diff --git a/.Rbuildignore b/.Rbuildignore index e05151613..b66ab8982 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -17,8 +17,8 @@ ^R/secure.global.ranking.md$ ^_pkgdown\.yml$ ^docs$ -^dsBase_6.3.4.tar.gz$ -^dsBase_6.3.4-permissive.tar.gz$ +^dsBase_6.3.5.tar.gz$ +^dsBase_6.3.5-permissive.tar.gz$ ^dsDanger_6.3.4.tar.gz$ ^\.circleci$ ^\.circleci/config\.yml$ diff --git a/.github/workflows/dsBaseClient_test_suite.yaml b/.github/workflows/dsBaseClient_test_suite.yaml new file mode 100644 index 000000000..17e13f1dc --- /dev/null +++ b/.github/workflows/dsBaseClient_test_suite.yaml @@ -0,0 +1,247 @@ +################################################################################ +# DataSHIELD GHA test suite - dsBaseClient +# Adapted from `armadillo_azure-pipelines.yml` by Roberto Villegas-Diaz +# +# Inside the root directory $(Pipeline.Workspace) will be a file tree like: +# /dsBaseClient <- Checked out version of datashield/dsBaseClient +# /dsBaseClient/logs <- Where results of tests and logs are collated +# /testStatus <- Checked out version of datashield/testStatus +# +# As of Sept. 2025 this takes ~ 95 mins to run. +################################################################################ +name: dsBaseClient tests' suite + +on: + push: + schedule: + - cron: '0 0 * * 6' # Weekly (on Saturdays @ 0.00) + +jobs: + dsBaseClient_test_suite: + runs-on: ubuntu-latest + timeout-minutes: 180 + permissions: + contents: read + + # These should all be constant, except TEST_FILTER. This can be used to test + # subsets of test files in the testthat directory. Options are like: + # '*' <- Run all tests. + # 'asNumericDS*' <- Run all asNumericDS tests, i.e. all the arg, etc. tests. + # '*_smk_*' <- Run all the smoke tests for all functions. + env: + TEST_FILTER: '_-|datachk-|smk-|arg-|disc-|perf-|smk_expt-|expt-|math-' + _r_check_system_clock_: 0 + WORKFLOW_ID: ${{ github.run_id }}-${{ github.run_attempt }} + PROJECT_NAME: dsBaseClient + BRANCH_NAME: ${{ github.head_ref || github.ref_name }} + REPO_OWNER: ${{ github.repository_owner }} + R_KEEP_PKG_SOURCE: yes + GITHUB_TOKEN: ${{ github.token || 'placeholder-token' }} + + steps: + - name: Checkout dsBaseClient + uses: actions/checkout@v4 + with: + path: dsBaseClient + + - name: Checkout testStatus + if: ${{ github.actor != 'nektos/act' }} # for local deployment only + uses: actions/checkout@v4 + with: + repository: ${{ env.REPO_OWNER }}/testStatus + ref: master + path: testStatus + persist-credentials: false + token: ${{ env.GITHUB_TOKEN }} + + - name: Uninstall default MySQL + run: | + curl https://bazel.build/bazel-release.pub.gpg | sudo apt-key add - + sudo service mysql stop || true + sudo apt-get update + sudo apt-get remove --purge mysql-client mysql-server mysql-common -y + sudo apt-get autoremove -y + sudo apt-get autoclean -y + sudo rm -rf /var/lib/mysql/ + + - uses: r-lib/actions/setup-pandoc@v2 + + - uses: r-lib/actions/setup-r@v2 + with: + r-version: release + http-user-agent: release + use-public-rspm: true + + - name: Install R and dependencies + run: | + sudo apt-get install --no-install-recommends software-properties-common dirmngr -y + wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc | sudo tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc + sudo add-apt-repository "deb https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran40/" + sudo apt-get update -qq + sudo apt-get upgrade -y + sudo apt-get install -qq libxml2-dev libcurl4-openssl-dev libssl-dev libgsl-dev libgit2-dev r-base -y + sudo apt-get install -qq libharfbuzz-dev libfribidi-dev libmagick++-dev xml-twig-tools -y + sudo R -q -e "install.packages(c('devtools','covr','fields','meta','metafor','ggplot2','gridExtra','data.table','DSI','DSOpal','DSLite','MolgenisAuth','MolgenisArmadillo','DSMolgenisArmadillo','DescTools','e1071'), repos='https://cloud.r-project.org')" + sudo R -q -e "devtools::install_github(repo='datashield/dsDangerClient', ref=Sys.getenv('BRANCH_NAME'))" + + - uses: r-lib/actions/setup-r-dependencies@v2 + with: + dependencies: 'c("Imports")' + extra-packages: | + any::rcmdcheck + cran::devtools + cran::git2r + cran::RCurl + cran::readr + cran::magrittr + cran::xml2 + cran::purrr + cran::dplyr + cran::stringr + cran::tidyr + cran::quarto + cran::knitr + cran::kableExtra + cran::rmarkdown + cran::downlit + needs: check + + - name: Check manual updated + run: | + orig_sum=$(find man -type f | sort -u | xargs cat | md5sum) + R -q -e "devtools::document()" + new_sum=$(find man -type f | sort -u | xargs cat | md5sum) + if [ "$orig_sum" != "$new_sum" ]; then + echo "Your committed man/*.Rd files are out of sync with the R headers." + exit 1 + fi + working-directory: dsBaseClient + continue-on-error: true + + - name: Devtools checks + run: | + R -q -e "devtools::check(args = c('--no-examples', '--no-tests'))" | tee azure-pipelines_check.Rout + grep --quiet "^0 errors" azure-pipelines_check.Rout && grep --quiet " 0 warnings" azure-pipelines_check.Rout && grep --quiet " 0 notes" azure-pipelines_check.Rout + working-directory: dsBaseClient + continue-on-error: true + + - name: Start Armadillo docker-compose + run: docker compose -f docker-compose_armadillo.yml up -d --build + working-directory: dsBaseClient + + - name: Install test datasets + run: | + sleep 60 + R -q -f "molgenis_armadillo-upload_testing_datasets.R" + working-directory: dsBaseClient/tests/testthat/data_files + + - name: Install dsBase to Armadillo + run: | + curl -u admin:admin -X GET http://localhost:8080/packages + curl -u admin:admin -H 'Content-Type: multipart/form-data' -F "file=@dsBase_6.3.5-permissive.tar.gz" -X POST http://localhost:8080/install-package + sleep 60 + docker restart dsbaseclient-armadillo-1 + sleep 30 + curl -u admin:admin -X POST http://localhost:8080/whitelist/dsBase + working-directory: dsBaseClient + + - name: Run tests with coverage & JUnit report + run: | + mkdir -p logs + R -q -e "devtools::reload();" + R -q -e ' + write.csv( + covr::coverage_to_list( + covr::package_coverage( + type = c("none"), + code = c('"'"' + output_file <- file("test_console_output.txt"); + sink(output_file); + sink(output_file, type = "message"); + junit_rep <- testthat::JunitReporter$new(file = file.path(getwd(), "test_results.xml")); + progress_rep <- testthat::ProgressReporter$new(max_failures = 999999); + multi_rep <- testthat::MultiReporter$new(reporters = list(progress_rep, junit_rep)); + options("datashield.return_errors" = FALSE, "default_driver" = "ArmadilloDriver"); + testthat::test_package("${{ env.PROJECT_NAME }}", filter = "${{ env.TEST_FILTER }}", reporter = multi_rep, stop_on_failure = FALSE)'"'"' + ) + ) + ), + "coveragelist.csv" + )' + + mv coveragelist.csv logs/ + mv test_* logs/ + working-directory: dsBaseClient + + - name: Check for JUnit errors + run: | + issue_count=$(sed 's/failures="0" errors="0"//' test_results.xml | grep -c errors= || true) + echo "Number of testsuites with issues: $issue_count" + sed 's/failures="0" errors="0"//' test_results.xml | grep errors= > issues.log || true + cat issues.log || true + # continue with workflow even when some tests fail + exit 0 + working-directory: dsBaseClient/logs + + - name: Write versions to file + run: | + echo "branch:${{ env.BRANCH_NAME }}" > ${{ env.WORKFLOW_ID }}.txt + echo "os:$(lsb_release -ds)" >> ${{ env.WORKFLOW_ID }}.txt + echo "R:$(R --version | head -n1)" >> ${{ env.WORKFLOW_ID }}.txt + Rscript --vanilla -e 'sessionInfo()' >> session_info_${{ env.WORKFLOW_ID }}.txt + working-directory: dsBaseClient/logs + + - name: Parse results from testthat and covr + run: | + Rscript --verbose --vanilla ../testStatus/source/parse_test_report.R logs/ logs/ https://github.com/datashield/${{ env.PROJECT_NAME }}/blob/${{ env.BRANCH_NAME }} '([^:]+)' '(?<=::)[^:]+(?=::)' + working-directory: dsBaseClient + env: + PROJECT_NAME: ${{ env.PROJECT_NAME }} + BRANCH_NAME: ${{ env.BRANCH_NAME }} + + - name: Render report + run: | + cd testStatus + + mkdir -p new/logs/${{ env.PROJECT_NAME }}/${{ env.BRANCH_NAME }}/${{ env.WORKFLOW_ID }}/ + mkdir -p new/docs/${{ env.PROJECT_NAME }}/${{ env.BRANCH_NAME }}/${{ env.WORKFLOW_ID }}/ + mkdir -p new/docs/${{ env.PROJECT_NAME }}/${{ env.BRANCH_NAME }}/latest/ + + # Copy logs to new logs directory location + cp -rv ../dsBaseClient/logs/* new/logs/${{ env.PROJECT_NAME }}/${{ env.BRANCH_NAME }}/${{ env.WORKFLOW_ID }}/ + cp -rv ../dsBaseClient/logs/${{ env.WORKFLOW_ID }}.txt new/logs/${{ env.PROJECT_NAME }}/${{ env.BRANCH_NAME }}/${{ env.WORKFLOW_ID }}/ + + R -e 'input_dir <- file.path("../new/logs", Sys.getenv("PROJECT_NAME"), Sys.getenv("BRANCH_NAME"), Sys.getenv("WORKFLOW_ID")); quarto::quarto_render("source/test_report.qmd", execute_params = list(input_dir = input_dir))' + mv source/test_report.html new/docs/${{ env.PROJECT_NAME }}/${{ env.BRANCH_NAME }}/${{ env.WORKFLOW_ID }}/index.html + cp -r new/docs/${{ env.PROJECT_NAME }}/${{ env.BRANCH_NAME }}/${{ env.WORKFLOW_ID }}/* new/docs/${{ env.PROJECT_NAME }}/${{ env.BRANCH_NAME }}/latest + + env: + PROJECT_NAME: ${{ env.PROJECT_NAME }} + BRANCH_NAME: ${{ env.BRANCH_NAME }} + WORKFLOW_ID: ${{ env.WORKFLOW_ID }} + + - name: Upload test logs + uses: actions/upload-artifact@v4 + with: + name: dsbaseclient-logs + path: testStatus/new + + - name: Dump environment info + run: | + echo -e "\n#############################" + echo -e "ls /: ######################" + ls -al . + echo -e "\n#############################" + echo -e "lscpu: ######################" + lscpu + echo -e "\n#############################" + echo -e "memory: #####################" + free -m + echo -e "\n#############################" + echo -e "env: ########################" + env + echo -e "\n#############################" + echo -e "R sessionInfo(): ############" + R -e 'sessionInfo()' + sudo apt install tree -y + tree . diff --git a/DESCRIPTION b/DESCRIPTION index cc110b7f7..e0f278a52 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,11 +1,11 @@ Package: dsBaseClient Title: 'DataSHIELD' Client Side Base Functions -Version: 6.3.4 +Version: 6.3.5 Description: Base 'DataSHIELD' functions for the client side. 'DataSHIELD' is a software package which allows you to do non-disclosive federated analysis on sensitive data. 'DataSHIELD' analytic functions have been designed to only share non disclosive summary statistics, with built in automated output checking based on statistical disclosure control. With data sites setting the threshold values for - the automated output checks. For more details, see 'citation("dsBaseClient")'. + the automated output checks. For more details, see citation('dsBaseClient'). Authors@R: c(person(given = "Paul", family = "Burton", role = c("aut"), @@ -36,10 +36,6 @@ Authors@R: c(person(given = "Paul", family = "Avraam", role = c("aut"), comment = c(ORCID = "0000-0001-8908-2441")), - person(given = "Demetris", - family = "Avraam", - role = c("aut"), - comment = c(ORCID = "0000-0001-8908-2441")), person(given = "Yannick", family = "Marcon", role = c("aut"), diff --git a/NAMESPACE b/NAMESPACE index ec905eb6e..289592525 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -1,6 +1,5 @@ # Generated by roxygen2: do not edit by hand -export(computeWeightedMeans) export(ds.Boole) export(ds.abs) export(ds.asCharacter) @@ -73,6 +72,7 @@ export(ds.matrixDimnames) export(ds.matrixInvert) export(ds.matrixMult) export(ds.matrixTranspose) +export(ds.mdPattern) export(ds.mean) export(ds.meanByClass) export(ds.meanSdGp) @@ -118,6 +118,7 @@ export(ds.unList) export(ds.unique) export(ds.var) export(ds.vectorCalc) +export(subsetHelper) import(DSI) import(data.table) importFrom(stats,as.formula) diff --git a/R/computeWeightedMeans.R b/R/computeWeightedMeans.R index 0f04fc915..1284ffc08 100644 --- a/R/computeWeightedMeans.R +++ b/R/computeWeightedMeans.R @@ -9,9 +9,11 @@ #' @param variables character name of the variable(s) to focus on. The variables must be in the data.table #' @param weight character name of the data.table column that contains a weight. #' @param by character vector of the columns to group by +#' @return Returns a data table object with computed weighted means. +#' #' @import data.table #' @importFrom stats as.formula na.omit ts weighted.mean -#' @export +#' @keywords internal computeWeightedMeans <- function(data_table, variables, weight, by) { if (is.null(weight)) { diff --git a/R/ds.asFactor.R b/R/ds.asFactor.R index 476f00f85..8e5fbd090 100644 --- a/R/ds.asFactor.R +++ b/R/ds.asFactor.R @@ -48,7 +48,7 @@ #' \code{baseline.level = 1} and \code{forced.factor.levels = c(1,2,3,4,5)}. #' The input vector is converted to the following matrix of dummy variables: #' -#' \tabular{rrrrr}{ +#' \tabular{rrrr}{ #' \strong{DV2} \tab \strong{DV3} \tab \strong{DV4} \tab \strong{DV5} \cr #' 0 \tab 0 \tab 0 \tab 0\cr #' 1 \tab 0 \tab 0 \tab 0\cr diff --git a/R/ds.boxPlot.R b/R/ds.boxPlot.R index d89c54709..7d86a79b1 100644 --- a/R/ds.boxPlot.R +++ b/R/ds.boxPlot.R @@ -21,7 +21,7 @@ #' ## Version 6, for version 5 see the Wiki #' #' ### Please ensure you have a training Virtual Machine running, -#' or that you have a live connection to a server. +#' # or that you have a live connection to a server. #' #' # Connecting to the Opal servers #' @@ -48,37 +48,37 @@ #' symbol = "D") #' #' ## Create a boxplot of one variable -#' ds.boxPlot("D", "LAB_HDL", datasources = connections) +#' ds.boxPlot("D", "LAB_HDL", datasources = connections) #' #' ## Create a boxplot that is split by study: -#' ds.boxPlot("D", "LAB_HDL", type= "split", datasources = connections) +#' ds.boxPlot("D", "LAB_HDL", type= "split", datasources = connections) #' #' ## Create a boxplot of two variables variable -#' ds.boxPlot("D", c("LAB_HDL", "LAB_TRIG", type="pooled", -#' datasources = connections) +#' ds.boxPlot("D", c("LAB_HDL", "LAB_TRIG"), type="pooled", +#' datasources = connections) #' # only one plot is created (of the aggregated results of all servers) #' #' ## Create a boxplot of two variables, which are split by a factor -#' ds.boxPlot("D", c("LAB_HDL", "LAB_TRIG"), group = "GENDER", +#' ds.boxPlot("D", c("LAB_HDL", "LAB_TRIG"), group = "GENDER", #' datasources = connections) #' #' ## Create a boxplot with x- and y-axis labels -#' ds.boxPlot("D", c("LAB_HDL", "LAB_TRIG"), group = "GENDER", +#' ds.boxPlot("D", c("LAB_HDL", "LAB_TRIG"), group = "GENDER", #' xlabel = "Variable", ylabel = "Measurement", datasources = connections) #' #' ## Improve the presentation of ds.boxplot output using ggplot: #' ### User must save the output, which is in a ggplot format already: -#' a <- ds.boxPlot("D", c("LAB_HDL", "LAB_TRIG"), group = "GENDER", +#' a <- ds.boxPlot("D", c("LAB_HDL", "LAB_TRIG"), group = "GENDER", #' xlabel = "Variable", ylabel = "Measurement", datasources = connections) #' #' ### Then customise output "a" using ggplot tools: #' a + ggplot2::scale_fill_discrete(name = "Gender", labels = c("Male", "Female")) #' #' ### Or use an alternative way, to maintain the aesthetics: -#' a + ggplot2::scale_fill_brewer(name = "Gender", labels = c("Male", "Female")) +#' a + ggplot2::scale_fill_brewer(name = "Gender", labels = c("Male", "Female")) #' #' # Clear the Datashield R sessions and logout -#' datashield.logout(connections) +#' datashield.logout(connections) #' #' } #' diff --git a/R/ds.cbind.R b/R/ds.cbind.R index d943e0175..e21cb961c 100644 --- a/R/ds.cbind.R +++ b/R/ds.cbind.R @@ -157,7 +157,7 @@ ds.cbind <- function(x=NULL, DataSHIELD.checks=FALSE, force.colnames=NULL, newob } colNames <- unlist(colNames) if(anyDuplicated(colNames) != 0){ - cat("\n Warning: Some column names in study", j, "are duplicated and a suffix '.k' will be added to the kth replicate \n") + message("\n Warning: Some column names in study", j, "are duplicated and a suffix '.k' will be added to the kth replicate \n") } } } @@ -198,7 +198,7 @@ ds.cbind <- function(x=NULL, DataSHIELD.checks=FALSE, force.colnames=NULL, newob next.class <- DSI::datashield.aggregate(datasources[std], calltext1) class.vector <- c(class.vector, next.class[[1]]) if (notify.of.progress){ - cat("\n",j," of ", length(x), " elements to combine in step 1 of 2 in study ", std, "\n") + message("\n",j," of ", length(x), " elements to combine in step 1 of 2 in study ", std, "\n") } } for(j in 1:length(x)){ @@ -206,14 +206,14 @@ ds.cbind <- function(x=NULL, DataSHIELD.checks=FALSE, force.colnames=NULL, newob if(class.vector[j]!="data.frame" && class.vector[j]!="matrix"){ colname.vector <- c(colname.vector, test.df) if (notify.of.progress){ - cat("\n",j," of ", length(x), " elements to combine in step 2 of 2 in study ", std, "\n") + message("\n",j," of ", length(x), " elements to combine in step 2 of 2 in study ", std, "\n") } }else{ calltext2 <- call('colnamesDS', test.df) df.names <- DSI::datashield.aggregate(datasources[std], calltext2) colname.vector <- c(colname.vector, df.names[[1]]) if (notify.of.progress){ - cat("\n", j," of ", length(x), " elements to combine in step 2 of 2 in study ", std, "\n") + message("\n", j," of ", length(x), " elements to combine in step 2 of 2 in study ", std, "\n") } } } @@ -221,7 +221,7 @@ ds.cbind <- function(x=NULL, DataSHIELD.checks=FALSE, force.colnames=NULL, newob } if (notify.of.progress){ - cat("\nBoth steps in all studies completed\n") + message("\nBoth steps in all studies completed\n") } # prepare name vectors for transmission diff --git a/R/ds.colnames.R b/R/ds.colnames.R index a4b98b1ad..a9e802523 100644 --- a/R/ds.colnames.R +++ b/R/ds.colnames.R @@ -1,51 +1,51 @@ #' #' @title Produces column names of the R object in the server-side -#' @description Retrieves column names of an R object on the server-side. +#' @description Retrieves column names of an R object on the server-side. #' This function is similar to R function \code{colnames}. -#' @details The input is restricted to the object of type \code{data.frame} or \code{matrix}. -#' +#' @details The input is restricted to the object of type \code{data.frame} or \code{matrix}. +#' #' Server function called: \code{colnamesDS} #' @param x a character string providing the name of the input data frame or matrix. -#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. #' If the \code{datasources} argument is not specified #' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. -#' @return \code{ds.colnames} returns the column names of -#' the specified server-side data frame or matrix. +#' @return \code{ds.colnames} returns the column names of +#' the specified server-side data frame or matrix. #' @author DataSHIELD Development Team #' @seealso \code{\link{ds.dim}} to obtain the dimensions of a matrix or a data frame. -#' @examples +#' @examples #' \dontrun{ -#' +#' #' ## Version 6, for version 5 see the Wiki #' # Connecting to the Opal servers -#' +#' #' require('DSI') #' require('DSOpal') #' require('dsBaseClient') -#' +#' #' builder <- DSI::newDSLoginBuilder() -#' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", +#' builder$append(server = "study1", +#' url = "http://192.168.56.100:8080/", +#' user = "administrator", password = "datashield_test&", #' table = "CNSIM.CNSIM1", driver = "OpalDriver") -#' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", +#' builder$append(server = "study2", +#' url = "http://192.168.56.100:8080/", +#' user = "administrator", password = "datashield_test&", #' table = "CNSIM.CNSIM2", driver = "OpalDriver") #' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", +#' url = "http://192.168.56.100:8080/", +#' user = "administrator", password = "datashield_test&", #' table = "CNSIM.CNSIM3", driver = "OpalDriver") #' logindata <- builder$build() -#' +#' #' # Log onto the remote Opal training servers -#' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") -#' +#' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") +#' #' # Getting column names of the R objects stored in the server-side #' ds.colnames(x = "D", #' datasources = connections[1]) #only the first server ("study1") is used #' # Clear the Datashield R sessions and logout -#' datashield.logout(connections) +#' datashield.logout(connections) #' } #' @export #' @@ -65,17 +65,6 @@ ds.colnames <- function(x=NULL, datasources=NULL) { stop("Please provide the name of a data.frame or matrix!", call.=FALSE) } - # check if the input object(s) is(are) defined in all the studies - defined <- isDefined(datasources, x) - - # call the internal function that checks the input object is of the same class in all studies. - typ <- checkClass(datasources, x) - - # if the input object is not a matrix or a dataframe stop - if(!('data.frame' %in% typ) & !('matrix' %in% typ)){ - stop("The input vector must be of type 'data.frame' or a 'matrix'!", call.=FALSE) - } - cally <- call("colnamesDS", x) column_names <- DSI::datashield.aggregate(datasources, cally) diff --git a/R/ds.contourPlot.R b/R/ds.contourPlot.R index 4e195e48b..f1fbb3bd8 100644 --- a/R/ds.contourPlot.R +++ b/R/ds.contourPlot.R @@ -120,6 +120,10 @@ ds.contourPlot <- function(x=NULL, y=NULL, type='combine', show='all', numints=2 stop("y=NULL. Please provide the names of two numeric vectors!", call.=FALSE) } + # Save par and setup reseting of par values + old_par <- graphics::par(no.readonly = TRUE) + on.exit(graphics::par(old_par), add = TRUE) + # check if the input objects are defined in all the studies isDefined(datasources, x) isDefined(datasources, y) diff --git a/R/ds.dataFrame.R b/R/ds.dataFrame.R index 5837747c6..eeddcdd90 100644 --- a/R/ds.dataFrame.R +++ b/R/ds.dataFrame.R @@ -137,7 +137,7 @@ ds.dataFrame <- function(x=NULL, row.names=NULL, check.rows=FALSE, check.names=T } colNames <- unlist(colNames) if(anyDuplicated(colNames) != 0){ - cat("\n Warning: Some column names in study", j, "are duplicated and a suffix '.k' will be added to the kth replicate \n") + message("\n Warning: Some column names in study", j, "are duplicated and a suffix '.k' will be added to the kth replicate \n") } } } @@ -178,7 +178,7 @@ ds.dataFrame <- function(x=NULL, row.names=NULL, check.rows=FALSE, check.names=T next.class <- DSI::datashield.aggregate(datasources[std], calltext1) class.vector <- c(class.vector, next.class[[1]]) if (notify.of.progress){ - cat("\n",j," of ", length(x), " elements to combine in step 1 of 2 in study ", std, "\n") + message("\n",j," of ", length(x), " elements to combine in step 1 of 2 in study ", std, "\n") } } for(j in 1:length(x)){ @@ -186,14 +186,14 @@ ds.dataFrame <- function(x=NULL, row.names=NULL, check.rows=FALSE, check.names=T if(class.vector[j]!="data.frame" && class.vector[j]!="matrix"){ colname.vector <- c(colname.vector, test.df) if (notify.of.progress){ - cat("\n",j," of ", length(x), " elements to combine in step 2 of 2 in study ", std, "\n") + message("\n",j," of ", length(x), " elements to combine in step 2 of 2 in study ", std, "\n") } }else{ calltext2 <- call('colnamesDS', test.df) df.names <- DSI::datashield.aggregate(datasources[std], calltext2) colname.vector <- c(colname.vector, df.names[[1]]) if (notify.of.progress){ - cat("\n", j," of ", length(x), " elements to combine in step 2 of 2 in study ", std, "\n") + message("\n", j," of ", length(x), " elements to combine in step 2 of 2 in study ", std, "\n") } } } @@ -201,7 +201,7 @@ ds.dataFrame <- function(x=NULL, row.names=NULL, check.rows=FALSE, check.names=T } if (notify.of.progress){ - cat("\nBoth steps in all studies completed\n") + message("\nBoth steps in all studies completed\n") } # prepare vectors for transmission diff --git a/R/ds.dataFrameSubset.R b/R/ds.dataFrameSubset.R index 1c5ff6a00..1ae6278db 100644 --- a/R/ds.dataFrameSubset.R +++ b/R/ds.dataFrameSubset.R @@ -231,13 +231,13 @@ if(!is.null(rm.cols)){ if (notify.of.progress) { if(num.messages==1){ - cat("\nSource",s,"\n",return.warning.message[[s]][[1]],"\n") + message("\nSource",s,"\n",return.warning.message[[s]][[1]],"\n") }else{ - cat("\nSource",s,"\n") + message("\nSource",s,"\n") for(m in 1:(num.messages-1)){ - cat(return.warning.message[[s]][[m]],"\n") + message(return.warning.message[[s]][[m]],"\n") } - cat(return.warning.message[[s]][[num.messages]],"\n") + message(return.warning.message[[s]][[num.messages]],"\n") } } } diff --git a/R/ds.densityGrid.R b/R/ds.densityGrid.R index b0766418a..fbd5b909b 100644 --- a/R/ds.densityGrid.R +++ b/R/ds.densityGrid.R @@ -66,11 +66,11 @@ #' # Example2: generate a grid density object for each study separately #' ds.densityGrid(x="D$LAB_TSC", #' y="D$LAB_HDL", -#' type="split" +#' type="split", #' datasources = connections[1])#only the first Opal server is used ("study1") #' #' # Example3: generate a grid density object where the number of intervals is set to 15, for -#' each study separately +#' # each study separately #' ds.densityGrid(x="D$LAB_TSC", #' y="D$LAB_HDL", #' type="split", diff --git a/R/ds.dmtC2S.R b/R/ds.dmtC2S.R index ee2e4be67..085d198fb 100644 --- a/R/ds.dmtC2S.R +++ b/R/ds.dmtC2S.R @@ -93,7 +93,7 @@ if(dplyr::is.tbl(dfdata)) if(!is.matrix(dfdata) && !is.data.frame(dfdata) && !dplyr::is.tbl(dfdata)) { - cat("\n FAILED: must either be a data.frame, matrix or tibble") + message("\n FAILED: must either be a data.frame, matrix or tibble") return('Please respecify') } diff --git a/R/ds.extractQuantiles.R b/R/ds.extractQuantiles.R index ba39dd51c..4068f8f3b 100644 --- a/R/ds.extractQuantiles.R +++ b/R/ds.extractQuantiles.R @@ -224,7 +224,7 @@ datasources.in.current.function<-datasources #CALL CLIENTSIDE FUNCTION ds.dmtC2S TO RETURN final.quantile.df TO SERVERSIDE dsBaseClient::ds.dmtC2S(dfdata=final.quantile.df,newobj="final.quantile.df",datasources = datasources.in.current.function) - cat("\n\n\n"," FINAL RANKING PROCEDURES COMPLETE: + message("\n\n\n"," FINAL RANKING PROCEDURES COMPLETE: PRIMARY RANKING OUTPUT IS IN DATA FRAME",extract.summary.output.ranks.df, " WHICH IS SORTED BY",extract.ranks.sort.by," AND HAS BEEN diff --git a/R/ds.forestplot.R b/R/ds.forestplot.R index 60227913c..e1bc21c13 100644 --- a/R/ds.forestplot.R +++ b/R/ds.forestplot.R @@ -10,6 +10,7 @@ #' See details from \code{?meta::metagen} for the different options. #' @param layout \code{character} (default \code{"JAMA"}) Layout of the plot. #' See details from \code{?meta::metagen} for the different options. +#' @return Results a foresplot object created with `meta::forest`. #' #' @export #' diff --git a/R/ds.glm.R b/R/ds.glm.R index 13cba2d96..8b1dbceb7 100644 --- a/R/ds.glm.R +++ b/R/ds.glm.R @@ -343,10 +343,10 @@ ds.glm <- function(formula=NULL, data=NULL, family=NULL, offset=NULL, weights=NU # to provide name of offset or weights variable if(sum(as.numeric(grepl('offset', formula, ignore.case=TRUE)))>0 || sum(as.numeric(grepl('weights', formula, ignore.case=TRUE)))>0){ - cat("\n\n WARNING: you may have specified an offset or regression weights") - cat("\n as part of the model formula. In ds.glm (unlike the usual glm in R)") - cat("\n you must specify an offset or weights separately from the formula") - cat("\n using the offset or weights argument.\n\n") + message("\n\n WARNING: you may have specified an offset or regression weights") + message("\n as part of the model formula. In ds.glm (unlike the usual glm in R)") + message("\n you must specify an offset or weights separately from the formula") + message("\n using the offset or weights argument.\n\n") } formula <- stats::as.formula(formula) @@ -451,12 +451,12 @@ ds.glm <- function(formula=NULL, data=NULL, family=NULL, offset=NULL, weights=NU "Any values of 1 in the following tables denote potential disclosure risks\n", "please use the argument to include only valid studies.\n", "Errors by study are as follows:\n") - print(as.matrix(y.invalid)) - print(as.matrix(Xpar.invalid)) - print(as.matrix(w.invalid)) - print(as.matrix(o.invalid)) - print(as.matrix(glm.saturation.invalid)) - print(as.matrix(errorMessage)) + message(as.matrix(y.invalid)) + message(as.matrix(Xpar.invalid)) + message(as.matrix(w.invalid)) + message(as.matrix(o.invalid)) + message(as.matrix(glm.saturation.invalid)) + message(as.matrix(errorMessage)) return(list( output.blocked.information.1, diff --git a/R/ds.glmSLMA.R b/R/ds.glmSLMA.R index 9b46a6a40..3c9d0edb5 100644 --- a/R/ds.glmSLMA.R +++ b/R/ds.glmSLMA.R @@ -398,10 +398,10 @@ ds.glmSLMA<-function(formula=NULL, family=NULL, offset=NULL, weights=NULL, combi if(sum(as.numeric(grepl('offset', formula, ignore.case=TRUE)))>0 || sum(as.numeric(grepl('weights', formula, ignore.case=TRUE)))>0) { - cat("\n\n WARNING: you may have specified an offset or regression weights") - cat("\n as part of the model formula. In ds.glm (unlike the usual glm in R)") - cat("\n you must specify an offset or weights separately from the formula") - cat("\n using the offset or weights argument.\n\n") + message("\n\n WARNING: you may have specified an offset or regression weights") + message("\n as part of the model formula. In ds.glm (unlike the usual glm in R)") + message("\n you must specify an offset or weights separately from the formula") + message("\n using the offset or weights argument.\n\n") } formula <- stats::as.formula(formula) @@ -617,7 +617,7 @@ if(at.least.one.study.data.error) } if (notify.of.progress) { - cat("\n\nSAVING SERVERSIDE glm OBJECT AS: <",newobj,">\n\n") + message("\n\nSAVING SERVERSIDE glm OBJECT AS: <",newobj,">\n\n") } calltext.2 <- call('glmSLMADS.assign', formula, family, offset, weights, dataName) @@ -664,17 +664,17 @@ if(!all.studies.valid) { for(sse in study.with.errors) { - cat("\n","Error report from second serverside function for study",sse,"\n") - cat("############################################################","\n") - cat(unlist(study.summary[[sse]][[1]]),"\n") - cat(unlist(study.summary[[sse]][[2]]),"\n\n") + message("\n","Error report from second serverside function for study",sse,"\n") + message("############################################################","\n") + message(unlist(study.summary[[sse]][[1]]),"\n") + message(unlist(study.summary[[sse]][[2]]),"\n\n") num.messages<-length(study.summary[[sse]])-2 for(m in 1:num.messages) { if(!is.null(unlist(study.summary[[sse]][[2+m]]))) { - cat(unlist(study.summary[[sse]][[2+m]]),"\n\n") + message(unlist(study.summary[[sse]][[2+m]]),"\n\n") } } } @@ -806,8 +806,8 @@ if(num.valid.studies>1){ if(!coefficient.vectors.match){ - cat("\n\nModels in different sources vary in structure\nplease match coefficients for meta-analysis individually\n") - cat("nYou can use the DataSHIELD generated estimates and standard errors as the basis for a meta-analysis\nbut carry out the final pooling step independently of DataSHIELD using whatever meta-analysis package you wish\n\n") + message("\n\nModels in different sources vary in structure\nplease match coefficients for meta-analysis individually\n") + message("nYou can use the DataSHIELD generated estimates and standard errors as the basis for a meta-analysis\nbut carry out the final pooling step independently of DataSHIELD using whatever meta-analysis package you wish\n\n") return(list(output.summary=output.summary)) } diff --git a/R/ds.glmSummary.R b/R/ds.glmSummary.R index 5629d937f..9fc259c5b 100644 --- a/R/ds.glmSummary.R +++ b/R/ds.glmSummary.R @@ -172,17 +172,17 @@ if(obj.name.exists.in.all.sources && obj.non.null.in.all.sources){ # # # # if(no.errors){ # -# cat("\n\nCREATE ASSIGN OBJECT\n") # +# message("\n\nCREATE ASSIGN OBJECT\n") # # # # validity.check<-paste0("<",test.obj.name, "> appears valid in all sources") # # print(list(is.object.created=return.message,validity.check=validity.check)) # # } # # if(!no.errors){ # - validity.check<-paste0("<",test.obj.name,"> invalid in at least one source. See studyside.messages:") # - print(list(is.object.created=return.message,validity.check=validity.check, # - studyside.messages=studyside.message)) # - } # + validity.check<-paste0("<",test.obj.name,"> invalid in at least one source. See studyside.messages:") # + message(list(is.object.created=return.message,validity.check=validity.check, # + studyside.messages=studyside.message)) # + } # # #END OF CHECK OBJECT CREATED CORECTLY MODULE # ############################################################################################################# diff --git a/R/ds.glmerSLMA.R b/R/ds.glmerSLMA.R index 8bb8aa36f..b996707ef 100644 --- a/R/ds.glmerSLMA.R +++ b/R/ds.glmerSLMA.R @@ -269,10 +269,10 @@ ds.glmerSLMA <- function(formula=NULL, offset=NULL, weights=NULL, combine.with.m if(sum(as.numeric(grepl('offset', formula, ignore.case=TRUE)))>0 || sum(as.numeric(grepl('weights', formula, ignore.case=TRUE)))>0) { - cat("\n\n WARNING: you may have specified an offset or regression weights") - cat("\n as part of the model formula. In ds.glm (unlike the usual glm in R)") - cat("\n you must specify an offset or weights separately from the formula") - cat("\n using the offset or weights argument.\n\n") + message("\n\n WARNING: you may have specified an offset or regression weights") + message("\n as part of the model formula. In ds.glm (unlike the usual glm in R)") + message("\n you must specify an offset or weights separately from the formula") + message("\n using the offset or weights argument.\n\n") } formula <- stats::as.formula(formula) @@ -363,7 +363,7 @@ ds.glmerSLMA <- function(formula=NULL, offset=NULL, weights=NULL, combine.with.m if (notify.of.progress) { - cat("\n\nSAVING SERVERSIDE glmerMod OBJECT AS: <",newobj,">\n\n") + message("\n\nSAVING SERVERSIDE glmerMod OBJECT AS: <",newobj,">\n\n") } calltext.2 <- call('glmerSLMADS.assign', formula, offset, weights, dataName, family, @@ -407,17 +407,17 @@ ds.glmerSLMA <- function(formula=NULL, offset=NULL, weights=NULL, combine.with.m { for(sse in study.with.errors) { - cat("\n","Error report from second serverside function for study",sse,"\n") - cat("############################################################","\n") - cat(unlist(study.summary[[sse]][[1]]),"\n") - cat(unlist(study.summary[[sse]][[2]]),"\n\n") + message("\n","Error report from second serverside function for study",sse,"\n") + message("############################################################","\n") + message(unlist(study.summary[[sse]][[1]]),"\n") + message(unlist(study.summary[[sse]][[2]]),"\n\n") num.messages<-length(study.summary[[sse]])-2 for(m in 1:num.messages) { if(!is.null(unlist(study.summary[[sse]][[2+m]]))) { - cat(unlist(study.summary[[sse]][[2+m]]),"\n\n") + message(unlist(study.summary[[sse]][[2+m]]),"\n\n") } } } @@ -425,8 +425,8 @@ ds.glmerSLMA <- function(formula=NULL, offset=NULL, weights=NULL, combine.with.m if(all.studies.valid) { - cat("\nAll studies passed disclosure tests\n") - cat("Please check for convergence warnings in the study summaries\n\n\n") + message("\nAll studies passed disclosure tests\n") + message("Please check for convergence warnings in the study summaries\n\n\n") } } @@ -551,8 +551,8 @@ ds.glmerSLMA <- function(formula=NULL, offset=NULL, weights=NULL, combine.with.m if(!coefficient.vectors.match){ - cat("\n\nModels in different sources vary in structure\nplease match coefficients for meta-analysis individually\n") - cat("nYou can use the DataSHIELD generated estimates and standard errors as the basis for a meta-analysis\nbut carry out the final pooling step independently of DataSHIELD using whatever meta-analysis package you wish\n\n") + message("\n\nModels in different sources vary in structure\nplease match coefficients for meta-analysis individually\n") + message("nYou can use the DataSHIELD generated estimates and standard errors as the basis for a meta-analysis\nbut carry out the final pooling step independently of DataSHIELD using whatever meta-analysis package you wish\n\n") return(list(output.summary=output.summary)) } @@ -615,10 +615,10 @@ ds.glmerSLMA <- function(formula=NULL, offset=NULL, weights=NULL, combine.with.m if (notify.of.progress) { - cat("Convergence information\n") + message("Convergence information\n") for(r in 1:numstudies) { - cat(full.error.message[r],"\n") + message(full.error.message[r],"\n") } } diff --git a/R/ds.heatmapPlot.R b/R/ds.heatmapPlot.R index 262b1d700..f42b6baf4 100644 --- a/R/ds.heatmapPlot.R +++ b/R/ds.heatmapPlot.R @@ -133,7 +133,7 @@ #' datasources = connections[1]) #only the first server is used (study1) #' #' # Example 3: Plot a combined heat map plot using the method 'deterministic' centroids of each -#' k = 7 nearest neighbours for numints = 40 +#' # k = 7 nearest neighbours for numints = 40 #' ds.heatmapPlot(x = 'D$LAB_TSC', #' y = 'D$LAB_HDL', #' numints = 40, @@ -169,6 +169,10 @@ ds.heatmapPlot <- function(x=NULL, y=NULL, type="combine", show="all", numints=2 stop("y=NULL. Please provide the names of the 2nd numeric vector!", call.=FALSE) } + # Save par and setup reseting of par values + old_par <- graphics::par(no.readonly = TRUE) + on.exit(graphics::par(old_par), add = TRUE) + # check if the input objects are defined in all the studies isDefined(datasources, x) isDefined(datasources, y) diff --git a/R/ds.histogram.R b/R/ds.histogram.R index 0f5357b77..562bebcb4 100644 --- a/R/ds.histogram.R +++ b/R/ds.histogram.R @@ -120,7 +120,7 @@ #' datasources = connections) #all studies are used #' #' # Example 2: generate a combined histogram with the default small cells counts -#' suppression rule +#' # suppression rule #' ds.histogram(x = 'D$PM_BMI_CONTINUOUS', #' method = 'smallCellsRule', #' type = 'combine', @@ -167,6 +167,10 @@ ds.histogram <- function(x=NULL, type="split", num.breaks=10, method="smallCells stop("Please provide the name of the input vector!", call.=FALSE) } + # Save par and setup reseting of par values + old_par <- graphics::par(no.readonly = TRUE) + on.exit(graphics::par(old_par), add = TRUE) + # check if the input object is defined in all the studies isDefined(datasources, x) diff --git a/R/ds.listClientsideFunctions.R b/R/ds.listClientsideFunctions.R index ba7c57a89..752401471 100644 --- a/R/ds.listClientsideFunctions.R +++ b/R/ds.listClientsideFunctions.R @@ -57,48 +57,30 @@ for(j in 1:length(search.path)) } - cat("\n### Full search path \n") print.search.list<-search() - print(print.search.list) if(test.userDefinedClient==TRUE) { - cat("\n### userDefinedClient functions \n") print.text<-ls(pos=".GlobalEnv",pattern="ds.*") if(identical(print.text,character(0)))print.text<-"No clientside functions in this repository" - print(print.text) print.text.full<-c(print.text.full,print.text) } if(test.dsBetaTestClient==TRUE) { - cat("\n### dsBetaTestClient functions \n") print.text<-ls(pos="package:dsBetaTestClient") if(identical(print.text,character(0)))print.text<-"No clientside functions in this repository" - print(print.text) print.text.full<-c(print.text.full,print.text) } if(test.dsBaseClient==TRUE) { - cat("\n### dsBaseClient functions \n") print.text<-ls(pos="package:dsBaseClient") if(identical(print.text,character(0)))print.text<-"No clientside functions in this repository" - print(print.text) print.text.full<-c(print.text.full,print.text) } - if(test.no.functions==TRUE) - { - cat("\n### No standard clientside functions identified \n") - } - - cat("\nIf you cannot see one or more of the clientside functions you expected to find", - "please see above for the full search path. If one of the paths is a possible clientside repository", - "issue the R command ls(pos='package:dsPackageName')", - "where 'package:dsPackageName' is the full name stated in the search path\n\n") - return(print.text.full) } # ds.listClientsideFunctions() diff --git a/R/ds.lmerSLMA.R b/R/ds.lmerSLMA.R index b6d05c9bf..8b7c69b2c 100644 --- a/R/ds.lmerSLMA.R +++ b/R/ds.lmerSLMA.R @@ -225,10 +225,10 @@ ds.lmerSLMA <- function(formula=NULL, offset=NULL, weights=NULL, combine.with.me if(sum(as.numeric(grepl('offset', formula, ignore.case=TRUE)))>0 || sum(as.numeric(grepl('weights', formula, ignore.case=TRUE)))>0) { - cat("\n\n WARNING: you may have specified an offset or regression weights") - cat("\n as part of the model formula. In ds.glm (unlike the usual glm in R)") - cat("\n you must specify an offset or weights separately from the formula") - cat("\n using the offset or weights argument.\n\n") + message("\n\n WARNING: you may have specified an offset or regression weights") + message("\n as part of the model formula. In ds.glm (unlike the usual glm in R)") + message("\n you must specify an offset or weights separately from the formula") + message("\n using the offset or weights argument.\n\n") } formula <- stats::as.formula(formula) @@ -286,7 +286,7 @@ ds.lmerSLMA <- function(formula=NULL, offset=NULL, weights=NULL, combine.with.me if(!is.null(optimizer)&&optimizer!="nloptwrap") { errorMessage.opt<-"ERROR: the only optimizer currently available for lmer is 'nloptwrap', please respecify" - cat("\n",errorMessage.opt,"\n") + message("\n",errorMessage.opt,"\n") return(list(errorMessage=errorMessage.opt)) } @@ -303,7 +303,7 @@ ds.lmerSLMA <- function(formula=NULL, offset=NULL, weights=NULL, combine.with.me } if (notify.of.progress) { - cat("\n\nSAVING SERVERSIDE lmerMod OBJECT AS: <",newobj,">\n\n") + message("\n\nSAVING SERVERSIDE lmerMod OBJECT AS: <",newobj,">\n\n") } calltext.2 <- call('lmerSLMADS.assign', formula, offset, weights, dataName, REML, @@ -343,17 +343,17 @@ ds.lmerSLMA <- function(formula=NULL, offset=NULL, weights=NULL, combine.with.me { for(sse in study.with.errors) { - cat("\n","Error report from second serverside function for study",sse,"\n") - cat("############################################################","\n") - cat(unlist(study.summary[[sse]][[1]]),"\n") - cat(unlist(study.summary[[sse]][[2]]),"\n\n") + message("\n","Error report from second serverside function for study",sse,"\n") + message("############################################################","\n") + message(unlist(study.summary[[sse]][[1]]),"\n") + message(unlist(study.summary[[sse]][[2]]),"\n\n") num.messages<-length(study.summary[[sse]])-2 for(m in 1:num.messages) { if(!is.null(unlist(study.summary[[sse]][[2+m]]))) { - cat(unlist(study.summary[[sse]][[2+m]]),"\n\n") + message(unlist(study.summary[[sse]][[2+m]]),"\n\n") } } } @@ -361,8 +361,8 @@ ds.lmerSLMA <- function(formula=NULL, offset=NULL, weights=NULL, combine.with.me if(all.studies.valid) { - cat("\nAll studies passed disclosure tests\n") - cat("Please check for convergence warnings in the study summaries\n\n\n") + message("\nAll studies passed disclosure tests\n") + message("Please check for convergence warnings in the study summaries\n\n\n") } } @@ -488,8 +488,8 @@ ds.lmerSLMA <- function(formula=NULL, offset=NULL, weights=NULL, combine.with.me if(!coefficient.vectors.match){ - cat("\n\nModels in different sources vary in structure\nplease match coefficients for meta-analysis individually\n") - cat("nYou can use the DataSHIELD generated estimates and standard errors as the basis for a meta-analysis\nbut carry out the final pooling step independently of DataSHIELD using whatever meta-analysis package you wish\n\n") + message("\n\nModels in different sources vary in structure\nplease match coefficients for meta-analysis individually\n") + message("nYou can use the DataSHIELD generated estimates and standard errors as the basis for a meta-analysis\nbut carry out the final pooling step independently of DataSHIELD using whatever meta-analysis package you wish\n\n") return(list(output.summary=output.summary)) } @@ -552,10 +552,10 @@ for(q in 1:numstudies) if (notify.of.progress) { - cat("Convergence information\n") + message("Convergence information\n") for(r in 1:numstudies) { - cat(full.error.message[r],"\n") + message(full.error.message[r],"\n") } } diff --git a/R/ds.matrix.R b/R/ds.matrix.R index b90356c59..69ad3a728 100644 --- a/R/ds.matrix.R +++ b/R/ds.matrix.R @@ -171,7 +171,7 @@ ds.matrix <- function(mdata = NA, from="clientside.scalar", nrows.scalar=NULL, n #Check that valid from has been specified if(from!="serverside.vector"&&from!="serverside.scalar"&&from!="clientside.scalar") { - cat(" FAILED: must be specified as one of the following - 'serverside.vector', + message(" FAILED: must be specified as one of the following - 'serverside.vector', 'serverside.scalar', 'clientside.scalar'\n\n") return('Please respecify') } diff --git a/R/ds.matrixDiag.R b/R/ds.matrixDiag.R index 8c8ca877a..2deef1a0a 100644 --- a/R/ds.matrixDiag.R +++ b/R/ds.matrixDiag.R @@ -112,7 +112,7 @@ #' datasources = connections) #' #' #Example 2: Create a square matrix with the server-side scalar as all diagonal values -#' and all the other values = 0 +#' #and all the other values = 0 #' #' #Create a scalar in the server-side #' @@ -152,7 +152,7 @@ #' datasources = connections) #' #' #Example 4: Create a square matrix with the client-side vector as a diagonal -#' and all the other values = 0 +#' #and all the other values = 0 #' #' ds.matrixDiag(x1 = c(2,6,9,10), #' aim = "clientside.vector.2.matrix", @@ -161,7 +161,7 @@ #' datasources = connections) #' #' #Example 5: Create a square matrix with the client-side scalar as all diagonal values -#' and all the other values = 0 +#' #and all the other values = 0 #' #' ds.matrixDiag(x1 = 4, #' aim = "clientside.scalar.2.matrix", @@ -203,7 +203,7 @@ ds.matrixDiag<-function(x1=NULL, aim=NULL, nrows.scalar=NULL, newobj=NULL, datas if(aim!="serverside.vector.2.matrix"&&aim!="serverside.scalar.2.matrix"&&aim!="serverside.matrix.2.vector"&& aim!="clientside.vector.2.matrix"&&aim!="clientside.scalar.2.matrix") { - cat(" FAILED: aim must be specified as one of the following - 'serverside.vector.2.matrix', + message(" FAILED: aim must be specified as one of the following - 'serverside.vector.2.matrix', 'serverside.scalar.2.matrix', 'serverside.matrix.2.vector', 'clientside.vector.2.matrix', 'clientside.scalar.2.matrix'\n\n") return('Please respecify') diff --git a/R/ds.mdPattern.R b/R/ds.mdPattern.R new file mode 100644 index 000000000..af59498e2 --- /dev/null +++ b/R/ds.mdPattern.R @@ -0,0 +1,305 @@ +#' +#' @title Display missing data patterns with disclosure control +#' @description This function is a client-side wrapper for the server-side mdPatternDS +#' function. It generates a missing data pattern matrix similar to mice::md.pattern but +#' with disclosure control applied to prevent revealing small cell counts. +#' @details The function calls the server-side mdPatternDS function which uses +#' mice::md.pattern to analyze missing data patterns. Patterns with counts below the +#' disclosure threshold (default: nfilter.tab = 3) are suppressed to maintain privacy. +#' +#' \strong{Output Format:} +#' - Each row represents a missing data pattern +#' - Pattern counts are shown in row names (e.g., "150", "25") +#' - Columns show 1 if the variable is observed, 0 if missing +#' - Last column shows the total number of missing values per pattern +#' - Last row shows the total number of missing values per variable +#' +#' \strong{Disclosure Control:} +#' +#' Suppressed patterns (count below threshold) are indicated by: +#' - Row name: "suppressed()" where N is the threshold +#' - All pattern values set to NA +#' - Summary row also suppressed to prevent back-calculation +#' +#' \strong{Pooling Behavior (type='combine'):} +#' +#' When pooling across studies, the function uses a \emph{conservative approach} +#' for disclosure control: +#' +#' 1. Identifies identical missing patterns across studies +#' 2. \strong{EXCLUDES suppressed patterns from pooling} - patterns suppressed in +#' ANY study are not included in the pooled count +#' 3. Sums counts only for non-suppressed identical patterns +#' 4. Re-validates pooled counts against disclosure threshold +#' +#' \strong{Important:} This conservative approach means: +#' - Pooled counts may be \emph{underestimates} if some studies had suppressed patterns +#' - This prevents disclosure through subtraction (e.g., if study A shows count=5 +#' and pool shows count=7, one could deduce study B has count=2, violating disclosure) +#' - Different patterns across studies are preserved separately in the pooled result +#' +#' @param x a character string specifying the name of a data frame or matrix on the +#' server-side containing the data to analyze. +#' @param type a character string specifying the output type. If 'split' (default), +#' returns separate patterns for each study. If 'combine', attempts to pool patterns +#' across studies. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained +#' after login. If the \code{datasources} argument is not specified, the default set of +#' connections will be used: see \code{\link[DSI]{datashield.connections_default}}. +#' @return For type='split': A list with one element per study, each containing: +#' \describe{ +#' \item{pattern}{The missing data pattern matrix for that study} +#' \item{valid}{Logical indicating if all patterns meet disclosure requirements} +#' \item{message}{A message describing the validity status} +#' } +#' +#' For type='combine': A list containing: +#' \describe{ +#' \item{pattern}{The pooled missing data pattern matrix across all studies} +#' \item{valid}{Logical indicating if all pooled patterns meet disclosure requirements} +#' \item{message}{A message describing the validity status} +#' } +#' @author Xavier Escribà montagut for DataSHIELD Development Team +#' @export +#' @examples +#' \dontrun{ +#' ## Version 6, for version 5 see the Wiki +#' +#' # Connecting to the Opal servers +#' +#' require('DSI') +#' require('DSOpal') +#' require('dsBaseClient') +#' +#' builder <- DSI::newDSLoginBuilder() +#' builder$append(server = "study1", +#' url = "http://192.168.56.100:8080/", +#' user = "administrator", password = "datashield_test&", +#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' builder$append(server = "study2", +#' url = "http://192.168.56.100:8080/", +#' user = "administrator", password = "datashield_test&", +#' table = "CNSIM.CNSIM2", driver = "OpalDriver") +#' logindata <- builder$build() +#' +#' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") +#' +#' # Get missing data patterns for each study separately +#' patterns_split <- ds.mdPattern(x = "D", type = "split", datasources = connections) +#' +#' # View results for study1 +#' print(patterns_split$study1$pattern) +#' # var1 var2 var3 +#' # 150 1 1 1 0 <- 150 obs complete +#' # 25 0 1 1 1 <- 25 obs missing var1 +#' # 25 0 0 25 <- Summary: 25 missing per variable +#' +#' # Get pooled missing data patterns across studies +#' patterns_pooled <- ds.mdPattern(x = "D", type = "combine", datasources = connections) +#' print(patterns_pooled$pattern) +#' +#' # Example with suppressed patterns: +#' # If study1 has a pattern with count=2 (suppressed) and study2 has same pattern +#' # with count=5 (valid), the pooled result will show count=5 (conservative approach) +#' # A warning will indicate: "Pooled counts may underestimate the true total" +#' +#' # Clear the Datashield R sessions and logout +#' datashield.logout(connections) +#' } +#' +ds.mdPattern <- function(x = NULL, type = 'split', datasources = NULL){ + + # Look for DS connections + if(is.null(datasources)){ + datasources <- datashield.connections_find() + } + + # Ensure datasources is a list of DSConnection-class + if(!(is.list(datasources) && all(unlist(lapply(datasources, function(d) {methods::is(d,"DSConnection")}))))){ + stop("The 'datasources' were expected to be a list of DSConnection-class objects", call.=FALSE) + } + + if(is.null(x)){ + stop("Please provide the name of a data frame or matrix!", call.=FALSE) + } + + # Get study names + study_names <- names(datasources) + + # Call the server side function + cally <- call("mdPatternDS", x) + results <- DSI::datashield.aggregate(datasources, cally) + + # Process results based on type + if(type == "split"){ + # Return individual study results + return(results) + + } else if(type == "combine"){ + # Pool results across studies + + # First check if any study has invalid patterns + any_invalid <- any(sapply(results, function(r) !r$valid)) + invalid_studies <- names(results)[sapply(results, function(r) !r$valid)] + + if(any_invalid){ + warning( + "Disclosure control: Some studies have suppressed patterns (below threshold).\n", + " Studies with suppressed patterns: ", paste(invalid_studies, collapse=", "), "\n", + " These patterns are EXCLUDED from pooling to prevent disclosure.\n", + " Pooled counts may underestimate the true total.", + call. = FALSE + ) + } + + # Extract patterns from each study + patterns_list <- lapply(results, function(r) r$pattern) + + # Check if all patterns have the same variables (columns) + n_vars <- sapply(patterns_list, ncol) + if(length(unique(n_vars)) > 1){ + stop("Cannot pool patterns: studies have different numbers of variables", call.=FALSE) + } + + var_names <- colnames(patterns_list[[1]]) + if(length(patterns_list) > 1){ + for(i in 2:length(patterns_list)){ + if(!identical(colnames(patterns_list[[i]]), var_names)){ + warning("Variable names differ across studies. Pooling by position.") + break + } + } + } + + # Pool the patterns + pooled_pattern <- .pool_md_patterns(patterns_list, study_names) + + # Check validity of pooled results + # Get threshold from first study's results or use a default check + nfilter.tab <- getOption("default.nfilter.tab") + if(is.null(nfilter.tab)) nfilter.tab <- 3 + + n_patterns <- nrow(pooled_pattern) - 1 + pooled_valid <- TRUE + + if(n_patterns > 0){ + # Pattern counts are in row names + pattern_counts <- as.numeric(rownames(pooled_pattern)[1:n_patterns]) + pattern_counts <- pattern_counts[!is.na(pattern_counts) & pattern_counts > 0] + + if(any(pattern_counts < nfilter.tab)){ + pooled_valid <- FALSE + } + } + + pooled_message <- ifelse(pooled_valid, + "Valid: all pooled pattern counts meet disclosure requirements", + "Some pooled pattern counts may be below threshold") + + return(list( + pattern = pooled_pattern, + valid = pooled_valid, + message = pooled_message, + studies = study_names + )) + + } else { + stop("Argument 'type' must be either 'split' or 'combine'", call.=FALSE) + } +} + +#' @title Pool missing data patterns across studies +#' @description Internal function to pool md.pattern results from multiple studies +#' @param patterns_list List of pattern matrices from each study +#' @param study_names Names of the studies +#' @return Pooled pattern matrix +#' @keywords internal +.pool_md_patterns <- function(patterns_list, study_names){ + + # Initialize with first study's pattern structure + pooled <- patterns_list[[1]] + n_vars <- ncol(pooled) + n_rows <- nrow(pooled) - 1 # Exclude summary row + + # Create a list to store unique patterns + unique_patterns <- list() + pattern_counts <- list() + + # Process each study + for(i in seq_along(patterns_list)){ + pattern <- patterns_list[[i]] + study_n_patterns <- nrow(pattern) - 1 + + if(study_n_patterns > 0){ + for(j in 1:study_n_patterns){ + # Get pattern (columns show 1/0 for observed/missing) + pat_vector <- pattern[j, 1:(n_vars-1)] + # Pattern count is in row name + pat_count_str <- rownames(pattern)[j] + pat_count <- suppressWarnings(as.numeric(pat_count_str)) + + # Skip if suppressed (non-numeric row name like "suppressed(<3)") + if(is.na(pat_count)){ + next + } + + # Convert pattern to string for comparison + pat_string <- paste(pat_vector, collapse="_") + + # Check if this pattern already exists + if(pat_string %in% names(unique_patterns)){ + # Add to existing count + pattern_counts[[pat_string]] <- pattern_counts[[pat_string]] + pat_count + } else { + # New pattern + unique_patterns[[pat_string]] <- pat_vector + pattern_counts[[pat_string]] <- pat_count + } + } + } + } + + # Build pooled pattern matrix + if(length(unique_patterns) == 0){ + # No valid patterns + pooled[1:n_rows, ] <- NA + } else { + # Sort patterns by count (descending) + sorted_idx <- order(unlist(pattern_counts), decreasing = TRUE) + sorted_patterns <- unique_patterns[sorted_idx] + sorted_counts <- pattern_counts[sorted_idx] + + # Create new pooled matrix + n_pooled_patterns <- length(sorted_patterns) + pooled <- matrix(NA, nrow = n_pooled_patterns + 1, ncol = n_vars) + colnames(pooled) <- colnames(patterns_list[[1]]) + + # Set row names (counts for patterns, empty for summary) + row_names <- c(as.character(unlist(sorted_counts)), "") + rownames(pooled) <- row_names + + # Fill in patterns + for(i in 1:n_pooled_patterns){ + pooled[i, 1:(n_vars-1)] <- sorted_patterns[[i]] + # Calculate number of missing for this pattern + pooled[i, n_vars] <- sum(sorted_patterns[[i]] == 0) + } + } + + # Calculate summary row (total missing per variable) + # Sum across studies + summary_row <- rep(0, n_vars) + for(i in seq_along(patterns_list)){ + study_summary <- patterns_list[[i]][nrow(patterns_list[[i]]), ] + # Only add if not suppressed + if(!all(is.na(study_summary))){ + summary_row <- summary_row + ifelse(is.na(study_summary), 0, study_summary) + } + } + + # Add summary row + pooled[nrow(pooled), ] <- summary_row + + return(pooled) +} + diff --git a/R/ds.rBinom.R b/R/ds.rBinom.R index 2f39f8b10..ec8b4f880 100644 --- a/R/ds.rBinom.R +++ b/R/ds.rBinom.R @@ -214,14 +214,14 @@ single.integer.seed<-c(single.integer.seed,seed.as.integer.study.specific) if(seed.as.text=="NULL"){ -cat("NO SEED SET IN STUDY",study.id,"\n\n") +message("NO SEED SET IN STUDY",study.id,"\n\n") } else { calltext <- paste0("setSeedDS(", seed.as.text, ")") ssDS.obj[[study.id]] <- DSI::datashield.aggregate(datasources[study.id], as.symbol(calltext)) } } -cat("\n\n") +message("\n\n") diff --git a/R/ds.rNorm.R b/R/ds.rNorm.R index 6100c8505..76d885f11 100644 --- a/R/ds.rNorm.R +++ b/R/ds.rNorm.R @@ -217,13 +217,13 @@ single.integer.seed<-c(single.integer.seed,seed.as.integer.study.specific) if(seed.as.text=="NULL"){ -cat("NO SEED SET IN STUDY",study.id,"\n\n") +message("NO SEED SET IN STUDY",study.id,"\n\n") } calltext <- paste0("setSeedDS(", seed.as.text, ")") ssDS.obj[[study.id]] <- DSI::datashield.aggregate(datasources[study.id], as.symbol(calltext)) } -cat("\n\n") +message("\n\n") diff --git a/R/ds.rPois.R b/R/ds.rPois.R index 2d2c7f019..74be7fdf7 100644 --- a/R/ds.rPois.R +++ b/R/ds.rPois.R @@ -190,13 +190,13 @@ single.integer.seed<-c(single.integer.seed,seed.as.integer.study.specific) if(seed.as.text=="NULL"){ -cat("NO SEED SET IN STUDY",study.id,"\n\n") +message("NO SEED SET IN STUDY",study.id,"\n\n") } calltext <- paste0("setSeedDS(", seed.as.text, ")") ssDS.obj[[study.id]] <- DSI::datashield.aggregate(datasources[study.id], as.symbol(calltext)) } -cat("\n\n") +message("\n\n") diff --git a/R/ds.rUnif.R b/R/ds.rUnif.R index d98fa28f0..ea74766b5 100644 --- a/R/ds.rUnif.R +++ b/R/ds.rUnif.R @@ -232,7 +232,7 @@ single.integer.seed<-c(single.integer.seed,seed.as.integer.study.specific) if(seed.as.text=="NULL"){ -cat("NO SEED SET IN STUDY",study.id,"\n") +message("NO SEED SET IN STUDY",study.id,"\n") } else { calltext <- paste0("setSeedDS(", seed.as.text, ")") diff --git a/R/ds.ranksSecure.R b/R/ds.ranksSecure.R index 1d9d98ed9..8ffa6a971 100644 --- a/R/ds.ranksSecure.R +++ b/R/ds.ranksSecure.R @@ -228,7 +228,7 @@ ds.ranksSecure <- function(input.var.name=NULL, quantiles.for.estimation="0.05-0 } if(monitor.progress){ -cat("\n\nStep 1 of 8 complete: +message("\n\nStep 1 of 8 complete: Cleaned up residual output from previous runs of ds.ranksSecure @@ -272,7 +272,7 @@ cat("\n\nStep 1 of 8 complete: dsBaseClient::ds.dmtC2S(dfdata=input.mean.sd.df,newobj="input.mean.sd.df") if(monitor.progress){ -cat("\n\nStep 2 of 8 complete: +message("\n\nStep 2 of 8 complete: Estimated mean and sd of v2br to standardise initial values @@ -308,7 +308,7 @@ cat("\n\nStep 2 of 8 complete: dsBaseClient::ds.dmtC2S(dfdata=min.max.df,newobj="min.max.df") if(monitor.progress){ -cat("\n\nStep 3 of 8 complete: +message("\n\nStep 3 of 8 complete: Generated ultra max and ultra min values to allocate to missing values if is NA.hi or NA.low @@ -316,9 +316,6 @@ cat("\n\nStep 3 of 8 complete: ") } -print(input.mean.sd.df) - - #CALL THE FIRST SERVER SIDE FUNCTION (ASSIGN) #WRITES ENCRYPTED DATA TO SERVERSIDE OBJECT "blackbox.output.df" calltext1 <- call("blackBoxDS", input.var.name=input.var.name, @@ -328,7 +325,7 @@ print(input.mean.sd.df) DSI::datashield.assign(datasources, "blackbox.output.df", calltext1) if(monitor.progress){ -cat("\n\nStep 4 of 8 complete: +message("\n\nStep 4 of 8 complete: Pseudo data synthesised,first set of rank-consistent transformations complete and blackbox.output.df created @@ -390,7 +387,7 @@ cat("\n\nStep 4 of 8 complete: ds.make("sR5.df$global.rank","testvar.ranks") if(monitor.progress){ -cat("\n\nStep 5 of 8 complete: + message("\n\nStep 5 of 8 complete: Global ranks generated and pseudodata stripped out. Now ready to proceed to transformation of global ranks @@ -445,7 +442,7 @@ cat("\n\nStep 5 of 8 complete: DSI::datashield.assign(datasources, "blackbox.ranks.df", calltext4) if(monitor.progress){ -cat("\n\nStep 6 of 8 complete: + message("\n\nStep 6 of 8 complete: Rank-consistent transformations of global ranks complete and blackbox.ranks.df created @@ -510,7 +507,7 @@ cat("\n\nStep 6 of 8 complete: DSI::datashield.assign(datasources,summary.output.ranks.df, calltext7) if(monitor.progress){ -cat("\n\nStep 7 of 8 complete: + message("\n\nStep 7 of 8 complete: Final global ranking of values in v2br complete and written to each serverside as appropriate @@ -544,7 +541,7 @@ cat("\n\nStep 7 of 8 complete: } if(monitor.progress && rm.residual.objects){ -cat("\n\nStep 8 of 8 complete: + message("\n\nStep 8 of 8 complete: Cleaned up residual output from running ds.ranksSecure @@ -552,7 +549,7 @@ cat("\n\nStep 8 of 8 complete: } if(monitor.progress && !rm.residual.objects){ - cat("\n\nStep 8 of 8 complete: + message("\n\nStep 8 of 8 complete: Residual output from running ds.ranksSecure NOT deleted @@ -562,14 +559,14 @@ cat("\n\nStep 8 of 8 complete: if(!generate.quantiles){ - cat("\n\n\n"," FINAL RANKING PROCEDURES COMPLETE: + message("\n\n\n"," FINAL RANKING PROCEDURES COMPLETE: PRIMARY RANKING OUTPUT IS IN DATA FRAME",summary.output.ranks.df, " WHICH IS SORTED BY",ranks.sort.by," AND HAS BEEN WRITTEN TO THE SERVERSIDE\n\n\n\n") info.message<-"As the argument was set to FALSE no quantiles have been estimated.Please set argument to TRUE if you want to estimate quantiles such as median, quartiles and 90th percentile" - cat("\n\n",info.message,"\n\n") + message("\n\n",info.message,"\n\n") return(info.message) } diff --git a/R/ds.rbind.R b/R/ds.rbind.R index 47e9165c2..d0aca96a8 100644 --- a/R/ds.rbind.R +++ b/R/ds.rbind.R @@ -133,7 +133,7 @@ calltext1<-call('classDS', testclass.var) next.class <- DSI::datashield.aggregate(datasources, calltext1) class.vector<-c(class.vector,next.class[[1]]) if (notify.of.progress) - cat("\n",j," of ", length(x), " elements to combine in step 1 of 2\n") + message("\n",j," of ", length(x), " elements to combine in step 1 of 2\n") } for(j in 1:length(x)) @@ -144,7 +144,7 @@ if(class.vector[j]!="data.frame" && class.vector[j]!="matrix") { colname.vector<-c(colname.vector,test.df) if (notify.of.progress) - cat("\n",j," of ", length(x), " elements to combine in step 2 of 2\n") + message("\n",j," of ", length(x), " elements to combine in step 2 of 2\n") } else { @@ -152,11 +152,11 @@ else df.names <- DSI::datashield.aggregate(datasources, calltext2) colname.vector<-c(colname.vector,df.names[[1]]) if (notify.of.progress) - cat("\n",j," of ", length(x), " elements to combine in step 2 of 2\n") + message("\n",j," of ", length(x), " elements to combine in step 2 of 2\n") } } if (notify.of.progress) - cat("\nBoth steps completed\n") + message("\nBoth steps completed\n") #CHECK FOR DUPLICATE NAMES IN COLUMN NAME VECTOR AND ADD ".k" TO THE kth REPLICATE num.duplicates<-rep(0,length(colname.vector)) diff --git a/R/ds.recodeValues.R b/R/ds.recodeValues.R index 184ccea2b..adeae5bf9 100644 --- a/R/ds.recodeValues.R +++ b/R/ds.recodeValues.R @@ -69,7 +69,7 @@ #' values2replace.vector = c(1,2), #' new.values.vector = c(1,2), #' missing = 99, -#' newobj = 'bmi_recoded' +#' newobj = 'bmi_recoded', #' datasources = connections) #' #' # Clear the Datashield R sessions and logout diff --git a/R/ds.rep.R b/R/ds.rep.R index 2d2ce9515..2f3e03010 100644 --- a/R/ds.rep.R +++ b/R/ds.rep.R @@ -151,7 +151,7 @@ if(source.each=='s')source.each<-'serverside' #Check that source has been specified if(source.x1!="serverside"&&source.x1!="clientside") { - cat(" FAILED: if source.x1 is non-null it must be specified as + message(" FAILED: if source.x1 is non-null it must be specified as one of the following: 'clientside','serverside','c', or 's'\n\n") return('Please respecify') } @@ -174,7 +174,7 @@ if(source.each=='s')source.each<-'serverside' #Check that source has been specified if(source.times!="serverside"&&source.times!="clientside"&&!is.null(source.times)) { - cat(" FAILED: if source.times is non-null it must be specified as + message(" FAILED: if source.times is non-null it must be specified as one of the following: 'clientside','serverside','c', or 's'\n\n") return('Please respecify') } @@ -208,7 +208,7 @@ if(source.each=='s')source.each<-'serverside' #Check that source has been specified if(source.length.out!="serverside"&&source.length.out!="clientside"&&!is.null(source.length.out)) { - cat(" FAILED: if source.length.out is non-null it must be specified as + message(" FAILED: if source.length.out is non-null it must be specified as one of the following: 'clientside','serverside','c', or 's'\n\n") return('Please respecify') } @@ -243,7 +243,7 @@ if(source.each=='s')source.each<-'serverside' #Check that source has been specified if(source.each!="serverside"&&source.each!="clientside"&&!is.null(source.each)) { - cat(" FAILED: if source.each is non-null it must be specified as + message(" FAILED: if source.each is non-null it must be specified as one of the following: 'clientside','serverside','c', or 's'\n\n") return('Please respecify') } diff --git a/R/ds.sample.R b/R/ds.sample.R index 08c1b04c1..9bd6780fb 100644 --- a/R/ds.sample.R +++ b/R/ds.sample.R @@ -207,18 +207,18 @@ single.integer.seed<-c(single.integer.seed,seed.as.integer.study.specific) if(seed.as.text=="NULL"){ if (notify.of.progress) - cat("NO SEED SET IN STUDY",study.id,"\n\n") + message("NO SEED SET IN STUDY",study.id,"\n\n") } calltext <- paste0("setSeedDS(", seed.as.text, ")") if (notify.of.progress) - print(calltext) + message(calltext) ssDS.obj[[study.id]] <- DSI::datashield.aggregate(datasources[study.id], as.symbol(calltext)) } if (notify.of.progress) - cat("\n\n") + message("\n\n") diff --git a/R/ds.scatterPlot.R b/R/ds.scatterPlot.R index 6c2c78058..55804b3b0 100644 --- a/R/ds.scatterPlot.R +++ b/R/ds.scatterPlot.R @@ -147,6 +147,10 @@ ds.scatterPlot <- function(x=NULL, y=NULL, method='deterministic', k=3, noise=0. stop("The 'datasources' were expected to be a list of DSConnection-class objects", call.=FALSE) } + # Save par and setup reseting of par values + old_par <- graphics::par(no.readonly = TRUE) + on.exit(graphics::par(old_par), add = TRUE) + # check if the input objects are defined in all the studies isDefined(datasources, x) isDefined(datasources, y) diff --git a/R/ds.table.R b/R/ds.table.R index 780f9f862..0f6ea996f 100644 --- a/R/ds.table.R +++ b/R/ds.table.R @@ -424,10 +424,10 @@ if(num.valid.studies==0) if ((! table.assign) || report.chisq.tests) { validity.message<-"All studies failed for reasons identified below" - cat("\n",validity.message,"\n\n") + message("\n",validity.message,"\n\n") for(ns in 1:numsources.orig) { - cat("\nStudy",ns,": ",error.messages[[ns]],"\n") + message("\nStudy",ns,": ",error.messages[[ns]],"\n") } return(list(validity.message=validity.message,error.messages=error.messages)) @@ -476,12 +476,12 @@ for(ns in 1:numsources.orig) validity.message<-c(validity.message,message.add) } -# cat("\n",validity.message,"\n") +# message("\n",validity.message,"\n") # for(ns in 1:numsources.orig) # { -# cat("\nStudy",ns,": ",error.messages[[ns]]) +# message("\nStudy",ns,": ",error.messages[[ns]]) # } -# cat("\n\n") +# message("\n\n") #table.out<-table.out.valid #numsources<-length(table.out) @@ -492,12 +492,12 @@ if(num.valid.studies==numsources.orig) validity.message<-"Data in all studies were valid" if (! table.assign) { - cat("\n",validity.message,"\n") + message("\n",validity.message,"\n") for(ns in 1:numsources.orig) { - cat("\nStudy",ns,": ",error.messages[[ns]]) + message("\nStudy",ns,": ",error.messages[[ns]]) } - cat("\n\n") + message("\n\n") } } @@ -520,7 +520,6 @@ if(numsources>1) { all.dims.same<-FALSE return.message<-"Warning: tables in different sources have different numbers of dimensions. Please analyse and combine yourself from study.specific tables above" - print(return.message) return(return.message) } } @@ -649,7 +648,7 @@ cells.so.far<-0 table.current.study<-cbind(rvar.mark,cvar.mark,stvar.mark,count.in.cell) table.current.study[is.na(table.current.study)]<-"NA" -#cat("current study =",ns) +#message("current study =",ns) #print(table.current.study) @@ -738,7 +737,7 @@ for(oo in 1:length(table.current.study[,1])) if(d1.a!=d1||d2.a!=d2||d3.a!=d3) { return.message= "Dimensions of tables not behaving sensibly across studies.Please check the data in each study and calculate counts and percentages, yourself, using the counts from the individual studies" - cat(return.message) + message(return.message) return(return.message) } @@ -875,7 +874,7 @@ cells.so.far<-0 table.current.study<-cbind(rvar.mark,cvar.mark,count.in.cell) table.current.study[is.na(table.current.study)]<-"NA" -#cat("current study =",ns) +#message("current study =",ns) #print(table.current.study) @@ -959,7 +958,7 @@ for(oo in 1:length(table.current.study[,1])) if(d1.a!=d1||d2.a!=d2) { return.message= "Dimensions of tables not behaving sensibly across studies.Please check the data in each study and calculate counts and percentages, yourself, using the counts from the individual studies" - cat(return.message) + message(return.message) return(return.message) } @@ -1082,7 +1081,7 @@ cells.so.far<-0 table.current.study<-cbind(rvar.mark,count.in.cell) table.current.study[is.na(table.current.study)]<-"NA" -#cat("current study =",ns) +#message("current study =",ns) #print(table.current.study) @@ -1153,7 +1152,7 @@ for(oo in 1:length(table.current.study[,1])) if(d1.a!=d1) { return.message= "Dimensions of tables not behaving sensibly across studies.Please check the data in each study and calculate counts and percentages, yourself, using the counts from the individual studies" - cat(return.message) + message(return.message) return(return.message) } @@ -1540,6 +1539,12 @@ if(num.table.dims==1) }#END second dim=1 loop +################################################# +# Setup on.exit() to restore options 'warn' value +################################################# + +old_warn_option <- base::getOption("warn") +on.exit(base::options(warn = old_warn_option), add = TRUE) ################################ #NOW UNDERTAKE CHISQUARED TESTS# diff --git a/R/ds.table2D.R b/R/ds.table2D.R index 0dee00abd..d632755a3 100644 --- a/R/ds.table2D.R +++ b/R/ds.table2D.R @@ -56,7 +56,7 @@ #' # Example 2: generate a two dimensional table, outputting study specific contingency tables #' ds.table2D(x='D$DIS_DIAB', y='D$GENDER', type='split') #' # display the 5 results items, one at a time to avoid having too much information displayed -#' at the same time +#' # at the same time #' output$counts #' output$rowPercent #' output$colPercent @@ -112,6 +112,13 @@ ds.table2D <- function(x=NULL, y=NULL, type='both', warningMessage=TRUE, datasou stop("Function argument 'type' has to be either 'combine', 'split' or 'both'") } + ################################################# + # Setup on.exit() to restore options 'warn' value + ################################################# + + old_warn_option <- base::getOption("warn") + on.exit(base::options(warn = old_warn_option), add = TRUE) + # the input variable might be given as column table (i.e. D$x) # or just as a vector not attached to a table (i.e. x) # we have to make sure the function deals with each case diff --git a/R/glmChecks.R b/R/glmChecks.R index 6dcfe2ee7..b469c7c71 100644 --- a/R/glmChecks.R +++ b/R/glmChecks.R @@ -52,6 +52,14 @@ glmChecks <- function(formula, data, offset, weights, datasources){ varIdentifier <- append(varIdentifier, "weights") } + ################################################# + # Setup on.exit() to restore options 'warn' value + ################################################# + + old_warn_option <- base::getOption("warn") + on.exit(base::options(warn = old_warn_option), add = TRUE) + + # check that each variable is defined and not empty and each study. Stop the process if any check fails stdnames <- names(datasources) for(i in 1:length(elts)){ diff --git a/R/subsetHelper.R b/R/subsetHelper.R index 025a06803..82eae7271 100644 --- a/R/subsetHelper.R +++ b/R/subsetHelper.R @@ -17,6 +17,7 @@ #' @keywords internal #' @return \code{subsetHelper} returns a message or the class of the object if the #' object has the same class in all studies. +#' @export #' @examples #' \dontrun{ #' diff --git a/README.md b/README.md index c82341b5f..616c30dcd 100644 --- a/README.md +++ b/README.md @@ -23,8 +23,8 @@ And the development version from install.packages("remotes") remotes::install_github("datashield/dsBaseClient", "") -# Install v6.3.4 with the following -remotes::install_github("datashield/dsBaseClient", "6.3.4") +# Install v6.3.5 with the following +remotes::install_github("datashield/dsBaseClient", "6.3.5") ``` For a full list of development branches, checkout https://github.com/datashield/dsBaseClient/branches @@ -50,7 +50,7 @@ The code here is organised as: [1] Burton P, Wilson R, Butters O, Ryser-Welch P, Westerberg A, Abarrategui L, Villegas-Diaz R, Avraam D, Marcon Y, Bishop T, Gaye A, Escribà Montagut X, Wheater S (2025). - _dsBaseClient: 'DataSHIELD' Client Side Base Functions_. R package version 6.3.4. + _dsBaseClient: 'DataSHIELD' Client Side Base Functions_. R package version 6.3.5. [2] Gaye A, Marcon Y, Isaeva J, LaFlamme P, Turner A, Jones E, Minion J, Boyd A, Newby C, Nuotio M, Wilson R, Butters O, Murtagh B, Demir I, Doiron D, Giepmans L, Wallace S, Budin-Ljøsne I, diff --git a/armadillo_azure-pipelines.yml b/armadillo_azure-pipelines.yml index 8439c8cef..4ff1f497d 100644 --- a/armadillo_azure-pipelines.yml +++ b/armadillo_azure-pipelines.yml @@ -58,10 +58,10 @@ schedules: - master always: true - cron: "0 2 * * *" - displayName: Nightly build - v6.3.4-dev + displayName: Nightly build - v6.3.5-dev branches: include: - - v6.3.4-dev + - v6.3.5-dev always: true ######################################################################################### @@ -132,7 +132,7 @@ jobs: sudo apt-get upgrade -y sudo apt-get install -qq libxml2-dev libcurl4-openssl-dev libssl-dev libgsl-dev libgit2-dev r-base -y - sudo apt-get install -qq libharfbuzz-dev libfribidi-dev libmagick++-dev -y + sudo apt-get install -qq libharfbuzz-dev libfribidi-dev libmagick++-dev libudunits2-dev -y sudo R -q -e "install.packages(c('devtools','covr'), dependencies=TRUE, repos='https://cloud.r-project.org')" sudo R -q -e "install.packages(c('fields','meta','metafor','ggplot2','gridExtra','data.table'), dependencies=TRUE, repos='https://cloud.r-project.org')" sudo R -q -e "install.packages(c('DSI','DSOpal','DSLite'), dependencies=TRUE, repos='https://cloud.r-project.org')" @@ -235,7 +235,7 @@ jobs: curl -u admin:admin -X GET http://localhost:8080/packages - curl -u admin:admin --max-time 300 -v -H 'Content-Type: multipart/form-data' -F "file=@dsBase_6.3.4-permissive.tar.gz" -X POST http://localhost:8080/install-package + curl -u admin:admin --max-time 300 -v -H 'Content-Type: multipart/form-data' -F "file=@dsBase_6.3.5-permissive.tar.gz" -X POST http://localhost:8080/install-package sleep 60 docker container restart dsbaseclient_armadillo_1 diff --git a/azure-pipelines.yml b/azure-pipelines.yml index 6c6103d4a..db3d7a186 100644 --- a/azure-pipelines.yml +++ b/azure-pipelines.yml @@ -3,11 +3,9 @@ # Starts with a vanilla Opal docker composition, installs dsBase # and dsBaseClient (as well as dependencies - including a fully functional # Opal server). -# Does checks and tests then saves results to testStatus repo. # # Inside the root directory $(Pipeline.Workspace) will be a file tree like: # /dsBaseClient <- Checked out version of datashield/dsBaseClient -# /testStatus <- Checked out version of datashield/testStatus # /logs <- Where results of tests and lots are collated # # As of May 2020 this takes ~ 70 mins to run. @@ -36,18 +34,6 @@ variables: _r_check_system_clock_: 0 -######################################################################################### -# Need to define all the GH repos and their access tokens, see: -# https://docs.microsoft.com/en-us/azure/devops/pipelines/library/service-endpoints?view=azure-devops&tabs=yaml -resources: - repositories: - - repository: testStatusRepo - type: github - endpoint: datashield-testing - name: datashield/testStatus - ref: master - - ######################################################################################### # When and under what condition to run the pipeline. schedules: @@ -58,10 +44,10 @@ schedules: - master always: true - cron: "0 2 * * *" - displayName: Nightly build - v6.3.4-dev + displayName: Nightly build - v6.3.5-dev branches: include: - - v6.3.4-dev + - v6.3.5-dev always: true ######################################################################################### @@ -82,11 +68,6 @@ jobs: - checkout: self path: 'dsBaseClient' - - checkout: testStatusRepo - path: 'testStatus' - persistCredentials: true - condition: and(eq(variables['Build.Repository.Name'], 'datashield/dsBaseClient'), ne(variables['Build.Reason'], 'PullRequest')) - ##################################################################################### # The MySQL install that comes with the VM doesn't seem compatable with our set up @@ -235,7 +216,7 @@ jobs: - bash: | R -q -e "library(opalr); opal <- opal.login(username = 'administrator', password = 'datashield_test&', url = 'https://localhost:8443', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); opal.put(opal, 'system', 'conf', 'general', '_rPackage'); opal.logout(o)" - R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsBase', username = 'datashield', ref = 'v6.3.4-dev'); opal.logout(opal)" + R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsBase', username = 'datashield', ref = 'v6.3.5-dev'); opal.logout(opal)" sleep 60 @@ -524,75 +505,6 @@ jobs: displayName: 'Down Opal Docker Composition' condition: succeeded() - ##################################################################################### - # Windup phase - ##################################################################################### - - ##################################################################################### - # Output some important version numbers to file. This gets added to the testStatus - # commit so it can be parsed and used on the status table. - - bash: | - - echo 'branch:'$(branchName) >> $(datetime).txt - echo 'os:'$(lsb_release -ds) >> $(datetime).txt - echo 'R:'$(R --version | head -n 1) >> $(datetime).txt - echo 'opal:'$(opal system --opal localhost:8443 --user administrator --password "datashield_test&" --version) >> $(datetime).txt - - workingDirectory: $(Pipeline.Workspace)/logs - displayName: 'Write versions to file' - condition: succeededOrFailed() - - - ##################################################################################### - # Checkout the testStatus repo, add the results from here, push back to GH. - # TODO: Automatically pull in better email/name info from somewhere. - # TODO: More debug info in commit message - - bash: | - - # Git needs some config set to be able to push to a repo. - git config --global user.email "you@example.com" - git config --global user.name "Azure pipeline" - - # This repo is checked out in detatched head state, so reconnect it here. - git checkout master - - # It is possible that other commits have been made to the testStatus repo since it - # was checked out. i.e. other pipeline runs might have finished. - git pull - - # Make the directories if they dont already exist - mkdir --parents logs/$(projectName)/$(branchName) - mkdir --parents docs/$(projectName)/$(branchName)/latest - - cp $(Pipeline.Workspace)/logs/coveragelist.csv logs/$(projectName)/$(branchName)/ - cp $(Pipeline.Workspace)/logs/coveragelist.csv logs/$(projectName)/$(branchName)/$(datetime).csv - - cp $(Pipeline.Workspace)/logs/test_results.xml logs/$(projectName)/$(branchName)/ - cp $(Pipeline.Workspace)/logs/test_results.xml logs/$(projectName)/$(branchName)/$(datetime).xml - - cp $(Pipeline.Workspace)/logs/$(datetime).txt logs/$(projectName)/$(branchName)/ - - # Run the script to parse the results and build the html pages. - # status.py JUnit_file.xml coverage_file.csv output_file.html local_repo_path remote_repo_name branch - source/status.py logs/$(projectName)/$(branchName)/$(datetime).xml logs/$(projectName)/$(branchName)/$(datetime).csv logs/$(projectName)/$(branchName)/$(datetime).txt status.html $(Pipeline.Workspace)/$(projectName) $(projectName) $(branchName) - - cp status.html docs/$(projectName)/$(branchName)/latest/index.html - git add logs/$(projectName)/$(branchName)/coveragelist.csv - git add logs/$(projectName)/$(branchName)/test_results.xml - git add logs/$(projectName)/$(branchName)/$(datetime).xml - git add logs/$(projectName)/$(branchName)/$(datetime).csv - git add logs/$(projectName)/$(branchName)/$(datetime).txt - git add docs/$(projectName)/$(branchName)/latest/index.html - - git commit -m "Azure auto test for $(projectName)/$(branchName) @ $(datetime)" -m "Debug info:\nProjectName:$(projectName)\nBranchName:$(branchName)\nDataTime:$(datetime)" - git push - exit 0 - - workingDirectory: $(Pipeline.Workspace)/testStatus - displayName: 'Parse test results' - condition: and(eq(variables['Build.Repository.Name'], 'datashield/dsBaseClient'), ne(variables['Build.Reason'], 'PullRequest')) - - ##################################################################################### # Output the environment information to the console. This is useful for debugging. # Always do this, even if some of the above has failed or the job has been cacelled. diff --git a/docker-compose_armadillo.yml b/docker-compose_armadillo.yml index 7a791d39f..37c44cdae 100644 --- a/docker-compose_armadillo.yml +++ b/docker-compose_armadillo.yml @@ -3,7 +3,7 @@ services: hostname: armadillo ports: - 8080:8080 - image: datashield/armadillo_citest:latest + image: datashield/armadillo_citest:5.11.0 environment: LOGGING_CONFIG: 'classpath:logback-file.xml' AUDIT_LOG_PATH: '/app/logs/audit.log' @@ -16,6 +16,7 @@ services: default: hostname: default - image: datashield/rock-omicron-karma-permissive:devel + image: datashield/rock-quebrada-lamda:latest +# image: datashield/rserver-panda-lamda:devel environment: DEBUG: "FALSE" diff --git a/docker-compose_opal.yml b/docker-compose_opal.yml index 40b3bf268..a62dec679 100644 --- a/docker-compose_opal.yml +++ b/docker-compose_opal.yml @@ -20,6 +20,6 @@ services: - MONGO_INITDB_ROOT_USERNAME=root - MONGO_INITDB_ROOT_PASSWORD=foobar rock: - image: datashield/rock-omicron-karma-permissive:devel + image: datashield/rock-quebrada-lamda-permissive:latest environment: DEBUG: "FALSE" diff --git a/docs/404.html b/docs/404.html index 761ee0b96..c37c451a9 100644 --- a/docs/404.html +++ b/docs/404.html @@ -32,7 +32,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -73,12 +73,12 @@

Page not found (404)

-

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/LICENSE.html b/docs/LICENSE.html index b495f5487..b18449a17 100644 --- a/docs/LICENSE.html +++ b/docs/LICENSE.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -256,11 +256,11 @@

NA

-

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/authors.html b/docs/authors.html index 177847f60..827877cec 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -71,10 +71,6 @@

Authors and Citation

Demetris Avraam. Author.

-
  • -

    Demetris Avraam. Author. -

    -

  • Yannick Marcon. Author.

    @@ -104,14 +100,14 @@

    Citation

    -

    Burton P, Wilson R, Butters O, Ryser-Welch P, Westerberg A, Abarrategui L, Villegas-Diaz R, Avraam D, Avraam D, Marcon Y, Bishop T, Gaye A, Escribà-Montagut X, Wheater S (2025). +

    Burton P, Wilson R, Butters O, Ryser-Welch P, Westerberg A, Abarrategui L, Villegas-Diaz R, Avraam D, Marcon Y, Bishop T, Gaye A, Escribà-Montagut X, Wheater S (????). dsBaseClient: 'DataSHIELD' Client Side Base Functions. -R package version 6.3.4. +R package version 6.3.5. 

    @Manual{,
   title = {dsBaseClient: 'DataSHIELD' Client Side Base Functions},
-  author = {Paul Burton and Rebecca Wilson and Olly Butters and Patricia Ryser-Welch and Alex Westerberg and Leire Abarrategui and Roberto Villegas-Diaz and Demetris Avraam and Demetris Avraam and Yannick Marcon and Tom Bishop and Amadou Gaye and Xavier Escribà-Montagut and Stuart Wheater},
-  note = {R package version 6.3.4},
+  author = {Paul Burton and Rebecca Wilson and Olly Butters and Patricia Ryser-Welch and Alex Westerberg and Leire Abarrategui and Roberto Villegas-Diaz and Demetris Avraam and Yannick Marcon and Tom Bishop and Amadou Gaye and Xavier Escribà-Montagut and Stuart Wheater},
+  note = {R package version 6.3.5},
 }

    Gaye A, Marcon Y, Isaeva J, LaFlamme P, Turner A, Jones E, Minion J, Boyd A, Newby C, Nuotio M, Wilson R, Butters O, Murtagh B, Demir I, Doiron D, Giepmans L, Wallace S, Budin-Ljøsne I, Schmidt C, Boffetta P, Boniol M, Bota M, Carter K, deKlerk N, Dibben C, Francis R, Hiekkalinna T, Hveem K, Kvaløy K, Millar S, Perry I, Peters A, Phillips C, Popham F, Raab G, Reischl E, Sheehan N, Waldenberger M, Perola M, van den Heuvel E, Macleod J, Knoppers B, Stolk R, Fortier I, Harris J, Woffenbuttel B, Murtagh M, Ferretti V, Burton P (2014). “DataSHIELD: taking the analysis to the data, not the data to the analysis.” @@ -168,11 +164,11 @@

    Citation

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/index.html b/docs/index.html index cc91e1494..b3d66be0a 100644 --- a/docs/index.html +++ b/docs/index.html @@ -12,7 +12,7 @@ - + Pool missing data patterns across studies — .pool_md_patterns • dsBaseClient + + +
    +
    + + + +
    +
    +
    +

    Pool missing data patterns across studies

    + + +
    + +
    +

    Internal function to pool md.pattern results from multiple studies

    +
    + +
    + 
    .pool_md_patterns(patterns_list, study_names)
    +
    + +
    +

    Arguments

    + + +
    patterns_list
    +

    List of pattern matrices from each study

    + + +
    study_names
    +

    Names of the studies

    + +
    +
    +

    Value

    +

    Pooled pattern matrix

    +
    + +
    + +
    + + +
    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +
    + +
    +

    Site built with pkgdown 2.2.0.

    +
    + +
    + + + + + + + + diff --git a/docs/reference/ds.Boole.html b/docs/reference/ds.Boole.html index b3e3b55e8..8024db82e 100644 --- a/docs/reference/ds.Boole.html +++ b/docs/reference/ds.Boole.html @@ -20,7 +20,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -200,11 +200,11 @@

    Examples

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.abs.html b/docs/reference/ds.abs.html index d986834af..3ca2945fd 100644 --- a/docs/reference/ds.abs.html +++ b/docs/reference/ds.abs.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -150,11 +150,11 @@

    Examples

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.asCharacter.html b/docs/reference/ds.asCharacter.html index 9b2b1fdaf..1ea041a6b 100644 --- a/docs/reference/ds.asCharacter.html +++ b/docs/reference/ds.asCharacter.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -132,11 +132,11 @@

    Examples

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.asDataMatrix.html b/docs/reference/ds.asDataMatrix.html index eb7b66e38..43145cc63 100644 --- a/docs/reference/ds.asDataMatrix.html +++ b/docs/reference/ds.asDataMatrix.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -135,11 +135,11 @@

    Examples

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.asFactor.html b/docs/reference/ds.asFactor.html index a2db6d261..7c3ea953c 100644 --- a/docs/reference/ds.asFactor.html +++ b/docs/reference/ds.asFactor.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -144,7 +144,7 @@

    Details

    If we set the argument fixed.dummy.vars = TRUE, baseline.level = 1 and forced.factor.levels = c(1,2,3,4,5). The input vector is converted to the following matrix of dummy variables:

    -
    DV2DV3DV4DV50
    00010
    00000
    00100
    00100
    01000
    00010
    00010

    For the same example if the baseline.level = 3 then the matrix is:

    +
    DV2DV3DV4DV5
    0000
    1000
    0000
    0100
    0010
    0010
    0000
    0100
    0010
    0001

    For the same example if the baseline.level = 3 then the matrix is:

    DV1DV2DV4DV5
    1000
    0100
    1000
    0000
    0010
    0010
    1000
    0000
    0010
    0001

    In the first instance the first row of the matrix has zeros in all entries indicating that the first data point belongs to level 1 (as the baseline level is equal to 1). The second row has 1 at the first (DV2) column and zeros elsewhere, @@ -229,11 +229,11 @@

    Examples

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.asFactorSimple.html b/docs/reference/ds.asFactorSimple.html index 32283795b..c29a0462f 100644 --- a/docs/reference/ds.asFactorSimple.html +++ b/docs/reference/ds.asFactorSimple.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -103,11 +103,11 @@

    Author

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.asInteger.html b/docs/reference/ds.asInteger.html index 0bb6cce03..f491af4a8 100644 --- a/docs/reference/ds.asInteger.html +++ b/docs/reference/ds.asInteger.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -148,11 +148,11 @@

    Examples

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.asList.html b/docs/reference/ds.asList.html index 45437c4b3..d9d70b03b 100644 --- a/docs/reference/ds.asList.html +++ b/docs/reference/ds.asList.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -133,11 +133,11 @@

    Examples

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.asLogical.html b/docs/reference/ds.asLogical.html index 58658647e..a30586d47 100644 --- a/docs/reference/ds.asLogical.html +++ b/docs/reference/ds.asLogical.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -134,11 +134,11 @@

    Examples

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.asMatrix.html b/docs/reference/ds.asMatrix.html index c961e2584..b49975539 100644 --- a/docs/reference/ds.asMatrix.html +++ b/docs/reference/ds.asMatrix.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -136,11 +136,11 @@

    Examples

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.asNumeric.html b/docs/reference/ds.asNumeric.html index 76ec51363..db255308d 100644 --- a/docs/reference/ds.asNumeric.html +++ b/docs/reference/ds.asNumeric.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -147,11 +147,11 @@

    Examples

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.assign.html b/docs/reference/ds.assign.html index af6b3e020..ff9c513d5 100644 --- a/docs/reference/ds.assign.html +++ b/docs/reference/ds.assign.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -131,11 +131,11 @@

    Examples

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.auc.html b/docs/reference/ds.auc.html index 2c93a3083..1343b260e 100644 --- a/docs/reference/ds.auc.html +++ b/docs/reference/ds.auc.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -89,11 +89,11 @@

    Author

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.boxPlot.html b/docs/reference/ds.boxPlot.html index c7b9a1e0b..00449f1e1 100644 --- a/docs/reference/ds.boxPlot.html +++ b/docs/reference/ds.boxPlot.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -103,7 +103,72 @@

    Value

    Examples

    - + 
    if (FALSE) { # \dontrun{
+  ## Version 6, for version 5 see the Wiki
+  
+  ### Please ensure you have a training Virtual Machine running,
+  # or that you have a live connection to a server.
+     
+  # Connecting to the Opal servers
+
+  require('DSI')
+  require('DSOpal')
+  require('dsBaseClient')
+
+  builder <- DSI::newDSLoginBuilder()
+  builder$append(server = "study1", 
+                 url = "http://192.168.56.100:8080/", 
+                 user = "administrator", password = "datashield_test&", 
+                 table = "CNSIM.CNSIM1", driver = "OpalDriver")
+  builder$append(server = "study2", 
+                 url = "http://192.168.56.100:8080/", 
+                 user = "administrator", password = "datashield_test&", 
+                 table = "CNSIM.CNSIM2", driver = "OpalDriver")
+  builder$append(server = "study3",
+                 url = "http://192.168.56.100:8080/", 
+                 user = "administrator", password = "datashield_test&", 
+                 table = "CNSIM.CNSIM3", driver = "OpalDriver")
+  logindata <- builder$build()
+  
+  connections <- DSI::datashield.login(logins = logindata, assign = TRUE,
+   symbol = "D") 
+  
+  ## Create a boxplot of one variable
+  ds.boxPlot("D", "LAB_HDL", datasources = connections) 
+ 
+  ## Create a boxplot that is split by study:
+  ds.boxPlot("D", "LAB_HDL", type= "split", datasources = connections) 
+  
+  ## Create a boxplot of two variables variable
+  ds.boxPlot("D", c("LAB_HDL", "LAB_TRIG"), type="pooled", 
+  datasources = connections)  
+  # only one plot is created (of the aggregated results of all servers)
+  
+  ## Create a boxplot of two variables, which are split by a factor
+  ds.boxPlot("D", c("LAB_HDL", "LAB_TRIG"), group = "GENDER", 
+  datasources = connections)
+  
+  ## Create a boxplot with x- and y-axis labels
+  ds.boxPlot("D", c("LAB_HDL", "LAB_TRIG"), group = "GENDER", 
+  xlabel = "Variable", ylabel = "Measurement", datasources = connections)
+  
+  ## Improve the presentation of ds.boxplot output using ggplot:
+  ### User must save the output, which is in a ggplot format already:
+  a <- ds.boxPlot("D", c("LAB_HDL", "LAB_TRIG"), group = "GENDER", 
+  xlabel = "Variable", ylabel = "Measurement", datasources = connections)
+                 
+  ### Then customise output "a" using ggplot tools:
+  a + ggplot2::scale_fill_discrete(name = "Gender", labels = c("Male", "Female"))
+  
+  ### Or use an alternative way, to maintain the aesthetics:
+  a + ggplot2::scale_fill_brewer(name = "Gender", labels = c("Male", "Female")) 
+                                                                                
+  # Clear the Datashield R sessions and logout                 
+  datashield.logout(connections) 
+  
+} # }   
+
+
    diff --git a/docs/reference/ds.boxPlotGG.html b/docs/reference/ds.boxPlotGG.html index 1d5456390..3e779c1ca 100644 --- a/docs/reference/ds.boxPlotGG.html +++ b/docs/reference/ds.boxPlotGG.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -108,11 +108,11 @@

    Value

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.boxPlotGG_data_Treatment.html b/docs/reference/ds.boxPlotGG_data_Treatment.html index 4ad0dbdc6..3fcb2e8c5 100644 --- a/docs/reference/ds.boxPlotGG_data_Treatment.html +++ b/docs/reference/ds.boxPlotGG_data_Treatment.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -95,11 +95,11 @@

    Value

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.boxPlotGG_data_Treatment_numeric.html b/docs/reference/ds.boxPlotGG_data_Treatment_numeric.html index 4e760a434..f4cdd49a1 100644 --- a/docs/reference/ds.boxPlotGG_data_Treatment_numeric.html +++ b/docs/reference/ds.boxPlotGG_data_Treatment_numeric.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -75,11 +75,11 @@

    Value

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.boxPlotGG_numeric.html b/docs/reference/ds.boxPlotGG_numeric.html index a2f69f988..c9c63d122 100644 --- a/docs/reference/ds.boxPlotGG_numeric.html +++ b/docs/reference/ds.boxPlotGG_numeric.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -91,11 +91,11 @@

    Value

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.boxPlotGG_table.html b/docs/reference/ds.boxPlotGG_table.html index 46f7ed910..267ba4616 100644 --- a/docs/reference/ds.boxPlotGG_table.html +++ b/docs/reference/ds.boxPlotGG_table.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -106,11 +106,11 @@

    Value

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.bp_standards.html b/docs/reference/ds.bp_standards.html index e3ab71fd8..27cc3024a 100644 --- a/docs/reference/ds.bp_standards.html +++ b/docs/reference/ds.bp_standards.html @@ -20,7 +20,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -126,11 +126,11 @@

    Author

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.c.html b/docs/reference/ds.c.html index d15251bad..a10858a7d 100644 --- a/docs/reference/ds.c.html +++ b/docs/reference/ds.c.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -132,11 +132,11 @@

    Examples

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.cbind.html b/docs/reference/ds.cbind.html index 91ef0d49a..5b12f78e1 100644 --- a/docs/reference/ds.cbind.html +++ b/docs/reference/ds.cbind.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -206,11 +206,11 @@

    Examples

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.changeRefGroup.html b/docs/reference/ds.changeRefGroup.html index 30b39d214..10b57d0bd 100644 --- a/docs/reference/ds.changeRefGroup.html +++ b/docs/reference/ds.changeRefGroup.html @@ -19,7 +19,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -199,11 +199,11 @@

    Examples

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.class.html b/docs/reference/ds.class.html index 7906dc578..67503eac8 100644 --- a/docs/reference/ds.class.html +++ b/docs/reference/ds.class.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -130,11 +130,11 @@

    Examples

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.colnames.html b/docs/reference/ds.colnames.html index 64853c41a..d4cbaf161 100644 --- a/docs/reference/ds.colnames.html +++ b/docs/reference/ds.colnames.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -94,28 +94,28 @@

    Examples

    require('dsBaseClient') builder <- DSI::newDSLoginBuilder() - builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", + builder$append(server = "study1", + url = "http://192.168.56.100:8080/", + user = "administrator", password = "datashield_test&", table = "CNSIM.CNSIM1", driver = "OpalDriver") - builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", + builder$append(server = "study2", + url = "http://192.168.56.100:8080/", + user = "administrator", password = "datashield_test&", table = "CNSIM.CNSIM2", driver = "OpalDriver") builder$append(server = "study3", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", + url = "http://192.168.56.100:8080/", + user = "administrator", password = "datashield_test&", table = "CNSIM.CNSIM3", driver = "OpalDriver") logindata <- builder$build() - + # Log onto the remote Opal training servers - connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") + connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") # Getting column names of the R objects stored in the server-side ds.colnames(x = "D", datasources = connections[1]) #only the first server ("study1") is used # Clear the Datashield R sessions and logout - datashield.logout(connections) + datashield.logout(connections) } # } @@ -127,11 +127,11 @@

    Examples

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.completeCases.html b/docs/reference/ds.completeCases.html index 6fa86c83f..5c54c1390 100644 --- a/docs/reference/ds.completeCases.html +++ b/docs/reference/ds.completeCases.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -147,11 +147,11 @@

    Examples

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.contourPlot.html b/docs/reference/ds.contourPlot.html index 2c4cd97d2..0a8a57fff 100644 --- a/docs/reference/ds.contourPlot.html +++ b/docs/reference/ds.contourPlot.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -203,11 +203,11 @@

    Examples

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.cor.html b/docs/reference/ds.cor.html index 19251198b..2690c2ca8 100644 --- a/docs/reference/ds.cor.html +++ b/docs/reference/ds.cor.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -156,11 +156,11 @@

    Examples

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.corTest.html b/docs/reference/ds.corTest.html index fdd369b9c..f508a53d7 100644 --- a/docs/reference/ds.corTest.html +++ b/docs/reference/ds.corTest.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -162,11 +162,11 @@

    Examples

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.cov.html b/docs/reference/ds.cov.html index 3637997c7..645ea7791 100644 --- a/docs/reference/ds.cov.html +++ b/docs/reference/ds.cov.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -181,11 +181,11 @@

    Examples

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.dataFrame.html b/docs/reference/ds.dataFrame.html index 791095af2..e197076d8 100644 --- a/docs/reference/ds.dataFrame.html +++ b/docs/reference/ds.dataFrame.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -199,11 +199,11 @@

    Examples

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.dataFrameFill.html b/docs/reference/ds.dataFrameFill.html index 7278740e1..e99a1b5b6 100644 --- a/docs/reference/ds.dataFrameFill.html +++ b/docs/reference/ds.dataFrameFill.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -150,11 +150,11 @@

    Examples

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.dataFrameSort.html b/docs/reference/ds.dataFrameSort.html index 99e75c797..a1e355fa8 100644 --- a/docs/reference/ds.dataFrameSort.html +++ b/docs/reference/ds.dataFrameSort.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -171,11 +171,11 @@

    Examples

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.dataFrameSubset.html b/docs/reference/ds.dataFrameSubset.html index 73448ea53..18b2ed85f 100644 --- a/docs/reference/ds.dataFrameSubset.html +++ b/docs/reference/ds.dataFrameSubset.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -216,11 +216,11 @@

    Examples

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.densityGrid.html b/docs/reference/ds.densityGrid.html index 4390d2b43..8b8ac9288 100644 --- a/docs/reference/ds.densityGrid.html +++ b/docs/reference/ds.densityGrid.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -110,7 +110,59 @@

    Author

    Examples

    - + 
    if (FALSE) { # \dontrun{
+
+ ## Version 6, for version 5 see the Wiki
+  # Connecting to the Opal servers
+
+  require('DSI')
+  require('DSOpal')
+  require('dsBaseClient')
+
+  builder <- DSI::newDSLoginBuilder()
+  builder$append(server = "study1", 
+                 url = "http://192.168.56.100:8080/", 
+                 user = "administrator", password = "datashield_test&", 
+                 table = "CNSIM.CNSIM1", driver = "OpalDriver")
+  builder$append(server = "study2", 
+                 url = "http://192.168.56.100:8080/", 
+                 user = "administrator", password = "datashield_test&", 
+                 table = "CNSIM.CNSIM2", driver = "OpalDriver")
+  builder$append(server = "study3",
+                 url = "http://192.168.56.100:8080/", 
+                 user = "administrator", password = "datashield_test&", 
+                 table = "CNSIM.CNSIM3", driver = "OpalDriver")
+  logindata <- builder$build()
+  
+  # Log onto the remote Opal training servers
+  connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") 
+ 
+  #Generate the density grid
+  # Example1: generate a combined grid density object (default)
+  ds.densityGrid(x="D$LAB_TSC",
+                 y="D$LAB_HDL",
+                 datasources = connections)#all opal servers are used
+
+  # Example2: generate a grid density object for each study separately
+  ds.densityGrid(x="D$LAB_TSC",
+                 y="D$LAB_HDL",
+                 type="split",
+                 datasources = connections[1])#only the first Opal server is used ("study1")
+
+  # Example3: generate a grid density object where the number of intervals is set to 15, for
+  #           each study separately
+  ds.densityGrid(x="D$LAB_TSC",
+                 y="D$LAB_HDL",
+                 type="split",
+                 numints=15,
+                 datasources = connections)
+
+  # clear the Datashield R sessions and logout
+  datashield.logout(connections)
+
+} # }
+
+
    diff --git a/docs/reference/ds.dim.html b/docs/reference/ds.dim.html index 037e87c70..3b979bac0 100644 --- a/docs/reference/ds.dim.html +++ b/docs/reference/ds.dim.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -167,11 +167,11 @@

    Examples

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.dmtC2S.html b/docs/reference/ds.dmtC2S.html index b0c531322..5992efa0c 100644 --- a/docs/reference/ds.dmtC2S.html +++ b/docs/reference/ds.dmtC2S.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -120,11 +120,11 @@

    Author

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.elspline.html b/docs/reference/ds.elspline.html index b2a8d5d83..ac1b671ec 100644 --- a/docs/reference/ds.elspline.html +++ b/docs/reference/ds.elspline.html @@ -20,7 +20,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -119,11 +119,11 @@

    Author

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.exists.html b/docs/reference/ds.exists.html index f5db40ba5..472c44855 100644 --- a/docs/reference/ds.exists.html +++ b/docs/reference/ds.exists.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -138,11 +138,11 @@

    Examples

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.exp.html b/docs/reference/ds.exp.html index eff914133..0922474a3 100644 --- a/docs/reference/ds.exp.html +++ b/docs/reference/ds.exp.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -132,11 +132,11 @@

    Examples

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.extractQuantiles.html b/docs/reference/ds.extractQuantiles.html index 0984ace64..f0f7af688 100644 --- a/docs/reference/ds.extractQuantiles.html +++ b/docs/reference/ds.extractQuantiles.html @@ -26,7 +26,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -176,11 +176,11 @@

    Author

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.forestplot.html b/docs/reference/ds.forestplot.html index 8ad597e4d..1a5a3f5b5 100644 --- a/docs/reference/ds.forestplot.html +++ b/docs/reference/ds.forestplot.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -73,6 +73,10 @@

    Arguments

    See details from ?meta::metagen for the different options.

    +
    +

    Value

    +

    Results a foresplot object created with `meta::forest`.

    +

    Examples

    @@ -118,11 +122,11 @@

    Examples

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.gamlss.html b/docs/reference/ds.gamlss.html index 6ea9d0609..6362d6b3f 100644 --- a/docs/reference/ds.gamlss.html +++ b/docs/reference/ds.gamlss.html @@ -23,7 +23,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -215,11 +215,11 @@

    Author

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.getWGSR.html b/docs/reference/ds.getWGSR.html index 2b697ccb4..f704cf593 100644 --- a/docs/reference/ds.getWGSR.html +++ b/docs/reference/ds.getWGSR.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -204,11 +204,11 @@

    Examples

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.glm.html b/docs/reference/ds.glm.html index 651c41e04..9bba08948 100644 --- a/docs/reference/ds.glm.html +++ b/docs/reference/ds.glm.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -427,11 +427,11 @@

    Examples

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.glmPredict.html b/docs/reference/ds.glmPredict.html index 2d4434a01..d1139d4a9 100644 --- a/docs/reference/ds.glmPredict.html +++ b/docs/reference/ds.glmPredict.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -227,11 +227,11 @@

    Author

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.glmSLMA.html b/docs/reference/ds.glmSLMA.html index d5ab72ff0..09833a2d4 100644 --- a/docs/reference/ds.glmSLMA.html +++ b/docs/reference/ds.glmSLMA.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -493,11 +493,11 @@

    Examples

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.glmSummary.html b/docs/reference/ds.glmSummary.html index 5bacf7ad5..dfffeb2a2 100644 --- a/docs/reference/ds.glmSummary.html +++ b/docs/reference/ds.glmSummary.html @@ -20,7 +20,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -154,11 +154,11 @@

    Author

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.glmerSLMA.html b/docs/reference/ds.glmerSLMA.html index ccc7ec131..7d1eea67b 100644 --- a/docs/reference/ds.glmerSLMA.html +++ b/docs/reference/ds.glmerSLMA.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -379,11 +379,11 @@

    Examples

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.heatmapPlot.html b/docs/reference/ds.heatmapPlot.html index b45a3e6f6..73d3a6843 100644 --- a/docs/reference/ds.heatmapPlot.html +++ b/docs/reference/ds.heatmapPlot.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -189,7 +189,65 @@

    Author

    Examples

    - + 
    if (FALSE) { # \dontrun{
+
+## Version 6, for version 5 see the Wiki
+  # Connecting to the Opal servers
+
+  require('DSI')
+  require('DSOpal')
+  require('dsBaseClient')
+
+  builder <- DSI::newDSLoginBuilder()
+  builder$append(server = "study1", 
+                 url = "http://192.168.56.100:8080/", 
+                 user = "administrator", password = "datashield_test&", 
+                 table = "CNSIM.CNSIM1", driver = "OpalDriver")
+  builder$append(server = "study2", 
+                 url = "http://192.168.56.100:8080/", 
+                 user = "administrator", password = "datashield_test&", 
+                 table = "CNSIM.CNSIM2", driver = "OpalDriver")
+  builder$append(server = "study3",
+                 url = "http://192.168.56.100:8080/", 
+                 user = "administrator", password = "datashield_test&", 
+                 table = "CNSIM.CNSIM3", driver = "OpalDriver")
+  logindata <- builder$build()
+  
+  # Log onto the remote Opal training servers
+  connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") 
+  
+  # Compute the heat map plot 
+  # Example 1: Plot a combined (default) heat map plot of the variables 'LAB_TSC'
+  # and 'LAB_HDL' using the method 'smallCellsRule' (default)
+  ds.heatmapPlot(x = 'D$LAB_TSC',
+                 y = 'D$LAB_HDL',
+                 datasources = connections) #all servers are used
+                 
+  # Example 2: Plot a split heat map  plot of the variables 'LAB_TSC'
+  # and 'LAB_HDL' using the method 'smallCellsRule' (default)
+  ds.heatmapPlot(x = 'D$LAB_TSC', 
+                 y = 'D$LAB_HDL',
+                 method = 'smallCellsRule', 
+                 type = 'split',
+                 datasources = connections[1]) #only the first server is used (study1)
+                 
+  # Example 3: Plot a combined heat map plot using the method 'deterministic' centroids of each 
+  # k = 7 nearest neighbours for numints = 40
+  ds.heatmapPlot(x = 'D$LAB_TSC',
+                 y = 'D$LAB_HDL', 
+                 numints = 40, 
+                 method = 'deterministic',
+                 k = 7,
+                 type = 'split',
+                 datasources = connections[2]) #only the second server is used (study2)
+
+
+  # clear the Datashield R sessions and logout
+  datashield.logout(connections)
+
+} # }
+
+
    diff --git a/docs/reference/ds.hetcor.html b/docs/reference/ds.hetcor.html index 2373f7117..79ad610cc 100644 --- a/docs/reference/ds.hetcor.html +++ b/docs/reference/ds.hetcor.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -124,11 +124,11 @@

    Author

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.histogram.html b/docs/reference/ds.histogram.html index 329bbf7aa..ee7427087 100644 --- a/docs/reference/ds.histogram.html +++ b/docs/reference/ds.histogram.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -180,7 +180,72 @@

    Author

    Examples

    - + 
    if (FALSE) { # \dontrun{
+
+## Version 6, for version 5 see the Wiki
+  # Connecting to the Opal servers
+
+  require('DSI')
+  require('DSOpal')
+  require('dsBaseClient')
+
+  builder <- DSI::newDSLoginBuilder()
+  builder$append(server = "study1", 
+                 url = "http://192.168.56.100:8080/", 
+                 user = "administrator", password = "datashield_test&", 
+                 table = "CNSIM.CNSIM1", driver = "OpalDriver")
+  builder$append(server = "study2", 
+                 url = "http://192.168.56.100:8080/", 
+                 user = "administrator", password = "datashield_test&", 
+                 table = "CNSIM.CNSIM2", driver = "OpalDriver")
+  builder$append(server = "study3",
+                 url = "http://192.168.56.100:8080/", 
+                 user = "administrator", password = "datashield_test&", 
+                 table = "CNSIM.CNSIM3", driver = "OpalDriver")
+  logindata <- builder$build()
+  
+  # Log onto the remote Opal training servers
+  connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") 
+  
+  # Compute the histogram
+  # Example 1: generate a histogram for each study separately 
+  ds.histogram(x = 'D$PM_BMI_CONTINUOUS',
+              type = "split",
+              datasources = connections) #all studies are used
+
+  # Example 2: generate a combined histogram with the default small cells counts
+  #             suppression rule
+  ds.histogram(x = 'D$PM_BMI_CONTINUOUS',
+               method = 'smallCellsRule',
+               type = 'combine',
+               datasources = connections[1]) #only the first study is used (study1)
+
+  # Example 3: if a variable is of type factor the function returns an error
+  ds.histogram(x = 'D$PM_BMI_CATEGORICAL',
+               datasources = connections)
+
+  # Example 4: generate a combined histogram with the deterministic method for k=50
+  ds.histogram(x = 'D$PM_BMI_CONTINUOUS',
+               k = 50, 
+               method = 'deterministic',
+               type = 'combine',
+               datasources = connections[2])#only the second study is used (study2)
+
+
+  # Example 5: create a histogram and the probability density on the plot
+  hist <- ds.histogram(x = 'D$PM_BMI_CONTINUOUS',
+                       method = 'probabilistic', type='combine',
+                       num.breaks = 30, 
+                       vertical.axis = 'Density',
+                       datasources = connections)
+  lines(hist$mids, hist$density)
+
+  # clear the Datashield R sessions and logout
+  datashield.logout(connections)
+  } # }
+
+
+
    diff --git a/docs/reference/ds.igb_standards.html b/docs/reference/ds.igb_standards.html index 1f04c7bbb..05c0bdf51 100644 --- a/docs/reference/ds.igb_standards.html +++ b/docs/reference/ds.igb_standards.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -141,11 +141,11 @@

    Author

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.isNA.html b/docs/reference/ds.isNA.html index 7fa98292c..1c8159682 100644 --- a/docs/reference/ds.isNA.html +++ b/docs/reference/ds.isNA.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -131,11 +131,11 @@

    Examples

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.isValid.html b/docs/reference/ds.isValid.html index 3ad491a01..51be2e36d 100644 --- a/docs/reference/ds.isValid.html +++ b/docs/reference/ds.isValid.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -131,11 +131,11 @@

    Examples

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.kurtosis.html b/docs/reference/ds.kurtosis.html index 8c2012bea..f77013ae3 100644 --- a/docs/reference/ds.kurtosis.html +++ b/docs/reference/ds.kurtosis.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -103,11 +103,11 @@

    Author

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.length.html b/docs/reference/ds.length.html index f71fef07e..98950b905 100644 --- a/docs/reference/ds.length.html +++ b/docs/reference/ds.length.html @@ -19,7 +19,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -157,11 +157,11 @@

    Examples

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.levels.html b/docs/reference/ds.levels.html index c2f42b3c1..addda2b48 100644 --- a/docs/reference/ds.levels.html +++ b/docs/reference/ds.levels.html @@ -19,7 +19,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -133,11 +133,11 @@

    Examples

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.lexis.html b/docs/reference/ds.lexis.html index 2f5e87db8..c01e94753 100644 --- a/docs/reference/ds.lexis.html +++ b/docs/reference/ds.lexis.html @@ -19,7 +19,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -298,11 +298,11 @@

    Examples

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.list.html b/docs/reference/ds.list.html index b6acfeb3c..48facb734 100644 --- a/docs/reference/ds.list.html +++ b/docs/reference/ds.list.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -129,11 +129,11 @@

    Examples

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.listClientsideFunctions.html b/docs/reference/ds.listClientsideFunctions.html index 46871aa7d..6e285862f 100644 --- a/docs/reference/ds.listClientsideFunctions.html +++ b/docs/reference/ds.listClientsideFunctions.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -86,11 +86,11 @@

    Examples

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.listDisclosureSettings.html b/docs/reference/ds.listDisclosureSettings.html index 205f07cfa..9fc5b9a18 100644 --- a/docs/reference/ds.listDisclosureSettings.html +++ b/docs/reference/ds.listDisclosureSettings.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -162,11 +162,11 @@

    Examples

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.listOpals.html b/docs/reference/ds.listOpals.html index 977c9afc3..01f2240e8 100644 --- a/docs/reference/ds.listOpals.html +++ b/docs/reference/ds.listOpals.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -80,11 +80,11 @@

    Author

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.listServersideFunctions.html b/docs/reference/ds.listServersideFunctions.html index 9dd4dc556..aad5a343b 100644 --- a/docs/reference/ds.listServersideFunctions.html +++ b/docs/reference/ds.listServersideFunctions.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -124,11 +124,11 @@

    Examples

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.lmerSLMA.html b/docs/reference/ds.lmerSLMA.html index acc1a8257..7564f289d 100644 --- a/docs/reference/ds.lmerSLMA.html +++ b/docs/reference/ds.lmerSLMA.html @@ -19,7 +19,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -328,11 +328,11 @@

    Examples

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.log.html b/docs/reference/ds.log.html index 2380a59fe..4b9682dcf 100644 --- a/docs/reference/ds.log.html +++ b/docs/reference/ds.log.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -138,11 +138,11 @@

    Examples

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.look.html b/docs/reference/ds.look.html index 398e30953..99845990f 100644 --- a/docs/reference/ds.look.html +++ b/docs/reference/ds.look.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -147,11 +147,11 @@

    Examples

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.ls.html b/docs/reference/ds.ls.html index 6fd23b812..f1083a610 100644 --- a/docs/reference/ds.ls.html +++ b/docs/reference/ds.ls.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -198,11 +198,11 @@

    Examples

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.lspline.html b/docs/reference/ds.lspline.html index 4b78e6ebb..224100e42 100644 --- a/docs/reference/ds.lspline.html +++ b/docs/reference/ds.lspline.html @@ -20,7 +20,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -116,11 +116,11 @@

    Author

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.make.html b/docs/reference/ds.make.html index fc0980558..eb70c3970 100644 --- a/docs/reference/ds.make.html +++ b/docs/reference/ds.make.html @@ -19,7 +19,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -201,11 +201,11 @@

    Examples

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.matrix.html b/docs/reference/ds.matrix.html index 6301c538f..c91744035 100644 --- a/docs/reference/ds.matrix.html +++ b/docs/reference/ds.matrix.html @@ -20,7 +20,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -246,11 +246,11 @@

    Examples

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.matrixDet.html b/docs/reference/ds.matrixDet.html index 09e6bab9a..958f7a637 100644 --- a/docs/reference/ds.matrixDet.html +++ b/docs/reference/ds.matrixDet.html @@ -20,7 +20,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -164,11 +164,11 @@

    Examples

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.matrixDet.report.html b/docs/reference/ds.matrixDet.report.html index 4fdbd6b1f..28c8f403d 100644 --- a/docs/reference/ds.matrixDet.report.html +++ b/docs/reference/ds.matrixDet.report.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -152,11 +152,11 @@

    Examples

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.matrixDiag.html b/docs/reference/ds.matrixDiag.html index 84200fc85..1429313a0 100644 --- a/docs/reference/ds.matrixDiag.html +++ b/docs/reference/ds.matrixDiag.html @@ -19,7 +19,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -145,7 +145,118 @@

    Author

    Examples

    - + 
    if (FALSE) { # \dontrun{
+
+ ## Version 6, for version 5 see the Wiki
+  
+  # connecting to the Opal servers
+
+  require('DSI')
+  require('DSOpal')
+  require('dsBaseClient')
+
+  builder <- DSI::newDSLoginBuilder()
+  builder$append(server = "study1", 
+                 url = "http://192.168.56.100:8080/", 
+                 user = "administrator", password = "datashield_test&", 
+                 table = "CNSIM.CNSIM1", driver = "OpalDriver")
+  builder$append(server = "study2", 
+                 url = "http://192.168.56.100:8080/", 
+                 user = "administrator", password = "datashield_test&", 
+                 table = "CNSIM.CNSIM2", driver = "OpalDriver")
+  builder$append(server = "study3",
+                 url = "http://192.168.56.100:8080/", 
+                 user = "administrator", password = "datashield_test&", 
+                 table = "CNSIM.CNSIM3", driver = "OpalDriver")
+  logindata <- builder$build()
+  
+  connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") 
+  
+  #Example 1: Create a square matrix with the server-side vector as its diagonal
+  #and all the other values = 0
+  
+  # Create a vector in the server-side 
+  
+  ds.rUnif(samp.size = 9,
+           min = -10.5,
+           max = 10.5,
+           newobj = "ss.vector.9",
+           seed.as.integer = 5575,
+           force.output.to.k.decimal.places = 0,
+           datasources = connections)
+   
+            
+  #Calculate the diagonal of the matrix
+  
+  ds.matrixDiag(x1 = "ss.vector.9",
+                aim = "serverside.vector.2.matrix",
+                nrows.scalar = NULL,
+                newobj = "matrix.diag1",
+                datasources = connections)
+                
+  #Example 2: Create a square matrix with the server-side scalar as all diagonal values 
+  #and all the other values = 0
+  
+  #Create a scalar in the server-side
+  
+  ds.rUnif(samp.size = 1,
+           min = -10.5,
+           max = 10.5,
+           newobj = "ss.scalar",
+           seed.as.integer = 5575,
+           force.output.to.k.decimal.places = 0,
+           datasources = connections)
+           
+  #Calculate the diagonal of the matrix
+           
+ ds.matrixDiag(x1 = "ss.scalar",
+               aim = "serverside.scalar.2.matrix",
+               nrows.scalar = 4,
+               newobj = "matrix.diag2",
+               datasources = connections)
+               
+ #Example 3: Create a vector that contains the server-side matrix diagonal values
+ 
+ #Create a matrix in the server-side
+ 
+ ds.matrix(mdata = 10,
+           from = "clientside.scalar",
+           nrows.scalar = 3,
+           ncols.scalar = 8,
+           newobj = "ss.matrix",
+           datasources = connections)
+           
+ #Extract the diagonal of the matrix
+     
+ ds.matrixDiag(x1 = "ss.matrix",
+               aim = "serverside.matrix.2.vector",
+               nrows.scalar = NULL,
+               newobj = "vector.diag3",
+               datasources = connections)
+                   
+ #Example 4: Create a square matrix with the client-side vector as a diagonal
+ #and all the other values = 0
+ 
+ ds.matrixDiag(x1 = c(2,6,9,10),
+               aim = "clientside.vector.2.matrix",
+               nrows.scalar = NULL,
+               newobj = "matrix.diag4",
+               datasources = connections)
+               
+ #Example 5: Create a square matrix with the client-side scalar as all diagonal values 
+ #and all the other values = 0
+ 
+ ds.matrixDiag(x1 = 4,
+               aim = "clientside.scalar.2.matrix",
+               nrows.scalar = 5,
+               newobj = "matrix.diag5",
+               datasources = connections)
+  
+  
+  # clear the Datashield R sessions and logout
+  datashield.logout(connections)
+} # }
+
    diff --git a/docs/reference/ds.matrixDimnames.html b/docs/reference/ds.matrixDimnames.html index 8cc27186a..5272176a7 100644 --- a/docs/reference/ds.matrixDimnames.html +++ b/docs/reference/ds.matrixDimnames.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -170,11 +170,11 @@

    Examples

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.matrixInvert.html b/docs/reference/ds.matrixInvert.html index 0937e4bd2..4d94199ab 100644 --- a/docs/reference/ds.matrixInvert.html +++ b/docs/reference/ds.matrixInvert.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -157,11 +157,11 @@

    Examples

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.matrixMult.html b/docs/reference/ds.matrixMult.html index 737b4cca5..0f7b11daf 100644 --- a/docs/reference/ds.matrixMult.html +++ b/docs/reference/ds.matrixMult.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -174,11 +174,11 @@

    Examples

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.matrixTranspose.html b/docs/reference/ds.matrixTranspose.html index 8e3dabe42..ff0f88cdc 100644 --- a/docs/reference/ds.matrixTranspose.html +++ b/docs/reference/ds.matrixTranspose.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -159,11 +159,11 @@

    Examples

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.mdPattern.html b/docs/reference/ds.mdPattern.html new file mode 100644 index 000000000..77d923ad3 --- /dev/null +++ b/docs/reference/ds.mdPattern.html @@ -0,0 +1,205 @@ + +Display missing data patterns with disclosure control — ds.mdPattern • dsBaseClient + + +
    +
    + + + +
    +
    +
    +

    Display missing data patterns with disclosure control

    + + +
    + +
    +

    This function is a client-side wrapper for the server-side mdPatternDS +function. It generates a missing data pattern matrix similar to mice::md.pattern but +with disclosure control applied to prevent revealing small cell counts.

    +
    + +
    + 
    ds.mdPattern(x = NULL, type = "split", datasources = NULL)
    +
    + +
    +

    Arguments

    + + +
    x
    +

    a character string specifying the name of a data frame or matrix on the +server-side containing the data to analyze.

    + + +
    type
    +

    a character string specifying the output type. If 'split' (default), +returns separate patterns for each study. If 'combine', attempts to pool patterns +across studies.

    + + +
    datasources
    +

    a list of DSConnection-class objects obtained +after login. If the datasources argument is not specified, the default set of +connections will be used: see datashield.connections_default.

    + +
    +
    +

    Value

    +

    For type='split': A list with one element per study, each containing:

    pattern
    +

    The missing data pattern matrix for that study

    + +
    valid
    +

    Logical indicating if all patterns meet disclosure requirements

    + +
    message
    +

    A message describing the validity status

    + + +

    For type='combine': A list containing:

    pattern
    +

    The pooled missing data pattern matrix across all studies

    + +
    valid
    +

    Logical indicating if all pooled patterns meet disclosure requirements

    + +
    message
    +

    A message describing the validity status

    + + +
    +
    +

    Details

    +

    The function calls the server-side mdPatternDS function which uses +mice::md.pattern to analyze missing data patterns. Patterns with counts below the +disclosure threshold (default: nfilter.tab = 3) are suppressed to maintain privacy.

    +

    Output Format: +- Each row represents a missing data pattern +- Pattern counts are shown in row names (e.g., "150", "25") +- Columns show 1 if the variable is observed, 0 if missing +- Last column shows the total number of missing values per pattern +- Last row shows the total number of missing values per variable

    +

    Disclosure Control:

    +

    Suppressed patterns (count below threshold) are indicated by: +- Row name: "suppressed(<N>)" where N is the threshold +- All pattern values set to NA +- Summary row also suppressed to prevent back-calculation

    +

    Pooling Behavior (type='combine'):

    +

    When pooling across studies, the function uses a conservative approach +for disclosure control:

    +

    1. Identifies identical missing patterns across studies +2. EXCLUDES suppressed patterns from pooling - patterns suppressed in + ANY study are not included in the pooled count +3. Sums counts only for non-suppressed identical patterns +4. Re-validates pooled counts against disclosure threshold

    +

    Important: This conservative approach means: +- Pooled counts may be underestimates if some studies had suppressed patterns +- This prevents disclosure through subtraction (e.g., if study A shows count=5 + and pool shows count=7, one could deduce study B has count=2, violating disclosure) +- Different patterns across studies are preserved separately in the pooled result

    +
    +
    +

    Author

    +

    Xavier Escribà montagut for DataSHIELD Development Team

    +
    + +
    +

    Examples

    + 
    if (FALSE) { # \dontrun{
+ ## Version 6, for version 5 see the Wiki
+
+  # Connecting to the Opal servers
+
+  require('DSI')
+  require('DSOpal')
+  require('dsBaseClient')
+
+  builder <- DSI::newDSLoginBuilder()
+  builder$append(server = "study1",
+                 url = "http://192.168.56.100:8080/",
+                 user = "administrator", password = "datashield_test&",
+                 table = "CNSIM.CNSIM1", driver = "OpalDriver")
+  builder$append(server = "study2",
+                 url = "http://192.168.56.100:8080/",
+                 user = "administrator", password = "datashield_test&",
+                 table = "CNSIM.CNSIM2", driver = "OpalDriver")
+  logindata <- builder$build()
+
+  connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D")
+
+  # Get missing data patterns for each study separately
+  patterns_split <- ds.mdPattern(x = "D", type = "split", datasources = connections)
+
+  # View results for study1
+  print(patterns_split$study1$pattern)
+  #      var1 var2 var3
+  # 150    1    1    1  0    <- 150 obs complete
+  #  25    0    1    1  1    <- 25 obs missing var1
+  #       25    0    0 25    <- Summary: 25 missing per variable
+
+  # Get pooled missing data patterns across studies
+  patterns_pooled <- ds.mdPattern(x = "D", type = "combine", datasources = connections)
+  print(patterns_pooled$pattern)
+
+  # Example with suppressed patterns:
+  # If study1 has a pattern with count=2 (suppressed) and study2 has same pattern 
+  # with count=5 (valid), the pooled result will show count=5 (conservative approach)
+  # A warning will indicate: "Pooled counts may underestimate the true total"
+
+  # Clear the Datashield R sessions and logout
+  datashield.logout(connections)
+} # }
+
+
    +
    +
    + +
    + + +
    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +
    + +
    +

    Site built with pkgdown 2.2.0.

    +
    + +
    + + + + + + + + diff --git a/docs/reference/ds.mean.html b/docs/reference/ds.mean.html index 5bac04db2..0bc64806f 100644 --- a/docs/reference/ds.mean.html +++ b/docs/reference/ds.mean.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -185,11 +185,11 @@

    Examples

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.meanByClass.html b/docs/reference/ds.meanByClass.html index 411ed7332..d7a1e210b 100644 --- a/docs/reference/ds.meanByClass.html +++ b/docs/reference/ds.meanByClass.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -169,11 +169,11 @@

    Examples

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.meanSdGp.html b/docs/reference/ds.meanSdGp.html index ffc0c2bfb..e472a3901 100644 --- a/docs/reference/ds.meanSdGp.html +++ b/docs/reference/ds.meanSdGp.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -214,11 +214,11 @@

    Examples

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.merge.html b/docs/reference/ds.merge.html index 1ad185efc..cefb07add 100644 --- a/docs/reference/ds.merge.html +++ b/docs/reference/ds.merge.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -232,11 +232,11 @@

    Examples

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.message.html b/docs/reference/ds.message.html index bbbb5cd76..edbb9df44 100644 --- a/docs/reference/ds.message.html +++ b/docs/reference/ds.message.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -144,11 +144,11 @@

    Examples

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.metadata.html b/docs/reference/ds.metadata.html index 64330a092..9a8646650 100644 --- a/docs/reference/ds.metadata.html +++ b/docs/reference/ds.metadata.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -122,11 +122,11 @@

    Examples

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.mice.html b/docs/reference/ds.mice.html index 2bc5ccc73..b92f4c727 100644 --- a/docs/reference/ds.mice.html +++ b/docs/reference/ds.mice.html @@ -25,7 +25,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -160,11 +160,11 @@

    Author

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.names.html b/docs/reference/ds.names.html index aa35230ec..8f246c3ba 100644 --- a/docs/reference/ds.names.html +++ b/docs/reference/ds.names.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -142,11 +142,11 @@

    Examples

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.ns.html b/docs/reference/ds.ns.html index 1a30398fe..f09603f1a 100644 --- a/docs/reference/ds.ns.html +++ b/docs/reference/ds.ns.html @@ -19,7 +19,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -129,11 +129,11 @@

    Author

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.numNA.html b/docs/reference/ds.numNA.html index 7cfea2cac..28cc8b354 100644 --- a/docs/reference/ds.numNA.html +++ b/docs/reference/ds.numNA.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -127,11 +127,11 @@

    Examples

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.qlspline.html b/docs/reference/ds.qlspline.html index b5039387a..29e9f7256 100644 --- a/docs/reference/ds.qlspline.html +++ b/docs/reference/ds.qlspline.html @@ -20,7 +20,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -128,11 +128,11 @@

    Author

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.quantileMean.html b/docs/reference/ds.quantileMean.html index 7f935afb7..7fc50ee5a 100644 --- a/docs/reference/ds.quantileMean.html +++ b/docs/reference/ds.quantileMean.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -146,11 +146,11 @@

    Examples

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.rBinom.html b/docs/reference/ds.rBinom.html index ea94d67c0..e512c35dc 100644 --- a/docs/reference/ds.rBinom.html +++ b/docs/reference/ds.rBinom.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -198,11 +198,11 @@

    Examples

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.rNorm.html b/docs/reference/ds.rNorm.html index bdddcf80f..837a091e2 100644 --- a/docs/reference/ds.rNorm.html +++ b/docs/reference/ds.rNorm.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -213,11 +213,11 @@

    Examples

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.rPois.html b/docs/reference/ds.rPois.html index cd46f0a0f..dec9552e7 100644 --- a/docs/reference/ds.rPois.html +++ b/docs/reference/ds.rPois.html @@ -19,7 +19,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -188,11 +188,11 @@

    Examples

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.rUnif.html b/docs/reference/ds.rUnif.html index 5823f42ff..1f5e91c37 100644 --- a/docs/reference/ds.rUnif.html +++ b/docs/reference/ds.rUnif.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -219,11 +219,11 @@

    Examples

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.ranksSecure.html b/docs/reference/ds.ranksSecure.html index 963c254e4..02253270f 100644 --- a/docs/reference/ds.ranksSecure.html +++ b/docs/reference/ds.ranksSecure.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -278,11 +278,11 @@

    Author

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.rbind.html b/docs/reference/ds.rbind.html index 6a117c6da..755e0e8a6 100644 --- a/docs/reference/ds.rbind.html +++ b/docs/reference/ds.rbind.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -171,11 +171,11 @@

    Examples

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.reShape.html b/docs/reference/ds.reShape.html index 069891e61..75859ac1a 100644 --- a/docs/reference/ds.reShape.html +++ b/docs/reference/ds.reShape.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -194,11 +194,11 @@

    Examples

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.recodeLevels.html b/docs/reference/ds.recodeLevels.html index 1272061bb..ca6c9f6ba 100644 --- a/docs/reference/ds.recodeLevels.html +++ b/docs/reference/ds.recodeLevels.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -144,11 +144,11 @@

    Examples

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.recodeValues.html b/docs/reference/ds.recodeValues.html index ef260dde7..c6013d53e 100644 --- a/docs/reference/ds.recodeValues.html +++ b/docs/reference/ds.recodeValues.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -122,7 +122,53 @@

    Author

    Examples

    - + 
    if (FALSE) { # \dontrun{
+
+  ## Version 6, for version 5 see the Wiki
+  
+  # connecting to the Opal servers
+
+  require('DSI')
+  require('DSOpal')
+  require('dsBaseClient')
+
+  builder <- DSI::newDSLoginBuilder()
+  builder$append(server = "study1", 
+                 url = "http://192.168.56.100:8080/", 
+                 user = "administrator", password = "datashield_test&", 
+                 table = "CNSIM.CNSIM1", driver = "OpalDriver")
+  builder$append(server = "study2", 
+                 url = "http://192.168.56.100:8080/", 
+                 user = "administrator", password = "datashield_test&", 
+                 table = "CNSIM.CNSIM2", driver = "OpalDriver")
+  builder$append(server = "study3",
+                 url = "http://192.168.56.100:8080/", 
+                 user = "administrator", password = "datashield_test&", 
+                 table = "CNSIM.CNSIM3", driver = "OpalDriver")
+  logindata <- builder$build()
+  
+  connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") 
+  
+  # Example 1: recode the levels of D$GENDER
+  ds.recodeValues(var.name = "D$GENDER", 
+                  values2replace.vector = c(0,1), 
+                  new.values.vector = c(10,20),
+                  newobj = 'gender_recoded',
+                  datasources = connections)
+                  
+  # Example 2: recode NAs in D$PM_BMI_CATEGORICAL          
+  ds.recodeValues(var.name = "D$PM_BMI_CATEGORICAL", 
+                  values2replace.vector = c(1,2), 
+                  new.values.vector = c(1,2),
+                  missing = 99, 
+                  newobj = 'bmi_recoded',
+                  datasources = connections)
+                 
+  # Clear the Datashield R sessions and logout                 
+  datashield.logout(connections) 
+  
+} # }   
+
    diff --git a/docs/reference/ds.rep.html b/docs/reference/ds.rep.html index 71db19a6d..91407cb60 100644 --- a/docs/reference/ds.rep.html +++ b/docs/reference/ds.rep.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -206,11 +206,11 @@

    Examples

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.replaceNA.html b/docs/reference/ds.replaceNA.html index 8fe3ba9a2..5ddb38a83 100644 --- a/docs/reference/ds.replaceNA.html +++ b/docs/reference/ds.replaceNA.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -170,11 +170,11 @@

    Examples

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.rm.html b/docs/reference/ds.rm.html index 7403ff28c..aa4d2c3a5 100644 --- a/docs/reference/ds.rm.html +++ b/docs/reference/ds.rm.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -140,11 +140,11 @@

    Examples

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.rowColCalc.html b/docs/reference/ds.rowColCalc.html index bfbd73861..558173f97 100644 --- a/docs/reference/ds.rowColCalc.html +++ b/docs/reference/ds.rowColCalc.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -143,11 +143,11 @@

    Examples

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.sample.html b/docs/reference/ds.sample.html index bd9e16792..c685e920f 100644 --- a/docs/reference/ds.sample.html +++ b/docs/reference/ds.sample.html @@ -19,7 +19,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -234,11 +234,11 @@

    Author

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.scatterPlot.html b/docs/reference/ds.scatterPlot.html index ae6518636..4235320cf 100644 --- a/docs/reference/ds.scatterPlot.html +++ b/docs/reference/ds.scatterPlot.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -222,11 +222,11 @@

    Examples

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.seq.html b/docs/reference/ds.seq.html index 08b34ac85..a76bf4772 100644 --- a/docs/reference/ds.seq.html +++ b/docs/reference/ds.seq.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -213,11 +213,11 @@

    Examples

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.setDefaultOpals.html b/docs/reference/ds.setDefaultOpals.html index 3b34696d1..2dc30336e 100644 --- a/docs/reference/ds.setDefaultOpals.html +++ b/docs/reference/ds.setDefaultOpals.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -93,11 +93,11 @@

    Author

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.setSeed.html b/docs/reference/ds.setSeed.html index eac16115c..fcf8633d8 100644 --- a/docs/reference/ds.setSeed.html +++ b/docs/reference/ds.setSeed.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -156,11 +156,11 @@

    Examples

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.skewness.html b/docs/reference/ds.skewness.html index ad9e9fa11..38222c0ba 100644 --- a/docs/reference/ds.skewness.html +++ b/docs/reference/ds.skewness.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -154,11 +154,11 @@

    Examples

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.sqrt.html b/docs/reference/ds.sqrt.html index c0f0612e9..693e97b5e 100644 --- a/docs/reference/ds.sqrt.html +++ b/docs/reference/ds.sqrt.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -145,11 +145,11 @@

    Examples

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.subset.html b/docs/reference/ds.subset.html index ff9d08f2d..0d8e25e24 100644 --- a/docs/reference/ds.subset.html +++ b/docs/reference/ds.subset.html @@ -19,7 +19,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -180,11 +180,11 @@

    Examples

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.subsetByClass.html b/docs/reference/ds.subsetByClass.html index b401a1562..25425047f 100644 --- a/docs/reference/ds.subsetByClass.html +++ b/docs/reference/ds.subsetByClass.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -142,11 +142,11 @@

    Examples

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.summary.html b/docs/reference/ds.summary.html index b0990fab8..67c1d6535 100644 --- a/docs/reference/ds.summary.html +++ b/docs/reference/ds.summary.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -139,11 +139,11 @@

    Examples

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.table.html b/docs/reference/ds.table.html index bcd1b6127..cb528a4d2 100644 --- a/docs/reference/ds.table.html +++ b/docs/reference/ds.table.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -284,11 +284,11 @@

    Author

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.table1D.html b/docs/reference/ds.table1D.html index 354a9ef6d..3e121b9da 100644 --- a/docs/reference/ds.table1D.html +++ b/docs/reference/ds.table1D.html @@ -19,7 +19,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -160,11 +160,11 @@

    Examples

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.table2D.html b/docs/reference/ds.table2D.html index 88dfcfd52..01da380a1 100644 --- a/docs/reference/ds.table2D.html +++ b/docs/reference/ds.table2D.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -129,7 +129,60 @@

    Author

    Examples

    - + 
    if (FALSE) { # \dontrun{
+
+  # load the file that contains the login details
+  data(logindata)
+
+  # login and assign all the variables to R
+  conns <- datashield.login(logins=logindata,assign=TRUE)
+
+  # Example 1: generate a two dimensional table, outputting combined contingency
+  # tables - default behaviour
+  output <- ds.table2D(x='D$DIS_DIAB', y='D$GENDER')
+  # display the 5 results items, one at a time to avoid having too much information
+  # displayed at the same time
+  output$counts
+  output$rowPercent
+  output$colPercent
+  output$chi2Test
+  output$validity
+
+  # Example 2: generate a two dimensional table, outputting study specific contingency tables
+  ds.table2D(x='D$DIS_DIAB', y='D$GENDER', type='split')
+  # display the 5 results items, one at a time to avoid having too much information displayed
+  # at the same time
+  output$counts
+  output$rowPercent
+  output$colPercent
+  output$chi2Test
+  output$validity
+
+  # Example 3: generate a two dimensional table, outputting combined contingency tables
+  # *** this example shows what happens when one or studies return an invalid table ***
+  output <- ds.table2D(x='D$DIS_CVA', y='D$GENDER', type='combine')
+  output$counts
+  output$rowPercent
+  output$colPercent
+  output$chi2Test
+  output$validity
+
+  # Example 4: same example as above but output is given for each study,
+  # separately (i.e. type='split')
+  # *** this example shows what happens when one or studies return an invalid table ***
+  output <- ds.table2D(x='D$DIS_CVA', y='D$GENDER', type='split')
+  output$counts
+  output$rowPercent
+  output$colPercent
+  output$chi2Test
+  output$validity
+
+  # clear the Datashield R sessions and logout
+  datashield.logout(conns)
+
+} # }
+
+
    diff --git a/docs/reference/ds.tapply.assign.html b/docs/reference/ds.tapply.assign.html index 158d62457..0c0eb0dfc 100644 --- a/docs/reference/ds.tapply.assign.html +++ b/docs/reference/ds.tapply.assign.html @@ -19,7 +19,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -212,11 +212,11 @@

    Examples

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.tapply.html b/docs/reference/ds.tapply.html index 99f9338ea..d87ec8f7c 100644 --- a/docs/reference/ds.tapply.html +++ b/docs/reference/ds.tapply.html @@ -19,7 +19,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -203,11 +203,11 @@

    Examples

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.testObjExists.html b/docs/reference/ds.testObjExists.html index 241fcd881..03f055362 100644 --- a/docs/reference/ds.testObjExists.html +++ b/docs/reference/ds.testObjExists.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -131,11 +131,11 @@

    Examples

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.unList.html b/docs/reference/ds.unList.html index c31ca868e..67ff6e08f 100644 --- a/docs/reference/ds.unList.html +++ b/docs/reference/ds.unList.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -149,11 +149,11 @@

    Examples

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.unique.html b/docs/reference/ds.unique.html index a887836e2..6fd1077cb 100644 --- a/docs/reference/ds.unique.html +++ b/docs/reference/ds.unique.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -122,11 +122,11 @@

    Examples

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.var.html b/docs/reference/ds.var.html index 109a1e78e..6bd495c97 100644 --- a/docs/reference/ds.var.html +++ b/docs/reference/ds.var.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -153,11 +153,11 @@

    Examples

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/ds.vectorCalc.html b/docs/reference/ds.vectorCalc.html index 385c3eca9..dd8deeb07 100644 --- a/docs/reference/ds.vectorCalc.html +++ b/docs/reference/ds.vectorCalc.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -120,11 +120,11 @@

    Examples

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/extract.html b/docs/reference/extract.html index ee10ef5d0..23b12fac3 100644 --- a/docs/reference/extract.html +++ b/docs/reference/extract.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -72,11 +72,11 @@

    Details

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/getPooledMean.html b/docs/reference/getPooledMean.html index 5f25fe1c9..3047a8e0c 100644 --- a/docs/reference/getPooledMean.html +++ b/docs/reference/getPooledMean.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -79,11 +79,11 @@

    Details

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/getPooledVar.html b/docs/reference/getPooledVar.html index b1136e230..109330eda 100644 --- a/docs/reference/getPooledVar.html +++ b/docs/reference/getPooledVar.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -79,11 +79,11 @@

    Details

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/glmChecks.html b/docs/reference/glmChecks.html index f2ea44350..8405d69c2 100644 --- a/docs/reference/glmChecks.html +++ b/docs/reference/glmChecks.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -100,11 +100,11 @@

    Author

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/index.html b/docs/reference/index.html index 66ffc0598..02009eb56 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -42,10 +42,6 @@

    All functions

    -

    computeWeightedMeans()

    - -

    Compute Weighted Mean by Group

    -

    ds.Boole()

    Converts a server-side R object into Boolean indicators

    @@ -353,6 +349,10 @@

    All functions ds.matrixTranspose()

    Transposes a server-side matrix

    + +

    ds.mdPattern()

    + +

    Display missing data patterns with disclosure control

    ds.mean()

    @@ -538,11 +538,11 @@

    All functions
    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/isAssigned.html b/docs/reference/isAssigned.html index 8044eb8b6..98ec0d4f5 100644 --- a/docs/reference/isAssigned.html +++ b/docs/reference/isAssigned.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -80,11 +80,11 @@

    Details

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/isDefined.html b/docs/reference/isDefined.html index f2cbb94bb..9621e0621 100644 --- a/docs/reference/isDefined.html +++ b/docs/reference/isDefined.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -91,11 +91,11 @@

    Author

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/logical2int.html b/docs/reference/logical2int.html index 34f4853fb..4be609896 100644 --- a/docs/reference/logical2int.html +++ b/docs/reference/logical2int.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -74,11 +74,11 @@

    Details

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/meanByClassHelper0a.html b/docs/reference/meanByClassHelper0a.html index 98dd1e0e7..377d13fcc 100644 --- a/docs/reference/meanByClassHelper0a.html +++ b/docs/reference/meanByClassHelper0a.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -93,11 +93,11 @@

    Author

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/meanByClassHelper0b.html b/docs/reference/meanByClassHelper0b.html index 4e4fb247f..024a5b4b2 100644 --- a/docs/reference/meanByClassHelper0b.html +++ b/docs/reference/meanByClassHelper0b.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -97,11 +97,11 @@

    Author

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/meanByClassHelper1.html b/docs/reference/meanByClassHelper1.html index 9df03a529..ed31d1ba4 100644 --- a/docs/reference/meanByClassHelper1.html +++ b/docs/reference/meanByClassHelper1.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -90,11 +90,11 @@

    Author

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/meanByClassHelper2.html b/docs/reference/meanByClassHelper2.html index 5466cbedf..f5801dd05 100644 --- a/docs/reference/meanByClassHelper2.html +++ b/docs/reference/meanByClassHelper2.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -91,11 +91,11 @@

    Author

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/meanByClassHelper3.html b/docs/reference/meanByClassHelper3.html index d3bcf8f14..8a4e29cdf 100644 --- a/docs/reference/meanByClassHelper3.html +++ b/docs/reference/meanByClassHelper3.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -90,11 +90,11 @@

    Author

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/meanByClassHelper4.html b/docs/reference/meanByClassHelper4.html index 2b8f40b7d..428c20649 100644 --- a/docs/reference/meanByClassHelper4.html +++ b/docs/reference/meanByClassHelper4.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -100,11 +100,11 @@

    Author

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/rowPercent.html b/docs/reference/rowPercent.html index df9685296..b89cc7464 100644 --- a/docs/reference/rowPercent.html +++ b/docs/reference/rowPercent.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -76,11 +76,11 @@

    Author

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/subsetHelper.html b/docs/reference/subsetHelper.html index 0a94aa1b3..e2080ac67 100644 --- a/docs/reference/subsetHelper.html +++ b/docs/reference/subsetHelper.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.4 + 6.3.5 @@ -131,11 +131,11 @@

    Examples

    -

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    +

    Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

    -

    Site built with pkgdown 2.1.3.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/sitemap.xml b/docs/sitemap.xml index 39df9eefa..fe21f864e 100644 --- a/docs/sitemap.xml +++ b/docs/sitemap.xml @@ -6,6 +6,7 @@ /reference/checkClass.html /reference/colPercent.html /reference/computeWeightedMeans.html +/reference/dot-pool_md_patterns.html /reference/ds.Boole.html /reference/ds.abs.html /reference/ds.asCharacter.html @@ -84,6 +85,7 @@ /reference/ds.matrixInvert.html /reference/ds.matrixMult.html /reference/ds.matrixTranspose.html +/reference/ds.mdPattern.html /reference/ds.mean.html /reference/ds.meanByClass.html /reference/ds.meanSdGp.html diff --git a/dsBase_6.3.4.tar.gz b/dsBase_6.3.5-permissive.tar.gz similarity index 57% rename from dsBase_6.3.4.tar.gz rename to dsBase_6.3.5-permissive.tar.gz index c7725adf9..3703315dd 100644 Binary files a/dsBase_6.3.4.tar.gz and b/dsBase_6.3.5-permissive.tar.gz differ diff --git a/dsBase_6.3.4-permissive.tar.gz b/dsBase_6.3.5.tar.gz similarity index 51% rename from dsBase_6.3.4-permissive.tar.gz rename to dsBase_6.3.5.tar.gz index c7c2f2b24..0ea538d0f 100644 Binary files a/dsBase_6.3.4-permissive.tar.gz and b/dsBase_6.3.5.tar.gz differ diff --git a/man/computeWeightedMeans.Rd b/man/computeWeightedMeans.Rd index 0b8b0879f..c1f9bfc15 100644 --- a/man/computeWeightedMeans.Rd +++ b/man/computeWeightedMeans.Rd @@ -15,6 +15,9 @@ computeWeightedMeans(data_table, variables, weight, by) \item{by}{character vector of the columns to group by} } +\value{ +Returns a data table object with computed weighted means. +} \description{ This function is originally from the panelaggregation package. It has been ported here in order to bypass the package being @@ -23,3 +26,4 @@ kicked off CRAN. \author{ Matthias Bannert, Gabriel Bucur } +\keyword{internal} diff --git a/man/dot-pool_md_patterns.Rd b/man/dot-pool_md_patterns.Rd new file mode 100644 index 000000000..baabf3e92 --- /dev/null +++ b/man/dot-pool_md_patterns.Rd @@ -0,0 +1,20 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/ds.mdPattern.R +\name{.pool_md_patterns} +\alias{.pool_md_patterns} +\title{Pool missing data patterns across studies} +\usage{ +.pool_md_patterns(patterns_list, study_names) +} +\arguments{ +\item{patterns_list}{List of pattern matrices from each study} + +\item{study_names}{Names of the studies} +} +\value{ +Pooled pattern matrix +} +\description{ +Internal function to pool md.pattern results from multiple studies +} +\keyword{internal} diff --git a/man/ds.asFactor.Rd b/man/ds.asFactor.Rd index c412df383..24125632b 100644 --- a/man/ds.asFactor.Rd +++ b/man/ds.asFactor.Rd @@ -95,7 +95,7 @@ If we set the argument \code{fixed.dummy.vars = TRUE}, \code{baseline.level = 1} and \code{forced.factor.levels = c(1,2,3,4,5)}. The input vector is converted to the following matrix of dummy variables: -\tabular{rrrrr}{ +\tabular{rrrr}{ \strong{DV2} \tab \strong{DV3} \tab \strong{DV4} \tab \strong{DV5} \cr 0 \tab 0 \tab 0 \tab 0\cr 1 \tab 0 \tab 0 \tab 0\cr diff --git a/man/ds.boxPlot.Rd b/man/ds.boxPlot.Rd index 0e8e7a336..993199251 100644 --- a/man/ds.boxPlot.Rd +++ b/man/ds.boxPlot.Rd @@ -46,7 +46,7 @@ of grouping using categorical variables on the dataset (only for data frames) ## Version 6, for version 5 see the Wiki ### Please ensure you have a training Virtual Machine running, - or that you have a live connection to a server. + # or that you have a live connection to a server. # Connecting to the Opal servers @@ -73,37 +73,37 @@ of grouping using categorical variables on the dataset (only for data frames) symbol = "D") ## Create a boxplot of one variable - ds.boxPlot("D", "LAB_HDL", datasources = connections) + ds.boxPlot("D", "LAB_HDL", datasources = connections) ## Create a boxplot that is split by study: - ds.boxPlot("D", "LAB_HDL", type= "split", datasources = connections) + ds.boxPlot("D", "LAB_HDL", type= "split", datasources = connections) ## Create a boxplot of two variables variable - ds.boxPlot("D", c("LAB_HDL", "LAB_TRIG", type="pooled", - datasources = connections) + ds.boxPlot("D", c("LAB_HDL", "LAB_TRIG"), type="pooled", + datasources = connections) # only one plot is created (of the aggregated results of all servers) ## Create a boxplot of two variables, which are split by a factor - ds.boxPlot("D", c("LAB_HDL", "LAB_TRIG"), group = "GENDER", + ds.boxPlot("D", c("LAB_HDL", "LAB_TRIG"), group = "GENDER", datasources = connections) ## Create a boxplot with x- and y-axis labels - ds.boxPlot("D", c("LAB_HDL", "LAB_TRIG"), group = "GENDER", + ds.boxPlot("D", c("LAB_HDL", "LAB_TRIG"), group = "GENDER", xlabel = "Variable", ylabel = "Measurement", datasources = connections) ## Improve the presentation of ds.boxplot output using ggplot: ### User must save the output, which is in a ggplot format already: - a <- ds.boxPlot("D", c("LAB_HDL", "LAB_TRIG"), group = "GENDER", + a <- ds.boxPlot("D", c("LAB_HDL", "LAB_TRIG"), group = "GENDER", xlabel = "Variable", ylabel = "Measurement", datasources = connections) ### Then customise output "a" using ggplot tools: a + ggplot2::scale_fill_discrete(name = "Gender", labels = c("Male", "Female")) ### Or use an alternative way, to maintain the aesthetics: - a + ggplot2::scale_fill_brewer(name = "Gender", labels = c("Male", "Female")) + a + ggplot2::scale_fill_brewer(name = "Gender", labels = c("Male", "Female")) # Clear the Datashield R sessions and logout - datashield.logout(connections) + datashield.logout(connections) } diff --git a/man/ds.colnames.Rd b/man/ds.colnames.Rd index e73910812..9460a567f 100644 --- a/man/ds.colnames.Rd +++ b/man/ds.colnames.Rd @@ -9,20 +9,20 @@ ds.colnames(x = NULL, datasources = NULL) \arguments{ \item{x}{a character string providing the name of the input data frame or matrix.} -\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ -\code{ds.colnames} returns the column names of +\code{ds.colnames} returns the column names of the specified server-side data frame or matrix. } \description{ -Retrieves column names of an R object on the server-side. +Retrieves column names of an R object on the server-side. This function is similar to R function \code{colnames}. } \details{ -The input is restricted to the object of type \code{data.frame} or \code{matrix}. +The input is restricted to the object of type \code{data.frame} or \code{matrix}. Server function called: \code{colnamesDS} } @@ -37,28 +37,28 @@ Server function called: \code{colnamesDS} require('dsBaseClient') builder <- DSI::newDSLoginBuilder() - builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", + builder$append(server = "study1", + url = "http://192.168.56.100:8080/", + user = "administrator", password = "datashield_test&", table = "CNSIM.CNSIM1", driver = "OpalDriver") - builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", + builder$append(server = "study2", + url = "http://192.168.56.100:8080/", + user = "administrator", password = "datashield_test&", table = "CNSIM.CNSIM2", driver = "OpalDriver") builder$append(server = "study3", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", + url = "http://192.168.56.100:8080/", + user = "administrator", password = "datashield_test&", table = "CNSIM.CNSIM3", driver = "OpalDriver") logindata <- builder$build() - + # Log onto the remote Opal training servers - connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") + connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") # Getting column names of the R objects stored in the server-side ds.colnames(x = "D", datasources = connections[1]) #only the first server ("study1") is used # Clear the Datashield R sessions and logout - datashield.logout(connections) + datashield.logout(connections) } } \seealso{ diff --git a/man/ds.densityGrid.Rd b/man/ds.densityGrid.Rd index 89cc4348d..0e2c5b783 100644 --- a/man/ds.densityGrid.Rd +++ b/man/ds.densityGrid.Rd @@ -88,11 +88,11 @@ Server function called: \code{densityGridDS} # Example2: generate a grid density object for each study separately ds.densityGrid(x="D$LAB_TSC", y="D$LAB_HDL", - type="split" + type="split", datasources = connections[1])#only the first Opal server is used ("study1") # Example3: generate a grid density object where the number of intervals is set to 15, for - each study separately + # each study separately ds.densityGrid(x="D$LAB_TSC", y="D$LAB_HDL", type="split", diff --git a/man/ds.forestplot.Rd b/man/ds.forestplot.Rd index 408dc2d30..66606601d 100644 --- a/man/ds.forestplot.Rd +++ b/man/ds.forestplot.Rd @@ -19,6 +19,9 @@ See details from \code{?meta::metagen} for the different options.} \item{layout}{\code{character} (default \code{"JAMA"}) Layout of the plot. See details from \code{?meta::metagen} for the different options.} } +\value{ +Results a foresplot object created with `meta::forest`. +} \description{ Draws a forestplot of the coefficients for Study-Level Meta-Analysis performed with DataSHIELD diff --git a/man/ds.heatmapPlot.Rd b/man/ds.heatmapPlot.Rd index 3ab17da98..dfd89d3c4 100644 --- a/man/ds.heatmapPlot.Rd +++ b/man/ds.heatmapPlot.Rd @@ -163,7 +163,7 @@ Server function called: \code{heatmapPlotDS} datasources = connections[1]) #only the first server is used (study1) # Example 3: Plot a combined heat map plot using the method 'deterministic' centroids of each - k = 7 nearest neighbours for numints = 40 + # k = 7 nearest neighbours for numints = 40 ds.heatmapPlot(x = 'D$LAB_TSC', y = 'D$LAB_HDL', numints = 40, diff --git a/man/ds.histogram.Rd b/man/ds.histogram.Rd index 17de73da6..d8173574f 100644 --- a/man/ds.histogram.Rd +++ b/man/ds.histogram.Rd @@ -148,7 +148,7 @@ Server function called: \code{histogramDS2} datasources = connections) #all studies are used # Example 2: generate a combined histogram with the default small cells counts - suppression rule + # suppression rule ds.histogram(x = 'D$PM_BMI_CONTINUOUS', method = 'smallCellsRule', type = 'combine', diff --git a/man/ds.matrixDiag.Rd b/man/ds.matrixDiag.Rd index 268e5148c..b58a0e625 100644 --- a/man/ds.matrixDiag.Rd +++ b/man/ds.matrixDiag.Rd @@ -136,7 +136,7 @@ Server function called: \code{matrixDiagDS} datasources = connections) #Example 2: Create a square matrix with the server-side scalar as all diagonal values - and all the other values = 0 + #and all the other values = 0 #Create a scalar in the server-side @@ -176,7 +176,7 @@ Server function called: \code{matrixDiagDS} datasources = connections) #Example 4: Create a square matrix with the client-side vector as a diagonal - and all the other values = 0 + #and all the other values = 0 ds.matrixDiag(x1 = c(2,6,9,10), aim = "clientside.vector.2.matrix", @@ -185,7 +185,7 @@ Server function called: \code{matrixDiagDS} datasources = connections) #Example 5: Create a square matrix with the client-side scalar as all diagonal values - and all the other values = 0 + #and all the other values = 0 ds.matrixDiag(x1 = 4, aim = "clientside.scalar.2.matrix", diff --git a/man/ds.mdPattern.Rd b/man/ds.mdPattern.Rd new file mode 100644 index 000000000..b1bacc0b1 --- /dev/null +++ b/man/ds.mdPattern.Rd @@ -0,0 +1,126 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/ds.mdPattern.R +\name{ds.mdPattern} +\alias{ds.mdPattern} +\title{Display missing data patterns with disclosure control} +\usage{ +ds.mdPattern(x = NULL, type = "split", datasources = NULL) +} +\arguments{ +\item{x}{a character string specifying the name of a data frame or matrix on the +server-side containing the data to analyze.} + +\item{type}{a character string specifying the output type. If 'split' (default), +returns separate patterns for each study. If 'combine', attempts to pool patterns +across studies.} + +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained +after login. If the \code{datasources} argument is not specified, the default set of +connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} +} +\value{ +For type='split': A list with one element per study, each containing: +\describe{ + \item{pattern}{The missing data pattern matrix for that study} + \item{valid}{Logical indicating if all patterns meet disclosure requirements} + \item{message}{A message describing the validity status} +} + +For type='combine': A list containing: +\describe{ + \item{pattern}{The pooled missing data pattern matrix across all studies} + \item{valid}{Logical indicating if all pooled patterns meet disclosure requirements} + \item{message}{A message describing the validity status} +} +} +\description{ +This function is a client-side wrapper for the server-side mdPatternDS +function. It generates a missing data pattern matrix similar to mice::md.pattern but +with disclosure control applied to prevent revealing small cell counts. +} +\details{ +The function calls the server-side mdPatternDS function which uses +mice::md.pattern to analyze missing data patterns. Patterns with counts below the +disclosure threshold (default: nfilter.tab = 3) are suppressed to maintain privacy. + +\strong{Output Format:} +- Each row represents a missing data pattern +- Pattern counts are shown in row names (e.g., "150", "25") +- Columns show 1 if the variable is observed, 0 if missing +- Last column shows the total number of missing values per pattern +- Last row shows the total number of missing values per variable + +\strong{Disclosure Control:} + +Suppressed patterns (count below threshold) are indicated by: +- Row name: "suppressed()" where N is the threshold +- All pattern values set to NA +- Summary row also suppressed to prevent back-calculation + +\strong{Pooling Behavior (type='combine'):} + +When pooling across studies, the function uses a \emph{conservative approach} +for disclosure control: + +1. Identifies identical missing patterns across studies +2. \strong{EXCLUDES suppressed patterns from pooling} - patterns suppressed in + ANY study are not included in the pooled count +3. Sums counts only for non-suppressed identical patterns +4. Re-validates pooled counts against disclosure threshold + +\strong{Important:} This conservative approach means: +- Pooled counts may be \emph{underestimates} if some studies had suppressed patterns +- This prevents disclosure through subtraction (e.g., if study A shows count=5 + and pool shows count=7, one could deduce study B has count=2, violating disclosure) +- Different patterns across studies are preserved separately in the pooled result +} +\examples{ +\dontrun{ + ## Version 6, for version 5 see the Wiki + + # Connecting to the Opal servers + + require('DSI') + require('DSOpal') + require('dsBaseClient') + + builder <- DSI::newDSLoginBuilder() + builder$append(server = "study1", + url = "http://192.168.56.100:8080/", + user = "administrator", password = "datashield_test&", + table = "CNSIM.CNSIM1", driver = "OpalDriver") + builder$append(server = "study2", + url = "http://192.168.56.100:8080/", + user = "administrator", password = "datashield_test&", + table = "CNSIM.CNSIM2", driver = "OpalDriver") + logindata <- builder$build() + + connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") + + # Get missing data patterns for each study separately + patterns_split <- ds.mdPattern(x = "D", type = "split", datasources = connections) + + # View results for study1 + print(patterns_split$study1$pattern) + # var1 var2 var3 + # 150 1 1 1 0 <- 150 obs complete + # 25 0 1 1 1 <- 25 obs missing var1 + # 25 0 0 25 <- Summary: 25 missing per variable + + # Get pooled missing data patterns across studies + patterns_pooled <- ds.mdPattern(x = "D", type = "combine", datasources = connections) + print(patterns_pooled$pattern) + + # Example with suppressed patterns: + # If study1 has a pattern with count=2 (suppressed) and study2 has same pattern + # with count=5 (valid), the pooled result will show count=5 (conservative approach) + # A warning will indicate: "Pooled counts may underestimate the true total" + + # Clear the Datashield R sessions and logout + datashield.logout(connections) +} + +} +\author{ +Xavier Escribà montagut for DataSHIELD Development Team +} diff --git a/man/ds.recodeValues.Rd b/man/ds.recodeValues.Rd index 6b775bc9d..8c8a75d80 100644 --- a/man/ds.recodeValues.Rd +++ b/man/ds.recodeValues.Rd @@ -97,7 +97,7 @@ Server function called: \code{recodeValuesDS} values2replace.vector = c(1,2), new.values.vector = c(1,2), missing = 99, - newobj = 'bmi_recoded' + newobj = 'bmi_recoded', datasources = connections) # Clear the Datashield R sessions and logout diff --git a/man/ds.table2D.Rd b/man/ds.table2D.Rd index 3d0e2a2c2..57982f3c0 100644 --- a/man/ds.table2D.Rd +++ b/man/ds.table2D.Rd @@ -77,7 +77,7 @@ identify the cell(s) that had the small counts which render the table invalid. # Example 2: generate a two dimensional table, outputting study specific contingency tables ds.table2D(x='D$DIS_DIAB', y='D$GENDER', type='split') # display the 5 results items, one at a time to avoid having too much information displayed - at the same time + # at the same time output$counts output$rowPercent output$colPercent diff --git a/opal_azure-pipelines.yml b/opal_azure-pipelines.yml index 6c6103d4a..6122fb035 100644 --- a/opal_azure-pipelines.yml +++ b/opal_azure-pipelines.yml @@ -58,10 +58,10 @@ schedules: - master always: true - cron: "0 2 * * *" - displayName: Nightly build - v6.3.4-dev + displayName: Nightly build - v6.3.5-dev branches: include: - - v6.3.4-dev + - v6.3.5-dev always: true ######################################################################################### @@ -233,9 +233,9 @@ jobs: # Install dsBase. # If previous steps have failed then don't run. - bash: | - R -q -e "library(opalr); opal <- opal.login(username = 'administrator', password = 'datashield_test&', url = 'https://localhost:8443', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); opal.put(opal, 'system', 'conf', 'general', '_rPackage'); opal.logout(o)" + R -q -e "library(opalr); opal <- opal.login(username = 'administrator', password = 'datashield_test&', url = 'https://localhost:8443', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); opal.put(opal, 'system', 'conf', 'general', '_rPackage'); opal.logout(opal)" - R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsBase', username = 'datashield', ref = 'v6.3.4-dev'); opal.logout(opal)" + R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsBase', username = 'datashield', ref = 'v6.3.5-dev'); opal.logout(opal)" sleep 60 diff --git a/tests/docker/armadillo/standard/config/application.yml b/tests/docker/armadillo/standard/config/application.yml index 12b78ec82..54e90c36a 100644 --- a/tests/docker/armadillo/standard/config/application.yml +++ b/tests/docker/armadillo/standard/config/application.yml @@ -14,17 +14,11 @@ armadillo: # oidc-admin-user: user@yourdomain.org profiles: - name: default - image: datashield/rock-omicron-karma:devel + image: datashield/rock-quebrada-lamda-permissive:latest port: 8085 host: default package-whitelist: # Packages for 'permissive' - dsBase - - dsMediation - - dsMTLBase - - dsSurvival - - dsTidyverse - - dsExposome - - dsOmics - resourcer function-blacklist: [ ] options: diff --git a/tests/testthat.R b/tests/testthat.R index 3e6bbe151..389ee66c5 100644 --- a/tests/testthat.R +++ b/tests/testthat.R @@ -9,4 +9,5 @@ library(testthat) library(dsBaseClient) -test_check("dsBaseClient") +if (identical(Sys.getenv("NOT_CRAN"), "true")) + test_check("dsBaseClient") diff --git a/tests/testthat/data_files/dataBootstrapUnitTests.R b/tests/testthat/data_files/dataBootstrapUnitTests.R deleted file mode 100644 index 4c51af16a..000000000 --- a/tests/testthat/data_files/dataBootstrapUnitTests.R +++ /dev/null @@ -1,117 +0,0 @@ -library(remotes) -install.packages("MolgenisArmadillo", repos = "https://registry.molgenis.org/repository/R") -library(MolgenisArmadillo) -library(DSI) - -# init_studies_dataset -CNSIM1 <- load("data_files/CNSIM/CNSIM1.rda") -CNSIM2 <- load("data_files/CNSIM/CNSIM2.rda") -CNSIM3 <- load("data_files/CNSIM/CNSIM3.rda") - -DASIM1 <- load("data_files/DASIM/DASIM1.rda") -DASIM2 <- load("data_files/DASIM/DASIM2.rda") -DASIM3 <- load("data_files/DASIM/DASIM3.rda") - -EXPAND_WITH_MISSING1 <- load("data_files/SURVIVAL/EXPAND_MISSING/expand_missing_study1.rda") -EXPAND_WITH_MISSING2 <- load("data_files/SURVIVAL/EXPAND_MISSING/expand_missing_study2.rda") -EXPAND_WITH_MISSING3 <- load("data_files/SURVIVAL/EXPAND_MISSING/expand_missing_study3.rda") - -CLUSTER_INT1 <- load("data_files/CLUSTER/CLUSTER_INT1.rda") -CLUSTER_INT2 <- load("data_files/CLUSTER/CLUSTER_INT2.rda") -CLUSTER_INT3 <- load("data_files/CLUSTER/CLUSTER_INT3.rda") - -CLUSTER_SLO1 <- load("data_files/CLUSTER/CLUSTER_SLO1.rda") -CLUSTER_SLO2 <- load("data_files/CLUSTER/CLUSTER_SLO2.rda") -CLUSTER_SLO3 <- load("data_files/CLUSTER/CLUSTER_SLO3.rda") - -# init_discordant_datasets -DISCORDANT_STUDY1 <- load("data_files/DISCORDANT/discordant_study1.rda") -DISCORDANT_STUDY2 <- load("data_files/DISCORDANT/discordant_study2.rda") -DISCORDANT_STUDY3 <- load("data_files/DISCORDANT/discordant_study3.rda") - -# init_testing_datasets -DATASET1 <- load("data_files/TESTING/DATASET1.rda") -DATASET2 <- load("data_files/TESTING/DATASET2.rda") -DATASET3 <- load("data_files/TESTING/DATASET3.rda") - -FACTOR_LEVELS_DATASET1 <- load("data_files/FACTOR_LEVELS/FACTOR_LEVELS_DATASET1.rda") -FACTOR_LEVELS_DATASET2 <- load("data_files/FACTOR_LEVELS/FACTOR_LEVELS_DATASET2.rda") -FACTOR_LEVELS_DATASET3 <- load("data_files/FACTOR_LEVELS/FACTOR_LEVELS_DATASET3.rda") - - -storage_url <- "http://localhost:9000" -# access_key and secret_key can be found in the minio configuration in the docker-compose.yml -MolgenisArmadillo::armadillo.set_credentials(server = storage_url, access_key = "molgenis", secret_key = "molgenis") -MolgenisArmadillo::armadillo.create_project("testdata") - - -# init_studies_datasets -MolgenisArmadillo::armadillo.upload_table("testdata", "cnsim", CNSIM1) -MolgenisArmadillo::armadillo.upload_table("testdata", "cnsim", CNSIM2) -MolgenisArmadillo::armadillo.upload_table("testdata", "cnsim", CNSIM3) - -MolgenisArmadillo::armadillo.upload_table("testdata", "dasim", DASIM1) -MolgenisArmadillo::armadillo.upload_table("testdata", "dasim", DASIM2) -MolgenisArmadillo::armadillo.upload_table("testdata", "dasim", DASIM3) - -MolgenisArmadillo::armadillo.upload_table("testdata", "survival", EXPAND_WITH_MISSING1) -MolgenisArmadillo::armadillo.upload_table("testdata", "survival", EXPAND_WITH_MISSING2) -MolgenisArmadillo::armadillo.upload_table("testdata", "survival", EXPAND_WITH_MISSING3) - -MolgenisArmadillo::armadillo.upload_table("testdata", "cluster", CLUSTER_INT1) -MolgenisArmadillo::armadillo.upload_table("testdata", "cluster", CLUSTER_INT2) -MolgenisArmadillo::armadillo.upload_table("testdata", "cluster", CLUSTER_INT3) - -MolgenisArmadillo::armadillo.upload_table("testdata", "cluster", CLUSTER_SLO1) -MolgenisArmadillo::armadillo.upload_table("testdata", "cluster", CLUSTER_SLO2) -MolgenisArmadillo::armadillo.upload_table("testdata", "cluster", CLUSTER_SLO3) - - -# init_discordant_datasets -MolgenisArmadillo::armadillo.upload_table("testdata", "discordant", DISCORDANT_STUDY1) -MolgenisArmadillo::armadillo.upload_table("testdata", "discordant", DISCORDANT_STUDY2) -MolgenisArmadillo::armadillo.upload_table("testdata", "discordant", DISCORDANT_STUDY3) - - -# remove first column -DATASET1 <- DATASET1[,-1] -DATASET2 <- DATASET2[,-1] -DATASET3 <- DATASET3[,-1] - -# init_testing_datasets -MolgenisArmadillo::armadillo.upload_table("testdata", "testing", DATASET1) -MolgenisArmadillo::armadillo.upload_table("testdata", "testing", DATASET2) -MolgenisArmadillo::armadillo.upload_table("testdata", "testing", DATASET3) - -MolgenisArmadillo::armadillo.upload_table("testdata", "factor_levels", FACTOR_LEVELS_DATASET1) -MolgenisArmadillo::armadillo.upload_table("testdata", "factor_levels", FACTOR_LEVELS_DATASET2) -MolgenisArmadillo::armadillo.upload_table("testdata", "factor_levels", FACTOR_LEVELS_DATASET3) - -class(CNSIM1$PM_BMI_CATEGORICAL) -levels(CNSIM1$PM_BMI_CATEGORICAL) - -devtools::test() -devtools::test(filter = "datachk", invert = TRUE) -devtools::test(filter = "dataFrameSort") - - # build the login dataframe -builder <- DSI::newDSLoginBuilder() -builder$append(server = "armadillo", - url = armadillo_url, - user = "admin", - password = "admin", - table = "testdata/testing/DISCORDANT_STUDY1", - driver = "ArmadilloDriver") - -# create loginframe -logindata <- builder$build() -logindata - -datashield.logout(conns) - -conns <- datashield.login(logins = logindata, assign = TRUE) -ds.ls() -dsGetInfo(conns$armadillo) -ds.colnames("D") -datashield.errors() -dsGetInfo(conns$armadillo) diff --git a/tests/testthat/perf_files/armadillo_azure-pipeline.csv b/tests/testthat/perf_files/armadillo_azure-pipeline.csv index 186e1d583..ca8a229ca 100644 --- a/tests/testthat/perf_files/armadillo_azure-pipeline.csv +++ b/tests/testthat/perf_files/armadillo_azure-pipeline.csv @@ -1,14 +1,14 @@ "refer_name","rate","lower_tolerance","upper_tolerance" -"conndisconn::perf::simple0","0.1275","0.5","2" -"ds.abs::perf::0","4.824","0.5","2" -"ds.asInteger::perf:0","4.366","0.5","2" -"ds.asList::perf:0","9.787","0.5","2" -"ds.asNumeric::perf:0","4.316","0.5","2" -"ds.assign::perf::0","8.055","0.5","2" -"ds.class::perf::combine:0","9.847","0.5","2" -"ds.colnames::perf:0","7.574","0.5","2" -"ds.exists::perf::combine:0","19.84","0.5","2" -"ds.length::perf::combine:0","19.58","0.5","2" -"ds.mean::perf::combine:0","19.66","0.5","2" -"ds.mean::perf::split:0","19.21","0.5","2" -"void::perf::void::0","41810.0","0.5","2" +"conndisconn::perf::simple0","0.1661","0.5","2" +"ds.abs::perf::0","6.247","0.5","2" +"ds.asInteger::perf:0","5.691","0.5","2" +"ds.asList::perf:0","12.50","0.5","2" +"ds.asNumeric::perf:0","5.723","0.5","2" +"ds.assign::perf::0","10.52","0.5","2" +"ds.class::perf::combine:0","13.73","0.5","2" +"ds.colnames::perf:0","25.64","0.5","2" +"ds.exists::perf::combine:0","25.73","0.5","2" +"ds.length::perf::combine:0","25.44","0.5","2" +"ds.mean::perf::combine:0","25.70","0.5","2" +"ds.mean::perf::split:0","25.72","0.5","2" +"void::perf::void::0","53016.0","0.5","2" diff --git a/tests/testthat/perf_files/armadillo_hp-laptop_quay.csv b/tests/testthat/perf_files/armadillo_hp-laptop_quay.csv index 6c6a3f337..9ac69853e 100644 --- a/tests/testthat/perf_files/armadillo_hp-laptop_quay.csv +++ b/tests/testthat/perf_files/armadillo_hp-laptop_quay.csv @@ -1,14 +1,14 @@ "refer_name","rate","lower_tolerance","upper_tolerance" -"conndisconn::perf::simple0","0.06225260028207","0.5","2" -"ds.abs::perf::0","2.602332538044","0.5","2" -"ds.asInteger::perf:0","2.16574645464856","0.5","2" -"ds.asList::perf:0","5.125787987349","0.5","2" -"ds.asNumeric::perf:0","2.02140793909654","0.5","2" -"ds.assign::perf::0","4.25379741119624","0.5","2" -"ds.class::perf::combine:0","5.03264832363257","0.5","2" -"ds.colnames::perf:0","3.61308626946146","0.5","2" -"ds.exists::perf::combine:0","8.47538336211864","0.5","2" -"ds.length::perf::combine:0","9.49818979827918","0.5","2" -"ds.mean::perf::combine:0","9.66558925664494","0.5","2" -"ds.mean::perf::split:0","8.6304479562724","0.5","2" -"void::perf::void::0","19351.7615914652","0.5","2" +"conndisconn::perf::simple0","0.04918","0.5","2" +"ds.abs::perf::0","1.184","0.5","2" +"ds.asInteger::perf:0","1.297","0.5","2" +"ds.asList::perf:0","2.884","0.5","2" +"ds.asNumeric::perf:0","1.354","0.5","2" +"ds.assign::perf::0","2.745","0.5","2" +"ds.class::perf::combine:0","3.261","0.5","2" +"ds.colnames::perf:0","2.404","0.5","2" +"ds.exists::perf::combine:0","6.342","0.5","2" +"ds.length::perf::combine:0","7.835","0.5","2" +"ds.mean::perf::combine:0","8.127","0.5","2" +"ds.mean::perf::split:0","8.109","0.5","2" +"void::perf::void::0","20280.0","0.5","2" diff --git a/tests/testthat/perf_files/default_perf_profile.csv b/tests/testthat/perf_files/default_perf_profile.csv index cff242360..ca8a229ca 100644 --- a/tests/testthat/perf_files/default_perf_profile.csv +++ b/tests/testthat/perf_files/default_perf_profile.csv @@ -1,14 +1,14 @@ "refer_name","rate","lower_tolerance","upper_tolerance" -"conndisconn::perf::simple0","0.2118","0.5","2" -"ds.abs::perf::0","1.718","0.5","2" -"ds.asInteger::perf:0","1.484","0.5","2" -"ds.asList::perf:0","3.050","0.5","2" -"ds.asNumeric::perf:0","1.508","0.5","2" -"ds.assign::perf::0","3.547","0.5","2" -"ds.class::perf::combine:0","3.061","0.5","2" -"ds.colnames::perf:0","2.456","0.5","2" -"ds.exists::perf::combine:0","6.904","0.5","2" -"ds.length::perf::combine:0","6.058","0.5","2" -"ds.mean::perf::combine:0","5.892","0.5","2" -"ds.mean::perf::split:0","6.881","0.5","2" -"void::perf::void::0","27070.0","0.5","2" +"conndisconn::perf::simple0","0.1661","0.5","2" +"ds.abs::perf::0","6.247","0.5","2" +"ds.asInteger::perf:0","5.691","0.5","2" +"ds.asList::perf:0","12.50","0.5","2" +"ds.asNumeric::perf:0","5.723","0.5","2" +"ds.assign::perf::0","10.52","0.5","2" +"ds.class::perf::combine:0","13.73","0.5","2" +"ds.colnames::perf:0","25.64","0.5","2" +"ds.exists::perf::combine:0","25.73","0.5","2" +"ds.length::perf::combine:0","25.44","0.5","2" +"ds.mean::perf::combine:0","25.70","0.5","2" +"ds.mean::perf::split:0","25.72","0.5","2" +"void::perf::void::0","53016.0","0.5","2" diff --git a/tests/testthat/perf_files/opal_azure-pipeline.csv b/tests/testthat/perf_files/opal_azure-pipeline.csv index cff242360..58614204f 100644 --- a/tests/testthat/perf_files/opal_azure-pipeline.csv +++ b/tests/testthat/perf_files/opal_azure-pipeline.csv @@ -1,14 +1,14 @@ "refer_name","rate","lower_tolerance","upper_tolerance" -"conndisconn::perf::simple0","0.2118","0.5","2" -"ds.abs::perf::0","1.718","0.5","2" -"ds.asInteger::perf:0","1.484","0.5","2" -"ds.asList::perf:0","3.050","0.5","2" -"ds.asNumeric::perf:0","1.508","0.5","2" -"ds.assign::perf::0","3.547","0.5","2" -"ds.class::perf::combine:0","3.061","0.5","2" -"ds.colnames::perf:0","2.456","0.5","2" -"ds.exists::perf::combine:0","6.904","0.5","2" -"ds.length::perf::combine:0","6.058","0.5","2" -"ds.mean::perf::combine:0","5.892","0.5","2" -"ds.mean::perf::split:0","6.881","0.5","2" -"void::perf::void::0","27070.0","0.5","2" +"conndisconn::perf::simple0","0.2725","0.5","2" +"ds.abs::perf::0","2.677","0.5","2" +"ds.asInteger::perf:0","2.294","0.5","2" +"ds.asList::perf:0","4.587","0.5","2" +"ds.asNumeric::perf:0","2.185","0.5","2" +"ds.assign::perf::0","5.490","0.5","2" +"ds.class::perf::combine:0","4.760","0.5","2" +"ds.colnames::perf:0","9.079","0.5","2" +"ds.exists::perf::combine:0","11.09","0.5","2" +"ds.length::perf::combine:0","9.479","0.5","2" +"ds.mean::perf::combine:0","9.650","0.5","2" +"ds.mean::perf::split:0","11.26","0.5","2" +"void::perf::void::0","46250.0","0.5","2" diff --git a/tests/testthat/perf_tests/perf_rate.R b/tests/testthat/perf_tests/perf_rate.R index 0384bf637..64b638db6 100644 --- a/tests/testthat/perf_tests/perf_rate.R +++ b/tests/testthat/perf_tests/perf_rate.R @@ -8,7 +8,8 @@ # along with this program. If not, see . #------------------------------------------------------------------------------- -.perf.reference.filename <- 'perf_files/default_perf_profile.csv' +.perf.reference.filename <- 'perf_files/default_perf_profile.csv' +.perf.reference.save.filename <- NULL .perf.reference <- NULL @@ -22,7 +23,13 @@ perf.reference.save <- function(perf.ref.name, rate, tolerance.lower, tolerance. .perf.reference[nrow(.perf.reference)+1,] <- c(perf.ref.name, rate, tolerance.lower, tolerance.upper) - write.csv(.perf.reference, .perf.reference.filename, row.names = FALSE) + if (is.null(.perf.reference.save.filename)) + { + .perf.reference.save.filename <<- base::tempfile(pattern = "perf_file_", fileext = ".csv") + message(paste0("Additional perf record added to '", .perf.reference.save.filename, "'")) + } + + write.csv(.perf.reference, .perf.reference.save.filename, row.names = FALSE) .perf.reference <<- .perf.reference } diff --git a/tests/testthat/setup.R b/tests/testthat/setup.R index 4c55c6e74..512e649c1 100644 --- a/tests/testthat/setup.R +++ b/tests/testthat/setup.R @@ -1,6 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. -# Copyright (c) 2022 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -8,11 +8,12 @@ # You should have received a copy of the GNU General Public License # along with this program. If not, see . #------------------------------------------------------------------------------- + # # Datashield test suite set up # -context("setup - start") +# context("setup - start") # Convert 'warnings' to 'errors' # options(warn = 2) @@ -33,4 +34,4 @@ source("connection_to_datasets/init_studies_datasets.R") source("connection_to_datasets/init_discordant_datasets.R") source("connection_to_datasets/init_mediation_datasets.R") -context("setup - done") +# context("setup - done") diff --git a/tests/testthat/teardown.R b/tests/testthat/teardown.R index 710dac810..5026a0dbf 100644 --- a/tests/testthat/teardown.R +++ b/tests/testthat/teardown.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -8,6 +9,6 @@ # along with this program. If not, see . #------------------------------------------------------------------------------- -context("teardown") +# context("teardown") -context("teardown - done") +# context("teardown - done") diff --git a/tests/testthat/test-_-vm-test.R b/tests/testthat/test-_-vm-test.R index 952425f56..7b5af1f4e 100644 --- a/tests/testthat/test-_-vm-test.R +++ b/tests/testthat/test-_-vm-test.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("vm-test::_::setup") +# context("vm-test::_::setup") init.testing.datasets() @@ -21,7 +22,7 @@ init.testing.datasets() # #connect to a server -context("vm-test::_::tests::vm") +# context("vm-test::_::tests::vm") test_that("The virtual machine is loaded. ", { @@ -33,11 +34,11 @@ test_that("The virtual machine is loaded. ", # Shutdown # -context("vm-test::_::shutdown") +# context("vm-test::_::shutdown") # # Done # -context("vm-test::_::done") +# context("vm-test::_::done") diff --git a/tests/testthat/test-arg-ds.Boole.R b/tests/testthat/test-arg-ds.Boole.R index fdfc45026..d8fb3bedf 100644 --- a/tests/testthat/test-arg-ds.Boole.R +++ b/tests/testthat/test-arg-ds.Boole.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC", "LAB_TRIG")) # Tests # -context("ds.Boole::arg::test errors") +# context("ds.Boole::arg::test errors") test_that("Boole_erros", { expect_error(ds.Boole(), "Please provide the name of the column or scalar that holds V1!", fixed=TRUE) expect_error(ds.Boole(V1="D$LAB_TSC"), "Please provide the name of a column or scalar holding V2 or declare a scalar in character format: eg '3'", fixed=TRUE) diff --git a/tests/testthat/test-arg-ds.asCharacter.R b/tests/testthat/test-arg-ds.asCharacter.R index a007ec6a3..8d7d35449 100644 --- a/tests/testthat/test-arg-ds.asCharacter.R +++ b/tests/testthat/test-arg-ds.asCharacter.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -18,7 +19,7 @@ connect.discordant.dataset.simple(list("A", "B", "C")) # Tests # -context("ds.asCharacter::arg::test errors") +# context("ds.asCharacter::arg::test errors") test_that("asCharacter_erros", { expect_error(ds.asCharacter(), "Please provide the name of the input vector!", fixed=TRUE) }) diff --git a/tests/testthat/test-arg-ds.asDataMatrix.R b/tests/testthat/test-arg-ds.asDataMatrix.R index e84e2281b..ca65f6cb0 100644 --- a/tests/testthat/test-arg-ds.asDataMatrix.R +++ b/tests/testthat/test-arg-ds.asDataMatrix.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.asDataMatrix::arg::test errors") +# context("ds.asDataMatrix::arg::test errors") test_that("asDataMatrix_erros", { expect_error(ds.asDataMatrix(), "Please provide the name of the input vector!", fixed=TRUE) }) diff --git a/tests/testthat/test-arg-ds.asFactor.R b/tests/testthat/test-arg-ds.asFactor.R index bfc4662dc..a264b040a 100644 --- a/tests/testthat/test-arg-ds.asFactor.R +++ b/tests/testthat/test-arg-ds.asFactor.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.asFactor::arg::test errors") +# context("ds.asFactor::arg::test errors") test_that("asFactor_erros", { expect_error(ds.asFactor(), "Please provide the name of the variable that is to be converted to a factor e.g. 'varname'", fixed=TRUE) expect_error(ds.asFactor(input.var.name=1), "Please provide the name of the variable that is to be converted to a factor in character format e.g. 'varname'", fixed=TRUE) diff --git a/tests/testthat/test-arg-ds.asInteger.R b/tests/testthat/test-arg-ds.asInteger.R index a6a1196ef..c6305012e 100644 --- a/tests/testthat/test-arg-ds.asInteger.R +++ b/tests/testthat/test-arg-ds.asInteger.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.asInteger::arg::test errors") +# context("ds.asInteger::arg::test errors") test_that("asInteger_erros", { expect_error(ds.asInteger(), "Please provide the name of the input vector!", fixed=TRUE) }) diff --git a/tests/testthat/test-arg-ds.asList.R b/tests/testthat/test-arg-ds.asList.R index c498d36cd..926401881 100644 --- a/tests/testthat/test-arg-ds.asList.R +++ b/tests/testthat/test-arg-ds.asList.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.asList::arg::test errors") +# context("ds.asList::arg::test errors") test_that("asList_erros", { expect_error(ds.asList(), "Please provide the name of the input vector!", fixed=TRUE) }) diff --git a/tests/testthat/test-arg-ds.asLogical.R b/tests/testthat/test-arg-ds.asLogical.R index 64912059a..39056cc38 100644 --- a/tests/testthat/test-arg-ds.asLogical.R +++ b/tests/testthat/test-arg-ds.asLogical.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.asLogical::arg::test errors") +# context("ds.asLogical::arg::test errors") test_that("asLogical_erros", { expect_error(ds.asLogical(), "Please provide the name of the input vector!", fixed=TRUE) }) diff --git a/tests/testthat/test-arg-ds.asMatrix.R b/tests/testthat/test-arg-ds.asMatrix.R index 5c7c8ebdf..4a199dd08 100644 --- a/tests/testthat/test-arg-ds.asMatrix.R +++ b/tests/testthat/test-arg-ds.asMatrix.R @@ -1,4 +1,6 @@ +# #Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # #This program and the accompanying materials are made available under the terms #of the GNU Public License v3.0. @@ -17,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.asMatrix::arg::test errors") +# context("ds.asMatrix::arg::test errors") test_that("asMatrix_erros", { expect_error(ds.asMatrix(), "Please provide the name of the input vector!", fixed=TRUE) }) diff --git a/tests/testthat/test-arg-ds.asNumeric.R b/tests/testthat/test-arg-ds.asNumeric.R index b821c8429..276260751 100644 --- a/tests/testthat/test-arg-ds.asNumeric.R +++ b/tests/testthat/test-arg-ds.asNumeric.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.asNumeric::arg::test errors") +# context("ds.asNumeric::arg::test errors") test_that("asNumeric_erros", { expect_error(ds.asNumeric(), "Please provide the name of the input vector!", fixed=TRUE) }) diff --git a/tests/testthat/test-arg-ds.assign.R b/tests/testthat/test-arg-ds.assign.R index 9c1cdac01..4fbd06c42 100644 --- a/tests/testthat/test-arg-ds.assign.R +++ b/tests/testthat/test-arg-ds.assign.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.assign::arg::test errors") +# context("ds.assign::arg::test errors") test_that("assign_erros", { expect_error(ds.assign(), "Please give the name of object to assign or an expression to evaluate and assign.!\n") }) diff --git a/tests/testthat/test-arg-ds.auc.R b/tests/testthat/test-arg-ds.auc.R index 7c42585f3..ade352110 100644 --- a/tests/testthat/test-arg-ds.auc.R +++ b/tests/testthat/test-arg-ds.auc.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,13 +13,13 @@ # Set up # -context("ds.auc::arg::setup") +# context("ds.auc::arg::setup") # # Tests # -context("ds.auc::arg::test errors") +# context("ds.auc::arg::test errors") test_that("ds.auc errors for null pred or y", { @@ -31,5 +32,5 @@ test_that("ds.auc errors for null pred or y", { # Done # -context("ds.auc::arg::shutdown") -context("ds.auc::arg::done") +# context("ds.auc::arg::shutdown") +# context("ds.auc::arg::done") diff --git a/tests/testthat/test-arg-ds.c.R b/tests/testthat/test-arg-ds.c.R index 3371d591d..7a85cecb4 100644 --- a/tests/testthat/test-arg-ds.c.R +++ b/tests/testthat/test-arg-ds.c.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.c::arg::test errors") +# context("ds.c::arg::test errors") test_that("simple c errors", { expect_error(ds.c(), "x=NULL. Please provide the names of the objects to concatenate!") }) diff --git a/tests/testthat/test-arg-ds.cbind.R b/tests/testthat/test-arg-ds.cbind.R index d600ac830..a51988136 100644 --- a/tests/testthat/test-arg-ds.cbind.R +++ b/tests/testthat/test-arg-ds.cbind.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.cbind::arg::test errors") +# context("ds.cbind::arg::test errors") test_that("cbind_erros", { ds.asList(x='D$LAB_TSC', newobj="as_list") diff --git a/tests/testthat/test-arg-ds.changeRefGroup.R b/tests/testthat/test-arg-ds.changeRefGroup.R index 1baffe404..91a0fe24c 100644 --- a/tests/testthat/test-arg-ds.changeRefGroup.R +++ b/tests/testthat/test-arg-ds.changeRefGroup.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("DIS_AMI", "LAB_TSC")) # Tests # -context("ds.changeRefGroup::arg::test errors") +# context("ds.changeRefGroup::arg::test errors") test_that("changeRefGroup_erros", { expect_error(ds.changeRefGroup(), "Please provide the name of a vector of type factor!") expect_error(ds.changeRefGroup(x="D$DIS_AMI"), " You must indicate a reference level - set the parameter 'ref'.") diff --git a/tests/testthat/test-arg-ds.class.R b/tests/testthat/test-arg-ds.class.R index c7240c7b0..c0bf5c7dd 100644 --- a/tests/testthat/test-arg-ds.class.R +++ b/tests/testthat/test-arg-ds.class.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.class::arg::test errors") +# context("ds.class::arg::test errors") test_that("class_erros", { expect_error(ds.class(), "Please provide the name of the input object!", fixed=TRUE) }) diff --git a/tests/testthat/test-arg-ds.colnames.R b/tests/testthat/test-arg-ds.colnames.R index bbbaa5e97..39ce9b87a 100644 --- a/tests/testthat/test-arg-ds.colnames.R +++ b/tests/testthat/test-arg-ds.colnames.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC", "LAB_TRIG")) # Tests # -context("ds.colnames::arg::test errors") +# context("ds.colnames::arg::test errors") test_that("simple colnames errors", { expect_error(ds.colnames(), "") }) diff --git a/tests/testthat/test-arg-ds.completeCases.R b/tests/testthat/test-arg-ds.completeCases.R index a13856380..8bb997338 100644 --- a/tests/testthat/test-arg-ds.completeCases.R +++ b/tests/testthat/test-arg-ds.completeCases.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.completeCases::arg::test errors") +# context("ds.completeCases::arg::test errors") test_that("completeCases_errors", { res <- ds.completeCases() expect_equal(res, "Error: x1 must be a character string naming a serverside data.frame, matrix or vector", fixed = TRUE) diff --git a/tests/testthat/test-arg-ds.cor.R b/tests/testthat/test-arg-ds.cor.R index 9f728e1a0..47b5a5abb 100644 --- a/tests/testthat/test-arg-ds.cor.R +++ b/tests/testthat/test-arg-ds.cor.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC", "LAB_TRIG")) # Tests # -context("ds.cor::arg::test errors") +# context("ds.cor::arg::test errors") test_that("cor_erros", { expect_error(ds.cor(), 'x=NULL. Please provide the name of a matrix or dataframe or the names of two numeric vectors!', fixed=TRUE) expect_error(ds.cor(x='D$LAB_TSC'), 'If x is a numeric vector, y must be a numeric vector!', fixed=TRUE) diff --git a/tests/testthat/test-arg-ds.corTest.R b/tests/testthat/test-arg-ds.corTest.R index ac80a40cc..76adc6f15 100644 --- a/tests/testthat/test-arg-ds.corTest.R +++ b/tests/testthat/test-arg-ds.corTest.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -18,7 +19,7 @@ connect.studies.dataset.survival(list("survtime", "time.id")) # Tests # -context("ds.corTest::arg") +# context("ds.corTest::arg") test_that("simple arg test", { expect_error(ds.corTest(), "x=NULL. Please provide the names of the 1st numeric vector!", fixed=TRUE) diff --git a/tests/testthat/test-arg-ds.cov.R b/tests/testthat/test-arg-ds.cov.R index 0958c65ad..29330c9de 100644 --- a/tests/testthat/test-arg-ds.cov.R +++ b/tests/testthat/test-arg-ds.cov.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC", "LAB_TRIG")) # Tests # -context("ds.cov::arg::test errors") +# context("ds.cov::arg::test errors") test_that("cov_erros", { expect_error(ds.cov(), 'x=NULL. Please provide the name of a matrix or dataframe or the names of two numeric vectors!', fixed=TRUE) expect_error(ds.cov(x='D$LAB_TSC'), 'If x is a numeric vector, y must be a numeric vector!', fixed=TRUE) diff --git a/tests/testthat/test-arg-ds.dataFrame.R b/tests/testthat/test-arg-ds.dataFrame.R index 9d76b7beb..33fa65cf6 100644 --- a/tests/testthat/test-arg-ds.dataFrame.R +++ b/tests/testthat/test-arg-ds.dataFrame.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.dataFrame::arg::test errors") +# context("ds.dataFrame::arg::test errors") test_that("dataframe_erros", { expect_error(ds.dataFrame(), "Please provide the name of the list that holds the input vectors!", fixed=TRUE) diff --git a/tests/testthat/test-arg-ds.dataFrameFill.R b/tests/testthat/test-arg-ds.dataFrameFill.R index 0e71d2e56..2eb77e4f1 100644 --- a/tests/testthat/test-arg-ds.dataFrameFill.R +++ b/tests/testthat/test-arg-ds.dataFrameFill.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.dataFrameFill::arg::test errors") +# context("ds.dataFrameFill::arg::test errors") test_that("dataFrameFill_erros", { expect_error(ds.dataFrameFill(), "Please provide the name of the data.frame to be filled as a character string: eg 'xxx'", fixed=TRUE) expect_error(ds.dataFrameFill("NonDF"), "The input object NonDF is not defined in sim1, sim2, sim3!", fixed=TRUE) diff --git a/tests/testthat/test-arg-ds.dataFrameSort.R b/tests/testthat/test-arg-ds.dataFrameSort.R index 65a1c2cfe..52061313f 100644 --- a/tests/testthat/test-arg-ds.dataFrameSort.R +++ b/tests/testthat/test-arg-ds.dataFrameSort.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC", "GENDER")) # Tests # -context("ds.dataFrameSort::arg::no args") +# context("ds.dataFrameSort::arg::no args") test_that("dataFrameSort_noargs", { expect_error(ds.dataFrameSort(), "There are some DataSHIELD errors, list them with datashield.errors()", fixed=TRUE) @@ -30,7 +31,7 @@ test_that("dataFrameSort_noargs", { expect_match(res.errors$sim3, "* Error in strsplit\\(df.name, split = \"\"\\) : non-character argument*") }) -context("ds.dataFrameSort::arg::sorted dataframe, of factors") +# context("ds.dataFrameSort::arg::sorted dataframe, of factors") test_that("dataFrameSort_factors", { myvectors <- c('D$LAB_TSC', 'D$GENDER') ds.dataFrame(x=myvectors, newobj="unsorted_df") diff --git a/tests/testthat/test-arg-ds.dataFrameSubset.R b/tests/testthat/test-arg-ds.dataFrameSubset.R index 4bd414e6e..53ec07e39 100644 --- a/tests/testthat/test-arg-ds.dataFrameSubset.R +++ b/tests/testthat/test-arg-ds.dataFrameSubset.R @@ -1,6 +1,7 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -13,7 +14,7 @@ # Set up # -context("ds.dataFrameSubset::arg::setup") +# context("ds.dataFrameSubset::arg::setup") connect.studies.dataset.cnsim(list("LAB_TSC")) @@ -25,27 +26,27 @@ test_that("setup", { # Tests # -context("ds.dataFrameSubset::arg::missing 'ds.name' arg errors") +# context("ds.dataFrameSubset::arg::missing 'ds.name' arg errors") test_that("dataFrameSubset_erros", { expect_error(ds.dataFrameSubset(), "Please provide the name of the data.frame to be subsetted as a character string: eg 'xxx'", fixed=TRUE) }) -context("ds.dataFrameSubset::arg::missing 'V1' arg error") +# context("ds.dataFrameSubset::arg::missing 'V1' arg error") test_that("dataFrameSubset_erros", { expect_error(ds.dataFrameSubset(df.name="D"), "Please provide the name of the column or scalar that holds V1 as a character string: eg 'xxx' or '3'", fixed=TRUE) }) -context("ds.dataFrameSubset::arg::missing 'V2' arg error") +# context("ds.dataFrameSubset::arg::missing 'V2' arg error") test_that("dataFrameSubset_erros", { expect_error(ds.dataFrameSubset(df.name="D", V1.name="LAB_TSC"), "Please provide the name of the column or scalar that holds V2 as a character string: eg 'xxx' or '3'", fixed=TRUE) }) -context("ds.dataFrameSubset::arg::missing 'Boolean.operator' arg error") +# context("ds.dataFrameSubset::arg::missing 'Boolean.operator' arg error") test_that("dataFrameSubset_erros", { expect_error(ds.dataFrameSubset(df.name="D", V1.name="LAB_TSC", V2.name="LAB_TSC"), "Unless you are only subsetting columns, please provide a Boolean operator in character format: eg '==' or '>=' or '<' or '!='. However, if either keep.cols or rm.cols is non-null because you want to subset columns and you specify both V1.name and V2.name as NULL (or 'ONES') and Boolean.operator as NULL,ds.dataFrameSubset will subset out the specified columns but will keep all rows.", fixed=TRUE) }) -context("ds.dataFrameSubset::arg::missing 'df.name' value server-side") +# context("ds.dataFrameSubset::arg::missing 'df.name' value server-side") test_that("dataFrameSubset_erros", { expect_error(ds.dataFrameSubset(df.name="M", V1.name="A", V2.name="B", Boolean.operator="=/="), "There are some DataSHIELD errors, list them with datashield.errors()", fixed=TRUE) @@ -57,7 +58,7 @@ test_that("dataFrameSubset_erros", { expect_match(res.errors$sim3, "* object 'M' not found*") }) -context("ds.dataFrameSubset::arg::missing 'V1' value server-side") +# context("ds.dataFrameSubset::arg::missing 'V1' value server-side") test_that("dataFrameSubset_erros", { expect_error(ds.dataFrameSubset(df.name="D", V1.name="A", V2.name="B", Boolean.operator="=/="), "There are some DataSHIELD errors, list them with datashield.errors()", fixed=TRUE) @@ -69,7 +70,7 @@ test_that("dataFrameSubset_erros", { expect_match(res.errors$sim3, "* Error in eval\\(parse\\(text = V1.name\\), envir = parent.frame\\(\\)\\) : \\n object 'A' not found*") }) -context("ds.dataFrameSubset::arg::missing 'V2' value server-side") +# context("ds.dataFrameSubset::arg::missing 'V2' value server-side") test_that("dataFrameSubset_erros", { expect_error(ds.dataFrameSubset(df.name="D", V1.name="D$LAB_TSC", V2.name="B", Boolean.operator="=/="), "There are some DataSHIELD errors, list them with datashield.errors()", fixed=TRUE) @@ -81,7 +82,7 @@ test_that("dataFrameSubset_erros", { expect_match(res.errors$sim3, "* Error in eval\\(parse\\(text = V2.name\\), envir = parent.frame\\(\\)\\) : \\n object 'B' not found*") }) -context("ds.dataFrameSubset::arg::invalid 'Boolean.operator' value server-side") +# context("ds.dataFrameSubset::arg::invalid 'Boolean.operator' value server-side") test_that("dataFrameSubset_erros", { expect_error(ds.dataFrameSubset(df.name="D", V1.name="D$LAB_TSC", V2.name="D$LAB_TSC", Boolean.operator="=/="), "There are some DataSHIELD errors, list them with datashield.errors()", fixed=TRUE) @@ -97,7 +98,7 @@ test_that("dataFrameSubset_erros", { # Shutdown # -context("ds.dataFrameSubset::arg::shutdown") +# context("ds.dataFrameSubset::arg::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -109,4 +110,4 @@ disconnect.studies.dataset.cnsim() # Done # -context("ds.dataFrameSubset::arg::done") +# context("ds.dataFrameSubset::arg::done") diff --git a/tests/testthat/test-arg-ds.dim.R b/tests/testthat/test-arg-ds.dim.R index 8ee681985..27b4e8bd8 100644 --- a/tests/testthat/test-arg-ds.dim.R +++ b/tests/testthat/test-arg-ds.dim.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.dim::arg::test errors") +# context("ds.dim::arg::test errors") test_that("dim_erros", { expect_error(ds.dim(), "Please provide the name of a data.frame or matrix!", fixed=TRUE) expect_error(ds.dim(x="F", checks = TRUE), "The input object must be a table structure!", fixed=TRUE) diff --git a/tests/testthat/test-arg-ds.exists.R b/tests/testthat/test-arg-ds.exists.R index 7e920395f..8ae2070d3 100644 --- a/tests/testthat/test-arg-ds.exists.R +++ b/tests/testthat/test-arg-ds.exists.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.exists::arg::test errors") +# context("ds.exists::arg::test errors") test_that("simple exists errors", { expect_error(ds.exists(), "Please provide the name of the input object!") }) diff --git a/tests/testthat/test-arg-ds.exp.R b/tests/testthat/test-arg-ds.exp.R index d3a6d1ef9..c851bba34 100644 --- a/tests/testthat/test-arg-ds.exp.R +++ b/tests/testthat/test-arg-ds.exp.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.exp::arg::test errors") +# context("ds.exp::arg::test errors") test_that("exp_erros", { expect_error(ds.exp(), "Please provide the name of the input object!", fixed=TRUE) }) diff --git a/tests/testthat/test-arg-ds.foobar.R b/tests/testthat/test-arg-ds.foobar.R index 05cbde701..19f959f28 100644 --- a/tests/testthat/test-arg-ds.foobar.R +++ b/tests/testthat/test-arg-ds.foobar.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.foobar::arg::setup") +# context("ds.foobar::arg::setup") connect.studies.dataset.cnsim(list("LAB_TSC")) @@ -24,14 +25,13 @@ test_that("setup", { # Tests # -context("ds.foobar::arg::aggregate") +# context("ds.foobar::arg::aggregate") test_that("NULL connections", { calltext <- call("fooBarDS") if (ds.test_env$driver == "ArmadilloDriver") { - expect_error(datashield.aggregate(conns=NULL, expr=calltext), "no applicable method for `@` applied to an object of class \"NULL\"", fixed=TRUE) -# expect_error(datashield.aggregate(conns=NULL, expr=calltext), "trying to get slot \"name\" from an object of a basic class (\"NULL\") with no slots", fixed=TRUE) + expect_error(datashield.aggregate(conns=NULL, expr=calltext), "unable to find an inherited method for function 'dsIsAsync' for signature 'conn = \"NULL\"'", fixed=TRUE) } else if (ds.test_env$driver == "OpalDriver") { - expect_error(datashield.aggregate(conns=NULL, expr=calltext), "no applicable method for `@` applied to an object of class \"NULL\"", fixed=TRUE) + expect_error(datashield.aggregate(conns=NULL, expr=calltext), "unable to find an inherited method for function 'dsIsAsync' for signature 'conn = \"NULL\"'", fixed=TRUE) } else { fail(message = "Unknown driver type", info = ds.test_env$driver) } @@ -40,7 +40,7 @@ test_that("NULL connections", { expect_length(errs, 0) }) -context("ds.foobar::arg::aggregate") +# context("ds.foobar::arg::aggregate") test_that("NULL expr", { calltext <- call("fooBarDS") expect_error(expect_warning(datashield.aggregate(conns=ds.test_env$connections, expr=NULL), "'x' is NULL so the result will be NULL", fixed = TRUE), "replacement has length zero", fixed = TRUE) @@ -49,7 +49,7 @@ test_that("NULL expr", { expect_length(errs, 0) }) -context("ds.foobar::arg::aggregate") +# context("ds.foobar::arg::aggregate") test_that("non existent aggregate foobarDS", { calltext <- call("fooBarDS") expect_error(datashield.aggregate(conns=ds.test_env$connections, expr=calltext)) @@ -65,14 +65,13 @@ test_that("non existent aggregate foobarDS", { expect_true(errs$sim3 %in% c("Command 'fooBarDS()' failed on 'sim3': No such DataSHIELD 'AGGREGATE' method with name: fooBarDS", "[Client error: (400) Bad Request] No such DataSHIELD 'AGGREGATE' method with name: fooBarDS", "Bad request: No such DataSHIELD 'AGGREGATE' method with name: fooBarDS")) }) -context("ds.foobar::arg::assign") +# context("ds.foobar::arg::assign") test_that("NULL connections", { calltext <- call("fooBarDS") if (ds.test_env$driver == "ArmadilloDriver") { - expect_error(datashield.assign(conns=NULL, symbol="new_obj", value=calltext), "no applicable method for `@` applied to an object of class \"NULL\"", fixed=TRUE) -# expect_error(datashield.assign(conns=NULL, symbol="new_obj", value=calltext), "trying to get slot \"name\" from an object of a basic class (\"NULL\") with no slots", fixed=TRUE) + expect_error(datashield.assign(conns=NULL, symbol="new_obj", value=calltext), "unable to find an inherited method for function 'dsIsAsync' for signature 'conn = \"NULL\"'", fixed=TRUE) } else if (ds.test_env$driver == "OpalDriver") { - expect_error(datashield.assign(conns=NULL, symbol="new_obj", value=calltext), "no applicable method for `@` applied to an object of class \"NULL\"", fixed=TRUE) + expect_error(datashield.assign(conns=NULL, symbol="new_obj", value=calltext), "unable to find an inherited method for function 'dsIsAsync' for signature 'conn = \"NULL\"'", fixed=TRUE) } else { fail(message = "Unknown driver type", info = ds.test_env$driver) } @@ -89,7 +88,7 @@ test_that("NULL connections", { # expect_length(res, 0) #}) -context("ds.foobar::arg::assign") +# context("ds.foobar::arg::assign") test_that("NULL value", { calltext <- call("fooBarDS") expect_error(datashield.assign(conns=ds.test_env$connections, symbol="new_obj", value=NULL), "Not a valid table name", fixed=TRUE) @@ -98,7 +97,7 @@ test_that("NULL value", { expect_length(errs, 0) }) -context("ds.foobar::arg::assign") +# context("ds.foobar::arg::assign") test_that("non existent assign foobarDS", { calltext <- call("fooBarDS") expect_error(datashield.assign(conns=ds.test_env$connections, symbol="new_obj", value=calltext)) @@ -117,7 +116,7 @@ test_that("non existent assign foobarDS", { # Tear down # -context("ds.foobar::arg::shutdown") +# context("ds.foobar::arg::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -125,4 +124,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.foobar::arg::done") +# context("ds.foobar::arg::done") diff --git a/tests/testthat/test-arg-ds.gamlss.R b/tests/testthat/test-arg-ds.gamlss.R index 7a4ec4737..c24f41efb 100644 --- a/tests/testthat/test-arg-ds.gamlss.R +++ b/tests/testthat/test-arg-ds.gamlss.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -18,7 +19,7 @@ connect.studies.dataset.gamlss(list("e3_bw", "e3_gac_None")) # Tests # -context("ds.gamlss::arg::test errors") +# context("ds.gamlss::arg::test errors") test_that("gamlss_errors", { expect_error(ds.gamlss(), " Please provide a valid formula!", fixed=TRUE) expect_error(ds.gamlss(formula="e3_bw ~ e3_gac_None", method="RG"), "Argument 'method' must be either 'RS', 'CG' or 'mixed'", fixed=TRUE) diff --git a/tests/testthat/test-arg-ds.glm.R b/tests/testthat/test-arg-ds.glm.R index 0724e206b..fbf1a880f 100644 --- a/tests/testthat/test-arg-ds.glm.R +++ b/tests/testthat/test-arg-ds.glm.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.glm::arg::test errors") +# context("ds.glm::arg::test errors") test_that("glm_errors", { expect_error(ds.glm(), " Please provide a valid regression formula!", fixed=TRUE) expect_error(ds.glm("D$LAB_TSC~D$LAB_TSC"), " Please provide a valid 'family' argument!", fixed=TRUE) diff --git a/tests/testthat/test-arg-ds.glmPredict.R b/tests/testthat/test-arg-ds.glmPredict.R index 579fa5b54..52c70b5c1 100644 --- a/tests/testthat/test-arg-ds.glmPredict.R +++ b/tests/testthat/test-arg-ds.glmPredict.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -18,14 +19,14 @@ connect.studies.dataset.cnsim(list("LAB_TSC", "LAB_TRIG", "DIS_AMI", "DIS_DIAB", # Tests # -context("ds.glmPredict::arg::test _glmname_ arg is correct object") +# context("ds.glmPredict::arg::test _glmname_ arg is correct object") test_that("glmPredict_errors", { expect_error(ds.glmPredict(), " is not set, please specify it as a character string containing the name of a valid glm class object on the serverside", fixed=TRUE) expect_error(ds.glmPredict("ABC"), "The input object ABC is not defined in sim1, sim2, sim3!", fixed=TRUE) }) -context("ds.glmPredict::arg::setting up glm obj for further testing") +# context("ds.glmPredict::arg::setting up glm obj for further testing") test_that("glmPredict_errors", { #glm.obj <- ds.glmSLMA('D$LAB_TSC~D$LAB_TSC', family="gaussian", newobj="gaussian.glmslma.obj") #glmSLMA.res <- ds.glmSLMA('D$DIS_DIAB~D$LAB_TRIG', family="binomial", newobj="binomial.glmslma.obj") @@ -37,7 +38,7 @@ test_that("glmPredict_errors", { expect_equal(glmSLMA.res$validity.check, " appears valid in all sources") }) -context("ds.glmPredict::arg::test _newdataname_ arg is correct object") +# context("ds.glmPredict::arg::test _newdataname_ arg is correct object") test_that("glmPredict_errors", { expect_error(ds.glmPredict("gaussian.glmslma.obj", newdataname = "help"),"There are some DataSHIELD errors, list them with datashield.errors()", fixed=TRUE) # TODO: "some DataSHIELD errors" is unhelpful and needs improvement @@ -46,13 +47,13 @@ test_that("glmPredict_errors", { expect_true(all(c("sim1","sim2","sim3") %in% names(datashield.errors()))) }) -context("ds.glmPredict::arg::test _output.type_ arg is correct object") +# context("ds.glmPredict::arg::test _output.type_ arg is correct object") test_that("glmPredict_errors", { expect_error(ds.glmPredict("gaussian.glmslma.obj", newdataname = NULL, output.type = NULL), "missing value where TRUE/FALSE needed", fixed=TRUE) expect_error(ds.glmPredict("gaussian.glmslma.obj", newdataname = NULL, output.type = 'blah'), " is not correctly set, please specify it as one of three character strings: 'link', 'response', or 'terms'", fixed=TRUE) }) -context("ds.glmPredict::arg::test _se.fit_ arg is correct object") +# context("ds.glmPredict::arg::test _se.fit_ arg is correct object") test_that("glmPredict_errors", { expect_error(ds.glmPredict("gaussian.glmslma.obj", newdataname = NULL, output.type = "response", se.fit = "1"), "There are some DataSHIELD errors, list them with datashield.errors()", fixed = TRUE) @@ -66,12 +67,12 @@ test_that("glmPredict_errors", { # res <- ds.glmPredict("gaussian.glmslma.obj", newdataname = NULL, output.type = "response", se.fit = FALSE, dispersion = "thereisnothingontheservercalledthis") #}) -context("ds.glmPredict::arg::test _terms_ arg is correct object") +# context("ds.glmPredict::arg::test _terms_ arg is correct object") test_that("glmPredict_errors", { expect_error(ds.glmPredict("gaussian.glmslma.obj", newdataname = NULL, output.type = "terms", se.fit = FALSE, dispersion = NULL, terms="thereisnothingontheservercalledthis2"), "There are some DataSHIELD errors, list them with datashield.errors()", fixed = TRUE) }) -context("ds.glmPredict::arg::test _na.action_ arg is correct object") +# context("ds.glmPredict::arg::test _na.action_ arg is correct object") test_that("glmPredict_errors", { expect_error(ds.glmPredict("gaussian.glmslma.obj", newdataname = NULL, output.type = "response", se.fit = FALSE, dispersion = NULL, terms=NULL, na.action= "na.other"), " is not correctly set, please specify it as one of four character strings: 'na.fail', 'na.omit', 'na.exclude' or 'na.pass'", fixed = TRUE) }) diff --git a/tests/testthat/test-arg-ds.glmSLMA.R b/tests/testthat/test-arg-ds.glmSLMA.R index ce4dbe735..4180f91af 100644 --- a/tests/testthat/test-arg-ds.glmSLMA.R +++ b/tests/testthat/test-arg-ds.glmSLMA.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.glmSLMA::arg::test errors") +# context("ds.glmSLMA::arg::test errors") test_that("glmSLMA_errors", { expect_error(ds.glmSLMA(), " Please provide a valid regression formula!", fixed=TRUE) diff --git a/tests/testthat/test-arg-ds.glmerSLMA.R b/tests/testthat/test-arg-ds.glmerSLMA.R index 84662f7f2..36c80bb5b 100644 --- a/tests/testthat/test-arg-ds.glmerSLMA.R +++ b/tests/testthat/test-arg-ds.glmerSLMA.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.glmerSLMA::arg::setup") +# context("ds.glmerSLMA::arg::setup") connect.studies.dataset.cluster.int(list("incid_rate", "trtGrp", "Male", "idDoctor", "idSurgery")) @@ -24,7 +25,7 @@ test_that("setup", { # Test # -context("ds.glmerSLMA::arg::testing") +# context("ds.glmerSLMA::arg::testing") test_that("simple glmerSLMA tesing (mis)use of arguments", { expect_error(ds.glmerSLMA(formula = 'incid_rate ~ trtGrp + Male + (1|idDoctor)', dataName = 'D'), " Please provide a valid 'family' argument!", fixed=TRUE) @@ -53,7 +54,7 @@ test_that("simple glmerSLMA tesing (mis)use of arguments", { # Shutdown # -context("ds.glmerSLMA::arg::shutdown") +# context("ds.glmerSLMA::arg::shutdown") test_that("setup", { ds_expect_variables(c("D", "offset", "weights")) @@ -65,4 +66,4 @@ disconnect.studies.dataset.cluster.int() # Done # -context("ds.glmerSLMA::arg::done") +# context("ds.glmerSLMA::arg::done") diff --git a/tests/testthat/test-arg-ds.isNA.R b/tests/testthat/test-arg-ds.isNA.R index 27c9bffcb..433857a75 100644 --- a/tests/testthat/test-arg-ds.isNA.R +++ b/tests/testthat/test-arg-ds.isNA.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_HDL")) # Tests # -context("ds.isNA::arg::errors") +# context("ds.isNA::arg::errors") test_that("isNA errors", { expect_error(ds.isNA(), "Please provide the name of the input vector!", fixed=TRUE) }) diff --git a/tests/testthat/test-arg-ds.isValid.R b/tests/testthat/test-arg-ds.isValid.R index 65d843cc7..37fbf21a5 100644 --- a/tests/testthat/test-arg-ds.isValid.R +++ b/tests/testthat/test-arg-ds.isValid.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_HDL")) # Tests # -context("ds.isValid::arg::errors") +# context("ds.isValid::arg::errors") test_that("isValid errors", { expect_error(ds.isValid(), "Please provide the name of the input vector!", fixed=TRUE) expect_error(ds.isValid("D$NOT_THERE"), "The input object D$NOT_THERE is not defined in sim1, sim2, sim3!", fixed=TRUE) diff --git a/tests/testthat/test-arg-ds.kurtosis.R b/tests/testthat/test-arg-ds.kurtosis.R index db80a0788..0d8118e12 100644 --- a/tests/testthat/test-arg-ds.kurtosis.R +++ b/tests/testthat/test-arg-ds.kurtosis.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.kurtosis::arg::setup") +# context("ds.kurtosis::arg::setup") connect.studies.dataset.cnsim(list("LAB_TSC")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.kurtosis::arg::test errors") +# context("ds.kurtosis::arg::test errors") test_that("kurtosis_erros", { expect_error(ds.kurtosis(), "Please provide the name of the input vector!", fixed=TRUE) expect_error(ds.kurtosis(x='D$LAB_TSC', type='datashield'), "Function argument \"type\" has to be either \"both\", \"combine\" or \"split\"", fixed=TRUE) @@ -36,7 +37,7 @@ test_that("kurtosis_erros", { # Done # -context("ds.kurtosis::arg::shutdown") +# context("ds.kurtosis::arg::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -44,4 +45,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.kurtosis::arg::done") +# context("ds.kurtosis::arg::done") diff --git a/tests/testthat/test-arg-ds.length.R b/tests/testthat/test-arg-ds.length.R index 87d5f3b3c..06ce3a7a5 100644 --- a/tests/testthat/test-arg-ds.length.R +++ b/tests/testthat/test-arg-ds.length.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.length::arg::test errors") +# context("ds.length::arg::test errors") test_that("length_erros", { ds.asMatrix(x='D$LAB_TSC', newobj="not_a_numeric") diff --git a/tests/testthat/test-arg-ds.levels.R b/tests/testthat/test-arg-ds.levels.R index 6f94c4ec9..cf6bf974b 100644 --- a/tests/testthat/test-arg-ds.levels.R +++ b/tests/testthat/test-arg-ds.levels.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.levels::arg") +# context("ds.levels::arg") test_that("simple levels", { expect_error(ds.levels(), "Please provide the name of the input vector!", fixed=TRUE) expect_error(ds.levels("LAB_TSC"), "The input object LAB_TSC is not defined in sim1, sim2, sim3!", fixed=TRUE) diff --git a/tests/testthat/test-arg-ds.lexis.R b/tests/testthat/test-arg-ds.lexis.R index 681598e07..52d1657df 100644 --- a/tests/testthat/test-arg-ds.lexis.R +++ b/tests/testthat/test-arg-ds.lexis.R @@ -1,6 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. -# Copyright (c) 2022 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -19,12 +19,12 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.lexis::arg::test errors") +# context("ds.lexis::arg::test errors") test_that("lexis_erros", { expect_error(ds.lexis(), "Please provide the name of the column that holds the subject IDs!", fixed=TRUE) }) -context("ds.lexis::arg::test intervalWidth") +# context("ds.lexis::arg::test intervalWidth") test_that("simple lexis", { expect_error(ds.lexis(data='D', intervalWidth = NA, idCol = 'D$id', entryCol = 'D$starttime', exitCol = 'D$endtime', statusCol = 'D$cens', variables = c('D$age.60'), expandDF = 'EM.new'), "Please provide a (non-zero) single numeric value or vector to identify the survival time intervals", fixed = TRUE) expect_error(ds.lexis(data='D', intervalWidth = NULL, idCol = 'D$id', entryCol = 'D$starttime', exitCol = 'D$endtime', statusCol = 'D$cens', variables = c('D$age.60'), expandDF = 'EM.new'), "Please provide a (non-zero) single numeric value or vector to identify the survival time intervals", fixed = TRUE) diff --git a/tests/testthat/test-arg-ds.list.R b/tests/testthat/test-arg-ds.list.R index ffbcb7496..b2bc229d6 100644 --- a/tests/testthat/test-arg-ds.list.R +++ b/tests/testthat/test-arg-ds.list.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.list::arg::test errors") +# context("ds.list::arg::test errors") test_that("simple ds.list errors", { expect_error(ds.list(), "x=NULL. Please provide the names of the objects to coerce into a list!") }) diff --git a/tests/testthat/test-arg-ds.lmerSLMA.R b/tests/testthat/test-arg-ds.lmerSLMA.R index bd229260b..d5f6510da 100644 --- a/tests/testthat/test-arg-ds.lmerSLMA.R +++ b/tests/testthat/test-arg-ds.lmerSLMA.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.lmerSLMA::arg::setup") +# context("ds.lmerSLMA::arg::setup") connect.studies.dataset.cluster.int(list("incid_rate", "trtGrp", "Male", "idDoctor", "BMI", "idSurgery")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.lmerSLMA::arg") +# context("ds.lmerSLMA::arg") test_that("simple lmerSLMA tesing (mis)use of arguments", { res <- ds.lmerSLMA(formula = 'incid_rate ~ trtGrp + Male', dataName = 'D') expect_equal(res$study1$errorMessage, "No random effects terms specified in formula", fixed=TRUE) @@ -50,7 +51,7 @@ test_that("simple lmerSLMA tesing (mis)use of arguments", { # Shutdown # -context("ds.lmerSLMA::arg::shutdown") +# context("ds.lmerSLMA::arg::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "offset", "offset.to.use", "weights", "weights.to.use")) @@ -62,4 +63,4 @@ disconnect.studies.dataset.cluster.int() # Done # -context("ds.lmerSLMA::arg::done") +# context("ds.lmerSLMA::arg::done") diff --git a/tests/testthat/test-arg-ds.log.R b/tests/testthat/test-arg-ds.log.R index d2510c08f..b51cdf7d4 100644 --- a/tests/testthat/test-arg-ds.log.R +++ b/tests/testthat/test-arg-ds.log.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.log::arg::test errors") +# context("ds.log::arg::test errors") test_that("log_erros", { expect_error(ds.log(), "Please provide the name of the input vector!", fixed=TRUE) }) diff --git a/tests/testthat/test-arg-ds.look.R b/tests/testthat/test-arg-ds.look.R index f1d7e6951..705660be7 100644 --- a/tests/testthat/test-arg-ds.look.R +++ b/tests/testthat/test-arg-ds.look.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.look::arg::test errors") +# context("ds.look::arg::test errors") test_that("look_erros", { expect_error(expect_warning(ds.look(checks=TRUE), "'ds.look' is deprecated.", fixed = TRUE), " missing, please give an expression/function in inverted commas\n", fixed=TRUE) }) diff --git a/tests/testthat/test-arg-ds.ls.R b/tests/testthat/test-arg-ds.ls.R index f4405ee77..bf24b112d 100644 --- a/tests/testthat/test-arg-ds.ls.R +++ b/tests/testthat/test-arg-ds.ls.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.ls::arg::setup") +# context("ds.ls::arg::setup") connect.studies.dataset.cnsim(list("LAB_TSC", "LAB_TRIG")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.ls::arg") +# context("ds.ls::arg") test_that("containing escape sequence", { res1 <- ds.ls(search.filter="_:A:_Environment") @@ -46,7 +47,7 @@ test_that("containing escape sequence", { # Shutdown # -context("ds.ls::arg::shutdown") +# context("ds.ls::arg::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -58,4 +59,4 @@ disconnect.studies.dataset.cnsim() # Done # -context("ds.ls::arg::done") +# context("ds.ls::arg::done") diff --git a/tests/testthat/test-arg-ds.make.R b/tests/testthat/test-arg-ds.make.R index d4a4a6e0a..170b6f113 100644 --- a/tests/testthat/test-arg-ds.make.R +++ b/tests/testthat/test-arg-ds.make.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.make::arg::test errors") +# context("ds.make::arg::test errors") test_that("make_erros", { expect_error(ds.make(), "Please give the name of object to assign or an expression to evaluate and assign.!\n", fixed=TRUE) }) diff --git a/tests/testthat/test-arg-ds.matrix.R b/tests/testthat/test-arg-ds.matrix.R index 2201a4f40..c6cf9089e 100644 --- a/tests/testthat/test-arg-ds.matrix.R +++ b/tests/testthat/test-arg-ds.matrix.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.matrix::arg::test errors") +# context("ds.matrix::arg::test errors") test_that("matrix_erros", { res <- ds.matrix(mdata=NULL) diff --git a/tests/testthat/test-arg-ds.matrixDet.R b/tests/testthat/test-arg-ds.matrixDet.R index 37d633fa9..c598d81b7 100644 --- a/tests/testthat/test-arg-ds.matrixDet.R +++ b/tests/testthat/test-arg-ds.matrixDet.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.matrixDet::arg::test errors") +# context("ds.matrixDet::arg::test errors") test_that("matrixDet_erros", { res <- ds.matrixDet() diff --git a/tests/testthat/test-arg-ds.matrixDet.report.R b/tests/testthat/test-arg-ds.matrixDet.report.R index 6bb0bc6c3..d76b92392 100644 --- a/tests/testthat/test-arg-ds.matrixDet.report.R +++ b/tests/testthat/test-arg-ds.matrixDet.report.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.matrixDet.report::arg::test errors") +# context("ds.matrixDet.report::arg::test errors") test_that("ds.matixDet.report erros", { res <- ds.matrixDet.report(M1=NULL) diff --git a/tests/testthat/test-arg-ds.matrixDiag.R b/tests/testthat/test-arg-ds.matrixDiag.R index e022d23cf..0dc152ff2 100644 --- a/tests/testthat/test-arg-ds.matrixDiag.R +++ b/tests/testthat/test-arg-ds.matrixDiag.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.matrixDiag::arg::test errors") +# context("ds.matrixDiag::arg::test errors") test_that("matrixDiag_erros", { res <- ds.matrixDiag() diff --git a/tests/testthat/test-arg-ds.matrixDimnames.R b/tests/testthat/test-arg-ds.matrixDimnames.R index 02a1f33b5..c6da09344 100644 --- a/tests/testthat/test-arg-ds.matrixDimnames.R +++ b/tests/testthat/test-arg-ds.matrixDimnames.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.matrixDimnames::arg::test errors") +# context("ds.matrixDimnames::arg::test errors") test_that("matrixDimnames_erros", { res <- ds.matrixDimnames() diff --git a/tests/testthat/test-arg-ds.matrixInvert.R b/tests/testthat/test-arg-ds.matrixInvert.R index 3718d6d07..dfed18dd6 100644 --- a/tests/testthat/test-arg-ds.matrixInvert.R +++ b/tests/testthat/test-arg-ds.matrixInvert.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.matrixInvert::arg::test errors") +# context("ds.matrixInvert::arg::test errors") test_that("matrixInvert_erros", { res <- ds.matrixInvert() diff --git a/tests/testthat/test-arg-ds.matrixMult.R b/tests/testthat/test-arg-ds.matrixMult.R index 1ab873494..95564e0d5 100644 --- a/tests/testthat/test-arg-ds.matrixMult.R +++ b/tests/testthat/test-arg-ds.matrixMult.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.matrixMult::arg::test errors") +# context("ds.matrixMult::arg::test errors") test_that("matrixMult_erros", { res <- ds.matrixMult() diff --git a/tests/testthat/test-arg-ds.matrixTranspose.R b/tests/testthat/test-arg-ds.matrixTranspose.R index ff94f60f0..d78c69041 100644 --- a/tests/testthat/test-arg-ds.matrixTranspose.R +++ b/tests/testthat/test-arg-ds.matrixTranspose.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.matrixTranspose::arg::test errors") +# context("ds.matrixTranspose::arg::test errors") test_that("matrixTranspose_erros", { res <- ds.matrixTranspose() diff --git a/tests/testthat/test-arg-ds.mean.R b/tests/testthat/test-arg-ds.mean.R index b28fdcbde..96ef958ba 100644 --- a/tests/testthat/test-arg-ds.mean.R +++ b/tests/testthat/test-arg-ds.mean.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.mean::arg::test errors") +# context("ds.mean::arg::test errors") test_that("mean_erros", { ds.asCharacter(x='D$LAB_TSC', newobj="not_a_numeric") diff --git a/tests/testthat/test-arg-ds.meanByClass.R b/tests/testthat/test-arg-ds.meanByClass.R index b829e05b9..c4de0a22b 100644 --- a/tests/testthat/test-arg-ds.meanByClass.R +++ b/tests/testthat/test-arg-ds.meanByClass.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC","LAB_HDL","GENDER","DIS_DIAB","PM_B # Tests # -context("ds.meanByClass::arg::test errors") +# context("ds.meanByClass::arg::test errors") test_that("meanByClass_erros", { ds.asCharacter(x='D$GENDER', newobj="not_a_numeric") ds.asCharacter(x='D$GENDER', newobj="not_a_factor") diff --git a/tests/testthat/test-arg-ds.meanSdGp.R b/tests/testthat/test-arg-ds.meanSdGp.R index bacc72410..bac7b2c46 100644 --- a/tests/testthat/test-arg-ds.meanSdGp.R +++ b/tests/testthat/test-arg-ds.meanSdGp.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.meanSdGp::arg::test errors") +# context("ds.meanSdGp::arg::test errors") test_that("meanSdGp_erros", { expect_error(ds.meanSdGp(), "Please provide the name of the input vector!", fixed=TRUE) }) diff --git a/tests/testthat/test-arg-ds.merge.R b/tests/testthat/test-arg-ds.merge.R index 5f6ccf385..4bb0bb8b4 100644 --- a/tests/testthat/test-arg-ds.merge.R +++ b/tests/testthat/test-arg-ds.merge.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.merge::arg::test errors") +# context("ds.merge::arg::test errors") test_that("merge_erros", { expect_error(ds.merge(), "Please provide the name (eg 'name1') of first dataframe to be merged (called x) ", fixed=TRUE) expect_error(ds.merge(x.name="A"), "Please provide the name (eg 'name2') of second dataframe to be merged (called y) ", fixed=TRUE) diff --git a/tests/testthat/test-arg-ds.message.R b/tests/testthat/test-arg-ds.message.R index 960e9811d..ea55ca136 100644 --- a/tests/testthat/test-arg-ds.message.R +++ b/tests/testthat/test-arg-ds.message.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.message::arg") +# context("ds.message::arg") test_that("request message for NULL", { expect_error(expect_warning(ds.message(NULL), "'ds.message' is deprecated.", fixed = TRUE), "Please provide the name of the studyside list object that holds the message\n in character format ie: 'object.name' in inverted commas", fixed=TRUE) }) diff --git a/tests/testthat/test-arg-ds.metadata.R b/tests/testthat/test-arg-ds.metadata.R index 6c05ee0a7..b31209f9a 100644 --- a/tests/testthat/test-arg-ds.metadata.R +++ b/tests/testthat/test-arg-ds.metadata.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.metadata::arg::setup") +# context("ds.metadata::arg::setup") connect.studies.dataset.cnsim(list('LAB_TSC', 'LAB_TRIG', 'LAB_HDL', 'LAB_GLUC_ADJUSTED', 'PM_BMI_CONTINUOUS', 'DIS_CVA', 'MEDI_LPD', 'DIS_DIAB', 'DIS_AMI', 'GENDER', 'PM_BMI_CATEGORICAL')) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.metadata::arg") +# context("ds.metadata::arg") test_that("missing variable", { expect_error(ds.metadata(x='E'), "The input object E is not defined in sim1, sim2, sim3!", fixed = TRUE) }) @@ -41,7 +42,7 @@ test_that("missing column", { # Tear down # -context("ds.metadata::arg::shutdown") +# context("ds.metadata::arg::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -49,4 +50,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.metadata::arg::done") +# context("ds.metadata::arg::done") diff --git a/tests/testthat/test-arg-ds.mice.R b/tests/testthat/test-arg-ds.mice.R index 4c2c21d33..a90c9c166 100644 --- a/tests/testthat/test-arg-ds.mice.R +++ b/tests/testthat/test-arg-ds.mice.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.mice::arg::test errors") +# context("ds.mice::arg::test errors") test_that("mice_errors", { expect_error(ds.mice(), "Please provide the name of the dataframe or matrix that contains the incomplete data!", fixed=TRUE) }) diff --git a/tests/testthat/test-arg-ds.names.R b/tests/testthat/test-arg-ds.names.R index 1c7fb10ae..f8c049106 100644 --- a/tests/testthat/test-arg-ds.names.R +++ b/tests/testthat/test-arg-ds.names.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.names::arg::test errors") +# context("ds.names::arg::test errors") test_that("simple ds.names errors", { expect_error(ds.names(), "Please provide the name of the input list!", fixed=TRUE) diff --git a/tests/testthat/test-arg-ds.ns.R b/tests/testthat/test-arg-ds.ns.R index b63c944a2..56fb58f5a 100644 --- a/tests/testthat/test-arg-ds.ns.R +++ b/tests/testthat/test-arg-ds.ns.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.ns::arg::setup") +# context("ds.ns::arg::setup") connect.studies.dataset.cnsim(list("PM_BMI_CONTINUOUS")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.ns::arg::test errors") +# context("ds.ns::arg::test errors") test_that("ns_errors", { expect_error(ds.ns(), "argument \"x\" is missing, with no default", fixed=TRUE) expect_error(ds.qlspline(x=NULL), "Please provide the name of the input variable x!", fixed=TRUE) @@ -34,7 +35,7 @@ test_that("ns_errors", { # Done # -context("ds.ns::arg::shutdown") +# context("ds.ns::arg::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -42,4 +43,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.ns::arg::done") +# context("ds.ns::arg::done") diff --git a/tests/testthat/test-arg-ds.numNA.R b/tests/testthat/test-arg-ds.numNA.R index 62d1af6d9..be436303a 100644 --- a/tests/testthat/test-arg-ds.numNA.R +++ b/tests/testthat/test-arg-ds.numNA.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.numNA::arg::test errors") +# context("ds.numNA::arg::test errors") test_that("simple ds.numNA errors", { expect_error(ds.numNA(), "Please provide the name of a vector!") }) diff --git a/tests/testthat/test-arg-ds.qlspline.R b/tests/testthat/test-arg-ds.qlspline.R index 697b2898e..c7ff7650a 100644 --- a/tests/testthat/test-arg-ds.qlspline.R +++ b/tests/testthat/test-arg-ds.qlspline.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.qlspline::arg::setup") +# context("ds.qlspline::arg::setup") connect.studies.dataset.cnsim(list("PM_BMI_CONTINUOUS")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.qlspline::arg::test errors") +# context("ds.qlspline::arg::test errors") test_that("qlspline_errors", { expect_error(ds.qlspline(), "argument \"x\" is missing, with no default", fixed=TRUE) expect_error(ds.qlspline(x=NULL), "Please provide the name of the input variable x!", fixed=TRUE) @@ -36,7 +37,7 @@ test_that("qlspline_errors", { # Done # -context("ds.qlspline::arg::shutdown") +# context("ds.qlspline::arg::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -44,4 +45,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.qlspline::arg::done") +# context("ds.qlspline::arg::done") diff --git a/tests/testthat/test-arg-ds.quantileMean.R b/tests/testthat/test-arg-ds.quantileMean.R index 2f94db2cc..4d1587628 100644 --- a/tests/testthat/test-arg-ds.quantileMean.R +++ b/tests/testthat/test-arg-ds.quantileMean.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list('LAB_HDL')) # Tests # -context("ds.quantileMean::arg::test errors") +# context("ds.quantileMean::arg::test errors") ds.asCharacter(x='D$LAB_HDL', newobj="not_a_numeric") test_that("quantileMean_erros", { expect_error(ds.quantileMean(), "Please provide the name of the input vector!", fixed=TRUE) diff --git a/tests/testthat/test-arg-ds.rBinom.R b/tests/testthat/test-arg-ds.rBinom.R index e031196a6..8d4100bde 100644 --- a/tests/testthat/test-arg-ds.rBinom.R +++ b/tests/testthat/test-arg-ds.rBinom.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.rBinom::arg::test errors") +# context("ds.rBinom::arg::test errors") test_that("rBinom_erros", { error.message <- ds.rBinom(seed.as.integer='Value') diff --git a/tests/testthat/test-arg-ds.rNorm.R b/tests/testthat/test-arg-ds.rNorm.R index 0f3cb82c5..d4ec8075b 100644 --- a/tests/testthat/test-arg-ds.rNorm.R +++ b/tests/testthat/test-arg-ds.rNorm.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.rNorm::arg::test errors") +# context("ds.rNorm::arg::test errors") test_that("rNorm_erros", { error.message <- ds.rNorm(seed.as.integer='Value') diff --git a/tests/testthat/test-arg-ds.rPois.R b/tests/testthat/test-arg-ds.rPois.R index 047064f97..707ca3813 100644 --- a/tests/testthat/test-arg-ds.rPois.R +++ b/tests/testthat/test-arg-ds.rPois.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.rPois::arg::test errors") +# context("ds.rPois::arg::test errors") test_that("rPois_erros", { error.message <- ds.rPois(seed.as.integer='Value') diff --git a/tests/testthat/test-arg-ds.rUnif.R b/tests/testthat/test-arg-ds.rUnif.R index bfe839e64..be046e8e5 100644 --- a/tests/testthat/test-arg-ds.rUnif.R +++ b/tests/testthat/test-arg-ds.rUnif.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.rUnif::arg::test errors") +# context("ds.rUnif::arg::test errors") test_that("rUnif_erros", { error.message <- ds.rUnif(seed.as.integer='Value') diff --git a/tests/testthat/test-arg-ds.ranksSecure.R b/tests/testthat/test-arg-ds.ranksSecure.R index 18778ccaf..fc6b99e1f 100644 --- a/tests/testthat/test-arg-ds.ranksSecure.R +++ b/tests/testthat/test-arg-ds.ranksSecure.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.ranksSecure::arg::setup") +# context("ds.ranksSecure::arg::setup") connect.all.datasets() @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.ranksSecure::arg::missing variable") +# context("ds.ranksSecure::arg::missing variable") test_that("missing variable", { expect_error(ds.ranksSecure("LAB_MISSING"), "There are some DataSHIELD errors, list them with datashield.errors()", fixed = TRUE) @@ -36,7 +37,7 @@ test_that("missing variable", { expect_match(res.errors$study3, "* object 'LAB_MISSING' not found") }) -context("ds.ranksSecure::arg::NULL variable") +# context("ds.ranksSecure::arg::NULL variable") test_that("NULL variable", { DSI::datashield.assign.expr(conns = ds.test_env$connections, symbol = "LAB_NULL", expr = "NULL") @@ -57,7 +58,7 @@ test_that("NULL variable", { expect_match(res.errors$study3, "* Error in stats::complete.cases\\(input.var\\) : \n no input has determined the number of cases") }) -context("ds.ranksSecure::arg::'text' variable") +# context("ds.ranksSecure::arg::'text' variable") test_that("'text' variable", { expect_error(ds.ranksSecure("D$CHARACTER"), "There are some DataSHIELD errors, list them with datashield.errors()", fixed = TRUE) @@ -69,12 +70,12 @@ test_that("'text' variable", { expect_match(res.errors$study3, "* Error in \\(1 - h\\) \\* qs\\[i\\] : non-numeric argument to binary operator") }) -context("ds.ranksSecure::arg::'logical' variable") +# context("ds.ranksSecure::arg::'logical' variable") test_that("'logical' variable", { expect_error(ds.ranksSecure("D$LOGICAL"), "FAILED: one of the extreme quantile estimates is NA probably because of a cluster of values at one end of the range of possible values. Try setting a narrower range of quantile values via the argument", fixed = TRUE) }) -context("ds.ranksSecure::arg::'integer factor' variable") +# context("ds.ranksSecure::arg::'integer factor' variable") test_that("'integer factor' variable", { expect_error(expect_warning(ds.ranksSecure("D$INTEGER_FACTOR"), "no non-missing arguments to max; returning -Inf", fixed = TRUE), "There are some DataSHIELD errors, list them with datashield.errors()", fixed = TRUE) @@ -90,7 +91,7 @@ test_that("'integer factor' variable", { # Done # -context("ds.ranksSecure::arg::shutdown") +# context("ds.ranksSecure::arg::shutdown") test_that("setup", { ds_expect_variables(c("D", "LAB_NULL", "input.mean.sd.df", "min.max.df", "summary.ranks.df", "testvar.ranks")) @@ -98,4 +99,4 @@ test_that("setup", { disconnect.all.datasets() -context("ds.ranksSecure::arg::done") +# context("ds.ranksSecure::arg::done") diff --git a/tests/testthat/test-arg-ds.rbind.R b/tests/testthat/test-arg-ds.rbind.R index e25b36a19..3a4ed9f27 100644 --- a/tests/testthat/test-arg-ds.rbind.R +++ b/tests/testthat/test-arg-ds.rbind.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.rbind::arg::test errors") +# context("ds.rbind::arg::test errors") test_that("rbind_erros", { expect_error(ds.rbind(), "Please provide a vector of character strings holding the name of the input elements!", fixed=TRUE) }) diff --git a/tests/testthat/test-arg-ds.reShape.R b/tests/testthat/test-arg-ds.reShape.R index f38f9ab7c..ed8e8102b 100644 --- a/tests/testthat/test-arg-ds.reShape.R +++ b/tests/testthat/test-arg-ds.reShape.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.reShape::arg::test errors") +# context("ds.reShape::arg::test errors") test_that("reShape_erros", { expect_error(ds.reShape(), "Please provide the name of the list that holds the input vectors!", fixed=TRUE) expect_error(ds.reShape(data.name="test", sep=TRUE), "'sep' must be a character string", fixed=TRUE) diff --git a/tests/testthat/test-arg-ds.recodeLevels.R b/tests/testthat/test-arg-ds.recodeLevels.R index 597b6e9ce..88b4b36e5 100644 --- a/tests/testthat/test-arg-ds.recodeLevels.R +++ b/tests/testthat/test-arg-ds.recodeLevels.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("PM_BMI_CATEGORICAL", "LAB_TSC")) # Tests # -context("ds.recodeLevels::arg::test errors") +# context("ds.recodeLevels::arg::test errors") test_that("recodeLevels_erros", { expect_error(expect_warning(ds.recodeLevels(), "'ds.recodeLevels' is deprecated.", fixed = TRUE), " End of process!", fixed=TRUE) expect_error(expect_warning(ds.recodeLevels(x='D$PM_BMI_CATEGORICAL'), "'ds.recodeLevels' is deprecated.", fixed = TRUE), " End of process!", fixed=TRUE) diff --git a/tests/testthat/test-arg-ds.recodeValues.R b/tests/testthat/test-arg-ds.recodeValues.R index a5b747dc4..74a2da507 100644 --- a/tests/testthat/test-arg-ds.recodeValues.R +++ b/tests/testthat/test-arg-ds.recodeValues.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.recodeValues::arg::test errors") +# context("ds.recodeValues::arg::test errors") test_that("recodeValues_erros", { expect_error(ds.recodeValues(), "Please provide the name of the variable to be recoded: eg 'xxx'", fixed=TRUE) expect_error(ds.recodeValues('D$LAB_TSC'), "Please provide a vector in the 'values2replace.vector' argument specifying\n the values to be replaced eg c(1,7)", fixed=TRUE) diff --git a/tests/testthat/test-arg-ds.rep.R b/tests/testthat/test-arg-ds.rep.R index 0ac3a0dfb..f9c2ec6ba 100644 --- a/tests/testthat/test-arg-ds.rep.R +++ b/tests/testthat/test-arg-ds.rep.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.rep::arg::setup") +# context("ds.rep::arg::setup") connect.studies.dataset.survival(list("survtime", "time.id", "female")) @@ -20,7 +21,7 @@ connect.studies.dataset.survival(list("survtime", "time.id", "female")) # Tests # -context("ds.rep::arg::test errors") +# context("ds.rep::arg::test errors") test_that("ds.rep erros", { res <- ds.rep() @@ -32,8 +33,8 @@ test_that("ds.rep erros", { # Done # -context("ds.rep::arg::shutdown") +# context("ds.rep::arg::shutdown") disconnect.studies.dataset.survival() -context("ds.rep::arg::done") +# context("ds.rep::arg::done") diff --git a/tests/testthat/test-arg-ds.replaceNA.R b/tests/testthat/test-arg-ds.replaceNA.R index b768a93fa..acd8c7b7e 100644 --- a/tests/testthat/test-arg-ds.replaceNA.R +++ b/tests/testthat/test-arg-ds.replaceNA.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.replaceNA::arg::test errors") +# context("ds.replaceNA::arg::test errors") test_that("simple ds.replaceNA errors", { expect_error(ds.replaceNA(), "Please provide the name of a vector!", fixed=TRUE) expect_error(ds.replaceNA(x="D$LAB_TSC"), "Please provide a list of replacement values!", fixed=TRUE) diff --git a/tests/testthat/test-arg-ds.rm.R b/tests/testthat/test-arg-ds.rm.R index ee4f5e3fb..bb674bca1 100644 --- a/tests/testthat/test-arg-ds.rm.R +++ b/tests/testthat/test-arg-ds.rm.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -18,7 +19,7 @@ connect.studies.dataset.survival(list("survtime", "time.id", "female")) # Tests # -context("ds.rm::arg::test errors") +# context("ds.rm::arg::test errors") test_that("ds.rm erros", { expect_error(ds.rm(), "Please provide the names of the objects to be deleted (eg 'object.name') as the x.names argument", fixed=TRUE) diff --git a/tests/testthat/test-arg-ds.rowColCalc.R b/tests/testthat/test-arg-ds.rowColCalc.R index 9fc14230f..76b8604bb 100644 --- a/tests/testthat/test-arg-ds.rowColCalc.R +++ b/tests/testthat/test-arg-ds.rowColCalc.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC", "LAB_HDL")) # Tests # -context("ds.rowColCalc::arg::test errors") +# context("ds.rowColCalc::arg::test errors") test_that("rowColCalc_errors", { expect_error(ds.rowColCalc(), "Please provide the name of a data.frame or matrix!", fixed=TRUE) expect_error(ds.rowColCalc(x='D', newobj="rsum_hdl_tsc"), "'operation' = NULL. Please set it to 'rowSums', 'colSums', 'rowMeans' or 'colMeans'", fixed=TRUE) diff --git a/tests/testthat/test-arg-ds.sample.R b/tests/testthat/test-arg-ds.sample.R index 0d14e79f4..f84f4c3e7 100644 --- a/tests/testthat/test-arg-ds.sample.R +++ b/tests/testthat/test-arg-ds.sample.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.sample::arg::setup") +# context("ds.sample::arg::setup") connect.studies.dataset.cnsim(list("LAB_TSC", "LAB_TRIG")) @@ -20,7 +21,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC", "LAB_TRIG")) # Tests # -context("ds.sample::arg::test errors") +# context("ds.sample::arg::test errors") test_that("cov_erros", { res1 <- ds.sample() expect_equal(res1, 'Error: x must denote a character string naming the serverside object to be sampled or an integer N denoting permute 1:N', fixed=TRUE) @@ -34,7 +35,7 @@ test_that("cov_erros", { # Shutdown # -context("ds.sample::arg::shutdown") +# context("ds.sample::arg::shutdown") disconnect.studies.dataset.cnsim() @@ -42,4 +43,4 @@ disconnect.studies.dataset.cnsim() # Done # -context("ds.sample::arg::done") +# context("ds.sample::arg::done") diff --git a/tests/testthat/test-arg-ds.seq.R b/tests/testthat/test-arg-ds.seq.R index 7ba77b7b0..3d047e7e4 100644 --- a/tests/testthat/test-arg-ds.seq.R +++ b/tests/testthat/test-arg-ds.seq.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.seq::arg::test errors") +# context("ds.seq::arg::test errors") test_that("seq_erros", { expect_error(ds.seq(FROM.value.char="Test"), "object 'Test' not found", fixed=TRUE) }) diff --git a/tests/testthat/test-arg-ds.setSeed.R b/tests/testthat/test-arg-ds.setSeed.R index 441275817..1bf41b5ca 100644 --- a/tests/testthat/test-arg-ds.setSeed.R +++ b/tests/testthat/test-arg-ds.setSeed.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.setSeed::arg::test errors") +# context("ds.setSeed::arg::test errors") test_that("setSeed_erros", { res <- ds.setSeed(seed.as.integer="Test") diff --git a/tests/testthat/test-arg-ds.skewness.R b/tests/testthat/test-arg-ds.skewness.R index cc1751a69..6a9440cc7 100644 --- a/tests/testthat/test-arg-ds.skewness.R +++ b/tests/testthat/test-arg-ds.skewness.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.skewness::arg::setup") +# context("ds.skewness::arg::setup") connect.studies.dataset.cnsim(list("LAB_TSC")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.skewness::arg::test errors") +# context("ds.skewness::arg::test errors") test_that("skewness_erros", { expect_error(ds.skewness(), "Please provide the name of the input vector!", fixed=TRUE) expect_error(ds.skewness(x='D$LAB_TSC', type='datashield'), "Function argument \"type\" has to be either \"both\", \"combine\" or \"split\"", fixed=TRUE) @@ -36,7 +37,7 @@ test_that("skewness_erros", { # Done # -context("ds.skewness::arg::shutdown") +# context("ds.skewness::arg::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -44,4 +45,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.skewness::arg::done") +# context("ds.skewness::arg::done") diff --git a/tests/testthat/test-arg-ds.subset.R b/tests/testthat/test-arg-ds.subset.R index a314d4906..65a96c814 100644 --- a/tests/testthat/test-arg-ds.subset.R +++ b/tests/testthat/test-arg-ds.subset.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("DIS_DIAB","PM_BMI_CONTINUOUS","LAB_HDL", "GE # Tests # -context("ds.subset::arg::test errors") +# context("ds.subset::arg::test errors") test_that("subset_erros", { expect_error(expect_warning(ds.subset(), "'ds.subset' is deprecated.", fixed = TRUE), "Please provide the name of the object to subset from!", fixed=TRUE) }) diff --git a/tests/testthat/test-arg-ds.subsetByClass.R b/tests/testthat/test-arg-ds.subsetByClass.R index 5aca7abfd..9645b195e 100644 --- a/tests/testthat/test-arg-ds.subsetByClass.R +++ b/tests/testthat/test-arg-ds.subsetByClass.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.subsetByClass::arg::test errors") +# context("ds.subsetByClass::arg::test errors") test_that("subsetByClass_erros", { expect_error(expect_warning(ds.subsetByClass(), "'ds.subsetByClass' is deprecated.", fixed = TRUE), "Please provide the name of the input data frame or factor!", fixed=TRUE) expect_error(expect_warning(ds.subsetByClass(x='D$LAB_TSC'), "'ds.subsetByClass' is deprecated.", fixed = TRUE), "The object to subset from must be a 'data.frame' or a 'factor'.", fixed=TRUE) diff --git a/tests/testthat/test-arg-ds.summary.R b/tests/testthat/test-arg-ds.summary.R index 5a2aa982c..e3d386568 100644 --- a/tests/testthat/test-arg-ds.summary.R +++ b/tests/testthat/test-arg-ds.summary.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.summary::arg::test errors") +# context("ds.summary::arg::test errors") test_that("summary_erros", { expect_error(ds.summary(), "Please provide the name of the input vector!", fixed=TRUE) }) diff --git a/tests/testthat/test-arg-ds.table.R b/tests/testthat/test-arg-ds.table.R index b18ff9497..094cf97ce 100644 --- a/tests/testthat/test-arg-ds.table.R +++ b/tests/testthat/test-arg-ds.table.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -18,14 +19,14 @@ connect.studies.dataset.cnsim(list("DIS_CVA", "DIS_AMI", "LAB_TSC", "LAB_HDL")) # Tests # -context("ds.table::arg::test rvar has value") +# context("ds.table::arg::test rvar has value") test_that("table rvar has value", { res <- ds.table() expect_equal(res, "Error: rvar must have a value which is a character string naming the row variable for the table", fixed=TRUE) }) -context("ds.table::arg::test rvar is not a variable") +# context("ds.table::arg::test rvar is not a variable") test_that("table rvar is not a variable", { expect_error(ds.table(rvar="D$NOT_VARIABLE"), "The input object D$NOT_VARIABLE is not defined in sim1, sim2, sim3!", fixed = TRUE) @@ -34,14 +35,14 @@ test_that("table rvar is not a variable", { expect_length(res.errors, 0) }) -context("ds.table::arg::test cvar has value") +# context("ds.table::arg::test cvar has value") test_that("table cvar has value", { res <- ds.table(rvar="D$LAB_TSC", cvar=30) expect_equal(res, "Error: if cvar is not null, it must have a value which is a character string naming the column variable for the table", fixed=TRUE) }) -context("ds.table::arg::test cvar is not a variable") +# context("ds.table::arg::test cvar is not a variable") test_that("table cvar is not a variable", { expect_error(ds.table(rvar="D$DIS_CVA", cvar="D$NOT_VARIABLE"), "The input object D$NOT_VARIABLE is not defined in sim1, sim2, sim3!", fixed = TRUE) @@ -50,14 +51,14 @@ test_that("table cvar is not a variable", { expect_length(res.errors, 0) }) -context("ds.table::arg::test stvar has value") +# context("ds.table::arg::test stvar has value") test_that("table stvar has value", { res <- ds.table(rvar="D$LAB_TSC", cvar=NULL, stvar=25) expect_equal(res, "Error: if stvar is not null, it must have a value which is a character string naming the variable coding separate tables for the table", fixed=TRUE) }) -context("ds.table::arg::test stvar is not a variable") +# context("ds.table::arg::test stvar is not a variable") test_that("table stvar is not a variable", { expect_error(ds.table(rvar="D$DIS_CVA", cvar="D$DIS_AMI", stvar="D$NOT_VARIABLE"), "The input object D$NOT_VARIABLE is not defined in sim1, sim2, sim3!", fixed = TRUE) @@ -66,12 +67,12 @@ test_that("table stvar is not a variable", { expect_length(res.errors, 0) }) -context("ds.table::arg::test stvar has CORRECT value") +# context("ds.table::arg::test stvar has CORRECT value") test_that("table useNA has value", { expect_error(ds.table(rvar="D$LAB_TSC", cvar=NULL, stvar=NULL, useNA = c("BEN")), "useNA must be either 'no' or 'always'.", fixed = TRUE) }) -context("ds.table::arg::test force.nfilter has value") +# context("ds.table::arg::test force.nfilter has value") test_that("table force.nfilter has value", { expect_error(ds.table(rvar="D$LAB_TSC", cvar=NULL, stvar=NULL, useNA = c("ifany"), force.nfilter =30), "useNA must be either 'no' or 'always'.", fixed = TRUE) }) diff --git a/tests/testthat/test-arg-ds.table1D.R b/tests/testthat/test-arg-ds.table1D.R index b0bf5e6d1..56c17dd4e 100644 --- a/tests/testthat/test-arg-ds.table1D.R +++ b/tests/testthat/test-arg-ds.table1D.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("DIS_CVA","GENDER")) # Tests # -context("ds.table1D::arg::test errors") +# context("ds.table1D::arg::test errors") test_that("table1D_erros", { expect_error(expect_warning(ds.table1D(), "'ds.table1D' is deprecated.", fixed = TRUE), "Please provide the name of the input vector!", fixed=TRUE) expect_error(expect_warning(ds.table1D(x='D$GENDER', type="datashield"), "'ds.table1D' is deprecated.", fixed = TRUE), "Function argument 'type' has to be either 'combine' or 'split'", fixed=TRUE) diff --git a/tests/testthat/test-arg-ds.table2D.R b/tests/testthat/test-arg-ds.table2D.R index 35fa39dba..e7b0623ee 100644 --- a/tests/testthat/test-arg-ds.table2D.R +++ b/tests/testthat/test-arg-ds.table2D.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.table2D::arg::test errors") +# context("ds.table2D::arg::test errors") test_that("table2D_erros", { expect_error(expect_warning(ds.table2D(), "'ds.table2D' is deprecated.", fixed = TRUE), "Please provide the name of the x vector!", fixed=TRUE) }) diff --git a/tests/testthat/test-arg-ds.tapply.R b/tests/testthat/test-arg-ds.tapply.R index 243de56e0..5ac42edf5 100644 --- a/tests/testthat/test-arg-ds.tapply.R +++ b/tests/testthat/test-arg-ds.tapply.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC", "GENDER")) # Tests # -context("ds.tapply::arg::test errors") +# context("ds.tapply::arg::test errors") test_that("tapply_erros", { res1 <- ds.tapply() diff --git a/tests/testthat/test-arg-ds.tapply.assign.R b/tests/testthat/test-arg-ds.tapply.assign.R index 787628d19..14ea83890 100644 --- a/tests/testthat/test-arg-ds.tapply.assign.R +++ b/tests/testthat/test-arg-ds.tapply.assign.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC", "GENDER")) # Tests # -context("ds.tapply.assign::arg::test errors") +# context("ds.tapply.assign::arg::test errors") test_that("tapply_erros", { res1 <- ds.tapply.assign() diff --git a/tests/testthat/test-arg-ds.testObjExists.R b/tests/testthat/test-arg-ds.testObjExists.R index c2f657810..bf01cc77a 100644 --- a/tests/testthat/test-arg-ds.testObjExists.R +++ b/tests/testthat/test-arg-ds.testObjExists.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.testObjExists::arg::test errors") +# context("ds.testObjExists::arg::test errors") test_that("testObjExists_erros", { res <- ds.testObjExists() diff --git a/tests/testthat/test-arg-ds.unList.R b/tests/testthat/test-arg-ds.unList.R index bddb5e06d..2d3aa4877 100644 --- a/tests/testthat/test-arg-ds.unList.R +++ b/tests/testthat/test-arg-ds.unList.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.unList::arg::test errors") +# context("ds.unList::arg::test errors") test_that("unList_erros", { expect_error(ds.unList(), "Please provide the name of the input vector!", fixed=TRUE) }) diff --git a/tests/testthat/test-arg-ds.unique.R b/tests/testthat/test-arg-ds.unique.R index bd619015e..a0e112a59 100644 --- a/tests/testthat/test-arg-ds.unique.R +++ b/tests/testthat/test-arg-ds.unique.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -18,12 +19,12 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.unique::arg::no arguments") +# context("ds.unique::arg::no arguments") test_that("simple ds.unique no arguments", { expect_error(ds.unique(), "x.name=NULL. Please provide the names of the objects to de-duplicated!", fixed = TRUE) }) -context("ds.unique::arg::NULL arguments") +# context("ds.unique::arg::NULL arguments") test_that("simple ds.unique NULL arguments", { expect_error(ds.unique(NULL), "x.name=NULL. Please provide the names of the objects to de-duplicated!", fixed = TRUE) }) diff --git a/tests/testthat/test-arg-ds.var.R b/tests/testthat/test-arg-ds.var.R index 71c2d89e8..8ececd0d0 100644 --- a/tests/testthat/test-arg-ds.var.R +++ b/tests/testthat/test-arg-ds.var.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.var::arg::test errors") +# context("ds.var::arg::test errors") test_that("var_erros", { ds.asCharacter(x='D$LAB_TSC', newobj="not_a_numeric") diff --git a/tests/testthat/test-arg-ds.vectorCalc.R b/tests/testthat/test-arg-ds.vectorCalc.R index 7a572365b..4c331b869 100644 --- a/tests/testthat/test-arg-ds.vectorCalc.R +++ b/tests/testthat/test-arg-ds.vectorCalc.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -18,7 +19,7 @@ connect.studies.dataset.survival(list("survtime")) # Tests # -context("ds.vectorCalc::arg::test errors") +# context("ds.vectorCalc::arg::test errors") test_that("ds.vectorCalc erros", { expect_error(expect_warning(ds.vectorCalc(), "'ds.vectorCalc' is deprecated.\nUse 'ds.make' instead.", fixed = TRUE), "x=NULL. Please provide the names of the objects to combine!", fixed=TRUE) diff --git a/tests/testthat/test-datachk-ANTHRO.R b/tests/testthat/test-datachk-ANTHRO.R index 2789755fa..41a53637d 100644 --- a/tests/testthat/test-datachk-ANTHRO.R +++ b/tests/testthat/test-datachk-ANTHRO.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ANTHRO::datachk::setup") +# context("ANTHRO::datachk::setup") connect.studies.dataset.anthro(list('age', 'sex', 'weight', 'height', 'muac')) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ANTHRO::datachk") +# context("ANTHRO::datachk") test_that("Check ANTHRO dataset", { res.class <- ds.class(x='D') expect_length(res.class, 3) @@ -159,7 +160,7 @@ test_that("Check ANTHRO dataset", { # Tear down # -context("ANTHRO::datachk::shutdown") +# context("ANTHRO::datachk::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -171,4 +172,4 @@ disconnect.studies.dataset.anthro() # Done # -context("ANTHRO::datachk::done") +# context("ANTHRO::datachk::done") diff --git a/tests/testthat/test-datachk-CLUSTER_INT.R b/tests/testthat/test-datachk-CLUSTER_INT.R index 8fc7deff2..d86eddd1a 100644 --- a/tests/testthat/test-datachk-CLUSTER_INT.R +++ b/tests/testthat/test-datachk-CLUSTER_INT.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("CLUSTER_INT::datachk::setup") +# context("CLUSTER_INT::datachk::setup") connect.studies.dataset.cluster.int(list("idSurgery", "trtGrp", "intSurgery", "nDoctors", "idDoctor", "intDoctor", "nPatients", "Male", "age", "BMI", "diabetes", "incid_rate", "private")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("CLUSTER_INT::datachk") +# context("CLUSTER_INT::datachk") test_that("Check CLUSTER INT dataset", { res.class <- ds.class(x='D') expect_length(res.class, 3) @@ -319,7 +320,7 @@ test_that("Check CLUSTER INT dataset", { # Tear down # -context("CLUSTER_INT::datachk::shutdown") +# context("CLUSTER_INT::datachk::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -327,4 +328,4 @@ test_that("shutdown", { disconnect.studies.dataset.cluster.int() -context("CLUSTER_INT::datachk::done") +# context("CLUSTER_INT::datachk::done") diff --git a/tests/testthat/test-datachk-CLUSTER_SLO.R b/tests/testthat/test-datachk-CLUSTER_SLO.R index 3c61c9cb7..842a5d409 100644 --- a/tests/testthat/test-datachk-CLUSTER_SLO.R +++ b/tests/testthat/test-datachk-CLUSTER_SLO.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("CLUSTER_SLO::datachk::setup") +# context("CLUSTER_SLO::datachk::setup") connect.studies.dataset.cluster.slo(list("idSurgery", "trtGrp", "intSurgery", "nDoctors", "idDoctor", "intDoctor", "sloDoctor", "nPatients", "Male", "age", "BMI", "private", "diabetes", "incid_rate")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("CLUSTER_SLO::datachk") +# context("CLUSTER_SLO::datachk") test_that("Check CLUSTER SLO dataset", { res.class <- ds.class(x='D') expect_length(res.class, 3) @@ -319,7 +320,7 @@ test_that("Check CLUSTER SLO dataset", { # Tear down # -context("CLUSTER_SLO::datachk::shutdown") +# context("CLUSTER_SLO::datachk::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -327,4 +328,4 @@ test_that("shutdown", { disconnect.studies.dataset.cluster.slo() -context("CLUSTER_SLO::datachk::done") +# context("CLUSTER_SLO::datachk::done") diff --git a/tests/testthat/test-datachk-CNSIM.R b/tests/testthat/test-datachk-CNSIM.R index 7296f51b7..afdfc8214 100644 --- a/tests/testthat/test-datachk-CNSIM.R +++ b/tests/testthat/test-datachk-CNSIM.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("CNSIM::datachk::setup") +# context("CNSIM::datachk::setup") connect.studies.dataset.cnsim(list('LAB_TSC', 'LAB_TRIG', 'LAB_HDL', 'LAB_GLUC_ADJUSTED', 'PM_BMI_CONTINUOUS', 'DIS_CVA', 'MEDI_LPD', 'DIS_DIAB', 'DIS_AMI', 'GENDER', 'PM_BMI_CATEGORICAL')) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("CNSIM::datachk") +# context("CNSIM::datachk") test_that("Check CNSIM dataset", { res.class <- ds.class(x='D') expect_length(res.class, 3) @@ -378,7 +379,7 @@ test_that("Check CNSIM dataset", { # Tear down # -context("CNSIM::datachk::shutdown") +# context("CNSIM::datachk::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -386,4 +387,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("CNSIM::datachk::done") +# context("CNSIM::datachk::done") diff --git a/tests/testthat/test-datachk-DISCORDANT.R b/tests/testthat/test-datachk-DISCORDANT.R index bb6c06a21..5254897b2 100644 --- a/tests/testthat/test-datachk-DISCORDANT.R +++ b/tests/testthat/test-datachk-DISCORDANT.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("DISCORDANT::datachk::setup") +# context("DISCORDANT::datachk::setup") connect.discordant.dataset.simple(list('A', 'B', 'C')) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("DISCORDANT::datachk") +# context("DISCORDANT::datachk") test_that("Check DISCORDANT dataset", { res.class <- ds.class(x='D') expect_length(res.class, 3) @@ -123,7 +124,7 @@ test_that("Check DISCORDANT dataset", { # Tear down # -context("DISCORDANT::datachk::shutdown") +# context("DISCORDANT::datachk::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -135,4 +136,4 @@ disconnect.discordant.dataset.simple() # Done # -context("DISCORDANT::datachk::done") +# context("DISCORDANT::datachk::done") diff --git a/tests/testthat/test-datachk-DNSIM.R b/tests/testthat/test-datachk-DNSIM.R index 73421dba4..f3a9e75c7 100644 --- a/tests/testthat/test-datachk-DNSIM.R +++ b/tests/testthat/test-datachk-DNSIM.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("DASIM::datachk::setup") +# context("DASIM::datachk::setup") connect.studies.dataset.dasim(list('LAB_TSC', 'LAB_TRIG', 'LAB_HDL', 'LAB_GLUC_FASTING', 'PM_BMI_CONTINUOUS', 'DIS_CVA', 'DIS_DIAB', 'DIS_AMI', 'GENDER', 'PM_BMI_CATEGORICAL')) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("DASIM::datachk") +# context("DASIM::datachk") test_that("Check DASIM dataset", { res.class <- ds.class(x='D') expect_length(res.class, 3) @@ -259,7 +260,7 @@ test_that("Check DASIM dataset", { # Tear down # -context("DASIM::datachk::shutdown") +# context("DASIM::datachk::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -267,4 +268,4 @@ test_that("shutdown", { disconnect.studies.dataset.dasim() -context("DASIM::datachk::done") +# context("DASIM::datachk::done") diff --git a/tests/testthat/test-datachk-FACTOR_LEVELS.R b/tests/testthat/test-datachk-FACTOR_LEVELS.R index d1db51fec..927e1cab6 100644 --- a/tests/testthat/test-datachk-FACTOR_LEVELS.R +++ b/tests/testthat/test-datachk-FACTOR_LEVELS.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("FACTOR_LEVELS::datachk::setup") +# context("FACTOR_LEVELS::datachk::setup") connect.testing.dataset.factor_levels() @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("FACTOR_LEVELS::datachk") +# context("FACTOR_LEVELS::datachk") test_that("Check FACTOR_LEVELS dataset", { res.class <- ds.class(x='D') expect_length(res.class, 3) @@ -259,7 +260,7 @@ test_that("Check FACTOR_LEVELS dataset", { # Tear down # -context("FACTOR_LEVELS::datachk::shutdown") +# context("FACTOR_LEVELS::datachk::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -267,4 +268,4 @@ test_that("shutdown", { disconnect.testing.dataset.factor_levels() -context("FACTOR_LEVELS::datachk::done") +# context("FACTOR_LEVELS::datachk::done") diff --git a/tests/testthat/test-datachk-SURVIVAL_EXPAND_WITH_MISSING.R b/tests/testthat/test-datachk-SURVIVAL_EXPAND_WITH_MISSING.R index bc8c12bce..0d28eff58 100644 --- a/tests/testthat/test-datachk-SURVIVAL_EXPAND_WITH_MISSING.R +++ b/tests/testthat/test-datachk-SURVIVAL_EXPAND_WITH_MISSING.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("SURVIVAL_EXPAND_WITH_MISSING::datachk::setup") +# context("SURVIVAL_EXPAND_WITH_MISSING::datachk::setup") connect.studies.dataset.survival(list('id', 'study.id', 'time.id', 'starttime', 'endtime', 'survtime', 'cens', 'age.60', 'female', 'noise.56', 'pm10.16', 'bmi.26')) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("SURVIVAL_EXPAND_WITH_MISSING::datachk") +# context("SURVIVAL_EXPAND_WITH_MISSING::datachk") test_that("Check SURVIVAL_EXPAND_WITH_MISSING dataset", { res.class <- ds.class(x='D') expect_length(res.class, 3) @@ -279,7 +280,7 @@ test_that("Check SURVIVAL_EXPAND_WITH_MISSING dataset", { # Tear down # -context("SURVIVAL_EXPAND_WITH_MISSING::datachk::shutdown") +# context("SURVIVAL_EXPAND_WITH_MISSING::datachk::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -291,4 +292,4 @@ disconnect.studies.dataset.survival() # Done # -context("SURVIVAL_EXPAND_WITH_MISSING::datachk::done") +# context("SURVIVAL_EXPAND_WITH_MISSING::datachk::done") diff --git a/tests/testthat/test-datachk-TESTING.R b/tests/testthat/test-datachk-TESTING.R index 5cc2332d0..f89d43643 100644 --- a/tests/testthat/test-datachk-TESTING.R +++ b/tests/testthat/test-datachk-TESTING.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("TESTING::datachk::setup") +# context("TESTING::datachk::setup") connect.all.datasets() @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("TESTING::datachk") +# context("TESTING::datachk") test_that("Check TESTING dataset", { res.class <- ds.class(x='D') expect_length(res.class, 3) @@ -419,7 +420,7 @@ test_that("Check TESTING dataset", { # Tear down # -context("TESTING::datachk::shutdown") +# context("TESTING::datachk::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -427,4 +428,4 @@ test_that("shutdown", { disconnect.all.datasets() -context("TESTING::datachk::done") +# context("TESTING::datachk::done") diff --git a/tests/testthat/test-disc-ds.cor.R b/tests/testthat/test-disc-ds.cor.R index eb61ada6f..88da21bbd 100644 --- a/tests/testthat/test-disc-ds.cor.R +++ b/tests/testthat/test-disc-ds.cor.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.cor::disc::setup") +# context("ds.cor::disc::setup") connect.studies.dataset.cnsim(list("LAB_TSC", "LAB_TRIG", "LAB_HDL", "LAB_GLUC_ADJUSTED", "GENDER")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.cor::disc") +# context("ds.cor::disc") test_that("simple D3 setup", { ds.dataFrameSubset('D',V1.name = 'D$GENDER', V2.name = '0', Boolean.operator = '==', newobj='D1') ds.dataFrameSubset('D1',V1.name = 'D1$LAB_TSC', V2.name = '3.5', Boolean.operator = '<', newobj='D2') @@ -107,7 +108,7 @@ test_that("simple disc test, naAction='pairwise.complete', type='combine'", { # Done # -context("ds.cor::disc::shutdown") +# context("ds.cor::disc::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "D1", "D2", "D3")) @@ -115,4 +116,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.cor::disc::done") +# context("ds.cor::disc::done") diff --git a/tests/testthat/test-disc-ds.cov.R b/tests/testthat/test-disc-ds.cov.R index 751d54bf9..2807a7b1c 100644 --- a/tests/testthat/test-disc-ds.cov.R +++ b/tests/testthat/test-disc-ds.cov.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.cov::disc::setup") +# context("ds.cov::disc::setup") connect.studies.dataset.cnsim(list("LAB_TSC", "LAB_TRIG", "LAB_HDL", "LAB_GLUC_ADJUSTED", "GENDER")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.cov::disc") +# context("ds.cov::disc") test_that("simple D3 setup", { ds.dataFrameSubset('D',V1.name = 'D$GENDER', V2.name = '0', Boolean.operator = '==', newobj='D1') ds.dataFrameSubset('D1',V1.name = 'D1$LAB_TSC', V2.name = '3.5', Boolean.operator = '<', newobj='D2') @@ -106,7 +107,7 @@ test_that("simple disc test, naAction='pairwise.complete', type='combine'", { # Done # -context("ds.cov::disc::shutdown") +# context("ds.cov::disc::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "D1", "D2", "D3")) @@ -114,4 +115,4 @@ test_that("shutdown", { disconnect.studies.dataset.survival() -context("ds.cov::disc::done") +# context("ds.cov::disc::done") diff --git a/tests/testthat/test-disc-ds.levels.R b/tests/testthat/test-disc-ds.levels.R index 6f00f1198..95d0c60b5 100644 --- a/tests/testthat/test-disc-ds.levels.R +++ b/tests/testthat/test-disc-ds.levels.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.levels::disc::setup") +# context("ds.levels::disc::setup") connect.studies.dataset.cnsim(list("GENDER", "PM_BMI_CATEGORICAL")) @@ -23,7 +24,7 @@ test_that("setup", { # # Tests # -context("ds.levels::disc") +# context("ds.levels::disc") test_that("simple levels", { # res <- ds.levels("D$GENDER") @@ -51,7 +52,7 @@ test_that("simple levels", { # Done # -context("ds.levels::disc::shutdown") +# context("ds.levels::disc::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -59,4 +60,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.levels::disc::done") +# context("ds.levels::disc::done") diff --git a/tests/testthat/test-disc-ds.mean.R b/tests/testthat/test-disc-ds.mean.R index f1b690c9d..cb8311d79 100644 --- a/tests/testthat/test-disc-ds.mean.R +++ b/tests/testthat/test-disc-ds.mean.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC", "LAB_TRIG")) # Tests # -context("ds.mean::disc::type=both") +# context("ds.mean::disc::type=both") test_that("mean values [both]", { # myvectors <- c("D$LAB_TSC", "D$LAB_TRIG") # ds.dataFrame(x=myvectors, newobj="unsubset_df") diff --git a/tests/testthat/test-disc-ds.meanByClass.R b/tests/testthat/test-disc-ds.meanByClass.R index 2b6147f8c..b1e7cedb6 100644 --- a/tests/testthat/test-disc-ds.meanByClass.R +++ b/tests/testthat/test-disc-ds.meanByClass.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.meanByClass::disc::setup") +# context("ds.meanByClass::disc::setup") connect.studies.dataset.cnsim(list("LAB_TSC","LAB_HDL","GENDER","DIS_DIAB","PM_BMI_CATEGORICAL")) @@ -20,7 +21,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC","LAB_HDL","GENDER","DIS_DIAB","PM_B # Tests # -context("ds.meanByClass::disc::test errors") +# context("ds.meanByClass::disc::test errors") test_that("meanByClass_erros", { # expect_error(ds.meanByClass(x='D', outvar='LAB_HDL', covar='GENDER', type='split'), 'Failed to get levels from study: FAILED: Result less than nfilter.subset', fixed=TRUE) }) @@ -29,7 +30,7 @@ test_that("meanByClass_erros", { # Tear down # -context("ds.meanByClass::disc::teardown") +# context("ds.meanByClass::disc::teardown") disconnect.studies.dataset.cnsim() @@ -37,4 +38,4 @@ disconnect.studies.dataset.cnsim() # Done # -context("ds.meanByClass::disc::done") +# context("ds.meanByClass::disc::done") diff --git a/tests/testthat/test-disc-ds.sample.R b/tests/testthat/test-disc-ds.sample.R index 08cc01c7f..ce74288a7 100644 --- a/tests/testthat/test-disc-ds.sample.R +++ b/tests/testthat/test-disc-ds.sample.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.sample::disc::setup") +# context("ds.sample::disc::setup") connect.studies.dataset.cnsim(list("LAB_TSC", "LAB_TRIG")) @@ -20,7 +21,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC", "LAB_TRIG")) # Tests # -context("ds.sample::disc::test disclosure") +# context("ds.sample::disc::test disclosure") test_that("cov_erros", { expect_error(ds.sample(x="This_line_is_very_very_very_very_very_very_long", size=1234, newobj="obj1"), "There are some DataSHIELD errors, list them with datashield.errors()", fixed = TRUE) res1.errors <- DSI::datashield.errors() @@ -64,7 +65,7 @@ test_that("cov_erros", { # Shutdown # -context("ds.sample::disc::shutdown") +# context("ds.sample::disc::shutdown") disconnect.studies.dataset.cnsim() @@ -72,4 +73,4 @@ disconnect.studies.dataset.cnsim() # Done # -context("ds.sample::disc::done") +# context("ds.sample::disc::done") diff --git a/tests/testthat/test-disc-ds.table.R b/tests/testthat/test-disc-ds.table.R index f82116940..b51a75f91 100644 --- a/tests/testthat/test-disc-ds.table.R +++ b/tests/testthat/test-disc-ds.table.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -13,7 +14,7 @@ # Set up - Phase 1 # -context("ds.table::disc::setup::phase 1") +# context("ds.table::disc::setup::phase 1") connect.all.datasets() @@ -25,7 +26,7 @@ test_that("setup", { # Tests - Phase 1 # -context("ds.table::disc::tests::phase 1::table.assign=FALSE") +# context("ds.table::disc::tests::phase 1::table.assign=FALSE") test_that("table disclosure table.assign=FALSE", { ds.asFactor(input.var.name="D$FACTOR_CHARACTER", newobj.name="factorCharacter") ds.asFactor(input.var.name="D$FACTOR_INTEGER", newobj.name="factorInteger") @@ -43,7 +44,7 @@ test_that("table disclosure table.assign=FALSE", { expect_equal(table.res$validity.message[4], "Study3: No errors reported from this study", fixed = TRUE) }) -context("ds.table::disc::tests::phase 1::table.assign=TRUE") +# context("ds.table::disc::tests::phase 1::table.assign=TRUE") test_that("table disclosure table.assign=TRUE", { ds.asFactor(input.var.name="D$FACTOR_CHARACTER", newobj.name="factorCharacter") ds.asFactor(input.var.name="D$FACTOR_INTEGER", newobj.name="factorInteger") @@ -55,7 +56,7 @@ test_that("table disclosure table.assign=TRUE", { expect_length(table.res, 0) }) -context("ds.table::disc::test rvar is big numeric") +# context("ds.table::disc::test rvar is big numeric") test_that("table rvar is big numeric", { expect_error(ds.table(rvar="D$NUMERIC"), "There are some DataSHIELD errors, list them with datashield.errors()", fixed = TRUE) @@ -71,7 +72,7 @@ test_that("table rvar is big numeric", { # Shutdown - Phase 1 # -context("ds.table::disc::shutdown::phase 1") +# context("ds.table::disc::shutdown::phase 1") test_that("setup", { ds_expect_variables(c("D", "factorCharacter", "factorInteger", "tablesource", "new_table2")) @@ -83,7 +84,7 @@ disconnect.all.datasets() # Set up - Phase 2 # -context("ds.table::disc::setup::phase 2") +# context("ds.table::disc::setup::phase 2") connect.studies.dataset.cnsim(list("GENDER", "DIS_AMI")) @@ -95,7 +96,7 @@ test_that("setup", { # Tests - Phase 2 # -context("ds.table::disc::tests::phase 2::table.assign=FALSE") +# context("ds.table::disc::tests::phase 2::table.assign=FALSE") test_that("table disclosure, table.assign=FALSE", { table.res <- ds.table(rvar='D$GENDER', cvar="D$DIS_AMI", table.assign=FALSE, newobj="new_table3") @@ -108,7 +109,7 @@ test_that("table disclosure, table.assign=FALSE", { expect_equal(table.res$error.message$sim3, "Failed: at least one cell has a non-zero count less than nfilter.tab i.e. 3", fixed = TRUE) }) -context("ds.table::disc::tests::phase 2::table.assign=TRUE") +# context("ds.table::disc::tests::phase 2::table.assign=TRUE") test_that("table disclosure, table.assign=TRUE", { table.res <- ds.table(rvar='D$GENDER', cvar="D$DIS_AMI", table.assign=TRUE, newobj="new_table4") @@ -119,7 +120,7 @@ test_that("table disclosure, table.assign=TRUE", { # Shutdown - Phase 2 # -context("ds.table::disc::shutdown::phase 2") +# context("ds.table::disc::shutdown::phase 2") test_that("setup", { ds_expect_variables(c("D", "new_table4")) @@ -131,4 +132,4 @@ disconnect.studies.dataset.cnsim() # Done # -context("ds.table::disc::done") +# context("ds.table::disc::done") diff --git a/tests/testthat/test-disc-ds.var.R b/tests/testthat/test-disc-ds.var.R index 08a445b92..39d6a506b 100644 --- a/tests/testthat/test-disc-ds.var.R +++ b/tests/testthat/test-disc-ds.var.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC", "LAB_TRIG")) # Tests # -context("ds.var::disc::type=both") +# context("ds.var::disc::type=both") test_that("var values [both]", { # myvectors <- c("D$LAB_TSC", "D$LAB_TRIG") # ds.dataFrame(x=myvectors, newobj="unsubset_df") diff --git a/tests/testthat/test-discctrl-ds.Boole.R b/tests/testthat/test-discctrl-ds.Boole.R index 80a5dc3d2..29591402e 100644 --- a/tests/testthat/test-discctrl-ds.Boole.R +++ b/tests/testthat/test-discctrl-ds.Boole.R @@ -1,6 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. -# Copyright (c) 2022 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -13,7 +13,7 @@ # Set up # -context("ds.Boole::discctrl::setup") +# context("ds.Boole::discctrl::setup") connect.studies.dataset.cnsim(list("LAB_TSC", "LAB_TRIG")) @@ -24,7 +24,7 @@ test_that("setup", { # # Tests # -context("ds.Boole::discctrl") +# context("ds.Boole::discctrl") test_that("simple rep", { expect_error(ds.Boole("D$LAB_TSC", "D$LAB_TRIG", "=="), "There are some DataSHIELD errors, list them with datashield.errors()", fixed = TRUE) @@ -43,7 +43,7 @@ test_that("simple rep", { # Done # -context("ds.Boole::discctrl::shutdown") +# context("ds.Boole::discctrl::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -51,4 +51,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.Boole::discctrl::done") +# context("ds.Boole::discctrl::done") diff --git a/tests/testthat/test-discctrl-ds.c.R b/tests/testthat/test-discctrl-ds.c.R index da4a0caa6..e4bfb577e 100644 --- a/tests/testthat/test-discctrl-ds.c.R +++ b/tests/testthat/test-discctrl-ds.c.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.c::discctrl::setup") +# context("ds.c::discctrl::setup") connect.studies.dataset.cnsim(list("GENDER", "PM_BMI_CATEGORICAL")) @@ -23,7 +24,7 @@ test_that("setup", { # # Tests # -context("ds.c::discctrl") +# context("ds.c::discctrl") test_that("simple c", { expect_error(ds.c("D$GENDER"), "There are some DataSHIELD errors, list them with datashield.errors()", fixed = TRUE) @@ -42,7 +43,7 @@ test_that("simple c", { # Done # -context("ds.c::discctrl::shutdown") +# context("ds.c::discctrl::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -50,4 +51,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.c::discctrl::done") +# context("ds.c::discctrl::done") diff --git a/tests/testthat/test-discctrl-ds.cbind.R b/tests/testthat/test-discctrl-ds.cbind.R index a829185e6..b1b3b79c2 100644 --- a/tests/testthat/test-discctrl-ds.cbind.R +++ b/tests/testthat/test-discctrl-ds.cbind.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.cbind::discctrl::setup") +# context("ds.cbind::discctrl::setup") connect.studies.dataset.cnsim(list("GENDER", "PM_BMI_CATEGORICAL")) @@ -23,7 +24,7 @@ test_that("setup", { # # Tests # -context("ds.cbind::discctrl") +# context("ds.cbind::discctrl") test_that("simple c", { expect_error(ds.cbind(x="D", DataSHIELD.checks=TRUE, datasources = ds.test_env$connections[1]), "There are some DataSHIELD errors, list them with datashield.errors()", fixed = TRUE) @@ -38,7 +39,7 @@ test_that("simple c", { # Done # -context("ds.cbind::discctrl::shutdown") +# context("ds.cbind::discctrl::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -46,4 +47,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.cbind::discctrl::done") +# context("ds.cbind::discctrl::done") diff --git a/tests/testthat/test-discctrl-ds.dataFrame.R b/tests/testthat/test-discctrl-ds.dataFrame.R index fe153c0e0..fedde1566 100644 --- a/tests/testthat/test-discctrl-ds.dataFrame.R +++ b/tests/testthat/test-discctrl-ds.dataFrame.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.dataFrame::discctrl::setup") +# context("ds.dataFrame::discctrl::setup") connect.studies.dataset.cnsim(list("GENDER", "PM_BMI_CATEGORICAL")) @@ -23,7 +24,7 @@ test_that("setup", { # # Tests # -context("ds.dataFrame::discctrl") +# context("ds.dataFrame::discctrl") test_that("simple c", { ds.assign('D$LAB_TSC', 'LAB_TSC') ds.assign('D$LAB_HDL', 'LAB_HDL') @@ -42,7 +43,7 @@ test_that("simple c", { # Done # -context("ds.dataFrame::discctrl::shutdown") +# context("ds.dataFrame::discctrl::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "LAB_TSC", "LAB_HDL")) @@ -50,4 +51,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.dataFrame::discctrl::done") +# context("ds.dataFrame::discctrl::done") diff --git a/tests/testthat/test-discctrl-ds.dataFrameSort.R b/tests/testthat/test-discctrl-ds.dataFrameSort.R index 027c5d8ec..e85a55bd2 100644 --- a/tests/testthat/test-discctrl-ds.dataFrameSort.R +++ b/tests/testthat/test-discctrl-ds.dataFrameSort.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.dataFrameSort::discctrl::setup") +# context("ds.dataFrameSort::discctrl::setup") connect.studies.dataset.cnsim(list("GENDER", "PM_BMI_CATEGORICAL")) @@ -23,7 +24,7 @@ test_that("setup", { # # Tests # -context("ds.dataFrameSort::discctrl") +# context("ds.dataFrameSort::discctrl") test_that("simple c", { expect_error(ds.dataFrameSort(df.name="D", sort.key.name="PM_BMI_CATEGORICAL", newobj="sorted_df"), "There are some DataSHIELD errors, list them with datashield.errors()", fixed = TRUE) @@ -42,7 +43,7 @@ test_that("simple c", { # Done # -context("ds.dataFrameSort::discctrl::shutdown") +# context("ds.dataFrameSort::discctrl::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -50,4 +51,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.dataFrameSort::discctrl::done") +# context("ds.dataFrameSort::discctrl::done") diff --git a/tests/testthat/test-discctrl-ds.dataFrameSubset.R b/tests/testthat/test-discctrl-ds.dataFrameSubset.R index c43d0c800..155313cba 100644 --- a/tests/testthat/test-discctrl-ds.dataFrameSubset.R +++ b/tests/testthat/test-discctrl-ds.dataFrameSubset.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.dataFrameSubset::discctrl::setup") +# context("ds.dataFrameSubset::discctrl::setup") connect.studies.dataset.cnsim(list("GENDER", "PM_BMI_CATEGORICAL")) @@ -23,7 +24,7 @@ test_that("setup", { # # Tests # -context("ds.dataFrameSubset::discctrl") +# context("ds.dataFrameSubset::discctrl") test_that("simple c", { expect_error(ds.dataFrameSubset(df.name="D", V1.name="D$LAB_TSC", V2.name="D$LAB_HDL", Boolean.operator="!=", newobj="subset_df"), "There are some DataSHIELD errors, list them with datashield.errors()", fixed = TRUE) @@ -42,7 +43,7 @@ test_that("simple c", { # Done # -context("ds.dataFrameSubset::discctrl::shutdown") +# context("ds.dataFrameSubset::discctrl::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -50,4 +51,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.dataFrameSubset::discctrl::done") +# context("ds.dataFrameSubset::discctrl::done") diff --git a/tests/testthat/test-discctrl-ds.dmtC2S.R b/tests/testthat/test-discctrl-ds.dmtC2S.R index fb2099a72..95af08e9c 100644 --- a/tests/testthat/test-discctrl-ds.dmtC2S.R +++ b/tests/testthat/test-discctrl-ds.dmtC2S.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.dmtC2S::discctrl::setup") +# context("ds.dmtC2S::discctrl::setup") connect.studies.dataset.cnsim(list("GENDER", "PM_BMI_CATEGORICAL")) @@ -23,7 +24,7 @@ test_that("setup", { # # Tests # -context("ds.dmtC2S::discctrl") +# context("ds.dmtC2S::discctrl") test_that("simple dmtC2S", { a <- data.frame(c(1, 2)) b <- data.frame(c(2, 3)) @@ -46,7 +47,7 @@ test_that("simple dmtC2S", { # Done # -context("ds.dmtC2S::discctrl::shutdown") +# context("ds.dmtC2S::discctrl::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -54,4 +55,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.dmtC2S::discctrl::done") +# context("ds.dmtC2S::discctrl::done") diff --git a/tests/testthat/test-discctrl-ds.levels.R b/tests/testthat/test-discctrl-ds.levels.R index 05325f543..5690859f5 100644 --- a/tests/testthat/test-discctrl-ds.levels.R +++ b/tests/testthat/test-discctrl-ds.levels.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.levels::discctrl::setup") +# context("ds.levels::discctrl::setup") connect.studies.dataset.cnsim(list("GENDER", "PM_BMI_CATEGORICAL")) @@ -23,7 +24,7 @@ test_that("setup", { # # Tests # -context("ds.levels::discctrl") +# context("ds.levels::discctrl") test_that("simple levels", { expect_error(ds.levels("D$GENDER"), "There are some DataSHIELD errors, list them with datashield.errors()", fixed = TRUE) @@ -42,7 +43,7 @@ test_that("simple levels", { # Done # -context("ds.levels::discctrl::shutdown") +# context("ds.levels::discctrl::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -50,4 +51,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.levels::discctrl::done") +# context("ds.levels::discctrl::done") diff --git a/tests/testthat/test-discctrl-ds.ns.R b/tests/testthat/test-discctrl-ds.ns.R index c7c4a43df..8f57c17d2 100644 --- a/tests/testthat/test-discctrl-ds.ns.R +++ b/tests/testthat/test-discctrl-ds.ns.R @@ -1,6 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. -# Copyright (c) 2022 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -13,7 +13,7 @@ # Set up # -context("ds.ns::discctrl::setup") +# context("ds.ns::discctrl::setup") connect.studies.dataset.cnsim(list("LAB_TRIG", "PM_BMI_CONTINUOUS")) @@ -24,7 +24,7 @@ test_that("setup", { # # Tests # -context("ds.ns::discctrl") +# context("ds.ns::discctrl") test_that("ns", { expect_error(ds.ns(x="D$PM_BMI_CONTINUOUS", knots=c(8,9,10,12,25,35), newobj="nsDS", datasources=ds.test_env$connections), "There are some DataSHIELD errors, list them with datashield.errors()", fixed = TRUE) @@ -43,7 +43,7 @@ test_that("ns", { # Done # -context("ds.ns::discctrl::shutdown") +# context("ds.ns::discctrl::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -51,4 +51,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.ns::discctrl::done") +# context("ds.ns::discctrl::done") diff --git a/tests/testthat/test-discctrl-ds.rBinom.R b/tests/testthat/test-discctrl-ds.rBinom.R index 19e2318ac..f8bc70d77 100644 --- a/tests/testthat/test-discctrl-ds.rBinom.R +++ b/tests/testthat/test-discctrl-ds.rBinom.R @@ -1,6 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. -# Copyright (c) 2022 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -13,7 +13,7 @@ # Set up # -context("ds.rBinom::discctrl::setup") +# context("ds.rBinom::discctrl::setup") connect.studies.dataset.cnsim(list("LAB_TSC")) @@ -24,7 +24,7 @@ test_that("setup", { # # Tests # -context("ds.rBinom::discctrl") +# context("ds.rBinom::discctrl") test_that("simple c", { expect_error(ds.rBinom(samp.size = 50, size = 50, prob = 0.25, newobj = "binom_dist", seed.as.integer = 27), "There are some DataSHIELD errors, list them with datashield.errors()", fixed = TRUE) @@ -39,7 +39,7 @@ test_that("simple c", { # Done # -context("ds.rBinom::discctrl::shutdown") +# context("ds.rBinom::discctrl::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -47,4 +47,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.rBinom::discctrl::done") +# context("ds.rBinom::discctrl::done") diff --git a/tests/testthat/test-discctrl-ds.rNorm.R b/tests/testthat/test-discctrl-ds.rNorm.R index 997e3fadb..153d84e03 100644 --- a/tests/testthat/test-discctrl-ds.rNorm.R +++ b/tests/testthat/test-discctrl-ds.rNorm.R @@ -1,6 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. -# Copyright (c) 2022 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -13,7 +13,7 @@ # Set up # -context("ds.rNorm::discctrl::setup") +# context("ds.rNorm::discctrl::setup") connect.studies.dataset.cnsim(list("GENDER", "PM_BMI_CATEGORICAL")) @@ -24,7 +24,7 @@ test_that("setup", { # # Tests # -context("ds.rNorm::discctrl") +# context("ds.rNorm::discctrl") test_that("simple c", { expect_error(ds.rNorm(samp.size = 50, mean = 10, sd = 5, newobj = "norm_dist", seed.as.integer = 27), "There are some DataSHIELD errors, list them with datashield.errors()", fixed = TRUE) @@ -39,7 +39,7 @@ test_that("simple c", { # Done # -context("ds.rNorm::discctrl::shutdown") +# context("ds.rNorm::discctrl::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -47,4 +47,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.rNorm::discctrl::done") +# context("ds.rNorm::discctrl::done") diff --git a/tests/testthat/test-discctrl-ds.rPois.R b/tests/testthat/test-discctrl-ds.rPois.R index 58b0667a0..b0176cedc 100644 --- a/tests/testthat/test-discctrl-ds.rPois.R +++ b/tests/testthat/test-discctrl-ds.rPois.R @@ -1,6 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. -# Copyright (c) 2022 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -13,7 +13,7 @@ # Set up # -context("ds.rPois::discctrl::setup") +# context("ds.rPois::discctrl::setup") connect.studies.dataset.cnsim(list("GENDER", "PM_BMI_CATEGORICAL")) @@ -24,7 +24,7 @@ test_that("setup", { # # Tests # -context("ds.rPois::discctrl") +# context("ds.rPois::discctrl") test_that("simple c", { expect_error(ds.rPois(samp.size = 50, lambda = 1, newobj = "pois_dist", seed.as.integer = 27), "There are some DataSHIELD errors, list them with datashield.errors()", fixed = TRUE) @@ -39,7 +39,7 @@ test_that("simple c", { # Done # -context("ds.rPois::discctrl::shutdown") +# context("ds.rPois::discctrl::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -47,4 +47,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.rPois::discctrl::done") +# context("ds.rPois::discctrl::done") diff --git a/tests/testthat/test-discctrl-ds.rUnif.R b/tests/testthat/test-discctrl-ds.rUnif.R index f2fd5e476..7327f366f 100644 --- a/tests/testthat/test-discctrl-ds.rUnif.R +++ b/tests/testthat/test-discctrl-ds.rUnif.R @@ -1,6 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. -# Copyright (c) 2022 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -13,7 +13,7 @@ # Set up # -context("ds.rUnif::discctrl::setup") +# context("ds.rUnif::discctrl::setup") connect.studies.dataset.cnsim(list("GENDER", "PM_BMI_CATEGORICAL")) @@ -24,7 +24,7 @@ test_that("setup", { # # Tests # -context("ds.rUnif::discctrl") +# context("ds.rUnif::discctrl") test_that("simple c", { expect_error(ds.rUnif(samp.size = 50, min = 0, max = 1, newobj = "unif_dist", seed.as.integer = 27), "There are some DataSHIELD errors, list them with datashield.errors()", fixed = TRUE) @@ -39,7 +39,7 @@ test_that("simple c", { # Done # -context("ds.rUnif::discctrl::shutdown") +# context("ds.rUnif::discctrl::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -47,4 +47,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.rUnif::discctrl::done") +# context("ds.rUnif::discctrl::done") diff --git a/tests/testthat/test-discctrl-ds.rbind.R b/tests/testthat/test-discctrl-ds.rbind.R index 28d3c0306..b80362070 100644 --- a/tests/testthat/test-discctrl-ds.rbind.R +++ b/tests/testthat/test-discctrl-ds.rbind.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.rbind::discctrl::setup") +# context("ds.rbind::discctrl::setup") connect.studies.dataset.survival(list("survtime", "time.id", "female", "age.60")) @@ -23,7 +24,7 @@ test_that("setup", { # # Tests # -context("ds.rbind::discctrl") +# context("ds.rbind::discctrl") test_that("simple c", { expect_error(ds.rbind(c("D$survtime", "D$time.id", "D$female", "D$age.60"), newobj="rbind_newobj"), "There are some DataSHIELD errors, list them with datashield.errors()", fixed = TRUE) @@ -42,7 +43,7 @@ test_that("simple c", { # Done # -context("ds.rbind::discctrl::shutdown") +# context("ds.rbind::discctrl::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -50,4 +51,4 @@ test_that("shutdown", { disconnect.studies.dataset.survival() -context("ds.rbind::discctrl::done") +# context("ds.rbind::discctrl::done") diff --git a/tests/testthat/test-discctrl-ds.reShape.R b/tests/testthat/test-discctrl-ds.reShape.R index 65f68eb6d..ec759b697 100644 --- a/tests/testthat/test-discctrl-ds.reShape.R +++ b/tests/testthat/test-discctrl-ds.reShape.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.reShape::discctrl::setup") +# context("ds.reShape::discctrl::setup") connect.studies.dataset.survival(list("id", "study.id", "time.id", "cens", "age.60", "female")) @@ -23,7 +24,7 @@ test_that("setup", { # # Tests # -context("ds.reShape::discctrl") +# context("ds.reShape::discctrl") test_that("simple reShape", { expect_error(ds.reShape(data.name="D", v.names="age.60", timevar.name="time.id", idvar.name="id", direction="wide", newobj="reshape1_obj"), "There are some DataSHIELD errors, list them with datashield.errors()", fixed = TRUE) @@ -42,7 +43,7 @@ test_that("simple reShape", { # Done # -context("ds.reShape::discctrl::shutdown") +# context("ds.reShape::discctrl::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -50,4 +51,4 @@ test_that("shutdown", { disconnect.studies.dataset.survival() -context("ds.reShape::discctrl::done") +# context("ds.reShape::discctrl::done") diff --git a/tests/testthat/test-discctrl-ds.recodeLevels.R b/tests/testthat/test-discctrl-ds.recodeLevels.R index 9f4ab0ca9..39551aa15 100644 --- a/tests/testthat/test-discctrl-ds.recodeLevels.R +++ b/tests/testthat/test-discctrl-ds.recodeLevels.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.recodeLevels::discctrl::setup") +# context("ds.recodeLevels::discctrl::setup") connect.studies.dataset.cnsim(list("PM_BMI_CATEGORICAL")) @@ -23,7 +24,7 @@ test_that("setup", { # # Tests # -context("ds.recodeLevels::discctrl") +# context("ds.recodeLevels::discctrl") test_that("simple recodeLevels", { expect_error(expect_warning(ds.recodeLevels(x='D$PM_BMI_CATEGORICAL', newCategories=c('normal', 'overweight', 'obesity'), newobj='bmi_new'), "", fixed = TRUE), "There are some DataSHIELD errors, list them with datashield.errors()", fixed = TRUE) @@ -42,7 +43,7 @@ test_that("simple recodeLevels", { # Done # -context("ds.recodeLevels::discctrl::shutdown") +# context("ds.recodeLevels::discctrl::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -50,4 +51,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.recodeLevels::discctrl::done") +# context("ds.recodeLevels::discctrl::done") diff --git a/tests/testthat/test-discctrl-ds.recodeValues.R b/tests/testthat/test-discctrl-ds.recodeValues.R index 71580510c..1bd6aa93e 100644 --- a/tests/testthat/test-discctrl-ds.recodeValues.R +++ b/tests/testthat/test-discctrl-ds.recodeValues.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.rep::discctrl::setup") +# context("ds.rep::discctrl::setup") connect.studies.dataset.survival(list("survtime", "time.id", "female", "age.60")) @@ -23,7 +24,7 @@ test_that("setup", { # # Tests # -context("ds.rep::discctrl") +# context("ds.rep::discctrl") test_that("simple recodeValues", { expect_error(ds.recodeValues("D$survtime", values2replace.vector=c(0,1), new.values.vector=c(-10,10), newobj="recodevalues_newobj"), "There are some DataSHIELD errors, list them with datashield.errors()", fixed = TRUE) @@ -42,7 +43,7 @@ test_that("simple recodeValues", { # Done # -context("ds.rep::discctrl::shutdown") +# context("ds.rep::discctrl::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -50,4 +51,4 @@ test_that("shutdown", { disconnect.studies.dataset.survival() -context("ds.rep::discctrl::done") +# context("ds.rep::discctrl::done") diff --git a/tests/testthat/test-discctrl-ds.rep.R b/tests/testthat/test-discctrl-ds.rep.R index feeb56c97..4828cc8ef 100644 --- a/tests/testthat/test-discctrl-ds.rep.R +++ b/tests/testthat/test-discctrl-ds.rep.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.rep::discctrl::setup") +# context("ds.rep::discctrl::setup") connect.studies.dataset.survival(list("survtime", "time.id", "female", "age.60")) @@ -23,7 +24,7 @@ test_that("setup", { # # Tests # -context("ds.rep::discctrl") +# context("ds.rep::discctrl") test_that("simple rep", { expect_error(ds.rep("D$survtime"), "There are some DataSHIELD errors, list them with datashield.errors()", fixed = TRUE) @@ -42,7 +43,7 @@ test_that("simple rep", { # Done # -context("ds.rep::discctrl::shutdown") +# context("ds.rep::discctrl::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -50,4 +51,4 @@ test_that("shutdown", { disconnect.studies.dataset.survival() -context("ds.rep::discctrl::done") +# context("ds.rep::discctrl::done") diff --git a/tests/testthat/test-discctrl-ds.sample.R b/tests/testthat/test-discctrl-ds.sample.R index 0991669ff..863112a49 100644 --- a/tests/testthat/test-discctrl-ds.sample.R +++ b/tests/testthat/test-discctrl-ds.sample.R @@ -1,6 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. -# Copyright (c) 2022 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -13,7 +13,7 @@ # Set up # -context("ds.sample::discctrl::setup") +# context("ds.sample::discctrl::setup") connect.studies.dataset.cnsim(list("GENDER", "PM_BMI_CATEGORICAL")) @@ -24,7 +24,7 @@ test_that("setup", { # # Tests # -context("ds.sample::discctrl") +# context("ds.sample::discctrl") test_that("simple c", { expect_error(ds.sample(x="D", size=20, seed.as.integer=27), "There are some DataSHIELD errors, list them with datashield.errors()", fixed = TRUE) @@ -39,7 +39,7 @@ test_that("simple c", { # Done # -context("ds.sample::discctrl::shutdown") +# context("ds.sample::discctrl::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -47,4 +47,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.sample::discctrl::done") +# context("ds.sample::discctrl::done") diff --git a/tests/testthat/test-discctrl-ds.seq.R b/tests/testthat/test-discctrl-ds.seq.R index 5045b06ae..a74ba73a7 100644 --- a/tests/testthat/test-discctrl-ds.seq.R +++ b/tests/testthat/test-discctrl-ds.seq.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.seq::discctrl::setup") +# context("ds.seq::discctrl::setup") connect.studies.dataset.survival(list("survtime", "time.id", "female", "age.60")) @@ -23,7 +24,7 @@ test_that("setup", { # # Tests # -context("ds.seq::discctrl") +# context("ds.seq::discctrl") test_that("simple rep", { expect_error(ds.seq(FROM.value.char="1", BY.value.char="1", LENGTH.OUT.value.char="10", ALONG.WITH.name=NULL, newobj="obj1"), "There are some DataSHIELD errors, list them with datashield.errors()", fixed = TRUE) @@ -42,7 +43,7 @@ test_that("simple rep", { # Done # -context("ds.seq::discctrl::shutdown") +# context("ds.seq::discctrl::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -50,4 +51,4 @@ test_that("shutdown", { disconnect.studies.dataset.survival() -context("ds.seq::discctrl::done") +# context("ds.seq::discctrl::done") diff --git a/tests/testthat/test-discctrl-ds.setSeed.R b/tests/testthat/test-discctrl-ds.setSeed.R index 351859c29..f32371b6b 100644 --- a/tests/testthat/test-discctrl-ds.setSeed.R +++ b/tests/testthat/test-discctrl-ds.setSeed.R @@ -1,6 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. -# Copyright (c) 2022 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -13,7 +13,7 @@ # Set up # -context("ds.setSeed::discctrl::setup") +# context("ds.setSeed::discctrl::setup") connect.studies.dataset.cnsim(list("GENDER", "PM_BMI_CATEGORICAL")) @@ -24,7 +24,7 @@ test_that("setup", { # # Tests # -context("ds.setSeed::discctrl") +# context("ds.setSeed::discctrl") test_that("simple c", { expect_error(ds.setSeed(4321), "There are some DataSHIELD errors, list them with datashield.errors()", fixed = TRUE) @@ -43,7 +43,7 @@ test_that("simple c", { # Done # -context("ds.setSeed::discctrl::shutdown") +# context("ds.setSeed::discctrl::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -51,4 +51,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.setSeed::discctrl::done") +# context("ds.setSeed::discctrl::done") diff --git a/tests/testthat/test-discctrl-ds.subset.R b/tests/testthat/test-discctrl-ds.subset.R index 6b99c7c83..6da2146d5 100644 --- a/tests/testthat/test-discctrl-ds.subset.R +++ b/tests/testthat/test-discctrl-ds.subset.R @@ -1,6 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. -# Copyright (c) 2022 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -13,7 +13,7 @@ # Set up # -context("ds.subset::discctrl::setup") +# context("ds.subset::discctrl::setup") connect.studies.dataset.cnsim(list("DIS_DIAB","PM_BMI_CONTINUOUS","LAB_HDL", "GENDER")) @@ -24,7 +24,7 @@ test_that("setup", { # # Tests # -context("ds.subset::discctrl") +# context("ds.subset::discctrl") test_that("simple subset", { expect_error(expect_warning(ds.subset(datasources=ds.test_env$connections, subset='subD', x='D', rows=c(1:50), cols=c(1,2)), "", fixed = TRUE), "There are some DataSHIELD errors, list them with datashield.errors()", fixed = TRUE) @@ -39,7 +39,7 @@ test_that("simple subset", { # Done # -context("ds.subset::discctrl::shutdown") +# context("ds.subset::discctrl::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -47,4 +47,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.subset::discctrl::done") +# context("ds.subset::discctrl::done") diff --git a/tests/testthat/test-discctrl-ds.subsetByClass.R b/tests/testthat/test-discctrl-ds.subsetByClass.R index 414efb4d5..a767cd546 100644 --- a/tests/testthat/test-discctrl-ds.subsetByClass.R +++ b/tests/testthat/test-discctrl-ds.subsetByClass.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.subsetByClass::discctrl::setup") +# context("ds.subsetByClass::discctrl::setup") connect.studies.dataset.cnsim(list("LAB_TSC", "GENDER")) @@ -23,7 +24,7 @@ test_that("setup", { # # Tests # -context("ds.subsetByClass::discctrl") +# context("ds.subsetByClass::discctrl") test_that("simple subsetByClass", { expect_error(expect_warning(ds.subsetByClass(x='D', subsets='subclasses1'), "", fixed = TRUE), "There are some DataSHIELD errors, list them with datashield.errors()", fixed = TRUE) @@ -42,7 +43,7 @@ test_that("simple subsetByClass", { # Done # -context("ds.subsetByClass::discctrl::shutdown") +# context("ds.subsetByClass::discctrl::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -50,4 +51,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.subsetByClass::discctrl::done") +# context("ds.subsetByClass::discctrl::done") diff --git a/tests/testthat/test-expt-ds.dataFrame.R b/tests/testthat/test-expt-ds.dataFrame.R index 0ec01ef2b..3660038c8 100644 --- a/tests/testthat/test-expt-ds.dataFrame.R +++ b/tests/testthat/test-expt-ds.dataFrame.R @@ -1,9 +1,20 @@ -context('ds.dataFrame::expt::setup') +#------------------------------------------------------------------------------- +# Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. +# +# This program and the accompanying materials +# are made available under the terms of the GNU Public License v3.0. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see . +#------------------------------------------------------------------------------- + +# context('ds.dataFrame::expt::setup') source('connection_to_datasets/init_testing_datasets.R') source('definition_tests/def-ds.data.frame.R') -context('ds.dataFrame::expt::one_column::single') +# context('ds.dataFrame::expt::one_column::single') test_that('numeric data', { connect.dataset.2() @@ -17,7 +28,7 @@ test_that('numeric data', .test.data.frame.creation(c('D$NEGATIVE_INTEGER'),'integer_7_df') }) -context('ds.dataFrame::expt::several_columns::single') +# context('ds.dataFrame::expt::several_columns::single') test_that('numeric data', { connect.dataset.2() @@ -25,7 +36,7 @@ test_that('numeric data', .test.data.frame.creation(c('D$INTEGER','D$NON_NEGATIVE_INTEGER','D$POSITIVE_INTEGER','D$NEGATIVE_INTEGER'),'integer_9_df') }) -context('ds.dataFrame::expt::one_column::multiple') +# context('ds.dataFrame::expt::one_column::multiple') test_that('numeric data', { connect.all.datasets() @@ -39,7 +50,7 @@ test_that('numeric data', .test.data.frame.creation(c('D$NEGATIVE_INTEGER'),'integer_16_df') }) -context('ds.dataFrame::expt::several_columns::single') +# context('ds.dataFrame::expt::several_columns::single') test_that('numeric data', { connect.all.datasets() @@ -47,7 +58,7 @@ test_that('numeric data', .test.data.frame.creation(c('D$INTEGER','D$NON_NEGATIVE_INTEGER','D$POSITIVE_INTEGER','D$NEGATIVE_INTEGER'),'integer_17_df') }) -context('ds.dataFrame::expt::one_column_from_objects::single') +# context('ds.dataFrame::expt::one_column_from_objects::single') test_that('numeric data', { connect.dataset.2() @@ -61,7 +72,7 @@ test_that('numeric data', .test.data.frame.from.objects('D$NEGATIVE_INTEGER','numeric_created','numeric_27_df') }) -context('ds.dataFrame::expt::object::multiple') +# context('ds.dataFrame::expt::object::multiple') test_that('numeric data', { connect.all.datasets() @@ -75,14 +86,14 @@ test_that('numeric data', .test.data.frame.from.objects('D$NEGATIVE_INTEGER','numeric_created','numeric_35_df') }) -context('ds.dataFrame::expt::several_objects::multiple') +# context('ds.dataFrame::expt::several_objects::multiple') test_that('several objects', { connect.all.datasets() .test.data.frame.from.different.objects('multiple_df') }) -context('ds.dataFrame::expt::non_numeric::multiple') +# context('ds.dataFrame::expt::non_numeric::multiple') test_that("non_numeric", { connect.all.datasets() @@ -93,7 +104,7 @@ test_that("non_numeric", .test.data.frame.from.objects('D$LOGICAL','boolean_created' ,'boolean_df') }) -context('ds.dataFrame::expt::non_numeric::multiple') +# context('ds.dataFrame::expt::non_numeric::multiple') { connect.dataset.2() .test.data.frame.creation(c('D$CHARACTER'),'character_df') @@ -103,6 +114,6 @@ context('ds.dataFrame::expt::non_numeric::multiple') .test.data.frame.from.objects('D$LOGICAL','boolean_created' ,'boolean_df') } -context('ds.dataFrame::expt::shutdown') +# context('ds.dataFrame::expt::shutdown') -context('ds.dataFrame::expt::done') +# context('ds.dataFrame::expt::done') diff --git a/tests/testthat/test-expt-ds.glmerSLMA.R b/tests/testthat/test-expt-ds.glmerSLMA.R index 0ce25e862..8c6fe40bc 100644 --- a/tests/testthat/test-expt-ds.glmerSLMA.R +++ b/tests/testthat/test-expt-ds.glmerSLMA.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.glmerSLMA::expt::setup") +# context("ds.glmerSLMA::expt::setup") #source("connection_to_datasets/init_all_datasets.R") connect.studies.dataset.cluster.int(list('idChild','idSurgery','trtGrp','s0','nDoctors', 'idDoctor','c0','nPatients','Male','age','BMI', @@ -26,7 +27,7 @@ test_that("setup", { # Tests # -context("ds.glmerSLMA::expt::int::multiple") +# context("ds.glmerSLMA::expt::int::multiple") test_that("linear mixed model with 2 levels of hierarchy", { @@ -76,7 +77,7 @@ test_that("linear mixed model with 2 levels of hierarchy", # Shutdown # -context("ds.lmerSLMA::expt::shutdown") +# context("ds.lmerSLMA::expt::shutdown") disconnect.studies.dataset.cluster.int() @@ -84,4 +85,4 @@ disconnect.studies.dataset.cluster.int() # Done # -context("ds.lmerSLMA::expt::done") +# context("ds.lmerSLMA::expt::done") diff --git a/tests/testthat/test-expt-ds.lmerSLMA.R b/tests/testthat/test-expt-ds.lmerSLMA.R index 271381c6a..703a589dd 100644 --- a/tests/testthat/test-expt-ds.lmerSLMA.R +++ b/tests/testthat/test-expt-ds.lmerSLMA.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.lmerSLMA::expt::setup") +# context("ds.lmerSLMA::expt::setup") #source("connection_to_datasets/init_all_datasets.R") connect.studies.dataset.cluster.int(list('idChild','idSurgery','trtGrp','s0','nDoctors', 'idDoctor','c0','nPatients','Male','age','BMI', @@ -27,7 +28,7 @@ test_that("setup", { # Tests # -context("ds.lmerSLMA::expt::int::multiple") +# context("ds.lmerSLMA::expt::int::multiple") test_that("linear mixed model with 2 levels of hierarchy", { @@ -79,4 +80,4 @@ test_that("linear mixed model with 2 levels of hierarchy", disconnect.studies.dataset.cluster.int() -context("ds.lmerSLMA::expt::done") +# context("ds.lmerSLMA::expt::done") diff --git a/tests/testthat/test-expt-ds.mean.R b/tests/testthat/test-expt-ds.mean.R index 8c6d6b44a..782a4acbe 100644 --- a/tests/testthat/test-expt-ds.mean.R +++ b/tests/testthat/test-expt-ds.mean.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -14,7 +15,7 @@ source("connection_to_datasets/init_testing_datasets.R") source("definition_tests/def-ds.mean.R") -context("ds.mean::expt::combine::multiple") +# context("ds.mean::expt::combine::multiple") test_that("combined data set", { connect.all.datasets() @@ -29,7 +30,7 @@ test_that("combined data set", .test.mean.combined('D$NEGATIVE_NUMERIC',ds.test_env$local.values[,'NEGATIVE_NUMERIC']) }) -context("ds.mean::expt::split::multiple") +# context("ds.mean::expt::split::multiple") test_that("split data set", { connect.all.datasets() @@ -44,7 +45,7 @@ test_that("split data set", .test.mean.split('D$NEGATIVE_NUMERIC',ds.test_env$local.values.1[,'NEGATIVE_NUMERIC'],ds.test_env$local.values.2[,'NEGATIVE_NUMERIC'],ds.test_env$local.values.3[,'NEGATIVE_NUMERIC']) }) -context("ds.mean::expt::single") +# context("ds.mean::expt::single") test_that("combined data set", { connect.dataset.1() @@ -58,7 +59,7 @@ test_that("combined data set", .test.mean.combined('D$NEGATIVE_NUMERIC',ds.test_env$local.values.1[,'NEGATIVE_NUMERIC']) }) -context("ds.mean::expt::large_values::single") +# context("ds.mean::expt::large_values::single") test_that("combined data set", { connect.dataset.1() @@ -72,7 +73,7 @@ test_that("combined data set", .test.mean.large('D$NEGATIVE_NUMERIC',ds.test_env$local.values.1[,'NEGATIVE_NUMERIC']) }) -context("ds.mean::expt::large_values::multiple") +# context("ds.mean::expt::large_values::multiple") test_that("combined data set", { connect.all.datasets() diff --git a/tests/testthat/test-expt-ds.reshape.R b/tests/testthat/test-expt-ds.reshape.R index 853d31af2..4e8f243b3 100644 --- a/tests/testthat/test-expt-ds.reshape.R +++ b/tests/testthat/test-expt-ds.reshape.R @@ -1,9 +1,20 @@ +#------------------------------------------------------------------------------- +# Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. +# +# This program and the accompanying materials +# are made available under the terms of the GNU Public License v3.0. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see . +#------------------------------------------------------------------------------- + source("connection_to_datasets/init_testing_datasets.R") source("definition_tests/def-ds.reshape.R") source("definition_tests/def-assign-stats.R") -context("ds.reShape::expt::multiple") +# context("ds.reShape::expt::multiple") test_that("copy and transform", { init.testing.datasets() diff --git a/tests/testthat/test-expt-ds.skewness.R b/tests/testthat/test-expt-ds.skewness.R index d43bdce86..268ac3a13 100644 --- a/tests/testthat/test-expt-ds.skewness.R +++ b/tests/testthat/test-expt-ds.skewness.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -13,7 +14,7 @@ source("connection_to_datasets/init_testing_datasets.R") source("definition_tests/def-ds.skewness.R") -context("ds.skewness::expt::combine::multiple") +# context("ds.skewness::expt::combine::multiple") test_that("combined data set", { @@ -28,7 +29,7 @@ test_that("combined data set", .test.skewness.combined('D$NEGATIVE_NUMERIC',ds.test_env$local.values[,'NEGATIVE_NUMERIC'], method = 1) }) -context("ds.skewness::expt::split::multiple") +# context("ds.skewness::expt::split::multiple") test_that("split data set", { connect.all.datasets() @@ -42,7 +43,7 @@ test_that("split data set", .test.skewness.split('D$NEGATIVE_NUMERIC',ds.test_env$local.values.1[,'NEGATIVE_NUMERIC'],ds.test_env$local.values.2[,'NEGATIVE_NUMERIC'],ds.test_env$local.values.3[,'NEGATIVE_NUMERIC'], method = 2) }) -context("ds.skewness::expt::single") +# context("ds.skewness::expt::single") test_that("combined data set", { connect.dataset.1() diff --git a/tests/testthat/test-expt-ds.var.R b/tests/testthat/test-expt-ds.var.R index e8a19fd4f..e4764f327 100644 --- a/tests/testthat/test-expt-ds.var.R +++ b/tests/testthat/test-expt-ds.var.R @@ -1,8 +1,19 @@ +#------------------------------------------------------------------------------- +# Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. +# +# This program and the accompanying materials +# are made available under the terms of the GNU Public License v3.0. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see . +#------------------------------------------------------------------------------- + source("connection_to_datasets/init_testing_datasets.R") source("definition_tests/def-ds.var.R") -context("ds.var::expt::multiple") +# context("ds.var::expt::multiple") test_that("combined data set", { connect.all.datasets() @@ -16,7 +27,7 @@ test_that("combined data set", .test.var.combined('D$NEGATIVE_NUMERIC',ds.test_env$local.values[,'NEGATIVE_NUMERIC']) }) -context("ds.var::expt::single") +# context("ds.var::expt::single") test_that("split data set", { connect.all.datasets() @@ -30,7 +41,7 @@ test_that("split data set", .test.var.split('D$NEGATIVE_NUMERIC',ds.test_env$local.values.1[,'NEGATIVE_NUMERIC'],ds.test_env$local.values.2[,'NEGATIVE_NUMERIC'],ds.test_env$local.values.3[,'NEGATIVE_NUMERIC']) }) -context("ds.var::expt::large_values::multiple") +# context("ds.var::expt::large_values::multiple") test_that("large values", { connect.all.datasets() @@ -44,7 +55,7 @@ test_that("large values", .test.variance.large('D$NEGATIVE_NUMERIC',ds.test_env$local.values[,'NEGATIVE_NUMERIC']) }) -context("ds.var::expt::large_values::single") +# context("ds.var::expt::large_values::single") test_that("large values", { connect.dataset.1() @@ -58,4 +69,3 @@ test_that("large values", .test.variance.large('D$NEGATIVE_NUMERIC',ds.test_env$local.values.1[,'NEGATIVE_NUMERIC']) }) - diff --git a/tests/testthat/test-expt_bug-ds.asFactor.R b/tests/testthat/test-expt_bug-ds.asFactor.R index 16ca08534..b7f26c9ee 100644 --- a/tests/testthat/test-expt_bug-ds.asFactor.R +++ b/tests/testthat/test-expt_bug-ds.asFactor.R @@ -1,7 +1,17 @@ -source("definition_tests/def-ds.asFactor.R") +#------------------------------------------------------------------------------- +# Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. +# +# This program and the accompanying materials +# are made available under the terms of the GNU Public License v3.0. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see . +#------------------------------------------------------------------------------- +source("definition_tests/def-ds.asFactor.R") -context("ds.asFactor::expt::multiple") +# context("ds.asFactor::expt::multiple") test_that("combined data set", { connect.all.datasets() @@ -16,7 +26,7 @@ test_that("combined data set", .test.find.factor('D$FACTOR_INTEGER', 'FACTOR_INT.f',ds.test_env$local.values,15) }) -context("ds.asFactor::expt::single") +# context("ds.asFactor::expt::single") test_that("single dataset ", { connect.dataset.1() diff --git a/tests/testthat/test-expt_bug-ds.dataFrameSort.R b/tests/testthat/test-expt_bug-ds.dataFrameSort.R index 7f4f065a3..522c28ca6 100644 --- a/tests/testthat/test-expt_bug-ds.dataFrameSort.R +++ b/tests/testthat/test-expt_bug-ds.dataFrameSort.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -8,12 +9,12 @@ # along with this program. If not, see . #------------------------------------------------------------------------------- -context('ds.dataFrameSort::expt::setup') +# context('ds.dataFrameSort::expt::setup') source('connection_to_datasets/init_testing_datasets.R') source('definition_tests/def-ds.dataFrameSort.R') -context("ds.dataFrameSort::expt::multiple::correct_parameter_class") +# context("ds.dataFrameSort::expt::multiple::correct_parameter_class") test_that('all datasets', { connect.all.datasets() @@ -31,7 +32,7 @@ test_that('all datasets', .test.function.parameters("D","D$NUMERIC_ONE_CHANGE",TRUE,"alphabetic","server.data") .test.function.parameters("D","D$INTEGER_ONE_CHANGE",TRUE,"numeric","server.data") }) -context("ds.dataFrameSort::expt::single::correct_parameter_class") +# context("ds.dataFrameSort::expt::single::correct_parameter_class") test_that('dataset 2', { connect.dataset.2() @@ -49,7 +50,7 @@ test_that('dataset 2', .test.function.parameters("D","D$NUMERIC_ONE_CHANGE",TRUE,"alphabetic","server.data") .test.function.parameters("D","D$INTEGER_ONE_CHANGE",TRUE,"numeric","server.data") }) -context("ds.dataFrameSort::expt::multiple::incorrect_parameter_class") +# context("ds.dataFrameSort::expt::multiple::incorrect_parameter_class") test_that('all datasets', { connect.all.datasets() @@ -65,7 +66,7 @@ test_that('all datasets', .test.function.parameters("D","D$NUMERIC_ONE_CHANGE",TRUE,"alphabetic",23) .test.function.parameters("dataframe","D$INTEGER_ONE_CHANGE",TRUE,"numeric","server.data") }) -context("ds.dataFrameSort::expt::single::incorrect_parameter_class") +# context("ds.dataFrameSort::expt::single::incorrect_parameter_class") test_that('dataset 2', { connect.dataset.2() @@ -82,7 +83,7 @@ test_that('dataset 2', .test.function.parameters("dataframe","D$INTEGER_ONE_CHANGE",TRUE,"numeric","server.data") }) -context("ds.dataFrameSort::expt::multiple::df::creation") +# context("ds.dataFrameSort::expt::multiple::df::creation") test_that('all datasets', { connect.all.datasets() @@ -98,7 +99,7 @@ test_that('all datasets', .test.data.frame.creation("D","NUMERIC_ONE_CHANGE",TRUE,"numeric","server.data") .test.data.frame.creation("D","INTEGER_ONE_CHANGE",TRUE,"numeric","server.data") }) -context("ds.dataFrameSort::expt::single::df::creation") +# context("ds.dataFrameSort::expt::single::df::creation") test_that('dataset 3', { connect.dataset.3() @@ -114,7 +115,7 @@ test_that('dataset 3', .test.data.frame.creation("D","NUMERIC_ONE_CHANGE",TRUE,"numeric","server.data") .test.data.frame.creation("D","INTEGER_ONE_CHANGE",FALSE,"alphabetic","server.data") }) -context("ds.dataFrameSort::expt::multiple::numeric::ascending") +# context("ds.dataFrameSort::expt::multiple::numeric::ascending") test_that('all datasets', { connect.all.datasets() @@ -140,7 +141,7 @@ test_that('all datasets', }) -context("ds.dataFrameSort::expt::single::numeric::ascending") +# context("ds.dataFrameSort::expt::single::numeric::ascending") test_that('dataset 1', { connect.dataset.1() @@ -166,7 +167,7 @@ test_that('dataset 1', }) -context("ds.dataFrameSort::expt::multiple::numeric::descending") +# context("ds.dataFrameSort::expt::multiple::numeric::descending") test_that('all datasets', { connect.all.datasets() @@ -192,7 +193,7 @@ test_that('all datasets', }) -context("ds.dataFrameSort::expt::single::numeric::descending") +# context("ds.dataFrameSort::expt::single::numeric::descending") test_that('dataset 1', { connect.dataset.1() @@ -220,7 +221,7 @@ test_that('dataset 1', }) -context("ds.dataFrameSort::expt::multiple::alphabetic::ascending") +# context("ds.dataFrameSort::expt::multiple::alphabetic::ascending") test_that('all datasets', { connect.all.datasets() @@ -246,7 +247,7 @@ test_that('all datasets', #.test.data.frame.sorting("D","FACTOR_CHARACTER",FALSE,"alphabetic","server.data",local.df.list) .test.data.frame.sorting("D","CHARACTER",FALSE,"alphabetic","server.data",local.df.list) }) -context("ds.dataFrameSort::expt::single::alphabetic::ascending") +# context("ds.dataFrameSort::expt::single::alphabetic::ascending") test_that('dataset 2', { connect.dataset.2() @@ -272,7 +273,7 @@ test_that('dataset 2', #.test.data.frame.sorting("D","FACTOR_CHARACTER",FALSE,"alphabetic","server.data",local.df.list) .test.data.frame.sorting("D","CHARACTER",FALSE,"alphabetic","server.data",local.df.list) }) -context("ds.dataFrameSort::expt::multiple::alphabetic::descending") +# context("ds.dataFrameSort::expt::multiple::alphabetic::descending") test_that('all datasets', { connect.all.datasets() @@ -296,7 +297,7 @@ test_that('all datasets', #.test.data.frame.sorting("D","FACTOR_CHARACTER",TRUE,"alphabetic","server.data",local.df.list) .test.data.frame.sorting("D","CHARACTER",TRUE,"alphabetic","server.data",local.df.list) }) -context("ds.dataFrameSort::expt::single::alphabetic::descending") +# context("ds.dataFrameSort::expt::single::alphabetic::descending") test_that('dataset 3', { connect.dataset.3() @@ -322,7 +323,7 @@ test_that('dataset 3', }) -context('ds.dataFrameSort::expt::shutdown') +# context('ds.dataFrameSort::expt::shutdown') -context('ds.dataFrameSort::expt::done') +# context('ds.dataFrameSort::expt::done') diff --git a/tests/testthat/test-expt_bug-ds.make.R b/tests/testthat/test-expt_bug-ds.make.R index 2b5005d03..1bcf320cc 100644 --- a/tests/testthat/test-expt_bug-ds.make.R +++ b/tests/testthat/test-expt_bug-ds.make.R @@ -1,9 +1,20 @@ +#------------------------------------------------------------------------------- +# Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. +# +# This program and the accompanying materials +# are made available under the terms of the GNU Public License v3.0. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see . +#------------------------------------------------------------------------------- + source("connection_to_datasets/init_testing_datasets.R") source("definition_tests/def-ds.make.R") source("definition_tests/def-assign-stats.R") -context("ds.make::expt::copy_transform:single") +# context("ds.make::expt::copy_transform:single") test_that("copy and transform", { connect.dataset.1() @@ -20,7 +31,7 @@ test_that("copy and transform", -context("ds.make::expt::copy_data::single") +# context("ds.make::expt::copy_data::single") test_that("copy data without any changes applied", { connect.dataset.1() @@ -35,7 +46,7 @@ test_that("copy data without any changes applied", .test.copy.data('D$FACTOR_INTEGER','FACTOR_INTEGER_created',ds.test_env$local.values.1[,15]) }) -context("ds.make::expt::copy_data::multiple") +# context("ds.make::expt::copy_data::multiple") test_that("copy data without any changes applied", { connect.all.datasets() @@ -50,7 +61,7 @@ test_that("copy data without any changes applied", .test.copy.data('D$FACTOR_INTEGER','FACTOR_INTEGER_created',ds.test_env$local.values[,15]) }) -context("ds.make::expt::sum_of_two_vectors::single") +# context("ds.make::expt::sum_of_two_vectors::single") test_that("apply the the sum some vectors", { connect.dataset.1() @@ -82,7 +93,7 @@ test_that("apply the the sum some vectors", }) -context("ds.make::expt::sum_of_two_vectors::multiple") +# context("ds.make::expt::sum_of_two_vectors::multiple") test_that("add some vectors", { connect.all.datasets() @@ -111,7 +122,7 @@ test_that("add some vectors", .test.operation.vectors('D$NUMERIC','D$NON_NEGATIVE_NUMERIC','NUMERIC_created',"+",result.local = .add.vectors(ds.test_env$local.values[,10],ds.test_env$local.values[,11])) }) -context("ds.make::expt::product_of_two_vectors::single") +# context("ds.make::expt::product_of_two_vectors::single") test_that("multiply two vectors", { connect.dataset.1() @@ -144,7 +155,7 @@ test_that("multiply two vectors", -context("ds.make::expt::product_of_two_vectors::multiple") +# context("ds.make::expt::product_of_two_vectors::multiple") test_that("multiply two vectors", { connect.all.datasets() @@ -173,7 +184,7 @@ test_that("multiply two vectors", .test.operation.vectors('D$NUMERIC','D$NON_NEGATIVE_NUMERIC','NUMERIC_created',"*",result.local = .mult.vectors(ds.test_env$local.values[,10],ds.test_env$local.values[,11])) }) -context("ds.make::expt::division_of_two_vectors::multiple") +# context("ds.make::expt::division_of_two_vectors::multiple") test_that("divide two vectors", { connect.all.datasets() @@ -202,7 +213,7 @@ test_that("divide two vectors", }) -context("ds.make::expt::division_of_two_vectors::single") +# context("ds.make::expt::division_of_two_vectors::single") test_that("divide two vectors", { connect.dataset.1() @@ -231,7 +242,7 @@ test_that("divide two vectors", }) -context("ds.make::expt::substract_of_two_vectors::multiple") +# context("ds.make::expt::substract_of_two_vectors::multiple") test_that("substract two vectors", { connect.all.datasets() @@ -260,7 +271,7 @@ test_that("substract two vectors", }) -context("ds.make::expt::substract_of_two_vectors::single") +# context("ds.make::expt::substract_of_two_vectors::single") test_that("substract two vectors", { connect.dataset.1() @@ -289,7 +300,7 @@ test_that("substract two vectors", }) -context("ds.make::expt::sum_of_constant::single") +# context("ds.make::expt::sum_of_constant::single") test_that("apply the the sum a vector and a constant value", { connect.dataset.1() @@ -306,7 +317,7 @@ test_that("apply the the sum a vector and a constant value", }) -context("ds.make::expt::substract_of_constant::single") +# context("ds.make::expt::substract_of_constant::single") test_that("substract a constant value to all the values of a vector", { connect.dataset.1() @@ -324,7 +335,7 @@ test_that("substract a constant value to all the values of a vector", }) -context("ds.make::expt::divide_of_constant::single") +# context("ds.make::expt::divide_of_constant::single") test_that("divide a constant value to all the values of a vector", { connect.dataset.1() @@ -341,7 +352,7 @@ test_that("divide a constant value to all the values of a vector", }) -context("ds.make::expt::multiply_of_constant::single") +# context("ds.make::expt::multiply_of_constant::single") test_that("multiply a constant value to all the values of a vector", { connect.dataset.1() @@ -359,7 +370,7 @@ test_that("multiply a constant value to all the values of a vector", }) -context("ds.make::expt::sum_of_constant::multiple") +# context("ds.make::expt::sum_of_constant::multiple") test_that("apply the the sum a vector and a constant value", { connect.all.datasets() @@ -376,7 +387,7 @@ test_that("apply the the sum a vector and a constant value", }) -context("ds.make::expt::substract_of_constant::multiple") +# context("ds.make::expt::substract_of_constant::multiple") test_that("substract a constant value to all the values of a vector", { connect.all.datasets() @@ -394,7 +405,7 @@ test_that("substract a constant value to all the values of a vector", }) -context("ds.make::expt::divide_of_constant::multiple") +# context("ds.make::expt::divide_of_constant::multiple") test_that("divide a constant value to all the values of a vector", { connect.all.datasets() @@ -411,7 +422,7 @@ test_that("divide a constant value to all the values of a vector", }) -context("ds.make::expt::multiply_of_constant::multiple") +# context("ds.make::expt::multiply_of_constant::multiple") test_that("multiply a constant value to all the values of a vector", { connect.all.datasets() diff --git a/tests/testthat/test-expt_bug-ds.rPois.R b/tests/testthat/test-expt_bug-ds.rPois.R index 5e2b808a6..41716ac90 100644 --- a/tests/testthat/test-expt_bug-ds.rPois.R +++ b/tests/testthat/test-expt_bug-ds.rPois.R @@ -1,8 +1,19 @@ +#------------------------------------------------------------------------------- +# Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. +# +# This program and the accompanying materials +# are made available under the terms of the GNU Public License v3.0. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see . +#------------------------------------------------------------------------------- + source("connection_to_datasets/init_testing_datasets.R") source("definition_tests/def-ds.rPois.R") -context("ds.rPois::expt::no seeds::single") +# context("ds.rPois::expt::no seeds::single") test_that("Poisson without seeds", { connect.dataset.1() @@ -15,7 +26,7 @@ test_that("Poisson without seeds", }) -context("ds.rPois::expt::no seeds::multiple") +# context("ds.rPois::expt::no seeds::multiple") test_that("Poisson without seeds", { connect.all.datasets() @@ -29,7 +40,7 @@ test_that("Poisson without seeds", -context("ds.rPois::expt::with seeds::single") +# context("ds.rPois::expt::with seeds::single") test_that("Poisson with seeds", { @@ -44,7 +55,7 @@ test_that("Poisson with seeds", .test.basic.expectation.with.seeds(2^31,'poisson_dist_7') }) -context("ds.rPois::expt::with seeds::multiple") +# context("ds.rPois::expt::with seeds::multiple") test_that("Poisson with seeds", { connect.all.datasets() diff --git a/tests/testthat/test-expt_bug-ds.rUnif.R b/tests/testthat/test-expt_bug-ds.rUnif.R index 845d3fa0f..f026843c8 100644 --- a/tests/testthat/test-expt_bug-ds.rUnif.R +++ b/tests/testthat/test-expt_bug-ds.rUnif.R @@ -1,7 +1,18 @@ +#------------------------------------------------------------------------------- +# Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. +# +# This program and the accompanying materials +# are made available under the terms of the GNU Public License v3.0. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see . +#------------------------------------------------------------------------------- + source("connection_to_datasets/init_testing_datasets.R") source("definition_tests/def-ds.rUnif.R") -context("ds.rUnif::expt::no_seeds::single") +# context("ds.rUnif::expt::no_seeds::single") test_that("basic expectation", { connect.dataset.2() @@ -14,7 +25,7 @@ test_that("basic expectation", .test.basic.expectation(2^31-1,'uniform_dist_6') }) -context("ds.rUnif::expt::no_seeds::multiple") +# context("ds.rUnif::expt::no_seeds::multiple") test_that("basic expectation", { connect.all.datasets() @@ -27,7 +38,7 @@ test_that("basic expectation", .test.basic.expectation(2^31-1,'uniform_dist_6') }) -context("ds.rUnif::expt::seeds::single") +# context("ds.rUnif::expt::seeds::single") test_that("basic expectation", { connect.dataset.2() @@ -40,7 +51,7 @@ test_that("basic expectation", .test.basic.expectation.with.seeds(2^31-1,'uniform_dist_6') }) -context("ds.rUnif::expt::seeds::multiple") +# context("ds.rUnif::expt::seeds::multiple") test_that("basic expectation", { connect.all.datasets() diff --git a/tests/testthat/test-expt_bug-ds.recodeValues.R b/tests/testthat/test-expt_bug-ds.recodeValues.R index 4a35f9b27..4f6bf6599 100644 --- a/tests/testthat/test-expt_bug-ds.recodeValues.R +++ b/tests/testthat/test-expt_bug-ds.recodeValues.R @@ -1,7 +1,18 @@ +#------------------------------------------------------------------------------- +# Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. +# +# This program and the accompanying materials +# are made available under the terms of the GNU Public License v3.0. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see . +#------------------------------------------------------------------------------- + source("connection_to_datasets/init_testing_datasets.R") source("definition_tests/def-ds.recodeValues.R") -context("ds.recodeValues::expt::changes_applied::single::") +# context("ds.recodeValues::expt::changes_applied::single::") test_that("changes must be applied", { @@ -40,7 +51,7 @@ test_that("changes must be applied", }) -context("ds.recodeValues::expt::changes_applied::multiple") +# context("ds.recodeValues::expt::changes_applied::multiple") test_that("changes must be applied", { @@ -81,7 +92,7 @@ test_that("changes must be applied", - context("ds.recodeValues::expt::no_change_applied::single") + # context("ds.recodeValues::expt::no_change_applied::single") test_that("no_change_applied", { connect.dataset.1() @@ -129,7 +140,7 @@ test_that("changes must be applied", }) -context("ds.recodeValues::expt::no_change_applied::multiple") +# context("ds.recodeValues::expt::no_change_applied::multiple") test_that("no_change_applied", { connect.all.datasets() diff --git a/tests/testthat/test-expt_bug-ds.table.R b/tests/testthat/test-expt_bug-ds.table.R index 23844fdf6..1834fca0a 100644 --- a/tests/testthat/test-expt_bug-ds.table.R +++ b/tests/testthat/test-expt_bug-ds.table.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- -# Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -8,10 +9,10 @@ # along with this program. If not, see . #------------------------------------------------------------------------------- -context("ds.table::expt::setup") +# context("ds.table::expt::setup") connect.testing.group.dataset.1() -context("ds.table::expt::single") +# context("ds.table::expt::single") test_that("combined data set", { #PRW AND ALEX WILL WRITE SOME CONNECT AND DISCONNECT FUNCTIONS ONCE WE KNOW THE DATA ARE SUITABLE - TO DO IMPORTANT !!!!!!!! COMPLETELY INEFFICIENT AT THE MOMENT 17/2/2020 diff --git a/tests/testthat/test-expt_dgr-ds.dataFrameSort.R b/tests/testthat/test-expt_dgr-ds.dataFrameSort.R index 251170e72..9ff0bca2b 100644 --- a/tests/testthat/test-expt_dgr-ds.dataFrameSort.R +++ b/tests/testthat/test-expt_dgr-ds.dataFrameSort.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context('ds.dataFrameSort::expt_dgr::setup') +# context('ds.dataFrameSort::expt_dgr::setup') source('connection_to_datasets/init_testing_datasets.R') source('definition_tests/def-ds.dataFrameSort.R') @@ -21,7 +22,7 @@ source('definition_tests/def-ds.dataFrameSort.R') # Tests # -context("ds.dataFrameSort::expt_dgr::multiple::correct_parameter_class") +# context("ds.dataFrameSort::expt_dgr::multiple::correct_parameter_class") test_that('all datasets', { connect.all.datasets() @@ -40,7 +41,7 @@ test_that('all datasets', .test.function.parameters("D","D$INTEGER_ONE_CHANGE",TRUE,"numeric","server.data") }) -context("ds.dataFrameSort::expt_dgr::single::correct_parameter_class") +# context("ds.dataFrameSort::expt_dgr::single::correct_parameter_class") test_that('dataset 2', { connect.dataset.2() @@ -59,7 +60,7 @@ test_that('dataset 2', .test.function.parameters("D","D$INTEGER_ONE_CHANGE",TRUE,"numeric","server.data") }) -context("ds.dataFrameSort::expt_dgr::multiple::incorrect_parameter_class") +# context("ds.dataFrameSort::expt_dgr::multiple::incorrect_parameter_class") test_that('all datasets', { connect.all.datasets() @@ -76,7 +77,7 @@ test_that('all datasets', .test.function.parameters("dataframe","D$INTEGER_ONE_CHANGE",TRUE,"numeric","server.data") }) -context("ds.dataFrameSort::expt_dgr::single::incorrect_parameter_class") +# context("ds.dataFrameSort::expt_dgr::single::incorrect_parameter_class") test_that('dataset 2', { connect.dataset.2() @@ -93,7 +94,7 @@ test_that('dataset 2', .test.function.parameters("dataframe","D$INTEGER_ONE_CHANGE",TRUE,"numeric","server.data") }) -context("ds.dataFrameSort::expt_dgr::multiple::df::creation") +# context("ds.dataFrameSort::expt_dgr::multiple::df::creation") test_that('all datasets', { connect.all.datasets() @@ -110,7 +111,7 @@ test_that('all datasets', .test.data.frame.creation("D","INTEGER_ONE_CHANGE",TRUE,"numeric","server.data") }) -context("ds.dataFrameSort::expt_dgr::single::df::creation") +# context("ds.dataFrameSort::expt_dgr::single::df::creation") test_that('dataset 3', { connect.dataset.3() @@ -127,7 +128,7 @@ test_that('dataset 3', .test.data.frame.creation("D","INTEGER_ONE_CHANGE",FALSE,"alphabetic","server.data") }) -context("ds.dataFrameSort::expt_dgr::multiple::numeric::ascending") +# context("ds.dataFrameSort::expt_dgr::multiple::numeric::ascending") test_that('all datasets', { connect.all.datasets() @@ -148,7 +149,7 @@ test_that('all datasets', #.test.data.frame.sorting("D","CHARACTER",FALSE,"numeric","server.data",all.local.values) }) -context("ds.dataFrameSort::expt_dgr::single::numeric::ascending") +# context("ds.dataFrameSort::expt_dgr::single::numeric::ascending") test_that('dataset 1', { connect.dataset.1() @@ -169,7 +170,7 @@ test_that('dataset 1', #.test.data.frame.sorting("D","CHARACTER",FALSE,"numeric","server.data",all.local.values) }) -context("ds.dataFrameSort::expt_dgr::multiple::numeric::descending") +# context("ds.dataFrameSort::expt_dgr::multiple::numeric::descending") test_that('all datasets', { connect.all.datasets() @@ -192,7 +193,7 @@ test_that('all datasets', }) -context("ds.dataFrameSort::expt_dgr::single::numeric::descending") +# context("ds.dataFrameSort::expt_dgr::single::numeric::descending") test_that('dataset 1', { connect.dataset.1() @@ -214,7 +215,7 @@ test_that('dataset 1', }) -context("ds.dataFrameSort::expt_dgr::multiple::alphabetic::ascending") +# context("ds.dataFrameSort::expt_dgr::multiple::alphabetic::ascending") test_that('all datasets', { #connect.all.datasets() @@ -242,7 +243,7 @@ test_that('all datasets', #.test.data.frame.sorting("D","CHARACTER",FALSE,"alphabetic","server.data",all.local.values) }) -context("ds.dataFrameSort::expt_dgr::single::alphabetic::ascending") +# context("ds.dataFrameSort::expt_dgr::single::alphabetic::ascending") test_that('dataset 2', { #connect.dataset.2() @@ -270,7 +271,7 @@ test_that('dataset 2', #.test.data.frame.sorting("D","CHARACTER",FALSE,"alphabetic","server.data",all.local.values) }) -context("ds.dataFrameSort::expt_dgr::multiple::alphabetic::descending") +# context("ds.dataFrameSort::expt_dgr::multiple::alphabetic::descending") test_that('all datasets', { #connect.all.datasets() @@ -296,7 +297,7 @@ test_that('all datasets', #.test.data.frame.sorting("D","CHARACTER",TRUE,"alphabetic","server.data",all.local.values) }) -context("ds.dataFrameSort::expt_dgr::single::alphabetic::descending") +# context("ds.dataFrameSort::expt_dgr::single::alphabetic::descending") test_that('dataset 3', { #connect.dataset.3() @@ -326,10 +327,10 @@ test_that('dataset 3', # Shutdown # -context('ds.dataFrameSort::expt_dgr::shutdown') +# context('ds.dataFrameSort::expt_dgr::shutdown') # # Done # -context('ds.dataFrameSort::expt_dgr::done') +# context('ds.dataFrameSort::expt_dgr::done') diff --git a/tests/testthat/test-expt_dgr-ds.dataFrameSubset.R b/tests/testthat/test-expt_dgr-ds.dataFrameSubset.R index 222d41bd5..278403ec9 100644 --- a/tests/testthat/test-expt_dgr-ds.dataFrameSubset.R +++ b/tests/testthat/test-expt_dgr-ds.dataFrameSubset.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.dataFrameSubset::expt_dgr::setup") +# context("ds.dataFrameSubset::expt_dgr::setup") source("connection_to_datasets/init_testing_datasets.R") source("definition_tests/def-ds.dataFrameSubset.R") @@ -21,7 +22,7 @@ source("definition_tests/def-ds.dataFrameSubset.R") # Tests # -context("ds.dataFrameSubset::expt_dgr::multiple::parameter_class") +# context("ds.dataFrameSubset::expt_dgr::multiple::parameter_class") test_that('all datasets', { connect.all.datasets() @@ -41,7 +42,7 @@ test_that('all datasets', }) -context("ds.dataFrameSubset::expt_dgr::single::parameter_class") +# context("ds.dataFrameSubset::expt_dgr::single::parameter_class") test_that('dataset 1', { connect.dataset.1() @@ -61,7 +62,7 @@ test_that('dataset 1', }) -context("ds.dataFrameSubset::expt_dgr::multiple::all_columns") +# context("ds.dataFrameSubset::expt_dgr::multiple::all_columns") test_that('all datasets', { connect.all.datasets() @@ -73,7 +74,7 @@ test_that('all datasets', .test.data.frame.creation("D","POSITIVE_NUMERIC","NON_NEGATIVE_NUMERIC","<=","subset.server") }) -context("ds.dataFrameSubset::expt_dgr::single::all_columns") +# context("ds.dataFrameSubset::expt_dgr::single::all_columns") test_that('dataset 2', { connect.dataset.2() @@ -85,7 +86,7 @@ test_that('dataset 2', .test.data.frame.creation("D","POSITIVE_NUMERIC","NON_NEGATIVE_NUMERIC","<=","subset.server") }) -context("ds.dataFrameSubset::expt_dgr::multiple::all_columns::subset_by_rows") +# context("ds.dataFrameSubset::expt_dgr::multiple::all_columns::subset_by_rows") test_that("all datasets", { connect.all.datasets() @@ -104,7 +105,7 @@ test_that("all datasets", subset.by.rows("D","POSITIVE_NUMERIC","NON_NEGATIVE_NUMERIC","<=",FALSE,"subset.server",local.df.list) }) -context("ds.dataFrameSubset::expt_dgr::single::all_columns::subset_by_rows") +# context("ds.dataFrameSubset::expt_dgr::single::all_columns::subset_by_rows") test_that("dataset 3", { connect.dataset.3() @@ -123,7 +124,7 @@ test_that("dataset 3", subset.by.rows("D","POSITIVE_NUMERIC","NON_NEGATIVE_NUMERIC","<=",FALSE,"subset.server",local.df.list) }) -context("ds.dataFrameSubset::expt_dgr::multiple::subset_by_rows_columns") +# context("ds.dataFrameSubset::expt_dgr::multiple::subset_by_rows_columns") test_that("all datasets", { connect.all.datasets() @@ -142,7 +143,7 @@ test_that("all datasets", subset.by.rows.cols("D","POSITIVE_NUMERIC","NON_NEGATIVE_NUMERIC",1:15,"<=",FALSE,"subset.server",local.df.list) }) -context("ds.dataFrameSubset::expt_dgr::single::subset_by_rows_columns") +# context("ds.dataFrameSubset::expt_dgr::single::subset_by_rows_columns") test_that("dataset 1", { connect.dataset.1() @@ -162,7 +163,7 @@ test_that("dataset 1", }) -context("ds.dataFrameSubset::expt_dgr::multiple::subset_by_rows_columns") +# context("ds.dataFrameSubset::expt_dgr::multiple::subset_by_rows_columns") test_that("all datasets", { connect.all.datasets() @@ -180,7 +181,7 @@ test_that("all datasets", subset.by.rows.cols("D","POSITIVE_NUMERIC","NON_NEGATIVE_NUMERIC",1:15,"<=",TRUE,"subset.server",local.df.list) subset.by.rows.cols("D","POSITIVE_NUMERIC","NON_NEGATIVE_NUMERIC",1:15,"<=",FALSE,"subset.server",local.df.list) }) -context("ds.dataFrameSubset::expt_dgr::single::subset_by_rows_columns") +# context("ds.dataFrameSubset::expt_dgr::single::subset_by_rows_columns") test_that("dataset 2", { connect.dataset.2() @@ -199,7 +200,7 @@ test_that("dataset 2", subset.by.rows.cols("D","POSITIVE_NUMERIC","NON_NEGATIVE_NUMERIC",1:15,"<=",FALSE,"subset.server",local.df.list) }) -context("ds.dataFrameSubset::expt_dgr::multiple::all_rows_subset_by_columns") +# context("ds.dataFrameSubset::expt_dgr::multiple::all_rows_subset_by_columns") test_that("all datasets", { connect.all.datasets() local.df.list<-list(ds.test_env$local.values.1,ds.test_env$local.values.2,ds.test_env$local.values.3) @@ -211,7 +212,7 @@ test_that("all datasets", subset.by.cols("D","NON_NEGATIVE_NUMERIC",c(1:7,13:16),FALSE,"subset.server",local.df.list) }) -context("ds.dataFrameSubset::expt_dgr::multiple::all_rows_subset_by_columns") +# context("ds.dataFrameSubset::expt_dgr::multiple::all_rows_subset_by_columns") test_that("dataset 3", { connect.dataset.3() local.df.list<-list(ds.test_env$local.values.3) diff --git a/tests/testthat/test-math-ds.mean.R b/tests/testthat/test-math-ds.mean.R index 601e6a502..4c2a15593 100644 --- a/tests/testthat/test-math-ds.mean.R +++ b/tests/testthat/test-math-ds.mean.R @@ -1,9 +1,18 @@ +#------------------------------------------------------------------------------- +# Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. +# +# This program and the accompanying materials +# are made available under the terms of the GNU Public License v3.0. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see . +#------------------------------------------------------------------------------- + source("connection_to_datasets/init_testing_datasets.R") source("definition_tests/def-ds.mean.R") - - -context("ds.mean::math::residual::multiple") +# context("ds.mean::math::residual::multiple") test_that("residual deviation tends to 0", { connect.all.datasets() @@ -27,7 +36,7 @@ test_that("residual deviation tends to 0", }) -context("ds.mean::math::residual::multiple") +# context("ds.mean::math::residual::multiple") test_that("residual deviation tends to 0", { connect.all.datasets() @@ -53,7 +62,7 @@ test_that("residual deviation tends to 0", }) -context("ds.mean::math::location_parameter::single") +# context("ds.mean::math::location_parameter::single") test_that("mean(X+a) - mean(X) = a", { connect.dataset.1() @@ -68,7 +77,7 @@ test_that("mean(X+a) - mean(X) = a", .test.location.parameter('D$NEGATIVE_NUMERIC') }) -context("ds.mean::math::location_parameter::multiple") +# context("ds.mean::math::location_parameter::multiple") test_that("mean(X+a) - mean(X) = a", { connect.all.datasets() @@ -86,7 +95,7 @@ test_that("mean(X+a) - mean(X) = a", -context("ds.mean::math::scale::multiple") +# context("ds.mean::math::scale::multiple") test_that("mean(X+a) / mean(X) = a", { connect.all.datasets() @@ -101,7 +110,7 @@ test_that("mean(X+a) / mean(X) = a", .test.scale('D$NEGATIVE_NUMERIC') }) -context("ds.mean::math::scale::single") +# context("ds.mean::math::scale::single") test_that("mean(X*a) / mean(X) = a", { connect.dataset.1() diff --git a/tests/testthat/test-math-ds.var.R b/tests/testthat/test-math-ds.var.R index 47a7270d7..e281c5d62 100644 --- a/tests/testthat/test-math-ds.var.R +++ b/tests/testthat/test-math-ds.var.R @@ -1,7 +1,18 @@ +#------------------------------------------------------------------------------- +# Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. +# +# This program and the accompanying materials +# are made available under the terms of the GNU Public License v3.0. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see . +#------------------------------------------------------------------------------- + source("connection_to_datasets/init_testing_datasets.R") source("definition_tests/def-ds.var.R") -context("ds.var::math::positive_result::multiple") +# context("ds.var::math::positive_result::multiple") test_that("variance >=0", { connect.all.datasets() @@ -25,7 +36,7 @@ test_that("variance >=0", }) -context("ds.var::math::positive_result::single") +# context("ds.var::math::positive_result::single") test_that("variance >=0", { connect.dataset.1() @@ -49,7 +60,7 @@ test_that("variance >=0", }) -context("ds.var::math::square_root_std::single") +# context("ds.var::math::square_root_std::single") test_that("variance is to the power of 2 of the standard deviation", { connect.dataset.1() @@ -65,7 +76,7 @@ test_that("variance is to the power of 2 of the standard deviation", }) -context("ds.var::math::square_root_std::multiple") +# context("ds.var::math::square_root_std::multiple") test_that("variance is to the power of 2 of the standard deviation", { connect.all.datasets() @@ -88,7 +99,7 @@ test_that("variance is to the power of 2 of the standard deviation", .test.standard.dev.split('D$NEGATIVE_NUMERIC',ds.test_env$local.values.1[,'NEGATIVE_NUMERIC'],ds.test_env$local.values.2[,'NEGATIVE_NUMERIC'],ds.test_env$local.values.3[,'NEGATIVE_NUMERIC']) }) -context("ds.var::math::location::parameter::single") +# context("ds.var::math::location::parameter::single") test_that("var (X+a) = Var(X)", { connect.dataset.1() @@ -102,7 +113,7 @@ test_that("var (X+a) = Var(X)", .test.location.parameter('D$NEGATIVE_NUMERIC') }) -context("ds.var::math::location::parameter::multiple") +# context("ds.var::math::location::parameter::multiple") test_that("var (X+a) = Var(X)", { connect.all.datasets() @@ -116,7 +127,7 @@ test_that("var (X+a) = Var(X)", .test.location.parameter('D$NEGATIVE_NUMERIC') }) -context("ds.var::math::scale::single") +# context("ds.var::math::scale::single") test_that("var (aX) = a^2Var(X)", { connect.dataset.1() @@ -130,7 +141,7 @@ test_that("var (aX) = a^2Var(X)", .test.scale('D$NEGATIVE_NUMERIC') }) -context("ds.var::math::scale::multiple") +# context("ds.var::math::scale::multiple") test_that("var (aX) = a^2Var(X)", { connect.all.datasets() @@ -143,5 +154,3 @@ test_that("var (aX) = a^2Var(X)", .test.scale('D$POSITIVE_NUMERIC') .test.scale('D$NEGATIVE_NUMERIC') }) - - diff --git a/tests/testthat/test-math_bug-ds.asFactor.R b/tests/testthat/test-math_bug-ds.asFactor.R index def587df6..cb44c2fa1 100644 --- a/tests/testthat/test-math_bug-ds.asFactor.R +++ b/tests/testthat/test-math_bug-ds.asFactor.R @@ -1,7 +1,19 @@ +#------------------------------------------------------------------------------- +# Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. +# +# This program and the accompanying materials +# are made available under the terms of the GNU Public License v3.0. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see . +#------------------------------------------------------------------------------- +# + source("connection_to_datasets/init_testing_datasets.R") source("definition_tests/def-ds.asFactor.R") -context("ds.asFactor::math::multiple") +# context("ds.asFactor::math::multiple") test_that("every factor should be unique", { connect.all.datasets() @@ -16,7 +28,7 @@ test_that("every factor should be unique", .test.uniqueness('D$FACTOR_INTEGER', 'FACTOR_INT.f') }) -context("ds.asFactor::math::multiple") +# context("ds.asFactor::math::multiple") test_that("every factor should be unique", { connect.dataset.1() diff --git a/tests/testthat/test-math_bug-ds.make.R b/tests/testthat/test-math_bug-ds.make.R index 4a5de5d98..2823af009 100644 --- a/tests/testthat/test-math_bug-ds.make.R +++ b/tests/testthat/test-math_bug-ds.make.R @@ -1,8 +1,18 @@ +#------------------------------------------------------------------------------- +# Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. +# +# This program and the accompanying materials +# are made available under the terms of the GNU Public License v3.0. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see . +#------------------------------------------------------------------------------- + source("connection_to_datasets/init_testing_datasets.R") source("definition_tests/def-ds.make.R") - -context("ds.make::math::transformation::multiple") +# context("ds.make::math::transformation::multiple") test_that("transformation", { connect.all.datasets() diff --git a/tests/testthat/test-math_bug-ds.rPois.R b/tests/testthat/test-math_bug-ds.rPois.R index 4aa6f803d..b920cfff0 100644 --- a/tests/testthat/test-math_bug-ds.rPois.R +++ b/tests/testthat/test-math_bug-ds.rPois.R @@ -1,9 +1,20 @@ +#------------------------------------------------------------------------------- +# Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. +# +# This program and the accompanying materials +# are made available under the terms of the GNU Public License v3.0. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see . +#------------------------------------------------------------------------------- + source("connection_to_datasets/init_testing_datasets.R") source("definition_tests/def-ds.rPois.R") random.number <- as.integer(as.POSIXct(Sys.time(), "GMT")) -context("ds.rPois::math::lambda equal mean and var::single") +# context("ds.rPois::math::lambda equal mean and var::single") test_that("lamdba == mean and lambda == var", { connect.dataset.1() @@ -14,7 +25,7 @@ test_that("lamdba == mean and lambda == var", }) -context("ds.rPois::math::lambda equal mean and var::multiple") +# context("ds.rPois::math::lambda equal mean and var::multiple") test_that("lamdba == mean and lambda == var", { connect.all.datasets() @@ -25,7 +36,7 @@ test_that("lamdba == mean and lambda == var", }) -context("ds.rPois::math::distributions comparison::multiple") +# context("ds.rPois::math::distributions comparison::multiple") test_that("changes in distribution", { connect.all.datasets() @@ -37,7 +48,7 @@ test_that("changes in distribution", .test.dispersions.stats.diff.distribution(seed/1000, c(1900),seed,c(1100)) }) -context("ds.rPois::math::distributions comparison::single") +# context("ds.rPois::math::distributions comparison::single") test_that("changes in distribution", { connect.dataset.3() diff --git a/tests/testthat/test-math_bug-ds.rUnif.R b/tests/testthat/test-math_bug-ds.rUnif.R index 123314a9f..7ca2da888 100644 --- a/tests/testthat/test-math_bug-ds.rUnif.R +++ b/tests/testthat/test-math_bug-ds.rUnif.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -13,7 +14,7 @@ source("definition_tests/def-ds.rUnif.R") random.number <- as.integer(as.POSIXct(Sys.time(), "GMT")) -context("ds.rUnif::math::mean_variance::single") +# context("ds.rUnif::math::mean_variance::single") test_that("mean_variance", { connect.dataset.1() @@ -23,7 +24,7 @@ test_that("mean_variance", .test.range.values(-200,-100,"uniform_3",seed) }) -context("ds.rUnif::math::distributions comparison::single") +# context("ds.rUnif::math::distributions comparison::single") test_that("changes in distribution", { connect.dataset.3() @@ -37,7 +38,7 @@ test_that("changes in distribution", }) -context("ds.rUnif::math::distributions comparison::multiple") +# context("ds.rUnif::math::distributions comparison::multiple") test_that("changes in distribution", { connect.all.datasets() diff --git a/tests/testthat/test-math_bug-ds.recodeValues.R b/tests/testthat/test-math_bug-ds.recodeValues.R index f34df1ea3..b5e452398 100644 --- a/tests/testthat/test-math_bug-ds.recodeValues.R +++ b/tests/testthat/test-math_bug-ds.recodeValues.R @@ -1,8 +1,18 @@ +#------------------------------------------------------------------------------- +# Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. +# +# This program and the accompanying materials +# are made available under the terms of the GNU Public License v3.0. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see . +#------------------------------------------------------------------------------- + source("connection_to_datasets/init_testing_datasets.R") source("definition_tests/def-ds.recodeValues.R") - -context("ds.recodeValues::math::single") +# context("ds.recodeValues::math::single") test_that("difference", { connect.dataset.1() @@ -65,7 +75,7 @@ test_that("difference", -context("ds.recodeValues::math::multiple") +# context("ds.recodeValues::math::multiple") test_that("difference", { connect.all.datasets() diff --git a/tests/testthat/test-math_bug-ds.table.R b/tests/testthat/test-math_bug-ds.table.R index 4f221c647..db0bd51ee 100644 --- a/tests/testthat/test-math_bug-ds.table.R +++ b/tests/testthat/test-math_bug-ds.table.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -9,7 +10,7 @@ #------------------------------------------------------------------------------- -context("ds.table::math::row and col proportions::multiple") +# context("ds.table::math::row and col proportions::multiple") test_that("row and col proportions sum to 1", { diff --git a/tests/testthat/test-math_dgr-ds.dataFrameSort.R b/tests/testthat/test-math_dgr-ds.dataFrameSort.R index e7d68279a..21d166472 100644 --- a/tests/testthat/test-math_dgr-ds.dataFrameSort.R +++ b/tests/testthat/test-math_dgr-ds.dataFrameSort.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context('ds.dataFrameSort::expt_dgr::setup') +# context('ds.dataFrameSort::expt_dgr::setup') source('connection_to_datasets/init_testing_datasets.R') source('definition_tests/def-ds.dataFrameSort.R') @@ -21,7 +22,7 @@ source('definition_tests/def-ds.dataFrameSort.R') # Tests # -context("ds.dataFrameSort::math_dgr::closure::multiple") +# context("ds.dataFrameSort::math_dgr::closure::multiple") test_that('server set %in% local set', { connect.all.datasets() @@ -43,7 +44,7 @@ test_that('server set %in% local set', }) -context("ds.dataFrameSort::math_dgr::closure::simple") +# context("ds.dataFrameSort::math_dgr::closure::simple") test_that('server set %in% local set', { connect.dataset.1() diff --git a/tests/testthat/test-math_dgr-ds.dataFrameSubset.R b/tests/testthat/test-math_dgr-ds.dataFrameSubset.R index 39ac712ba..c9a8e176e 100644 --- a/tests/testthat/test-math_dgr-ds.dataFrameSubset.R +++ b/tests/testthat/test-math_dgr-ds.dataFrameSubset.R @@ -1,3 +1,10 @@ +#------------------------------------------------------------------------------- +# Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. +# +# This program and the accompanying materials +# are made available under the terms of the GNU Public License v3.0. +# # You should have received a copy of the GNU General Public License # along with this program. If not, see . #------------------------------------------------------------------------------- @@ -6,7 +13,7 @@ # Set up # -context('ds.dataFrameSubset::expt_dgr::setup') +# context('ds.dataFrameSubset::expt_dgr::setup') source('connection_to_datasets/init_testing_datasets.R') source('definition_tests/def-ds.dataFrameSubset.R') @@ -15,7 +22,7 @@ source('definition_tests/def-ds.dataFrameSubset.R') # Tests # -context("ds.dataFrameSubset::math_dgr::closure::multiple") +# context("ds.dataFrameSubset::math_dgr::closure::multiple") test_that('server set %in% local set', { connect.all.datasets() @@ -33,7 +40,7 @@ test_that('server set %in% local set', # .closure.test("D","POSITIVE_NUMERIC","NON_NEGATIVE_NUMERIC","<=",FALSE,"subset.server",local.df.list) }) -context("ds.dataFrameSubset::math_dgr::closure::simple") +# context("ds.dataFrameSubset::math_dgr::closure::simple") test_that('server set %in% local set', { connect.dataset.2() diff --git a/tests/testthat/test-math_dgr-ds.skewness.R b/tests/testthat/test-math_dgr-ds.skewness.R index d6c8ab219..d743de0b1 100644 --- a/tests/testthat/test-math_dgr-ds.skewness.R +++ b/tests/testthat/test-math_dgr-ds.skewness.R @@ -1,7 +1,18 @@ +#------------------------------------------------------------------------------- +# Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. +# +# This program and the accompanying materials +# are made available under the terms of the GNU Public License v3.0. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see . +#------------------------------------------------------------------------------- + source("connection_to_datasets/init_testing_datasets.R") source("definition_tests/def-ds.skewness.R") -context("ds.skewness::math_dgr::mean.median.mode::multiple") +# context("ds.skewness::math_dgr::mean.median.mode::multiple") test_that("skewness >0 & mode0 & mode0 & Q3-Q2>Q2-Q1 or skewness<0 & Q3-Q2 appears valid in all sources") }) -context("ds.dataFrameSubset::smk::create a subset dataframe, based on scalar") +# context("ds.dataFrameSubset::smk::create a subset dataframe, based on scalar") test_that("dataFrameSubset_exists scalar", { myvectors <- c('D$LAB_TSC', 'D$LAB_HDL', 'D$PM_BMI_CATEGORICAL') ds.dataFrame(x=myvectors, newobj="unsubset_df") @@ -100,7 +101,7 @@ test_that("dataFrameSubset_exists scalar", { # Done # -context("ds.dataFrameSubset::smk::shutdown") +# context("ds.dataFrameSubset::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "unsubset_df", "subset_df")) @@ -108,4 +109,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.dataFrameSubset::smk::down") +# context("ds.dataFrameSubset::smk::down") diff --git a/tests/testthat/test-smk-ds.dim.R b/tests/testthat/test-smk-ds.dim.R index c1d1d9b5a..3c8caf0e1 100644 --- a/tests/testthat/test-smk-ds.dim.R +++ b/tests/testthat/test-smk-ds.dim.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.dim::smk::setup") +# context("ds.dim::smk::setup") connect.studies.dataset.cnsim(list("LAB_TSC")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.dim::smk") +# context("ds.dim::smk") test_that("simple dim, both", { dim.res <- ds.dim('D', type='both') @@ -43,7 +44,7 @@ test_that("simple dim, both", { expect_equal(dim.res$`dimensions of D in combined studies`[[2]], 1) }) -context("ds.dim::smk") +# context("ds.dim::smk") test_that("simple dim, split", { dim.res <- ds.dim('D', type='split') @@ -59,7 +60,7 @@ test_that("simple dim, split", { expect_equal(dim.res$`dimensions of D in sim3`[[2]], 1) }) -context("ds.dim::smk") +# context("ds.dim::smk") test_that("simple dim, combine", { dim.res <- ds.dim('D', type='combine') @@ -73,7 +74,7 @@ test_that("simple dim, combine", { # Done # -context("ds.dim::smk::shutdown") +# context("ds.dim::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -81,4 +82,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.dim::smk::done") +# context("ds.dim::smk::done") diff --git a/tests/testthat/test-smk-ds.dmtC2S.R b/tests/testthat/test-smk-ds.dmtC2S.R index fb56fb435..5a1ba2737 100644 --- a/tests/testthat/test-smk-ds.dmtC2S.R +++ b/tests/testthat/test-smk-ds.dmtC2S.R @@ -1,6 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. -# Copyright (c) 2022 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -13,7 +13,7 @@ # Set up # -context("ds.dmtC2S::smk::setup") +# context("ds.dmtC2S::smk::setup") connect.studies.dataset.cnsim(list("LAB_TSC")) @@ -25,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.dmtC2S::smk::data.frame") +# context("ds.dmtC2S::smk::data.frame") test_that("simple dmtC2S - data.frame", { a <- data.frame(c(1, 2, 3, 4)) b <- data.frame(c(2, 3, 4, 1)) @@ -44,7 +44,7 @@ test_that("simple dmtC2S - data.frame", { expect_true(all(c("data.frame") %in% res.class$sim3)) }) -context("ds.dmtC2S::smk::matrix") +# context("ds.dmtC2S::smk::matrix") test_that("simple dmtC2S - matrix", { a <- c(1, 2, 3, 4, 2, 3, 4, 1, 3) cm <- matrix(a, nrow = 3, ncol = 3, byrow = TRUE) @@ -61,7 +61,7 @@ test_that("simple dmtC2S - matrix", { expect_true(all(c("matrix", "array") %in% res.class$sim3)) }) -context("ds.dmtC2S::smk::tibble") +# context("ds.dmtC2S::smk::tibble") test_that("simple dmtC2S - tibble", { a <- data.frame(c(1, 2, 3, 4)) b <- data.frame(c(2, 3, 4, 1)) @@ -84,7 +84,7 @@ test_that("simple dmtC2S - tibble", { # Done # -context("ds.dmtC2S::smk::shutdown") +# context("ds.dmtC2S::smk::shutdown") test_that("setup", { ds_expect_variables(c("D", "dataframe.newobj", "matrix.newobj", "tibble.newobj")) @@ -92,4 +92,4 @@ test_that("setup", { disconnect.studies.dataset.cnsim() -context("ds.dmtC2S::smk::done") +# context("ds.dmtC2S::smk::done") diff --git a/tests/testthat/test-smk-ds.elspline.R b/tests/testthat/test-smk-ds.elspline.R index 72753d624..aa8d3d787 100644 --- a/tests/testthat/test-smk-ds.elspline.R +++ b/tests/testthat/test-smk-ds.elspline.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.elspline::smk::setup") +# context("ds.elspline::smk::setup") connect.studies.dataset.cnsim(list("LAB_TRIG", "PM_BMI_CONTINUOUS")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.elspline::smk::test1") +# context("ds.elspline::smk::test1") test_that("elspline", { ds.elspline(x="D$PM_BMI_CONTINUOUS", n=3, newobj="elsplineDS", datasources=ds.test_env$connections) @@ -74,7 +75,7 @@ test_that("elspline", { }) -context("ds.elspline::smk::test2") +# context("ds.elspline::smk::test2") test_that("elspline", { ds.elspline(x="D$PM_BMI_CONTINUOUS", n=5, newobj="elsplineDS2", datasources=ds.test_env$connections) @@ -132,7 +133,7 @@ test_that("elspline", { # Done # -context("ds.elspline::smk::shutdown") +# context("ds.elspline::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "elsplineDS", "elsplineDS2", "LAB_TRIG")) @@ -140,4 +141,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.elspline::smk::done") +# context("ds.elspline::smk::done") diff --git a/tests/testthat/test-smk-ds.exists.R b/tests/testthat/test-smk-ds.exists.R index 4590bbe44..5f95ea242 100644 --- a/tests/testthat/test-smk-ds.exists.R +++ b/tests/testthat/test-smk-ds.exists.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.exists::smk::setup") +# context("ds.exists::smk::setup") connect.studies.dataset.cnsim(list("LAB_TSC")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.exists::smk") +# context("ds.exists::smk") test_that("simple exists", { res <- ds.exists("no_exists_obj") @@ -39,7 +40,7 @@ test_that("simple exists", { # ds.exists(...) can't be used to check within environment -context("ds.exists::smk") +# context("ds.exists::smk") test_that("simple exists, with dollar", { res <- ds.exists('D$LAB_TSC') @@ -52,7 +53,7 @@ test_that("simple exists, with dollar", { expect_equal(res$sim3, FALSE) }) -context("ds.exists::smk") +# context("ds.exists::smk") test_that("simple exists", { ds.assign('D$LAB_TSC', 'exists_obj') @@ -71,7 +72,7 @@ test_that("simple exists", { # Done # -context("ds.exists::smk::shutdown") +# context("ds.exists::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "exists_obj")) @@ -79,4 +80,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.exists::smk::done") +# context("ds.exists::smk::done") diff --git a/tests/testthat/test-smk-ds.exp.R b/tests/testthat/test-smk-ds.exp.R index af09ede61..fa850fb81 100644 --- a/tests/testthat/test-smk-ds.exp.R +++ b/tests/testthat/test-smk-ds.exp.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.exp::smk::setup") +# context("ds.exp::smk::setup") connect.studies.dataset.cnsim(list("LAB_TSC")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.exp::smk") +# context("ds.exp::smk") test_that("simple exp", { res1 <- ds.exp("D$LAB_TSC", newobj="exp1_obj") @@ -81,7 +82,7 @@ test_that("simple exp", { # Done # -context("ds.exp::smk::shutdown") +# context("ds.exp::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "exp1_obj", "new_data", "exp2_obj")) @@ -89,4 +90,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.exp::smk::done") +# context("ds.exp::smk::done") diff --git a/tests/testthat/test-smk-ds.gamlss.R b/tests/testthat/test-smk-ds.gamlss.R index c9c084e44..1e4ad232c 100644 --- a/tests/testthat/test-smk-ds.gamlss.R +++ b/tests/testthat/test-smk-ds.gamlss.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.gamlss::smk::setup") +# context("ds.gamlss::smk::setup") connect.studies.dataset.gamlss(list("e3_bw", "e3_gac_None", "hs_zbmi_who", "hs_child_age_None", "h_mbmi_None", "hs_correct_raven", "hs_wgtgain_None")) @@ -25,7 +26,7 @@ test_that("setup", { # Tests # -context("ds.gamlss::smk::mod1") +# context("ds.gamlss::smk::mod1") test_that("gamlss, birth weight", { model_e3_bw.DS <- ds.gamlss(formula = 'e3_bw ~ e3_gac_None', sigma.formula = 'e3_bw ~ e3_gac_None', @@ -111,7 +112,7 @@ test_that("gamlss, birth weight", { expect_equal(as.numeric(model_e3_bw.DS$study1$centiles[9,'per']), 99.3410214, tolerance=1e-7) }) -context("ds.gamlss::smk::mod2") +# context("ds.gamlss::smk::mod2") test_that("gamlss, Z BMI", { model_zbmi_who.DS <- ds.gamlss(formula = 'hs_zbmi_who ~ hs_child_age_None+h_mbmi_None', sigma.formula = 'hs_zbmi_who ~ hs_child_age_None', @@ -199,7 +200,7 @@ test_that("gamlss, Z BMI", { }) -context("ds.gamlss::smk::mod3") +# context("ds.gamlss::smk::mod3") test_that("gamlss, RAVEN TEST", { ds.dataFrameSort(df.name = 'D', sort.key.name = 'D$hs_correct_raven', newobj = 'D2') @@ -291,7 +292,7 @@ test_that("gamlss, RAVEN TEST", { expect_equal(as.numeric(model_correct_raven.DS$study1$centiles[9,'per']), 100.000000, tolerance=1e-7) }) -context("ds.gamlss::smk::mod4") +# context("ds.gamlss::smk::mod4") test_that("gamlss, WEIGHT GAIN", { model_wgtgain.DS <- ds.gamlss(formula = 'hs_wgtgain_None ~ (e3_bw)', sigma.formula = 'hs_wgtgain_None ~ (e3_bw)', @@ -381,7 +382,7 @@ test_that("gamlss, WEIGHT GAIN", { # Done # -context("ds.gamlss::smk::shutdown") +# context("ds.gamlss::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "D2", "z_scores_e3_bw", "z_scores_hs_correct_raven", "z_scores_hs_wgtgain_None", @@ -390,4 +391,4 @@ test_that("shutdown", { disconnect.studies.dataset.gamlss() -context("ds.gamlss::smk::done") +# context("ds.gamlss::smk::done") diff --git a/tests/testthat/test-smk-ds.getWGSR.R b/tests/testthat/test-smk-ds.getWGSR.R index b11e59993..c5034a717 100644 --- a/tests/testthat/test-smk-ds.getWGSR.R +++ b/tests/testthat/test-smk-ds.getWGSR.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.getWGSR::smk::setup") +# context("ds.getWGSR::smk::setup") connect.studies.dataset.anthro(list("age", "sex", "weight", "height", "muac")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.getWGSR::smk") +# context("ds.getWGSR::smk") test_that("simple getWGSR", { res <- ds.getWGSR('D$sex', 'D$weight', 'D$height', 'wfh', newobj='newobj.getwgsr') @@ -61,7 +62,7 @@ test_that("simple getWGSR", { # Done # -context("ds.getWGSR::smk::shutdown") +# context("ds.getWGSR::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "newobj.getwgsr")) @@ -69,4 +70,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.getWGSR::smk::done") +# context("ds.getWGSR::smk::done") diff --git a/tests/testthat/test-smk-ds.glm-binomial.R b/tests/testthat/test-smk-ds.glm-binomial.R index 133a93e18..666188efd 100644 --- a/tests/testthat/test-smk-ds.glm-binomial.R +++ b/tests/testthat/test-smk-ds.glm-binomial.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.glm::smk::binomial::setup") +# context("ds.glm::smk::binomial::setup") connect.studies.dataset.cnsim(list("DIS_DIAB", "GENDER", "PM_BMI_CONTINUOUS", "LAB_HDL")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.glm::smk::binomial") +# context("ds.glm::smk::binomial") test_that("glm_binomial", { res <- ds.glm('D$DIS_DIAB~D$GENDER*D$PM_BMI_CONTINUOUS+D$LAB_HDL', family="binomial", checks=FALSE) @@ -50,7 +51,7 @@ test_that("glm_binomial", { expect_equal(res$output.information, "SEE TOP OF OUTPUT FOR INFORMATION ON MISSING DATA AND ERROR MESSAGES") }) -context("ds.glm::smk::binomial, with check") +# context("ds.glm::smk::binomial, with check") test_that("glm_binomial, with check", { expect_warning(res <- ds.glm('D$DIS_DIAB~D$GENDER*D$PM_BMI_CONTINUOUS+D$LAB_HDL', family="binomial", checks=TRUE), "NAs introduced by coercion") @@ -80,7 +81,7 @@ test_that("glm_binomial, with check", { # Done # -context("ds.glm::smk::binomial::shutdown") +# context("ds.glm::smk::binomial::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "DIS_DIAB", "GENDER", "LAB_HDL", "PM_BMI_CONTINUOUS")) @@ -88,4 +89,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.glm::smk::binomial::done") +# context("ds.glm::smk::binomial::done") diff --git a/tests/testthat/test-smk-ds.glm-gaussian.R b/tests/testthat/test-smk-ds.glm-gaussian.R index f482d54b7..569fbdd91 100644 --- a/tests/testthat/test-smk-ds.glm-gaussian.R +++ b/tests/testthat/test-smk-ds.glm-gaussian.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.glm::smk::gaussian::setup") +# context("ds.glm::smk::gaussian::setup") connect.studies.dataset.cnsim(list("LAB_TSC", "LAB_TRIG")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.glm::smk::gaussian") +# context("ds.glm::smk::gaussian") test_that("glm_gaussian", { res <- ds.glm('D$LAB_TSC~D$LAB_TRIG',family="gaussian",checks=FALSE) @@ -50,7 +51,7 @@ test_that("glm_gaussian", { expect_equal(res$output.information, "SEE TOP OF OUTPUT FOR INFORMATION ON MISSING DATA AND ERROR MESSAGES") }) -context("ds.glm::smk::gaussian, with check") +# context("ds.glm::smk::gaussian, with check") test_that("glm_gaussian, with check", { expect_warning(res <- ds.glm('D$LAB_TSC~D$LAB_TRIG', family="gaussian", checks=TRUE), "NAs introduced by coercion") @@ -80,7 +81,7 @@ test_that("glm_gaussian, with check", { # Done # -context("ds.glm::smk::gaussian::shutdown") +# context("ds.glm::smk::gaussian::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "LAB_TRIG", "LAB_TSC")) @@ -88,4 +89,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.glm::smk::gaussian::done") +# context("ds.glm::smk::gaussian::done") diff --git a/tests/testthat/test-smk-ds.glm-poisson.R b/tests/testthat/test-smk-ds.glm-poisson.R index a8385bfb4..19c56ebc7 100644 --- a/tests/testthat/test-smk-ds.glm-poisson.R +++ b/tests/testthat/test-smk-ds.glm-poisson.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.glm::smk::poisson::setup") +# context("ds.glm::smk::poisson::setup") connect.studies.dataset.survival(list("survtime", "time.id", "female", "age.60")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.glm::smk::poisson") +# context("ds.glm::smk::poisson") test_that("glm_gaussian", { res <- ds.glm("D$survtime~1+D$time.id+D$female", family="poisson", checks=FALSE) @@ -50,7 +51,7 @@ test_that("glm_gaussian", { expect_equal(res$output.information, "SEE TOP OF OUTPUT FOR INFORMATION ON MISSING DATA AND ERROR MESSAGES") }) -context("ds.glm::smk::poisson, with check") +# context("ds.glm::smk::poisson, with check") test_that("glm_gaussian, which check", { expect_warning(res <- ds.glm("D$survtime~1+D$time.id+D$female", family="poisson", checks=TRUE), "NAs introduced by coercion") @@ -80,7 +81,7 @@ test_that("glm_gaussian, which check", { # Done # -context("ds.glm::smk::poisson::shutdown") +# context("ds.glm::smk::poisson::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "female", "survtime", "time.id")) @@ -88,4 +89,4 @@ test_that("shutdown", { disconnect.studies.dataset.survival() -context("ds.glm::smk::poisson::done") +# context("ds.glm::smk::poisson::done") diff --git a/tests/testthat/test-smk-ds.glmPredict-binomial.R b/tests/testthat/test-smk-ds.glmPredict-binomial.R index 59ec5438d..12570b9c5 100644 --- a/tests/testthat/test-smk-ds.glmPredict-binomial.R +++ b/tests/testthat/test-smk-ds.glmPredict-binomial.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.glmPredict::smk::binomial::setup") +# context("ds.glmPredict::smk::binomial::setup") connect.studies.dataset.cnsim(list("LAB_TSC", "LAB_TRIG", "DIS_AMI", "DIS_DIAB", "GENDER")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.glmPredict::smk::binomial::without_newobj") +# context("ds.glmPredict::smk::binomial::without_newobj") test_that("simple glmPredict, binomial, without newobj, se.fit=FALSE",{ glmSLMA.res <- ds.glmSLMA('D$DIS_DIAB~D$LAB_TRIG', family="binomial", newobj="binomial.glmslma.obj") @@ -106,7 +107,7 @@ test_that("simple glmPredict, binomial, without newobj, se.fit=FALSE",{ }) -context("ds.glmPredict::smk::binomial::with_newobj") +# context("ds.glmPredict::smk::binomial::with_newobj") test_that("simple glmPredict, binomial, with newobj, se.fit=FALSE", { glmSLMA.res <- ds.glmSLMA('D$DIS_DIAB~D$LAB_TRIG', family="binomial", newobj="binomial.glmslma.obj") @@ -187,7 +188,7 @@ test_that("simple glmPredict, binomial, with newobj, se.fit=FALSE", { expect_equal(res$sim3$safe.list$fit.quantiles[[7]], 0.029020811, tolerance = ds.test_env$tolerance) }) -context("ds.glmPredict::smk::binomial::sefit_true") +# context("ds.glmPredict::smk::binomial::sefit_true") test_that("simple glmPredict, binomial, with newobj, se.fit=TRUE", { glmSLMA.res <- ds.glmSLMA('D$DIS_DIAB~D$LAB_TRIG', family="binomial", newobj="binomial.glmslma.obj") @@ -318,7 +319,7 @@ test_that("simple glmPredict, binomial, with newobj, se.fit=TRUE", { # Shutdown # -context("ds.glmPredict::smk::binomial::shutdown") +# context("ds.glmPredict::smk::binomial::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "binomial.glmslma.obj", "binomial.glm.predict.obj", "binomial.glm.predict.sefit.obj", "predict_glm" )) @@ -330,4 +331,4 @@ disconnect.studies.dataset.cnsim() # Done # -context("ds.glmPredict::smk::binomial::done") +# context("ds.glmPredict::smk::binomial::done") diff --git a/tests/testthat/test-smk-ds.glmPredict-gaussian.R b/tests/testthat/test-smk-ds.glmPredict-gaussian.R index e810f118c..934aba3e7 100644 --- a/tests/testthat/test-smk-ds.glmPredict-gaussian.R +++ b/tests/testthat/test-smk-ds.glmPredict-gaussian.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.glmPredict::smk::gaussian::setup") +# context("ds.glmPredict::smk::gaussian::setup") connect.studies.dataset.cnsim(list("LAB_TSC", "LAB_TRIG", "DIS_AMI", "DIS_DIAB", "GENDER")) @@ -23,7 +24,7 @@ test_that("setup", { # # Tests # -context("ds.glmPredict::smk::gaussian::without_newobj") +# context("ds.glmPredict::smk::gaussian::without_newobj") test_that("simple glmPredict, gaussian, without newobj, se.fit=FALSE",{ glmSLMA.res <- ds.glmSLMA('D$LAB_TSC~D$LAB_TRIG', family="gaussian", newobj="gaussian.glmslma.obj") @@ -104,7 +105,7 @@ test_that("simple glmPredict, gaussian, without newobj, se.fit=FALSE",{ expect_equal(res$sim3$safe.list$fit.quantiles[[7]], 6.054574, tolerance = ds.test_env$tolerance) }) -context("ds.glmPredict::smk::gaussian::with_newobj") +# context("ds.glmPredict::smk::gaussian::with_newobj") test_that("simple glmPredict, gaussian, with newobj, se.fit=FALSE", { glmSLMA.res <- ds.glmSLMA('D$LAB_TSC~D$LAB_TRIG', family="gaussian", newobj="gaussian.glmslma.obj") @@ -185,7 +186,7 @@ test_that("simple glmPredict, gaussian, with newobj, se.fit=FALSE", { expect_equal(res$sim3$safe.list$fit.quantiles[[7]], 6.054574, tolerance = ds.test_env$tolerance) }) -context("ds.glmPredict::smk::gaussian::sefit_true") +# context("ds.glmPredict::smk::gaussian::sefit_true") test_that("simple glmPredict, gaussian, with newobj, se.fit=TRUE", { glmSLMA.res <- ds.glmSLMA('D$LAB_TSC~D$LAB_TRIG', family="gaussian", newobj="gaussian.glmslma.obj") @@ -316,7 +317,7 @@ test_that("simple glmPredict, gaussian, with newobj, se.fit=TRUE", { # Shutdown # -context("ds.glmPredict::smk::gaussian::shutdown") +# context("ds.glmPredict::smk::gaussian::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "gaussian.glm.predict.obj", "gaussian.glm.predict.sefit.obj", "gaussian.glmslma.obj", "predict_glm" )) @@ -328,4 +329,4 @@ disconnect.studies.dataset.cnsim() # Done # -context("ds.glmPredict::smk::gaussian::done") +# context("ds.glmPredict::smk::gaussian::done") diff --git a/tests/testthat/test-smk-ds.glmPredict-poisson.R b/tests/testthat/test-smk-ds.glmPredict-poisson.R index 83a0af2b1..d8f830c14 100644 --- a/tests/testthat/test-smk-ds.glmPredict-poisson.R +++ b/tests/testthat/test-smk-ds.glmPredict-poisson.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.glmPredict::smk::poisson::setup") +# context("ds.glmPredict::smk::poisson::setup") connect.studies.dataset.cnsim(list("LAB_TSC", "LAB_TRIG", "DIS_AMI", "DIS_DIAB", "GENDER")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.glmPredict::smk::poisson::without_newobj") +# context("ds.glmPredict::smk::poisson::without_newobj") test_that("simple glmPredict, poisson, without newobj, se.fit=FALSE", { glmSLMA.res <- ds.glmSLMA('D$LAB_TSC~D$LAB_TRIG', family="poisson", newobj="poisson.glmslma.obj") @@ -105,7 +106,7 @@ test_that("simple glmPredict, poisson, without newobj, se.fit=FALSE", { expect_equal(res$sim3$safe.list$fit.quantiles[[7]], 6.056664, tolerance = ds.test_env$tolerance) }) -context("ds.glmPredict::smk::poisson::with_newobj") +# context("ds.glmPredict::smk::poisson::with_newobj") test_that("simple glmPredict, poisson, with newobj, se.fit=FALSE", { glmSLMA.res <- ds.glmSLMA('D$LAB_TSC~D$LAB_TRIG', family="poisson", newobj="poisson.glmslma.obj") @@ -186,7 +187,7 @@ test_that("simple glmPredict, poisson, with newobj, se.fit=FALSE", { expect_equal(res$sim3$safe.list$fit.quantiles[[7]], 6.056664, tolerance = ds.test_env$tolerance) }) -context("ds.glmPredict::smk::poisson::sefit_true") +# context("ds.glmPredict::smk::poisson::sefit_true") test_that("simple glmPredict, poisson, with newobj, se.fit=TRUE", { glmSLMA.res <- ds.glmSLMA('D$LAB_TSC~D$LAB_TRIG', family="poisson", newobj="poisson.glmslma.obj") @@ -316,7 +317,7 @@ test_that("simple glmPredict, poisson, with newobj, se.fit=TRUE", { # Shutdown # -context("ds.glmPredict::smk::poisson::shutdown") +# context("ds.glmPredict::smk::poisson::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "poisson.glm.predict.obj", "poisson.glm.predict.sefit.obj", "poisson.glmslma.obj", "predict_glm" )) @@ -328,4 +329,4 @@ disconnect.studies.dataset.cnsim() # Done # -context("ds.glmPredict::smk::poisson::done") +# context("ds.glmPredict::smk::poisson::done") diff --git a/tests/testthat/test-smk-ds.glmSLMA.R b/tests/testthat/test-smk-ds.glmSLMA.R index 37532ba44..b0769bfdf 100644 --- a/tests/testthat/test-smk-ds.glmSLMA.R +++ b/tests/testthat/test-smk-ds.glmSLMA.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.glmSLMA::smk::setup") +# context("ds.glmSLMA::smk::setup") connect.studies.dataset.cnsim(list("LAB_TSC", "LAB_TRIG", "MEDI_LPD", "DIS_AMI", "DIS_DIAB", "GENDER")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.glmSLMA::smk::gaussian") +# context("ds.glmSLMA::smk::gaussian") test_that("simple glmSLMA, gaussian", { glmSLMA.res <- ds.glmSLMA('D$LAB_TSC~D$LAB_TRIG', family="gaussian") @@ -77,7 +78,7 @@ test_that("simple glmSLMA, gaussian", { expect_equal(glmSLMA.res$validity.check, " appears valid in all sources") }) -context("ds.glmSLMA::smk::gaussian-assigned") +# context("ds.glmSLMA::smk::gaussian-assigned") test_that("simple glmSLMA, gaussian-assigned", { glmSLMA.res <- ds.glmSLMA('D$LAB_TSC~D$LAB_TRIG', family="gaussian", newobj="glmSLMA_1.newobj") @@ -130,7 +131,7 @@ test_that("simple glmSLMA, gaussian-assigned", { expect_equal(glmSLMA.res$validity.check, " appears valid in all sources") }) -context("ds.glmSLMA::smk::binomial") +# context("ds.glmSLMA::smk::binomial") test_that("simple glmSLMA, binomial", { ds.asCharacter('D$MEDI_LPD', 'str.medi.lpd') ds.asNumeric('str.medi.lpd', 'num.medi.lpd') @@ -190,7 +191,7 @@ test_that("simple glmSLMA, binomial", { expect_equal(glmSLMA.res$validity.check, " appears valid in all sources") }) -context("ds.glmSLMA::smk::binomial-assigned") +# context("ds.glmSLMA::smk::binomial-assigned") test_that("simple glmSLMA, binomial-assigned", { ds.asCharacter('D$MEDI_LPD', 'str.medi.lpd') ds.asNumeric('str.medi.lpd', 'num.medi.lpd') @@ -250,7 +251,7 @@ test_that("simple glmSLMA, binomial-assigned", { expect_equal(glmSLMA.res$validity.check, " appears valid in all sources") }) -context("ds.glmSLMA::smk::poisson") +# context("ds.glmSLMA::smk::poisson") test_that("simple glmSLMA, poisson", { glmSLMA.res <- ds.glmSLMA('D$LAB_TSC~D$LAB_TRIG', family="poisson") @@ -303,7 +304,7 @@ test_that("simple glmSLMA, poisson", { expect_equal(glmSLMA.res$validity.check, " appears valid in all sources") }) -context("ds.glmSLMA::smk::poisson-assigned") +# context("ds.glmSLMA::smk::poisson-assigned") test_that("simple glmSLMA, poisson-assigned", { glmSLMA.res <- ds.glmSLMA('D$LAB_TSC~D$LAB_TRIG', family="poisson", newobj="glmSLMA_3.newobj") @@ -360,7 +361,7 @@ test_that("simple glmSLMA, poisson-assigned", { # Done # -context("ds.glmSLMA::smk::shutdown") +# context("ds.glmSLMA::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "new.glm.obj", "glmSLMA_1.newobj", "glmSLMA_2.newobj", "glmSLMA_3.newobj", "num.medi.lpd", "num.dis.diab", "num.gender", "str.medi.lpd", "str.dis.diab", "str.gender")) @@ -369,4 +370,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.glmSLMA::smk::done") +# context("ds.glmSLMA::smk::done") diff --git a/tests/testthat/test-smk-ds.glmSummary.R b/tests/testthat/test-smk-ds.glmSummary.R index 68efb105e..c6a827dfc 100644 --- a/tests/testthat/test-smk-ds.glmSummary.R +++ b/tests/testthat/test-smk-ds.glmSummary.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.glmSummary::smk::setup") +# context("ds.glmSummary::smk::setup") connect.studies.dataset.cnsim(list("LAB_TSC", "LAB_TRIG", "DIS_AMI", "DIS_DIAB", "GENDER")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.glmSummary::smk::gaussian") +# context("ds.glmSummary::smk::gaussian") test_that("simple glmSummary, gaussian, without newobj", { glmSLMA.res <- ds.glmSLMA('D$LAB_TSC~D$LAB_TRIG', family="gaussian", newobj="gaussian.glmslma.obj") @@ -87,7 +88,7 @@ test_that("simple glmSummary, gaussian", { expect_equal(class(res$sim3$glm.summary.obj), 'summary.glm') }) -context("ds.glmSummary::smk::poisson") +# context("ds.glmSummary::smk::poisson") test_that("simple glmSummary, poisson, without newobj", { glmSLMA.res <- ds.glmSLMA('D$LAB_TSC~D$LAB_TRIG', family="poisson", newobj="poisson.glmslma.obj") @@ -154,7 +155,7 @@ test_that("simple glmSummary, poisson", { # Shutdown # -context("ds.glmSummary::smk::shutdown") +# context("ds.glmSummary::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "gaussian.glmslma.obj", "gaussian.glmsummary.obj", "poisson.glmslma.obj", "poisson.glmsummary.obj", "summary_glm.newobj")) @@ -166,4 +167,4 @@ disconnect.studies.dataset.cnsim() # Done # -context("ds.glmSummary::smk::done") +# context("ds.glmSummary::smk::done") diff --git a/tests/testthat/test-smk-ds.glmerSLMA.R b/tests/testthat/test-smk-ds.glmerSLMA.R index 0d9720063..4ad25a02f 100644 --- a/tests/testthat/test-smk-ds.glmerSLMA.R +++ b/tests/testthat/test-smk-ds.glmerSLMA.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up Phase 1 # -context("ds.glmerSLMA::smk::setup - phase 1") +# context("ds.glmerSLMA::smk::setup - phase 1") connect.studies.dataset.cluster.int(list("incid_rate", "trtGrp", "Male", "idDoctor", "idSurgery")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests Phase 1 # -context("ds.glmerSLMA::smk::phase 1") +# context("ds.glmerSLMA::smk::phase 1") test_that("simple glmerSLMA tesing (mis)use of arguments", { res = ds.glmerSLMA(formula = 'incid_rate ~ trtGrp + Male + (1|idDoctor)', family='poisson', dataName = "D", start_theta = c(1)) expect_length(res, 8) @@ -74,7 +75,7 @@ test_that("simple glmerSLMA with assign=TRUE", { # Shutdown phase 1 # -context("ds.glmerSLMA::smk::shutdown - phase 1") +# context("ds.glmerSLMA::smk::shutdown - phase 1") test_that("setup", { #note the offset and weights objects below are artefacts @@ -87,7 +88,7 @@ disconnect.studies.dataset.cluster.int() # Set up phase 2 # -context("ds.glmerSLMA::smk::setup - phase 2") +# context("ds.glmerSLMA::smk::setup - phase 2") connect.studies.dataset.cluster.slo(list("incid_rate", "trtGrp", "Male", "idDoctor", "BMI", "idSurgery")) @@ -99,7 +100,7 @@ test_that("setup", { # Tests phase 2 # -context("ds.glmerSLMA::smk::test - phase 2") +# context("ds.glmerSLMA::smk::test - phase 2") test_that("check slope formulae - 1", { res = ds.glmerSLMA(formula = 'incid_rate ~ trtGrp + Male + (1|idDoctor) + (1|idSurgery) + (0+trtGrp|idSurgery)', family='poisson', dataName = 'D', control_type = 'check.conv.grad', control_value = 0.1) @@ -249,7 +250,7 @@ test_that("check slope formulae - 2", { # Shutdown phase 2 # -context("ds.glmerSLMA::smk::shutdown - phase 2") +# context("ds.glmerSLMA::smk::shutdown - phase 2") test_that("setup", { ds_expect_variables(c("D", "offset", "weights")) @@ -261,4 +262,4 @@ disconnect.studies.dataset.cluster.slo() # Done # -context("ds.glmerSLMA::smk::done") +# context("ds.glmerSLMA::smk::done") diff --git a/tests/testthat/test-smk-ds.hetcor.R b/tests/testthat/test-smk-ds.hetcor.R index 7d029fb30..906c1cdd9 100644 --- a/tests/testthat/test-smk-ds.hetcor.R +++ b/tests/testthat/test-smk-ds.hetcor.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.hetcor::smk::setup") +# context("ds.hetcor::smk::setup") connect.studies.dataset.cnsim(list("LAB_TSC", "LAB_TRIG", "LAB_HDL", "LAB_GLUC_ADJUSTED", "PM_BMI_CONTINUOUS", "DIS_CVA", "MEDI_LPD", "DIS_DIAB", "DIS_AMI", "GENDER", "PM_BMI_CATEGORICAL")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.hetcor::smk::test1") +# context("ds.hetcor::smk::test1") test_that("hetcor", { ds.dataFrame(c("D$LAB_TSC", "D$LAB_TRIG", "D$LAB_HDL", "D$LAB_GLUC_ADJUSTED", "D$PM_BMI_CONTINUOUS", "D$DIS_CVA", "D$MEDI_LPD", "D$DIS_DIAB", "D$DIS_AMI", "D$GENDER", "D$PM_BMI_CATEGORICAL"), newobj="df") @@ -177,7 +178,7 @@ test_that("hetcor", { # Done # -context("ds.hetcor::smk::shutdown") +# context("ds.hetcor::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "df")) @@ -185,4 +186,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.hetcor::smk::done") +# context("ds.hetcor::smk::done") diff --git a/tests/testthat/test-smk-ds.isNA.R b/tests/testthat/test-smk-ds.isNA.R index fb7213747..a0419eff8 100644 --- a/tests/testthat/test-smk-ds.isNA.R +++ b/tests/testthat/test-smk-ds.isNA.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.isNA::smk::setup") +# context("ds.isNA::smk::setup") connect.studies.dataset.cnsim(list("LAB_HDL")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.isNA::smk") +# context("ds.isNA::smk") res <- ds.isNA(x='D$LAB_HDL') test_that("isNA", { expect_false(res$sim1) @@ -36,7 +37,7 @@ test_that("isNA", { # Tear down # -context("ds.isNA::smk::shutdown") +# context("ds.isNA::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -44,5 +45,5 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.isNA::smk::done") +# context("ds.isNA::smk::done") diff --git a/tests/testthat/test-smk-ds.isValid.R b/tests/testthat/test-smk-ds.isValid.R index 302412ba5..59b72dcce 100644 --- a/tests/testthat/test-smk-ds.isValid.R +++ b/tests/testthat/test-smk-ds.isValid.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.isValid::smk::setup") +# context("ds.isValid::smk::setup") connect.studies.dataset.cnsim(list("LAB_TSC", "LAB_TRIG")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.isValid::smk") +# context("ds.isValid::smk") test_that("isValid", { res1 <- ds.isValid(x='D$LAB_TSC') @@ -55,7 +56,7 @@ test_that("isValid", { # Tear down # -context("ds.isValid::smk::shutdown") +# context("ds.isValid::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -63,4 +64,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.isValid::smk::done") +# context("ds.isValid::smk::done") diff --git a/tests/testthat/test-smk-ds.kurtosis.R b/tests/testthat/test-smk-ds.kurtosis.R index 76cedb049..297f87e46 100644 --- a/tests/testthat/test-smk-ds.kurtosis.R +++ b/tests/testthat/test-smk-ds.kurtosis.R @@ -1,6 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. -# Copyright (c) 2022 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -13,7 +13,7 @@ # Set up # -context("ds.kurtosis::smk::setup") +# context("ds.kurtosis::smk::setup") connect.studies.dataset.cnsim(list("LAB_TSC", "LAB_TRIG", "LAB_HDL", "LAB_GLUC_ADJUSTED", "PM_BMI_CONTINUOUS")) @@ -27,7 +27,7 @@ test_that("setup", { # Method 1 -context("ds.kurtosis::smk::method 1::split") +# context("ds.kurtosis::smk::method 1::split") test_that("simple kurtosis, method 1, split, on LAB_TSC", { kurtosis.res <- ds.kurtosis(x = 'D$LAB_TSC', method = 1, type='split') @@ -128,7 +128,7 @@ test_that("simple kurtosis, method 1, split, on PM_BMI_CONTINUOUS", { expect_equal(kurtosis.res$ValidityMessage[3], "VALID ANALYSIS") }) -context("ds.kurtosis::smk::method 1::combine") +# context("ds.kurtosis::smk::method 1::combine") test_that("simple kurtosis, combine, on LAB_TSC", { kurtosis.res <- ds.kurtosis(x = 'D$LAB_TSC', method = 1, type='combine') @@ -199,7 +199,7 @@ test_that("simple kurtosis, method 1, combine, on PM_BMI_CONTINUOUS", { expect_equal(kurtosis.res$ValidityMessage[1], "VALID ANALYSIS") }) -context("ds.kurtosis::smk::method 1::both") +# context("ds.kurtosis::smk::method 1::both") test_that("simple kurtosis, both, on LAB_TSC", { kurtosis.res <- ds.kurtosis(x = 'D$LAB_TSC', method = 1, type='both') @@ -342,7 +342,7 @@ test_that("simple kurtosis, method 1, both, on PM_BMI_CONTINUOUS", { # Method 2 -context("ds.kurtosis::smk::method 2::split") +# context("ds.kurtosis::smk::method 2::split") test_that("simple kurtosis, method 2, split, on LAB_TSC", { kurtosis.res <- ds.kurtosis(x = 'D$LAB_TSC', method = 2, type='split') @@ -443,7 +443,7 @@ test_that("simple kurtosis, method 2, split, on PM_BMI_CONTINUOUS", { expect_equal(kurtosis.res$ValidityMessage[3], "VALID ANALYSIS") }) -context("ds.kurtosis::smk::method 2::combine") +# context("ds.kurtosis::smk::method 2::combine") test_that("simple kurtosis, combine, on LAB_TSC", { kurtosis.res <- ds.kurtosis(x = 'D$LAB_TSC', method = 2, type='combine') @@ -514,7 +514,7 @@ test_that("simple kurtosis, method 2, combine, on PM_BMI_CONTINUOUS", { expect_equal(kurtosis.res$ValidityMessage[1], "VALID ANALYSIS") }) -context("ds.kurtosis::smk::method 2::both") +# context("ds.kurtosis::smk::method 2::both") test_that("simple kurtosis, both, on LAB_TSC", { kurtosis.res <- ds.kurtosis(x = 'D$LAB_TSC', method = 2, type='both') @@ -657,7 +657,7 @@ test_that("simple kurtosis, method 2, both, on PM_BMI_CONTINUOUS", { # Method 3 -context("ds.kurtosis::smk::method 3::split") +# context("ds.kurtosis::smk::method 3::split") test_that("simple kurtosis, method 3, split, on LAB_TSC", { kurtosis.res <- ds.kurtosis(x = 'D$LAB_TSC', method = 3, type='split') @@ -758,7 +758,7 @@ test_that("simple kurtosis, method 3, split, on PM_BMI_CONTINUOUS", { expect_equal(kurtosis.res$ValidityMessage[3], "VALID ANALYSIS") }) -context("ds.kurtosis::smk::method 3::combine") +# context("ds.kurtosis::smk::method 3::combine") test_that("simple kurtosis, combine, on LAB_TSC", { kurtosis.res <- ds.kurtosis(x = 'D$LAB_TSC', method = 3, type='combine') @@ -829,7 +829,7 @@ test_that("simple kurtosis, method 3, combine, on PM_BMI_CONTINUOUS", { expect_equal(kurtosis.res$ValidityMessage[1], "VALID ANALYSIS") }) -context("ds.kurtosis::smk::method 3::both") +# context("ds.kurtosis::smk::method 3::both") test_that("simple kurtosis, both, on LAB_TSC", { kurtosis.res <- ds.kurtosis(x = 'D$LAB_TSC', method = 3, type='both') @@ -974,7 +974,7 @@ test_that("simple kurtosis, method 3, both, on PM_BMI_CONTINUOUS", { # Done # -context("ds.kurtosis::smk::shutdown") +# context("ds.kurtosis::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -982,4 +982,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.kurtosis::smk::done") +# context("ds.kurtosis::smk::done") diff --git a/tests/testthat/test-smk-ds.length.R b/tests/testthat/test-smk-ds.length.R index 58d85b33e..b7c9bd764 100644 --- a/tests/testthat/test-smk-ds.length.R +++ b/tests/testthat/test-smk-ds.length.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.length::smk::setup") +# context("ds.length::smk::setup") connect.studies.dataset.cnsim(list("LAB_TSC")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.length::smk") +# context("ds.length::smk") test_that("basic length, both", { res.length <- ds.length('D$LAB_TSC', type='both') @@ -81,7 +82,7 @@ test_that("basic length, combine", { # Done # -context("ds.length::smk::shutdown") +# context("ds.length::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -89,4 +90,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.length::smk::done") +# context("ds.length::smk::done") diff --git a/tests/testthat/test-smk-ds.levels.R b/tests/testthat/test-smk-ds.levels.R index cc262a1ed..022758937 100644 --- a/tests/testthat/test-smk-ds.levels.R +++ b/tests/testthat/test-smk-ds.levels.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.levels::smk::setup") +# context("ds.levels::smk::setup") connect.studies.dataset.cnsim(list("GENDER", "PM_BMI_CATEGORICAL")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.levels::smk") +# context("ds.levels::smk") test_that("simple levels", { ds.asFactor("D$GENDER", newobj.name = "gender") @@ -51,7 +52,7 @@ test_that("simple levels", { expect_equal(res$sim3$Levels[2], "1") }) -context("ds.levels::smk") +# context("ds.levels::smk") test_that("simple levels", { ds.asFactor("D$PM_BMI_CATEGORICAL", newobj.name = "pm_bmi_categorical") @@ -85,7 +86,7 @@ test_that("simple levels", { # Done # -context("ds.levels::smk::shutdown") +# context("ds.levels::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "gender", "pm_bmi_categorical")) @@ -93,5 +94,5 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.levels::smk::done") +# context("ds.levels::smk::done") diff --git a/tests/testthat/test-smk-ds.lexis.R b/tests/testthat/test-smk-ds.lexis.R index 2ad3b717d..c0c302339 100644 --- a/tests/testthat/test-smk-ds.lexis.R +++ b/tests/testthat/test-smk-ds.lexis.R @@ -1,6 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. -# Copyright (c) 2022 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -13,7 +13,7 @@ # Set up # -context("ds.lexis::smk::setup") +# context("ds.lexis::smk::setup") connect.studies.dataset.survival(list("id", "starttime", "endtime", "cens", "age.60")) @@ -25,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.lexis::smk") +# context("ds.lexis::smk") test_that("simple lexis", { res <- ds.lexis(data='D', intervalWidth = c(1.0, 1.5, 2.5), idCol = 'D$id', entryCol = 'D$starttime', exitCol = 'D$endtime', statusCol = 'D$cens', variables = c('D$age.60'), expandDF = 'EM.new') @@ -55,7 +55,7 @@ test_that("simple lexis", { # Done # -context("ds.lexis::smk::shutdown") +# context("ds.lexis::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "EM.new", "messageobj")) @@ -63,4 +63,4 @@ test_that("shutdown", { disconnect.studies.dataset.survival() -context("ds.lexis::smk::done") +# context("ds.lexis::smk::done") diff --git a/tests/testthat/test-smk-ds.list.R b/tests/testthat/test-smk-ds.list.R index d369bedfc..85ff10d86 100644 --- a/tests/testthat/test-smk-ds.list.R +++ b/tests/testthat/test-smk-ds.list.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.list::smk::setup") +# context("ds.list::smk::setup") connect.studies.dataset.cnsim(list("LAB_TSC", "LAB_HDL")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.list::smk") +# context("ds.list::smk") test_that("Is List", { myobjects <- c('D$LAB_TSC', 'D$LAB_HDL') res <- ds.list(x=myobjects, newobj='my_newobj') @@ -72,7 +73,7 @@ test_that("Is List", { # Tear down # -context("ds.list::smk::shutdown") +# context("ds.list::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "my_newobj")) @@ -80,4 +81,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.list::smk::down") +# context("ds.list::smk::down") diff --git a/tests/testthat/test-smk-ds.listClientsideFunctions.R b/tests/testthat/test-smk-ds.listClientsideFunctions.R index 31b053eb1..4e5f67914 100644 --- a/tests/testthat/test-smk-ds.listClientsideFunctions.R +++ b/tests/testthat/test-smk-ds.listClientsideFunctions.R @@ -1,6 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. -# Copyright (c) 2022 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -13,7 +13,7 @@ # Set up # -context("ds.listClientsideFunctions::smk::setup") +# context("ds.listClientsideFunctions::smk::setup") connect.studies.dataset.cnsim(list("LAB_TSC", "LAB_HDL")) @@ -25,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.listClientsideFunctions::smk::check results") +# context("ds.listClientsideFunctions::smk::check results") test_that("check results", { output <- list( "ds.abs", @@ -141,7 +141,7 @@ test_that("check results", { "ds.vectorCalc" ) - expect_output(res <- ds.listClientsideFunctions(), "*") + res <- ds.listClientsideFunctions() for (func.name in output) { expect_true(func.name %in% res, info = func.name) @@ -152,7 +152,7 @@ test_that("check results", { # Done # -context("ds.listClientsideFunctions::smk::shutdown") +# context("ds.listClientsideFunctions::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -160,4 +160,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.listClientsideFunctions::smk::done") +# context("ds.listClientsideFunctions::smk::done") diff --git a/tests/testthat/test-smk-ds.listDisclosureSettings.R b/tests/testthat/test-smk-ds.listDisclosureSettings.R index e1b136951..2d8e34842 100644 --- a/tests/testthat/test-smk-ds.listDisclosureSettings.R +++ b/tests/testthat/test-smk-ds.listDisclosureSettings.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.listDisclosureSettings::smk::setup") +# context("ds.listDisclosureSettings::smk::setup") connect.studies.dataset.cnsim(list("LAB_TSC", "LAB_HDL")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.listDisclosureSettings::smk::check results") +# context("ds.listDisclosureSettings::smk::check results") test_that("check results", { res <- ds.listDisclosureSettings() @@ -78,7 +79,7 @@ test_that("check results", { # Done # -context("ds.listDisclosureSettings::smk::shutdown") +# context("ds.listDisclosureSettings::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -86,4 +87,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.listDisclosureSettings::smk::down") +# context("ds.listDisclosureSettings::smk::down") diff --git a/tests/testthat/test-smk-ds.listServersideFunctions.R b/tests/testthat/test-smk-ds.listServersideFunctions.R index 4e098b128..0e3221fb2 100644 --- a/tests/testthat/test-smk-ds.listServersideFunctions.R +++ b/tests/testthat/test-smk-ds.listServersideFunctions.R @@ -1,6 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. -# Copyright (c) 2022 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -19,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC", "LAB_HDL")) # Tests # -context("ds.listServersideFunctions::smk::check results") +# context("ds.listServersideFunctions::smk::check results") test_that("check results", { assign.functions <- factor(c( "BooleDS", "abs", "absDS", "acos", "as.character", "as.null", "as.numeric", "asCharacterDS", "asDataMatrixDS", diff --git a/tests/testthat/test-smk-ds.lmerSLMA.R b/tests/testthat/test-smk-ds.lmerSLMA.R index c552a65ff..7d352a9c2 100644 --- a/tests/testthat/test-smk-ds.lmerSLMA.R +++ b/tests/testthat/test-smk-ds.lmerSLMA.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up phase 1 # -context("ds.lmerSLMA::smk::setup phase 1") +# context("ds.lmerSLMA::smk::setup phase 1") connect.studies.dataset.cluster.int(list("incid_rate", "trtGrp", "Male", "idDoctor", "BMI", "idSurgery")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.lmerSLMA::smk::phase 1") +# context("ds.lmerSLMA::smk::phase 1") test_that("simple lmerSLMA", { res <- ds.lmerSLMA(formula = 'incid_rate ~ trtGrp + Male + (1|idDoctor)', dataName = "D") @@ -75,7 +76,7 @@ test_that("test offsets and weights", { # Shutdown # -context("ds.lmerSLMA::smk::shutdown phase 1") +# context("ds.lmerSLMA::smk::shutdown phase 1") test_that("shutdown", { #note the offset and weights objects below are artefacts @@ -89,7 +90,7 @@ disconnect.studies.dataset.cluster.int() # Set up # -context("ds.lmerSLMA::smk::setup phase 2") +# context("ds.lmerSLMA::smk::setup phase 2") connect.studies.dataset.cluster.slo(list("incid_rate", "trtGrp", "Male", "idDoctor", "BMI", "idSurgery")) @@ -101,7 +102,7 @@ test_that("setup", { # Tests # -context("ds.lmerSLMA::smk::test phase 2") +# context("ds.lmerSLMA::smk::test phase 2") test_that("check slope formulae", { res = ds.lmerSLMA(formula = 'BMI ~ trtGrp + Male + (1|idDoctor) + (1|idSurgery) + (0+trtGrp|idSurgery)', dataName = 'D', control_type = 'check.conv.grad',control_value = 0.1) @@ -251,7 +252,7 @@ test_that("check slope formulae", { # Shutdown # -context("ds.lmerSLMA::smk::shutdown phase 2") +# context("ds.lmerSLMA::smk::shutdown phase 2") test_that("shutdown", { ds_expect_variables(c("D", "offset", "weights")) @@ -263,4 +264,4 @@ disconnect.studies.dataset.cluster.slo() # Done # -context("ds.lmerSLMA::smk::done") +# context("ds.lmerSLMA::smk::done") diff --git a/tests/testthat/test-smk-ds.log.R b/tests/testthat/test-smk-ds.log.R index cd18e6f1f..c857408db 100644 --- a/tests/testthat/test-smk-ds.log.R +++ b/tests/testthat/test-smk-ds.log.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.log::smk::setup") +# context("ds.log::smk::setup") connect.studies.dataset.cnsim(list("LAB_TSC")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.log::smk") +# context("ds.log::smk") test_that("simple log", { res1 <- ds.log("D$LAB_TSC", newobj="log1_obj") @@ -81,7 +82,7 @@ test_that("simple log", { # Done # -context("ds.log::smk::shutdown") +# context("ds.log::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "new_data", "log1_obj", "log2_obj")) @@ -89,4 +90,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.log::smk::done") +# context("ds.log::smk::done") diff --git a/tests/testthat/test-smk-ds.look.R b/tests/testthat/test-smk-ds.look.R index c8167430c..f4a656837 100644 --- a/tests/testthat/test-smk-ds.look.R +++ b/tests/testthat/test-smk-ds.look.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.look::smk::setup") +# context("ds.look::smk::setup") connect.studies.dataset.cnsim(list("LAB_TSC", "LAB_TRIG", "LAB_HDL")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.look::smk") +# context("ds.look::smk") test_that("simple look", { res <- ds.look("lengthDS('D$LAB_TSC')") @@ -39,7 +40,7 @@ test_that("simple look", { # Done # -context("ds.look::smk::shutdown") +# context("ds.look::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -47,4 +48,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.look::smk::done") +# context("ds.look::smk::done") diff --git a/tests/testthat/test-smk-ds.ls.R b/tests/testthat/test-smk-ds.ls.R index 1a9afe3d4..91dd745a4 100644 --- a/tests/testthat/test-smk-ds.ls.R +++ b/tests/testthat/test-smk-ds.ls.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.ls::smk::setup") +# context("ds.ls::smk::setup") connect.studies.dataset.cnsim(list("LAB_TSC", "LAB_TRIG")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.ls::smk") +# context("ds.ls::smk") test_that("simple ls", { res <- ds.ls() @@ -107,7 +108,7 @@ test_that("simple ls, with envir, with wildcard prefix", { # Shutdown # -context("ds.ls::smk::shutdown") +# context("ds.ls::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -119,4 +120,4 @@ disconnect.studies.dataset.cnsim() # Done # -context("ds.ls::smk::done") +# context("ds.ls::smk::done") diff --git a/tests/testthat/test-smk-ds.lspline.R b/tests/testthat/test-smk-ds.lspline.R index 9529babd7..08d45470d 100644 --- a/tests/testthat/test-smk-ds.lspline.R +++ b/tests/testthat/test-smk-ds.lspline.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.lspline::smk::setup") +# context("ds.lspline::smk::setup") connect.studies.dataset.cnsim(list("LAB_TRIG", "PM_BMI_CONTINUOUS")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.lspline::smk::test1") +# context("ds.lspline::smk::test1") test_that("lspline", { ds.lspline(x="D$PM_BMI_CONTINUOUS", knots=c(15,25,35), newobj="lsplineDS", datasources=ds.test_env$connections) @@ -81,7 +82,7 @@ test_that("lspline", { # Done # -context("ds.lspline::smk::shutdown") +# context("ds.lspline::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "LAB_TRIG", "lsplineDS")) @@ -89,4 +90,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.qlspline::smk::done") +# context("ds.qlspline::smk::done") diff --git a/tests/testthat/test-smk-ds.make.R b/tests/testthat/test-smk-ds.make.R index 57565fbe5..cadb04707 100644 --- a/tests/testthat/test-smk-ds.make.R +++ b/tests/testthat/test-smk-ds.make.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.make::smk::setup") +# context("ds.make::smk::setup") connect.studies.dataset.cnsim(list("LAB_TSC", "LAB_TRIG", "LAB_HDL")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.make::smk") +# context("ds.make::smk") test_that("simple make", { res <- ds.make("(D$LAB_TSC*D$LAB_TRIG*D$LAB_HDL)", "maded.rand") @@ -33,7 +34,7 @@ test_that("simple make", { expect_equal(res$validity.check, " appears valid in all sources") }) -context("ds.make::smk") +# context("ds.make::smk") test_that("simple make", { res <- ds.make("(D$LAB_TSC*10)", "maded.rand") @@ -42,7 +43,7 @@ test_that("simple make", { expect_equal(res$validity.check, " appears valid in all sources") }) -context("ds.make::smk") +# context("ds.make::smk") test_that("simple make", { res <- ds.make("(D$LAB_TSC)*10", "maded.rand") @@ -55,7 +56,7 @@ test_that("simple make", { # Done # -context("ds.make::smk::shutdown") +# context("ds.make::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "maded.rand")) @@ -63,4 +64,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.make::smk::done") +# context("ds.make::smk::done") diff --git a/tests/testthat/test-smk-ds.matrix.R b/tests/testthat/test-smk-ds.matrix.R index c9295bd9a..d48367603 100644 --- a/tests/testthat/test-smk-ds.matrix.R +++ b/tests/testthat/test-smk-ds.matrix.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.matrix::smk::setup") +# context("ds.matrix::smk::setup") connect.studies.dataset.cnsim(list("LAB_TSC")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.matrix::smk") +# context("ds.matrix::smk") test_that("simplest ds.matrix", { matrix <- c(0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11) @@ -46,7 +47,7 @@ test_that("simplest ds.matrix", { # Tear down # -context("ds.matrix::smk::shutdown") +# context("ds.matrix::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "matrix.newobj")) @@ -54,4 +55,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.matrix::smk::done") +# context("ds.matrix::smk::done") diff --git a/tests/testthat/test-smk-ds.matrixDet.R b/tests/testthat/test-smk-ds.matrixDet.R index 3cf8f8b50..74626cbc4 100644 --- a/tests/testthat/test-smk-ds.matrixDet.R +++ b/tests/testthat/test-smk-ds.matrixDet.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.matrixDet::smk::setup") +# context("ds.matrixDet::smk::setup") connect.studies.dataset.cnsim(list("LAB_TSC")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.matrixDet::smk") +# context("ds.matrixDet::smk") test_that("simplest ds.matrixDet", { matrix <- c(-2, 1, 3, 0, -1, 1, 1, 2, 0) @@ -47,7 +48,7 @@ test_that("simplest ds.matrixDet", { # Tear down # -context("ds.matrixDet::smk::shutdown") +# context("ds.matrixDet::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "matrix.newobj", "matrixdet.newobj")) @@ -55,4 +56,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.matrixDet::smk::done") +# context("ds.matrixDet::smk::done") diff --git a/tests/testthat/test-smk-ds.matrixDet.report.R b/tests/testthat/test-smk-ds.matrixDet.report.R index 5854fbde3..20850a5a3 100644 --- a/tests/testthat/test-smk-ds.matrixDet.report.R +++ b/tests/testthat/test-smk-ds.matrixDet.report.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.matrixDet.report::smk::setup") +# context("ds.matrixDet.report::smk::setup") connect.studies.dataset.cnsim(list("LAB_TSC")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.matrixDet.report::smk") +# context("ds.matrixDet.report::smk") test_that("simplest ds.matrixDet.report", { matrix <- c(-2, 1, 3, 0, -1, 1, 1, 2, 0) @@ -51,7 +52,7 @@ test_that("simplest ds.matrixDet.report", { # Tear down # -context("ds.matrixDet.report::smk::shutdown") +# context("ds.matrixDet.report::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "matrix.newobj")) @@ -59,4 +60,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.matrixDet.report::smk::done") +# context("ds.matrixDet.report::smk::done") diff --git a/tests/testthat/test-smk-ds.matrixDiag.R b/tests/testthat/test-smk-ds.matrixDiag.R index 14bc8baba..2a9b30d75 100644 --- a/tests/testthat/test-smk-ds.matrixDiag.R +++ b/tests/testthat/test-smk-ds.matrixDiag.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.matrixDiag::smk::setup") +# context("ds.matrixDiag::smk::setup") connect.studies.dataset.cnsim(list("LAB_TSC")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.matrixDiag::smk") +# context("ds.matrixDiag::smk") test_that("simplest ds.matrixDiag", { matrix <- c(0, 1, 2, 3, 4, 5) @@ -42,7 +43,7 @@ test_that("simplest ds.matrixDiag", { expect_true("matrix" %in% check.class$sim3) }) -context("ds.matrixDiag::smk") +# context("ds.matrixDiag::smk") test_that("simplest ds.matrixDiag", { matrix <- c(0, 1, 2, 3, 4, 5) @@ -64,7 +65,7 @@ test_that("simplest ds.matrixDiag", { # Tear down # -context("ds.matrixDiag::smk::shutdown") +# context("ds.matrixDiag::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "matrix_diag", "matrixdiag.newobj")) @@ -72,4 +73,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.matrixDiag::smk::done") +# context("ds.matrixDiag::smk::done") diff --git a/tests/testthat/test-smk-ds.matrixDimnames.R b/tests/testthat/test-smk-ds.matrixDimnames.R index f39a04799..6ac87d2ff 100644 --- a/tests/testthat/test-smk-ds.matrixDimnames.R +++ b/tests/testthat/test-smk-ds.matrixDimnames.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.matrixDimnames::smk::setup") +# context("ds.matrixDimnames::smk::setup") connect.studies.dataset.cnsim(list("LAB_TSC")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.matrixDimnames::smk") +# context("ds.matrixDimnames::smk") test_that("simplest ds.matrixDimnames", { matrix <- c(-2, 1, 3, 0, -1, 1, 1, 2, 0) @@ -50,7 +51,7 @@ test_that("simplest ds.matrixDimnames", { # Tear down # -context("ds.matrixDimnames::smk::shutdown") +# context("ds.matrixDimnames::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "matrix.newobj", "matrixdimnames.newobj")) @@ -58,4 +59,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.matrixDimnames::smk::done") +# context("ds.matrixDimnames::smk::done") diff --git a/tests/testthat/test-smk-ds.matrixInvert.R b/tests/testthat/test-smk-ds.matrixInvert.R index b0ab7f41e..8cd89a415 100644 --- a/tests/testthat/test-smk-ds.matrixInvert.R +++ b/tests/testthat/test-smk-ds.matrixInvert.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.matrixInvert::smk::setup") +# context("ds.matrixInvert::smk::setup") connect.studies.dataset.cnsim(list("LAB_TSC")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.matrixInvert::smk") +# context("ds.matrixInvert::smk") test_that("simplest ds.matrixInvert", { matrix <- c(-2, 1, 3, 0, -1, 1, 1, 2, 0) @@ -47,7 +48,7 @@ test_that("simplest ds.matrixInvert", { # Tear down # -context("ds.matrixInvert::smk::shutdown") +# context("ds.matrixInvert::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "matrix.newobj", "matrixinvert.newobj")) @@ -55,4 +56,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.matrixInvert::smk::done") +# context("ds.matrixInvert::smk::done") diff --git a/tests/testthat/test-smk-ds.matrixMult.R b/tests/testthat/test-smk-ds.matrixMult.R index 76ddb9af3..001e36efb 100644 --- a/tests/testthat/test-smk-ds.matrixMult.R +++ b/tests/testthat/test-smk-ds.matrixMult.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.matrixMult::smk::setup") +# context("ds.matrixMult::smk::setup") connect.studies.dataset.cnsim(list("LAB_TSC")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.matrixMult::smk") +# context("ds.matrixMult::smk") test_that("simplest ds.matrixMult", { matrix1 <- c(-2, 1, 3, 0, -1, 1, 1, 2, 0) matrix2 <- c(-2, 1, 3, 1, -1, 1, 1, 2, 1) @@ -49,7 +50,7 @@ test_that("simplest ds.matrixMult", { # Tear down # -context("ds.matrixMult::smk::shutdown") +# context("ds.matrixMult::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "mat1", "mat2", "matrixmult.newobj")) @@ -57,4 +58,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.matrixMult::smk::done") +# context("ds.matrixMult::smk::done") diff --git a/tests/testthat/test-smk-ds.matrixTranspose.R b/tests/testthat/test-smk-ds.matrixTranspose.R index 234fbb383..fa1920a78 100644 --- a/tests/testthat/test-smk-ds.matrixTranspose.R +++ b/tests/testthat/test-smk-ds.matrixTranspose.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.matrixTranspose::smk::setup") +# context("ds.matrixTranspose::smk::setup") connect.studies.dataset.cnsim(list("LAB_TSC")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.matrixTranspose::smk") +# context("ds.matrixTranspose::smk") test_that("simplest ds.matrixTranspose", { matrix <- c(0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11) @@ -47,7 +48,7 @@ test_that("simplest ds.matrixTranspose", { # Tear down # -context("ds.matrixTranspose::smk::shutdown") +# context("ds.matrixTranspose::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "matrix.newobj", "matrixtranspose.newobj")) @@ -55,4 +56,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.matrixTranspose::smk::done") +# context("ds.matrixTranspose::smk::done") diff --git a/tests/testthat/test-smk-ds.mean.R b/tests/testthat/test-smk-ds.mean.R index be89553c5..5b2d7360e 100644 --- a/tests/testthat/test-smk-ds.mean.R +++ b/tests/testthat/test-smk-ds.mean.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.mean::smk::setup") +# context("ds.mean::smk::setup") connect.studies.dataset.cnsim(list("LAB_TSC")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.mean::smk::type=combine") +# context("ds.mean::smk::type=combine") test_that("mean values [combine]", { ds.rm("mean.all.studies") ds.rm("mean.study.specific") @@ -60,7 +61,7 @@ test_that("mean values [combine]", { expect_false("Nvalid.study.specific" %in% ls.res$sim3$objects.found) }) -context("ds.mean::smk::type=split") +# context("ds.mean::smk::type=split") test_that("mean values [split]", { ds.rm("mean.all.studies") ds.rm("mean.study.specific") @@ -104,7 +105,7 @@ test_that("mean values [split]", { expect_false("Nvalid.study.specific" %in% ls.res$sim3$objects.found) }) -context("ds.mean::smk::type=both") +# context("ds.mean::smk::type=both") test_that("mean values [both]", { ds.rm("mean.all.studies") ds.rm("mean.study.specific") @@ -153,7 +154,7 @@ test_that("mean values [both]", { expect_false("Nvalid.study.specific" %in% ls.res$sim3$objects.found) }) -context("ds.mean::smk::type=combine,save.mean.Nvalid=TRUE") +# context("ds.mean::smk::type=combine,save.mean.Nvalid=TRUE") test_that("mean values [combine]", { ds.rm("mean.all.studies") ds.rm("mean.study.specific") @@ -189,7 +190,7 @@ test_that("mean values [combine]", { expect_true("Nvalid.study.specific" %in% ls.res$sim3$objects.found) }) -context("ds.mean::smk::type=split,save.mean.Nvalid=TRUE") +# context("ds.mean::smk::type=split,save.mean.Nvalid=TRUE") test_that("mean values [split]", { ds.rm("mean.all.studies") ds.rm("mean.study.specific") @@ -233,7 +234,7 @@ test_that("mean values [split]", { expect_true("Nvalid.study.specific" %in% ls.res$sim3$objects.found) }) -context("ds.mean::smk::type=both,save.mean.Nvalid=TRUE") +# context("ds.mean::smk::type=both,save.mean.Nvalid=TRUE") test_that("mean values [both]", { stat.mean <- ds.mean(x='D$LAB_TSC', type='both', save.mean.Nvalid=TRUE) @@ -281,7 +282,7 @@ test_that("mean values [both]", { # Done # -context("ds.mean::smk::shutdown") +# context("ds.mean::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "mean.all.studies", "mean.study.specific", "Nvalid.all.studies", "Nvalid.study.specific")) @@ -289,4 +290,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.mean::smk::done") +# context("ds.mean::smk::done") diff --git a/tests/testthat/test-smk-ds.meanByClass.R b/tests/testthat/test-smk-ds.meanByClass.R index a9d1ef7c4..2c5aba86a 100644 --- a/tests/testthat/test-smk-ds.meanByClass.R +++ b/tests/testthat/test-smk-ds.meanByClass.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.meanByClass::smk::setup") +# context("ds.meanByClass::smk::setup") connect.studies.dataset.cnsim(list("LAB_TSC","LAB_HDL","PM_BMI_CATEGORICAL")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.meanByClass::smk::LAB_TSC across PM_BMI_CATEGORICAL categories where both vectors are 'loose'") +# context("ds.meanByClass::smk::LAB_TSC across PM_BMI_CATEGORICAL categories where both vectors are 'loose'") ds.assign("D$LAB_TSC", "ldl") ds.assign("D$PM_BMI_CATEGORICAL", "pm_bmi") test_that("LAB_TSC_across_", { @@ -39,7 +40,7 @@ test_that("LAB_TSC_across_", { expect_equal(res[[6]], '5.89(1.15)') }) -context("ds.meanByClass::smk::calculate the mean proportion for LAB_HDL across PM_BMI_CATEGORICAL categories") +# context("ds.meanByClass::smk::calculate the mean proportion for LAB_HDL across PM_BMI_CATEGORICAL categories") res <- ds.meanByClass(x='D', outvar='LAB_HDL', covar='PM_BMI_CATEGORICAL') test_that("LAB_HDL_across_PM_BMI_CATEGORICAL", { @@ -53,7 +54,7 @@ test_that("LAB_HDL_across_PM_BMI_CATEGORICAL", { }) -context("ds.meanByClass::smk::calculate the mean proportion for LAB_HDL & LAB_TSC across bmi categories") +# context("ds.meanByClass::smk::calculate the mean proportion for LAB_HDL & LAB_TSC across bmi categories") res <- ds.meanByClass(x='D', outvar=c('LAB_HDL','LAB_TSC'), covar=c('PM_BMI_CATEGORICAL')) test_that("LAB_HDL-LAB_TSC_across_PM_BMI_CATEGORICAL", { @@ -77,7 +78,7 @@ test_that("LAB_HDL-LAB_TSC_across_PM_BMI_CATEGORICAL", { # res <- ds.meanByClass(datasources=ds.test_env$connection.opal, x='D', outvar=c('LAB_HDL','LAB_TSC'), covar=c('GENDER','PM_BMI_CATEGORICAL','DIS_DIAB')) -context("ds.meanByClass::smk::calculate the mean proportion for LAB_HDL across PM_BMI_CATEGORICAL categories, split") +# context("ds.meanByClass::smk::calculate the mean proportion for LAB_HDL across PM_BMI_CATEGORICAL categories, split") res <- ds.meanByClass(x='D', outvar='LAB_HDL', covar='PM_BMI_CATEGORICAL', type='split') test_that("LAB_HDL_across_PM_BMI_CATEGORICAL", { @@ -110,7 +111,7 @@ test_that("LAB_HDL_across_PM_BMI_CATEGORICAL", { # Tear down # -context("ds.meanByClass::smk::shutdown") +# context("ds.meanByClass::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "D.PM_BMI_CATEGORICAL1", "D.PM_BMI_CATEGORICAL2", "D.PM_BMI_CATEGORICAL3", @@ -119,4 +120,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.meanByClass::smk::done") +# context("ds.meanByClass::smk::done") diff --git a/tests/testthat/test-smk-ds.meanSdGp.R b/tests/testthat/test-smk-ds.meanSdGp.R index 45da49e34..14561fd09 100644 --- a/tests/testthat/test-smk-ds.meanSdGp.R +++ b/tests/testthat/test-smk-ds.meanSdGp.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.meanSdGp::smk::setup") +# context("ds.meanSdGp::smk::setup") connect.studies.dataset.survival(list("age.60", "female")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.meanSdGp::smk::type=split") +# context("ds.meanSdGp::smk::type=split") test_that("meanSdGp values [split]", { stat.meanSdGp <- ds.meanSdGp(x='D$age.60', y='D$female', type='split') @@ -38,7 +39,7 @@ test_that("meanSdGp values [split]", { expect_true("numeric" %in% class(stat.meanSdGp$Total_Ntotal)) }) -context("ds.meanSdGp::smk::type=combine") +# context("ds.meanSdGp::smk::type=combine") test_that("meanSdGp values [combine]", { stat.meanSdGp <- ds.meanSdGp(x='D$age.60', y='D$female', type='combine') @@ -52,7 +53,7 @@ test_that("meanSdGp values [combine]", { expect_true("numeric" %in% class(stat.meanSdGp$Total_Ntotal)) }) -context("ds.meanSdGp::smk::type=both") +# context("ds.meanSdGp::smk::type=both") test_that("meanSdGp values [both]", { stat.meanSdGp <- ds.meanSdGp(x='D$age.60', y='D$female', type='both') @@ -70,7 +71,7 @@ test_that("meanSdGp values [both]", { # Done # -context("ds.meanSdGp::smk::shutdown") +# context("ds.meanSdGp::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -78,4 +79,4 @@ test_that("shutdown", { disconnect.studies.dataset.survival() -context("ds.meanSdGp::smk::done") +# context("ds.meanSdGp::smk::done") diff --git a/tests/testthat/test-smk-ds.merge.R b/tests/testthat/test-smk-ds.merge.R index 521483eb9..fb58dcf5b 100644 --- a/tests/testthat/test-smk-ds.merge.R +++ b/tests/testthat/test-smk-ds.merge.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.merge::smk::setup") +# context("ds.merge::smk::setup") connect.studies.dataset.cnsim(list("LAB_TSC", "LAB_TRIG", "LAB_HDL", "DIS_CVA", "DIS_AMI")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.merge::smk") +# context("ds.merge::smk") test_that("simple test", { spec_vectors_1 <- c('D$LAB_TSC', 'D$LAB_HDL') spec_vectors_2 <- c('D$LAB_TSC', 'D$DIS_AMI') @@ -49,7 +50,7 @@ test_that("simple test", { # Done # -context("ds.merge::smk::shutdown") +# context("ds.merge::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "test_1_df", "test_2_df", "merge_newobj")) @@ -57,4 +58,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.merge::smk::done") +# context("ds.merge::smk::done") diff --git a/tests/testthat/test-smk-ds.message.R b/tests/testthat/test-smk-ds.message.R index ec9675870..bc3572633 100644 --- a/tests/testthat/test-smk-ds.message.R +++ b/tests/testthat/test-smk-ds.message.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.message::smk::setup") +# context("ds.message::smk::setup") connect.studies.dataset.cnsim(list("LAB_TSC")) @@ -25,7 +26,7 @@ test_that("setup", { # Tests # -context("ds.message::smk") +# context("ds.message::smk") test_that("not exists - request message", { message.res <- ds.message('Test') @@ -94,7 +95,7 @@ test_that("partial - request message - conn 3", { # # Done # -context("ds.message::smk::shutdown") +# context("ds.message::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "Test")) @@ -102,4 +103,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.message::smk::done") +# context("ds.message::smk::done") diff --git a/tests/testthat/test-smk-ds.metadata.R b/tests/testthat/test-smk-ds.metadata.R index a3f5329af..5acbb2ad6 100644 --- a/tests/testthat/test-smk-ds.metadata.R +++ b/tests/testthat/test-smk-ds.metadata.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.metadata::smk::setup") +# context("ds.metadata::smk::setup") connect.studies.dataset.cnsim(list('LAB_TSC', 'LAB_TRIG', 'LAB_HDL', 'LAB_GLUC_ADJUSTED', 'PM_BMI_CONTINUOUS', 'DIS_CVA', 'MEDI_LPD', 'DIS_DIAB', 'DIS_AMI', 'GENDER', 'PM_BMI_CATEGORICAL')) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.metadata::smk") +# context("ds.metadata::smk") test_that("data.frame metadata", { res <- ds.metadata(x='D') @@ -113,7 +114,7 @@ test_that("column metadata", { # Tear down # -context("ds.metadata::smk::shutdown") +# context("ds.metadata::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -121,4 +122,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.metadata::smk::done") +# context("ds.metadata::smk::done") diff --git a/tests/testthat/test-smk-ds.mice.R b/tests/testthat/test-smk-ds.mice.R index 802cf8663..71c0464a4 100644 --- a/tests/testthat/test-smk-ds.mice.R +++ b/tests/testthat/test-smk-ds.mice.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.mice::smk::setup") +# context("ds.mice::smk::setup") connect.studies.dataset.cnsim(list("LAB_TSC","LAB_TRIG","LAB_HDL","LAB_GLUC_ADJUSTED", "PM_BMI_CONTINUOUS","DIS_CVA","MEDI_LPD","DIS_DIAB", @@ -26,7 +27,7 @@ test_that("setup", { # Tests # -context("ds.mice::smk::imp1") +# context("ds.mice::smk::imp1") test_that("mice, initial imputation", { initialImp <- ds.mice(data="D", m=1, method=NULL, predictorMatrix=NULL, post=NULL, seed="NA", newobj_df='impSet') @@ -60,7 +61,7 @@ test_that("mice, initial imputation", { }) -context("ds.mice::smk::imp2") +# context("ds.mice::smk::imp2") test_that("mice, second imputation", { initialImp <- ds.mice(data="D", m=1, method=NULL, predictorMatrix=NULL, post=NULL, seed="NA", @@ -126,7 +127,7 @@ test_that("mice, second imputation", { # Done # -context("ds.mice::smk::shutdown") +# context("ds.mice::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "impSet.1", "imp_new.1","imp_new.2","imp_new.3","imp_new.4","imp_new.5", @@ -135,4 +136,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.mice::smk::done") +# context("ds.mice::smk::done") diff --git a/tests/testthat/test-smk-ds.names.R b/tests/testthat/test-smk-ds.names.R index 97f3fef9e..e73b7b57c 100644 --- a/tests/testthat/test-smk-ds.names.R +++ b/tests/testthat/test-smk-ds.names.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.names::smk::setup") +# context("ds.names::smk::setup") connect.studies.dataset.cnsim(list("LAB_TSC", "DIS_DIAB", "PM_BMI_CONTINUOUS", "LAB_HDL", "GENDER")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.names::smk") +# context("ds.names::smk") test_that("level_names", { myobjects <- c('D$LAB_TSC', 'D$LAB_HDL') res_list <- ds.list(x=myobjects, newobj='my_newobj') @@ -47,7 +48,7 @@ test_that("level_names", { # Tear down # -context("ds.names::smk::shutdown") +# context("ds.names::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "my_newobj")) @@ -55,4 +56,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.names::smk::done") +# context("ds.names::smk::done") diff --git a/tests/testthat/test-smk-ds.ns.R b/tests/testthat/test-smk-ds.ns.R index a1f66c791..d925aa1e9 100644 --- a/tests/testthat/test-smk-ds.ns.R +++ b/tests/testthat/test-smk-ds.ns.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.ns::smk::setup") +# context("ds.ns::smk::setup") connect.studies.dataset.cnsim(list("LAB_TRIG", "PM_BMI_CONTINUOUS")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.ns::smk::test1") +# context("ds.ns::smk::test1") test_that("ns", { ds.ns(x="D$PM_BMI_CONTINUOUS", knots=c(15,25,35), newobj="nsDS", datasources=ds.test_env$connections) @@ -85,7 +86,7 @@ test_that("ns", { # Done # -context("ds.ns::smk::shutdown") +# context("ds.ns::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "LAB_TRIG", "nsDS")) @@ -93,4 +94,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.ns::smk::done") +# context("ds.ns::smk::done") diff --git a/tests/testthat/test-smk-ds.numNA.R b/tests/testthat/test-smk-ds.numNA.R index ed332d7a5..0c71e93f9 100644 --- a/tests/testthat/test-smk-ds.numNA.R +++ b/tests/testthat/test-smk-ds.numNA.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.numNA::smk::setup") +# context("ds.numNA::smk::setup") connect.studies.dataset.cnsim(list("LAB_HDL", "LAB_TRIG", "DIS_CVA")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.numNA::smk") +# context("ds.numNA::smk") test_that("simple numNA", { res1 <- ds.numNA(x='D$LAB_HDL') @@ -52,7 +53,7 @@ test_that("simple numNA", { # Done # -context("ds.numNA::smk::shutdown") +# context("ds.numNA::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -60,4 +61,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.numNA::smk::done") +# context("ds.numNA::smk::done") diff --git a/tests/testthat/test-smk-ds.qlspline.R b/tests/testthat/test-smk-ds.qlspline.R index 2c55b0d50..e8b89701e 100644 --- a/tests/testthat/test-smk-ds.qlspline.R +++ b/tests/testthat/test-smk-ds.qlspline.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.qlspline::smk::setup") +# context("ds.qlspline::smk::setup") connect.studies.dataset.cnsim(list("LAB_TRIG", "PM_BMI_CONTINUOUS")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.qlspline::smk::test1") +# context("ds.qlspline::smk::test1") test_that("qlspline", { ds.qlspline(x="D$PM_BMI_CONTINUOUS", q=4, na.rm=TRUE, newobj="qlsplineDS", datasources=ds.test_env$connections) @@ -76,7 +77,7 @@ test_that("qlspline", { }) -context("ds.qlspline::smk::test2") +# context("ds.qlspline::smk::test2") test_that("qlspline", { ds.qlspline(x="D$PM_BMI_CONTINUOUS", q=c(0.3,0.6), na.rm=TRUE, newobj="qlsplineDS2", datasources=ds.test_env$connections) @@ -130,7 +131,7 @@ test_that("qlspline", { # Done # -context("ds.qlspline::smk::shutdown") +# context("ds.qlspline::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "LAB_TRIG", "qlsplineDS", "qlsplineDS2")) @@ -138,4 +139,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.qlspline::smk::done") +# context("ds.qlspline::smk::done") diff --git a/tests/testthat/test-smk-ds.quantileMean.R b/tests/testthat/test-smk-ds.quantileMean.R index 59c5479db..1438fb772 100644 --- a/tests/testthat/test-smk-ds.quantileMean.R +++ b/tests/testthat/test-smk-ds.quantileMean.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.quantileMean::smk::setup") +# context("ds.quantileMean::smk::setup") connect.studies.dataset.cnsim(list('LAB_HDL')) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.quantileMean::smk::standard") +# context("ds.quantileMean::smk::standard") test_that("quantileMean", { res <- ds.quantileMean(x='D$LAB_HDL') @@ -39,7 +40,7 @@ test_that("quantileMean", { expect_equal(res[[8]], 1.5676188, tolerance = .000001) }) -context("ds.quantileMean::smk::split") +# context("ds.quantileMean::smk::split") test_that("quantileMean_split", { ds.assign("D$LAB_HDL", "hdl") res <- ds.quantileMean(x='hdl', type='split') @@ -78,7 +79,7 @@ test_that("quantileMean_split", { # Tear down # -context("ds.quantileMean::smk::shutdown") +# context("ds.quantileMean::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "hdl")) @@ -86,4 +87,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.quantileMean::smk::done") +# context("ds.quantileMean::smk::done") diff --git a/tests/testthat/test-smk-ds.rBinom.R b/tests/testthat/test-smk-ds.rBinom.R index 000f41833..657466933 100644 --- a/tests/testthat/test-smk-ds.rBinom.R +++ b/tests/testthat/test-smk-ds.rBinom.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.rBinom::smk::setup") +# context("ds.rBinom::smk::setup") connect.studies.dataset.cnsim(list("LAB_TSC")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.rBinom::smk::simple test") +# context("ds.rBinom::smk::simple test") test_that("simple test", { res <- ds.rBinom(samp.size = 50, size = 50, prob = 0.25, newobj = "binom_dist", seed.as.integer = 27) @@ -45,7 +46,7 @@ test_that("simple test", { # Done # -context("ds.rBinom::smk::shutdown") +# context("ds.rBinom::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "binom_dist")) @@ -53,4 +54,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.rBinom::smk::done") +# context("ds.rBinom::smk::done") diff --git a/tests/testthat/test-smk-ds.rNorm.R b/tests/testthat/test-smk-ds.rNorm.R index 9996db9a8..cc63c1c04 100644 --- a/tests/testthat/test-smk-ds.rNorm.R +++ b/tests/testthat/test-smk-ds.rNorm.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.rNorm::smk::setup") +# context("ds.rNorm::smk::setup") connect.studies.dataset.cnsim(list("LAB_TSC")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.rNorm::smk::simple test") +# context("ds.rNorm::smk::simple test") test_that("simple test", { res <- ds.rNorm(samp.size = 50, mean = 10, sd = 5, newobj = "norm_dist", seed.as.integer = 27, force.output.to.k.decimal.places = 4) @@ -45,7 +46,7 @@ test_that("simple test", { # Done # -context("ds.rNorm::smk::shutdown") +# context("ds.rNorm::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "norm_dist")) @@ -53,4 +54,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.rNorm::smk::done") +# context("ds.rNorm::smk::done") diff --git a/tests/testthat/test-smk-ds.rPois.R b/tests/testthat/test-smk-ds.rPois.R index 38ebe55c2..68e74802c 100644 --- a/tests/testthat/test-smk-ds.rPois.R +++ b/tests/testthat/test-smk-ds.rPois.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.rPois::smk::setup") +# context("ds.rPois::smk::setup") connect.studies.dataset.cnsim(list("LAB_TSC")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.rPois::smk::simple test") +# context("ds.rPois::smk::simple test") test_that("simple test", { res <- ds.rPois(samp.size = 50, lambda = 1, newobj = "pois_dist", seed.as.integer = 27) @@ -45,7 +46,7 @@ test_that("simple test", { # Done # -context("ds.rPois::smk::shutdown") +# context("ds.rPois::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "pois_dist")) @@ -53,4 +54,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.rPois::smk::done") +# context("ds.rPois::smk::done") diff --git a/tests/testthat/test-smk-ds.rUnif.R b/tests/testthat/test-smk-ds.rUnif.R index 3682a0c30..f8fa681bd 100644 --- a/tests/testthat/test-smk-ds.rUnif.R +++ b/tests/testthat/test-smk-ds.rUnif.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.rUnif::smk::setup") +# context("ds.rUnif::smk::setup") connect.studies.dataset.cnsim(list("LAB_TSC")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.rUnif::smk::simple test") +# context("ds.rUnif::smk::simple test") test_that("simple test", { res <- ds.rUnif(samp.size = 50, min = 0, max = 1, newobj = "unif_dist", seed.as.integer = 27, force.output.to.k.decimal.places = 4) @@ -45,7 +46,7 @@ test_that("simple test", { # Done # -context("ds.rUnif::smk::shutdown") +# context("ds.rUnif::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "unif_dist")) @@ -53,4 +54,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.rUnif::smk::done") +# context("ds.rUnif::smk::done") diff --git a/tests/testthat/test-smk-ds.ranksSecure.R b/tests/testthat/test-smk-ds.ranksSecure.R index 890ac2633..43720c1f9 100644 --- a/tests/testthat/test-smk-ds.ranksSecure.R +++ b/tests/testthat/test-smk-ds.ranksSecure.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.ranksSecure::smk::setup") +# context("ds.ranksSecure::smk::setup") connect.studies.dataset.cnsim(list("LAB_TRIG", "LAB_TSC")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.ranksSecure::smk::continous, without NAs, all positive") +# context("ds.ranksSecure::smk::continous, without NAs, all positive") test_that("continous, without NAs, all positive", { res.cc <- ds.completeCases("D$LAB_TSC", newobj="CC_LAB_TSC") expect_equal(res.cc$validity.check, " appears valid in all sources") @@ -51,7 +52,7 @@ test_that("continous, without NAs, all positive", { expect_true(all(class(res$final.quantile.vector) %in% c('numeric'))) }) -context("ds.ranksSecure::smk::continous, without NAs, with negative") +# context("ds.ranksSecure::smk::continous, without NAs, with negative") test_that("continous, without NAs, with negative", { res.cc <- ds.completeCases("D$LAB_TRIG", newobj="CC_LAB_TRIG") expect_equal(res.cc$validity.check, " appears valid in all sources") @@ -78,7 +79,7 @@ test_that("continous, without NAs, with negative", { expect_true(all(class(res$final.quantile.vector) %in% c('numeric'))) }) -context("ds.ranksSecure::smk::continous, with NAs, all positive") +# context("ds.ranksSecure::smk::continous, with NAs, all positive") test_that("continous, with NAs, all positive", { res <- ds.ranksSecure("D$LAB_TSC") @@ -96,7 +97,7 @@ test_that("continous, with NAs, all positive", { expect_true(all(class(res$final.quantile.vector) %in% c('numeric'))) }) -context("ds.ranksSecure::smk::continous, with NAs, with negative") +# context("ds.ranksSecure::smk::continous, with NAs, with negative") test_that("continous, with NAs, with negative", { res <- ds.ranksSecure("D$LAB_TRIG") @@ -119,7 +120,7 @@ test_that("continous, with NAs, with negative", { # Done # -context("ds.ranksSecure::smk::shutdown") +# context("ds.ranksSecure::smk::shutdown") test_that("setup", { ds_expect_variables(c("D", "CC_LAB_TSC", "CC_LAB_TRIG", "final.quantile.df", "summary.ranks.df", "testvar.ranks")) @@ -127,4 +128,4 @@ test_that("setup", { disconnect.studies.dataset.cnsim() -context("ds.ranksSecure::smk::done") +# context("ds.ranksSecure::smk::done") diff --git a/tests/testthat/test-smk-ds.rbind.R b/tests/testthat/test-smk-ds.rbind.R index 20cc910c7..af01b50e7 100644 --- a/tests/testthat/test-smk-ds.rbind.R +++ b/tests/testthat/test-smk-ds.rbind.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.rbind::smk::setup") +# context("ds.rbind::smk::setup") connect.studies.dataset.survival(list("survtime", "time.id", "female", "age.60")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.rbind::smk") +# context("ds.rbind::smk") test_that("simple test", { res <- ds.rbind(c("D$survtime", "D$time.id", "D$female", "D$age.60"), newobj="rbind_newobj") @@ -42,7 +43,7 @@ test_that("simple test", { # Done # -context("ds.rbind::smk::shutdown") +# context("ds.rbind::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "rbind_newobj")) @@ -50,4 +51,4 @@ test_that("shutdown", { disconnect.studies.dataset.survival() -context("ds.rbind::smk::done") +# context("ds.rbind::smk::done") diff --git a/tests/testthat/test-smk-ds.reShape.R b/tests/testthat/test-smk-ds.reShape.R index 5b96a861c..2836d20be 100644 --- a/tests/testthat/test-smk-ds.reShape.R +++ b/tests/testthat/test-smk-ds.reShape.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.reShape::smk::setup") +# context("ds.reShape::smk::setup") connect.studies.dataset.survival(list("id", "study.id", "time.id", "cens", "age.60", "female")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.reShape::smk") +# context("ds.reShape::smk") test_that("simplest ds.reShape, wide", { res <- ds.reShape(data.name="D", v.names="age.60", timevar.name="time.id", idvar.name="id", direction="wide", newobj="reshape1_obj") @@ -45,7 +46,7 @@ test_that("simplest ds.reShape, wide", { # Done # -context("ds.reShape::smk::shutdown") +# context("ds.reShape::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "reshape1_obj")) @@ -53,4 +54,4 @@ test_that("shutdown", { disconnect.studies.dataset.survival() -context("ds.reShape::smk::done") +# context("ds.reShape::smk::done") diff --git a/tests/testthat/test-smk-ds.recodeLevels.R b/tests/testthat/test-smk-ds.recodeLevels.R index cdc3d7879..3b813074f 100644 --- a/tests/testthat/test-smk-ds.recodeLevels.R +++ b/tests/testthat/test-smk-ds.recodeLevels.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.recodeLevels::smk::setup") +# context("ds.recodeLevels::smk::setup") connect.studies.dataset.cnsim(list("PM_BMI_CATEGORICAL")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.recodeLevels::smk") +# context("ds.recodeLevels::smk") test_that("new levels", { expect_warning(ds.recodeLevels(x='D$PM_BMI_CATEGORICAL', newCategories=c('normal', 'overweight', 'obesity'), newobj='bmi_new'), "'ds.recodeLevels' is deprecated.\nUse 'ds.recodeValues' instead.", fixed = TRUE) levels <- ds.levels(x='bmi_new') @@ -39,7 +40,7 @@ test_that("new levels", { expect_equal(levels$sim3$Levels, expected) }) -context("ds.recodeLevels::smk::no connections or newobj") +# context("ds.recodeLevels::smk::no connections or newobj") test_that("new levels auto", { expect_warning(ds.recodeLevels(x='D$PM_BMI_CATEGORICAL', newCategories=c('normal', 'overweight', 'obesity')), "'ds.recodeLevels' is deprecated.\nUse 'ds.recodeValues' instead.", fixed = TRUE) levels <- ds.levels(x='PM_BMI_CATEGORICAL_new') @@ -58,7 +59,7 @@ test_that("new levels auto", { # Tear down # -context("ds.recodeLevels::smk::shutdown") +# context("ds.recodeLevels::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "bmi_new", "PM_BMI_CATEGORICAL_new")) @@ -66,4 +67,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.recodeLevels::smk::done") +# context("ds.recodeLevels::smk::done") diff --git a/tests/testthat/test-smk-ds.recodeValues.R b/tests/testthat/test-smk-ds.recodeValues.R index 187ec63d5..a20d4db47 100644 --- a/tests/testthat/test-smk-ds.recodeValues.R +++ b/tests/testthat/test-smk-ds.recodeValues.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.recodeValues::smk::setup") +# context("ds.recodeValues::smk::setup") connect.studies.dataset.survival(list("survtime", "time.id", "female", "age.60")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.recodeValues::smk") +# context("ds.recodeValues::smk") test_that("simple test", { res <- ds.recodeValues("D$survtime", values2replace.vector=c(0,1), new.values.vector=c(-10,10), newobj="recodevalues_newobj") @@ -43,7 +44,7 @@ test_that("simple test", { # # Done # -context("ds.recodeValues::smk::shutdown") +# context("ds.recodeValues::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "recodevalues_newobj")) @@ -51,4 +52,4 @@ test_that("shutdown", { disconnect.studies.dataset.survival() -context("ds.recodeValues::smk::done") +# context("ds.recodeValues::smk::done") diff --git a/tests/testthat/test-smk-ds.rep-complex.R b/tests/testthat/test-smk-ds.rep-complex.R index 1a42fdbc3..7d86a8266 100644 --- a/tests/testthat/test-smk-ds.rep-complex.R +++ b/tests/testthat/test-smk-ds.rep-complex.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.rep::smk::complex setup") +# context("ds.rep::smk::complex setup") connect.studies.dataset.cnsim(list("LAB_TSC", "GENDER")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.rep::smk::complex") +# context("ds.rep::smk::complex") test_that("complex test", { res1 <- ds.rep(x1 = 4, times = 6, length.out = NA, each = 1, source.x1 = "clientside", source.times = "c", source.length.out = NULL, source.each = "c", x1.includes.characters = FALSE, newobj = "rep1.seq") @@ -44,7 +45,7 @@ test_that("complex test", { # Done # -context("ds.rep::smk::complex shutdown") +# context("ds.rep::smk::complex shutdown") test_that("shutdown", { ds_expect_variables(c("D", "rep1.seq", "rep2.seq")) @@ -52,4 +53,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.rep::smk::complex done") +# context("ds.rep::smk::complex done") diff --git a/tests/testthat/test-smk-ds.rep.R b/tests/testthat/test-smk-ds.rep.R index c65cba69c..e3819cc76 100644 --- a/tests/testthat/test-smk-ds.rep.R +++ b/tests/testthat/test-smk-ds.rep.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.rep::smk::setup") +# context("ds.rep::smk::setup") connect.studies.dataset.survival(list("survtime", "time.id", "female")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.rep::smk") +# context("ds.rep::smk") test_that("simple test", { res <- ds.rep("D$survtime") @@ -37,7 +38,7 @@ test_that("simple test", { # Done # -context("ds.rep::smk::shutdown") +# context("ds.rep::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "seq.vect")) @@ -45,4 +46,4 @@ test_that("shutdown", { disconnect.studies.dataset.survival() -context("ds.rep::smk::done") +# context("ds.rep::smk::done") diff --git a/tests/testthat/test-smk-ds.replaceNA.R b/tests/testthat/test-smk-ds.replaceNA.R index 9aad07feb..04bdfdf45 100644 --- a/tests/testthat/test-smk-ds.replaceNA.R +++ b/tests/testthat/test-smk-ds.replaceNA.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.replaceNA::smk::setup") +# context("ds.replaceNA::smk::setup") connect.studies.dataset.cnsim(list("LAB_HDL", "LAB_TRIG", "DIS_CVA")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.replaceNA::smk") +# context("ds.replaceNA::smk") test_that("simple replaceNA", { res1 <- ds.replaceNA(x='D$LAB_HDL', forNA=c(1.0, 2.0, 3.0), newobj="newobj1") expect_length(res1, 0) @@ -40,7 +41,7 @@ test_that("simple replaceNA", { # Done # -context("ds.replaceNA::smk::shutdown") +# context("ds.replaceNA::smk::shutdown") test_that("setup", { ds_expect_variables(c("D", "newobj1", "newobj2", "newobj3")) @@ -48,4 +49,4 @@ test_that("setup", { disconnect.studies.dataset.cnsim() -context("ds.replaceNA::smk::done") +# context("ds.replaceNA::smk::done") diff --git a/tests/testthat/test-smk-ds.rm.R b/tests/testthat/test-smk-ds.rm.R index 75be387a5..f13b1dcfd 100644 --- a/tests/testthat/test-smk-ds.rm.R +++ b/tests/testthat/test-smk-ds.rm.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.rm::smk::setup") +# context("ds.rm::smk::setup") connect.studies.dataset.survival(list("survtime", "time.id", "female")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.rm::smk") +# context("ds.rm::smk") test_that("simple test", { res1 <- ds.rm("nonexistant_object") @@ -67,7 +68,7 @@ test_that("simple test", { expect_equal(res2$survival1$problem.objects, "") }) -context("ds.rm::smk") +# context("ds.rm::smk") test_that("multiple test", { res1 <- ds.rm("nonexistant_object1,nonexistant_object2") @@ -136,7 +137,7 @@ test_that("multiple test", { # Done # -context("ds.rm::smk::shutdown") +# context("ds.rm::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -144,4 +145,4 @@ test_that("shutdown", { disconnect.studies.dataset.survival() -context("ds.rm::smk::done") +# context("ds.rm::smk::done") diff --git a/tests/testthat/test-smk-ds.rowColCalc.R b/tests/testthat/test-smk-ds.rowColCalc.R index 002d763db..792bfb5e4 100644 --- a/tests/testthat/test-smk-ds.rowColCalc.R +++ b/tests/testthat/test-smk-ds.rowColCalc.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.rowColCalc::smk::setup") +# context("ds.rowColCalc::smk::setup") connect.studies.dataset.cnsim(list("LAB_TSC", "LAB_HDL")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.rowColCalc::smk") +# context("ds.rowColCalc::smk") ds.rowColCalc(x='D', operation="rowSums", newobj="rsum_hdl_tsc") res <- ds.exists('rsum_hdl_tsc') test_that("rowColCalc_exists", { @@ -34,7 +35,7 @@ test_that("rowColCalc_exists", { expect_true(res$sim3) }) -context("ds.rowColCalc::smk::no newobj") +# context("ds.rowColCalc::smk::no newobj") ds.rowColCalc(x='D', operation="rowSums") res <- ds.exists('rowcolcalc.newobj') test_that("rowColCalc_out_exists", { @@ -48,7 +49,7 @@ test_that("rowColCalc_out_exists", { # # Tear down # -context("ds.rowColCalc::smk::shutdown") +# context("ds.rowColCalc::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "rsum_hdl_tsc", "rowcolcalc.newobj")) @@ -56,4 +57,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.rowColCalc::smk::done") +# context("ds.rowColCalc::smk::done") diff --git a/tests/testthat/test-smk-ds.sample.R b/tests/testthat/test-smk-ds.sample.R index 8a251e3bb..797caefaa 100644 --- a/tests/testthat/test-smk-ds.sample.R +++ b/tests/testthat/test-smk-ds.sample.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.sample::smk::setup") +# context("ds.sample::smk::setup") connect.studies.dataset.survival(list("survtime", "time.id", "female")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.sample::smk::test") +# context("ds.sample::smk::test") test_that("simple test", { res1 <- ds.sample(x="D", size=30) @@ -115,7 +116,7 @@ test_that("simple test", { expect_equal(res2_survtime_length$`total length of test.obj$in.sample in all studies combined`, 126) }) -context("ds.sample::smk::test error") +# context("ds.sample::smk::test error") test_that("simple test, error", { expect_error(ds.sample(x="D$survtime", size="30", newobj="no.obj"), "There are some DataSHIELD errors, list them with datashield.errors()", fixed = TRUE) @@ -131,7 +132,7 @@ test_that("simple test, error", { # Done # -context("ds.sample::smk::shutdown") +# context("ds.sample::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "newobj.sample", "test.obj")) @@ -139,4 +140,4 @@ test_that("shutdown", { disconnect.studies.dataset.survival() -context("ds.sample::smk::done") +# context("ds.sample::smk::done") diff --git a/tests/testthat/test-smk-ds.seq.R b/tests/testthat/test-smk-ds.seq.R index f44c7e46e..7da50458a 100644 --- a/tests/testthat/test-smk-ds.seq.R +++ b/tests/testthat/test-smk-ds.seq.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.seq::smk::setup") +# context("ds.seq::smk::setup") connect.studies.dataset.cnsim(list("LAB_TSC")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.seq::smk") +# context("ds.seq::smk") test_that("simplest ds.seq", { seq.res <- ds.seq(FROM.value.char="1", BY.value.char="1", LENGTH.OUT.value.char="10", ALONG.WITH.name=NULL, newobj="obj1") @@ -45,7 +46,7 @@ test_that("simplest ds.seq", { # Tear down # -context("ds.seq::smk::shutdown") +# context("ds.seq::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "obj1", "obj2")) @@ -53,4 +54,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.seq::smk::done") +# context("ds.seq::smk::done") diff --git a/tests/testthat/test-smk-ds.setSeed.R b/tests/testthat/test-smk-ds.setSeed.R index eadf7fe18..fadeaae9f 100644 --- a/tests/testthat/test-smk-ds.setSeed.R +++ b/tests/testthat/test-smk-ds.setSeed.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.setSeed::smk::setup") +# context("ds.setSeed::smk::setup") connect.studies.dataset.cnsim(list("LAB_TSC")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.setSeed::smk") +# context("ds.setSeed::smk") test_that("basic setSeed", { res.setSeed <- ds.setSeed(1234) @@ -43,7 +44,7 @@ test_that("basic setSeed", { # Done # -context("ds.setSeed::smk::shutdown") +# context("ds.setSeed::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -51,4 +52,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.setSeed::smk::done") +# context("ds.setSeed::smk::done") diff --git a/tests/testthat/test-smk-ds.skewness.R b/tests/testthat/test-smk-ds.skewness.R index e607b9a93..d6f7eaec4 100644 --- a/tests/testthat/test-smk-ds.skewness.R +++ b/tests/testthat/test-smk-ds.skewness.R @@ -1,6 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. -# Copyright (c) 2022 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -13,7 +13,7 @@ # Set up # -context("ds.skewness::smk::setup") +# context("ds.skewness::smk::setup") connect.studies.dataset.cnsim(list("LAB_TSC", "LAB_TRIG", "LAB_HDL", "LAB_GLUC_ADJUSTED", "PM_BMI_CONTINUOUS")) @@ -27,7 +27,7 @@ test_that("setup", { # Method 1 -context("ds.skewness::smk::method 1::split") +# context("ds.skewness::smk::method 1::split") test_that("simple skewness, method 1, split, on LAB_TSC", { skewness.res <- ds.skewness(x = 'D$LAB_TSC', method = 1, type='split') @@ -128,7 +128,7 @@ test_that("simple skewness, method 1, split, on PM_BMI_CONTINUOUS", { expect_equal(skewness.res$ValidityMessage[3], "VALID ANALYSIS") }) -context("ds.skewness::smk::method 1::combine") +# context("ds.skewness::smk::method 1::combine") test_that("simple skewness, combine, on LAB_TSC", { skewness.res <- ds.skewness(x = 'D$LAB_TSC', method = 1, type='combine') @@ -199,7 +199,7 @@ test_that("simple skewness, method 1, combine, on PM_BMI_CONTINUOUS", { expect_equal(skewness.res$ValidityMessage[1], "VALID ANALYSIS") }) -context("ds.skewness::smk::method 1::both") +# context("ds.skewness::smk::method 1::both") test_that("simple skewness, both, on LAB_TSC", { skewness.res <- ds.skewness(x = 'D$LAB_TSC', method = 1, type='both') @@ -342,7 +342,7 @@ test_that("simple skewness, method 1, both, on PM_BMI_CONTINUOUS", { # Method 2 -context("ds.skewness::smk::method 2::split") +# context("ds.skewness::smk::method 2::split") test_that("simple skewness, method 2, split, on LAB_TSC", { skewness.res <- ds.skewness(x = 'D$LAB_TSC', method = 2, type='split') @@ -443,7 +443,7 @@ test_that("simple skewness, method 2, split, on PM_BMI_CONTINUOUS", { expect_equal(skewness.res$ValidityMessage[3], "VALID ANALYSIS") }) -context("ds.skewness::smk::method 2::combine") +# context("ds.skewness::smk::method 2::combine") test_that("simple skewness, combine, on LAB_TSC", { skewness.res <- ds.skewness(x = 'D$LAB_TSC', method = 2, type='combine') @@ -514,7 +514,7 @@ test_that("simple skewness, method 2, combine, on PM_BMI_CONTINUOUS", { expect_equal(skewness.res$ValidityMessage[1], "VALID ANALYSIS") }) -context("ds.skewness::smk::method 2::both") +# context("ds.skewness::smk::method 2::both") test_that("simple skewness, both, on LAB_TSC", { skewness.res <- ds.skewness(x = 'D$LAB_TSC', method = 2, type='both') @@ -657,7 +657,7 @@ test_that("simple skewness, method 2, both, on PM_BMI_CONTINUOUS", { # Method 3 -context("ds.skewness::smk::method 3::split") +# context("ds.skewness::smk::method 3::split") test_that("simple skewness, method 3, split, on LAB_TSC", { skewness.res <- ds.skewness(x = 'D$LAB_TSC', method = 3, type='split') @@ -758,7 +758,7 @@ test_that("simple skewness, method 3, split, on PM_BMI_CONTINUOUS", { expect_equal(skewness.res$ValidityMessage[3], "VALID ANALYSIS") }) -context("ds.skewness::smk::method 3::combine") +# context("ds.skewness::smk::method 3::combine") test_that("simple skewness, combine, on LAB_TSC", { skewness.res <- ds.skewness(x = 'D$LAB_TSC', method = 3, type='combine') @@ -829,7 +829,7 @@ test_that("simple skewness, method 3, combine, on PM_BMI_CONTINUOUS", { expect_equal(skewness.res$ValidityMessage[1], "VALID ANALYSIS") }) -context("ds.skewness::smk::method 3::both") +# context("ds.skewness::smk::method 3::both") test_that("simple skewness, both, on LAB_TSC", { skewness.res <- ds.skewness(x = 'D$LAB_TSC', method = 3, type='both') @@ -974,7 +974,7 @@ test_that("simple skewness, method 3, both, on PM_BMI_CONTINUOUS", { # Done # -context("ds.skewness::smk::shutdown") +# context("ds.skewness::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -982,4 +982,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.skewness::smk::done") +# context("ds.skewness::smk::done") diff --git a/tests/testthat/test-smk-ds.sqrt.R b/tests/testthat/test-smk-ds.sqrt.R index 9c106c736..ccb50c0ca 100644 --- a/tests/testthat/test-smk-ds.sqrt.R +++ b/tests/testthat/test-smk-ds.sqrt.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.sqrt::smk::setup") +# context("ds.sqrt::smk::setup") connect.studies.dataset.cnsim(list("LAB_TSC")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.sqrt::smk") +# context("ds.sqrt::smk") test_that("simple c", { res <- ds.sqrt("D$LAB_TSC", newobj = "sqrt.newobj") @@ -50,7 +51,7 @@ test_that("simple c", { # Done # -context("ds.sqrt::smk::shutdown") +# context("ds.sqrt::smk::shutdown") test_that("setup", { ds_expect_variables(c("D", "sqrt.newobj")) @@ -58,4 +59,4 @@ test_that("setup", { disconnect.studies.dataset.cnsim() -context("ds.sqrt::smk::done") +# context("ds.sqrt::smk::done") diff --git a/tests/testthat/test-smk-ds.subset.R b/tests/testthat/test-smk-ds.subset.R index 4accdfe5e..88fecdd2d 100644 --- a/tests/testthat/test-smk-ds.subset.R +++ b/tests/testthat/test-smk-ds.subset.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.subset::smk::setup") +# context("ds.subset::smk::setup") connect.studies.dataset.cnsim(list("DIS_DIAB","PM_BMI_CONTINUOUS","LAB_HDL", "GENDER")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.subset::smk::generate a subset of the assigned table (by default the table is named 'D') with the first 50 observations and the two first columns") +# context("ds.subset::smk::generate a subset of the assigned table (by default the table is named 'D') with the first 50 observations and the two first columns") ds.subset(datasources=ds.test_env$connections, subset='subD', x='D', rows=c(1:50), cols=c(1,2)) res <- ds.exists('subD') test_that("subD_exists", { @@ -34,7 +35,7 @@ test_that("subD_exists", { expect_true(res$sim3) }) -context("ds.subset::smk::generate a subset of the assigned table (by default the table is named 'D') with the first 50 observations and the two first columns referred to by their names") +# context("ds.subset::smk::generate a subset of the assigned table (by default the table is named 'D') with the first 50 observations and the two first columns referred to by their names") ds.subset(subset='subD2', x='D', rows=c(1:50), cols = c('DIS_DIAB','PM_BMI_CONTINUOUS')) res <- ds.exists('subD2') test_that("subD2_exists", { @@ -44,7 +45,7 @@ test_that("subD2_exists", { expect_true(res$sim3) }) -context("ds.subset::smk::generate a subset of the table D with bmi values greater than or equal to 25.") +# context("ds.subset::smk::generate a subset of the table D with bmi values greater than or equal to 25.") ds.subset(datasources=ds.test_env$connections, subset='subD3', x='D', logical='PM_BMI_CONTINUOUS>=', threshold=25) res <- ds.exists('subD3') test_that("subD3_exists", { @@ -80,7 +81,7 @@ test_that("subD3_exists", { # Tear down # -context("ds.subset::smk::shutdown") +# context("ds.subset::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "subD", "subD2", "subD3")) @@ -88,4 +89,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.subset::smk::done") +# context("ds.subset::smk::done") diff --git a/tests/testthat/test-smk-ds.subsetByClass.R b/tests/testthat/test-smk-ds.subsetByClass.R index 95bf16ebf..71420fcbe 100644 --- a/tests/testthat/test-smk-ds.subsetByClass.R +++ b/tests/testthat/test-smk-ds.subsetByClass.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.subsetByClass::smk::setup") +# context("ds.subsetByClass::smk::setup") connect.studies.dataset.cnsim(list("LAB_TSC", "GENDER")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.subsetByClass::smk") +# context("ds.subsetByClass::smk") test_that("gender implicit", { res <- ds.subsetByClass(x='D', subsets='subclasses1') @@ -67,7 +68,7 @@ test_that("gender explicit", { # Tear down # -context("ds.subsetByClass::smk::shutdown") +# context("ds.subsetByClass::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "subclasses1", "subclasses2")) @@ -75,4 +76,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.subsetByClass::smk::done") +# context("ds.subsetByClass::smk::done") diff --git a/tests/testthat/test-smk-ds.summary.R b/tests/testthat/test-smk-ds.summary.R index fd39b021c..750c0392d 100644 --- a/tests/testthat/test-smk-ds.summary.R +++ b/tests/testthat/test-smk-ds.summary.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.summary::smk::setup") +# context("ds.summary::smk::setup") connect.studies.dataset.cnsim(list('LAB_TSC', 'LAB_TRIG', 'LAB_HDL', 'LAB_GLUC_ADJUSTED', 'PM_BMI_CONTINUOUS', 'DIS_CVA', 'MEDI_LPD', 'DIS_DIAB', 'DIS_AMI', 'GENDER', 'PM_BMI_CATEGORICAL')) @@ -23,7 +24,7 @@ test_that("setup", { # # Tests # -context("ds.summary::smk::summary of a dataframe variable") +# context("ds.summary::smk::summary of a dataframe variable") test_that("summary_dataframe_variable", { res <- ds.summary(x='D') @@ -42,7 +43,7 @@ test_that("summary_dataframe_variable", { expect_length(res$sim3$`variables held`, 11) }) -context("ds.summary::smk::summary of a numerical variable") +# context("ds.summary::smk::summary of a numerical variable") test_that("summary_numerical_variable", { res <- ds.summary(x='D$LAB_TSC') @@ -51,7 +52,7 @@ test_that("summary_numerical_variable", { expect_equal(res$sim3$`quantiles & mean`[[4]], 5.786) }) -context("ds.summary::smk::summary of a character variable") +# context("ds.summary::smk::summary of a character variable") test_that("summary_character_variable", { ds.asCharacter(x='D$GENDER', newobj="a_character") res <- ds.summary(x='a_character') @@ -60,7 +61,7 @@ test_that("summary_character_variable", { expect_equal(res$sim2$length, 3088) }) -context("ds.summary::smk::summary of a factor variable") +# context("ds.summary::smk::summary of a factor variable") test_that("summary_factor_variable", { ds.asFactor('D$PM_BMI_CATEGORICAL', newobj="a_factor") res <- ds.summary(x='a_factor') @@ -89,7 +90,7 @@ test_that("summary_factor_variable", { expect_equal(res$sim3$`count of '3'`, 1154) }) -context("ds.summary::smk::summary of a list variable") +# context("ds.summary::smk::summary of a list variable") test_that("summary_list_variable", { ds.asList(x.name='D$PM_BMI_CATEGORICAL', newobj="a_list") res <- ds.summary(x='a_list') @@ -106,7 +107,7 @@ test_that("summary_list_variable", { expect_equal(res$sim3$length, 4128) }) -context("ds.summary::smk::summary of a data frame") +# context("ds.summary::smk::summary of a data frame") test_that("summary_data_frame", { res <- ds.summary(x='D') @@ -122,7 +123,7 @@ test_that("summary_data_frame", { # Tear down # -context("ds.summary::smk::teardown") +# context("ds.summary::smk::teardown") test_that("shutdown", { ds_expect_variables(c("D", "a_character", "a_factor", "a_list")) @@ -130,4 +131,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.summary::smk::done") +# context("ds.summary::smk::done") diff --git a/tests/testthat/test-smk-ds.table.R b/tests/testthat/test-smk-ds.table.R index bae8aae42..0dd48cef1 100644 --- a/tests/testthat/test-smk-ds.table.R +++ b/tests/testthat/test-smk-ds.table.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -11,7 +12,7 @@ # # Set up # -context("ds.table::smk::setup") +# context("ds.table::smk::setup") connect.all.datasets() @@ -23,7 +24,7 @@ test_that("setup", { # Tests # -context("ds.table::smk::dataframe setup") +# context("ds.table::smk::dataframe setup") test_that("simple dataframe input setup", { ds.asFactor(input.var.name="D$FACTOR_CHARACTER", newobj.name="factorCharacter") ds.asFactor(input.var.name="D$FACTOR_INTEGER", newobj.name="factorInteger") @@ -38,7 +39,7 @@ test_that("simple dataframe input setup", { expect_equal(subset.res$validity.check, " appears valid in all sources") }) -context("ds.table::smk::simple table 1D") +# context("ds.table::smk::simple table 1D") test_that("simple table 1D", { table1.res <- ds.table(rvar='tablesource_subset$factorCharacter') @@ -53,7 +54,7 @@ test_that("simple table 1D", { expect_equal(table1.res$validity.message, "Data in all studies were valid") }) -context("ds.table::smk::simple table 2D") +# context("ds.table::smk::simple table 2D") test_that("simple table 2D", { table1.res <- ds.table(rvar='tablesource_subset$factorInteger', cvar='tablesource_subset$factorCharacter') @@ -75,7 +76,7 @@ test_that("simple table 2D", { expect_equal(table1.res$validity.message, "Data in all studies were valid") }) -context("ds.table::smk::simple table 3D") +# context("ds.table::smk::simple table 3D") test_that("simple table 3D", { expect_error(ds.table(rvar='tablesource_subset$factorInteger', cvar='tablesource_subset$factorCharacter', stvar='tablesource_subset$factorCategory'), "There are some DataSHIELD errors, list them with datashield.errors()", fixed = TRUE) @@ -141,7 +142,7 @@ test_that("simple table 3D, with assign", { # Done # -context("ds.table::smk::shutdown") +# context("ds.table::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "factorCharacter", "factorInteger", "factorCategory", "tablesource", "tablesource_subset", "new_table1", "new_table2", "new_table3")) @@ -149,4 +150,4 @@ test_that("shutdown", { disconnect.all.datasets() -context("ds.table::smk::done") +# context("ds.table::smk::done") diff --git a/tests/testthat/test-smk-ds.table1D.R b/tests/testthat/test-smk-ds.table1D.R index 013cdf322..a875f5929 100644 --- a/tests/testthat/test-smk-ds.table1D.R +++ b/tests/testthat/test-smk-ds.table1D.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.table1D::smk::setup") +# context("ds.table1D::smk::setup") connect.studies.dataset.cnsim(list("DIS_CVA","GENDER")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.table1D::smk::generate a one dimensional table, outputting combined contingency tables") +# context("ds.table1D::smk::generate a one dimensional table, outputting combined contingency tables") test_that("GENDER_normal", { res <- expect_warning(ds.table1D(x='D$GENDER'), "'ds.table1D' is deprecated.\nUse 'ds.table' instead.", fixed = TRUE) @@ -33,7 +34,7 @@ test_that("GENDER_normal", { expect_equal(res$counts[3], 9379) }) -context("ds.table1D::smk::generate a one dimensional table, outputting combined contingency tables fail") +# context("ds.table1D::smk::generate a one dimensional table, outputting combined contingency tables fail") test_that("DIS_CVA_invalid", { res <- expect_warning(ds.table1D(x='D$DIS_CVA'), "'ds.table1D' is deprecated.\nUse 'ds.table' instead.", fixed = TRUE) @@ -45,7 +46,7 @@ test_that("DIS_CVA_invalid", { expect_equal(res$validity, "All tables are valid!") }) -context("ds.table1D::smk::generate a one dimensional table, outputting combined contingency tables fail split") +# context("ds.table1D::smk::generate a one dimensional table, outputting combined contingency tables fail split") test_that("DIS_CVA_invalid_split", { res <- expect_warning(ds.table1D(x='D$DIS_CVA', type="split"), "'ds.table1D' is deprecated.\nUse 'ds.table' instead.", fixed = TRUE) @@ -57,7 +58,7 @@ test_that("DIS_CVA_invalid_split", { expect_equal(res$validity, "All tables are valid!") }) -context("ds.table1D::smk::generate a one dimensional table, outputting study specific contingency tables") +# context("ds.table1D::smk::generate a one dimensional table, outputting study specific contingency tables") test_that("GENDER_split", { res <- expect_warning(ds.table1D(x='D$GENDER', type="split"), "'ds.table1D' is deprecated.\nUse 'ds.table' instead.", fixed = TRUE) @@ -67,7 +68,7 @@ test_that("GENDER_split", { expect_equal(res$counts$sim3[1], 2091) }) -context("ds.table1D::smk::generate a one dimensional table, outputting study specific contingency tables for study 1 and 2") +# context("ds.table1D::smk::generate a one dimensional table, outputting study specific contingency tables for study 1 and 2") test_that("GENDER_split_12", { res <- expect_warning(ds.table1D(datasources=ds.test_env$connections[1:2], x='D$GENDER', type="split"), "'ds.table1D' is deprecated.\nUse 'ds.table' instead.", fixed = TRUE) @@ -77,7 +78,7 @@ test_that("GENDER_split_12", { expect_equal(res$counts$sim3[1], NULL) }) -context("ds.table1D::smk::generate a one dimensional table, outputting study specific and combined contingency tables") +# context("ds.table1D::smk::generate a one dimensional table, outputting study specific and combined contingency tables") test_that("GENDER_normal_2", { res <- expect_warning(ds.table1D(datasources=ds.test_env$connections, x='D$GENDER'), "'ds.table1D' is deprecated.\nUse 'ds.table' instead.", fixed = TRUE) @@ -90,7 +91,7 @@ test_that("GENDER_normal_2", { # Tear down # -context("ds.table1D::smk::shutdown") +# context("ds.table1D::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -98,4 +99,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.table1D::smk::done") +# context("ds.table1D::smk::done") diff --git a/tests/testthat/test-smk-ds.table2D.R b/tests/testthat/test-smk-ds.table2D.R index 09fc859ce..596ae5080 100644 --- a/tests/testthat/test-smk-ds.table2D.R +++ b/tests/testthat/test-smk-ds.table2D.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.table2D::smk::setup") +# context("ds.table2D::smk::setup") connect.studies.dataset.cnsim(list("DIS_DIAB", "GENDER")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.table2D::smk") +# context("ds.table2D::smk") test_that("simple table2D", { table2D.res <- expect_warning(ds.table2D(x='D$DIS_DIAB', y='D$GENDER'), "'ds.table2D' is deprecated.\nUse 'ds.table' instead.", fixed = TRUE) @@ -56,7 +57,7 @@ test_that("simple table2D", { # Done # -context("ds.table2D::smk::shutdown") +# context("ds.table2D::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -64,4 +65,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.table2D::smk::done") +# context("ds.table2D::smk::done") diff --git a/tests/testthat/test-smk-ds.tapply.R b/tests/testthat/test-smk-ds.tapply.R index b79876ff0..67aad82c9 100644 --- a/tests/testthat/test-smk-ds.tapply.R +++ b/tests/testthat/test-smk-ds.tapply.R @@ -1,6 +1,7 @@ #------------------------------------------------------------------------------- # Copyright (c) 2014 OBiBa, # 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -13,7 +14,7 @@ # Set up # -context("ds.tapply::smk::setup") +# context("ds.tapply::smk::setup") connect.studies.dataset.cnsim(list("LAB_TSC", "GENDER")) @@ -28,7 +29,7 @@ test_that("setup", { ds.assign('D$LAB_TSC', 'LAB_TSC') ds.assign('D$GENDER', 'GENDER') -context("ds.tapply::smk::fun=mean") +# context("ds.tapply::smk::fun=mean") test_that("simplest 'ds.tapply', fun=mean", { list <- ds.tapply('LAB_TSC', INDEX.names=c('GENDER'), FUN.name='mean') @@ -56,7 +57,7 @@ test_that("simplest 'ds.tapply', fun=mean", { expect_equal(list$sim3$N[[2]], 1700) }) -context("ds.tapply::smk::fun=sd") +# context("ds.tapply::smk::fun=sd") test_that("simplest 'ds.tapply', fun=sd", { list <- ds.tapply('LAB_TSC', INDEX.names=c('GENDER'), FUN.name='sd') @@ -84,7 +85,7 @@ test_that("simplest 'ds.tapply', fun=sd", { expect_equal(list$sim3$N[[2]], 1700) }) -context("ds.tapply::smk::fun=sum") +# context("ds.tapply::smk::fun=sum") test_that("simplest 'ds.tapply', fun=sum", { list <- ds.tapply('LAB_TSC', INDEX.names=c('GENDER'), FUN.name='sum') @@ -112,7 +113,7 @@ test_that("simplest 'ds.tapply', fun=sum", { expect_equal(list$sim3$N[[2]], 1700) }) -context("ds.tapply::smk::fun=quantile") +# context("ds.tapply::smk::fun=quantile") test_that("simplest 'ds.tapply', fun=quantile", { list <- ds.tapply('LAB_TSC', INDEX.names=c('GENDER'), FUN.name='quantile') @@ -132,7 +133,7 @@ test_that("simplest 'ds.tapply', fun=quantile", { # Tear down # -context("ds.tapply::smk::shutdown") +# context("ds.tapply::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "GENDER", "LAB_TSC")) @@ -140,4 +141,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.tapply::smk::done") +# context("ds.tapply::smk::done") diff --git a/tests/testthat/test-smk-ds.tapply.assign.R b/tests/testthat/test-smk-ds.tapply.assign.R index ba13f39df..8fd4918d2 100644 --- a/tests/testthat/test-smk-ds.tapply.assign.R +++ b/tests/testthat/test-smk-ds.tapply.assign.R @@ -1,6 +1,7 @@ #------------------------------------------------------------------------------- # Copyright (c) 2014 OBiBa, # 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -13,7 +14,7 @@ # Set up # -context("ds.tapply.assign::smk::setup") +# context("ds.tapply.assign::smk::setup") connect.studies.dataset.cnsim(list("LAB_TSC", "GENDER")) @@ -28,7 +29,7 @@ test_that("setup", { ds.assign('D$LAB_TSC', 'LAB_TSC') ds.assign('D$GENDER', 'GENDER') -context("ds.tapply.assign::smk::fun=mean") +# context("ds.tapply.assign::smk::fun=mean") test_that("simplest 'ds.tapply.assign', fun=mean", { list <- ds.tapply.assign('LAB_TSC', INDEX.names=c('GENDER'), FUN.name='mean', newobj="fun_mean.newobj") @@ -44,7 +45,7 @@ test_that("simplest 'ds.tapply.assign', fun=mean", { expect_equal(res.length$`total length of fun_mean.newobj in all studies combined`, 6) }) -context("ds.tapply.assign::smk::fun=sd") +# context("ds.tapply.assign::smk::fun=sd") test_that("simplest 'ds.tapply.assign', fun=sd", { list <- ds.tapply.assign('LAB_TSC', INDEX.names=c('GENDER'), FUN.name='sd', newobj="fun_sd.newobj") @@ -60,7 +61,7 @@ test_that("simplest 'ds.tapply.assign', fun=sd", { expect_equal(res.length$`total length of fun_sd.newobj in all studies combined`, 6) }) -context("ds.tapply.assign::smk::fun=sum") +# context("ds.tapply.assign::smk::fun=sum") test_that("simplest 'ds.tapply.assign', fun=sum", { list <- ds.tapply.assign('LAB_TSC', INDEX.names=c('GENDER'), FUN.name='sum', newobj="fun_sum.newobj") @@ -76,7 +77,7 @@ test_that("simplest 'ds.tapply.assign', fun=sum", { expect_equal(res.length$`total length of fun_sum.newobj in all studies combined`, 6) }) -context("ds.tapply.assign::smk::fun=quantile") +# context("ds.tapply.assign::smk::fun=quantile") test_that("simplest 'ds.tapply.assign', fun=quantile", { list <- ds.tapply.assign('LAB_TSC', INDEX.names=c('GENDER'), FUN.name='quantile', newobj="fun_quantile.newobj") @@ -96,7 +97,7 @@ test_that("simplest 'ds.tapply.assign', fun=quantile", { # Tear down # -context("ds.tapply.assign::smk::shutdown") +# context("ds.tapply.assign::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "GENDER", "LAB_TSC", "fun_mean.newobj", "fun_sd.newobj", "fun_sum.newobj", "fun_quantile.newobj")) @@ -108,4 +109,4 @@ disconnect.studies.dataset.cnsim() # Done # -context("ds.tapply.assign::smk::done") +# context("ds.tapply.assign::smk::done") diff --git a/tests/testthat/test-smk-ds.testObjExists-discordant.R b/tests/testthat/test-smk-ds.testObjExists-discordant.R index a7d89a3ec..5163217fd 100644 --- a/tests/testthat/test-smk-ds.testObjExists-discordant.R +++ b/tests/testthat/test-smk-ds.testObjExists-discordant.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.testObjExists::smk::setup") +# context("ds.testObjExists::smk::setup") connect.discordant.dataset.simple(list("A", "B", "C")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.testObjExists::smk::discordant") +# context("ds.testObjExists::smk::discordant") test_that("simple testObjExists, discordant", { res <- ds.testObjExists('D') @@ -59,7 +60,7 @@ test_that("data.frame testObjExists, discordant", { # Done # -context("ds.testObjExists::smk::shutdown") +# context("ds.testObjExists::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -67,4 +68,4 @@ test_that("shutdown", { disconnect.discordant.dataset.simple() -context("ds.testObjExists::smk::done") +# context("ds.testObjExists::smk::done") diff --git a/tests/testthat/test-smk-ds.testObjExists.R b/tests/testthat/test-smk-ds.testObjExists.R index 5b2b2c383..857fe823c 100644 --- a/tests/testthat/test-smk-ds.testObjExists.R +++ b/tests/testthat/test-smk-ds.testObjExists.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.testObjExists::smk::setup") +# context("ds.testObjExists::smk::setup") connect.studies.dataset.cnsim(list("LAB_TSC", "LAB_HDL")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.testObjExists::smk") +# context("ds.testObjExists::smk") test_that("simple testObjExists", { res <- ds.testObjExists('D') @@ -92,7 +93,7 @@ test_that("data.frame testObjExists", { # Done # -context("ds.testObjExists::smk::shutdown") +# context("ds.testObjExists::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "dataframe.newobj")) @@ -100,4 +101,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.testObjExists::smk::done") +# context("ds.testObjExists::smk::done") diff --git a/tests/testthat/test-smk-ds.unList.R b/tests/testthat/test-smk-ds.unList.R index 98fbaa986..806b13315 100644 --- a/tests/testthat/test-smk-ds.unList.R +++ b/tests/testthat/test-smk-ds.unList.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.unList::smk::setup") +# context("ds.unList::smk::setup") connect.studies.dataset.cnsim(list("GENDER")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.unList::smk::simple test") +# context("ds.unList::smk::simple test") test_that("simple test", { ds.asList(x.name="D$GENDER", newobj="GENDER.list") @@ -39,7 +40,7 @@ test_that("simple test", { # Done # -context("ds.unList::smk::shutdown") +# context("ds.unList::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "GENDER.list", "unlist.newobj")) @@ -47,4 +48,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.unList::smk::done") +# context("ds.unList::smk::done") diff --git a/tests/testthat/test-smk-ds.unique.R b/tests/testthat/test-smk-ds.unique.R index 9aca375ca..21f6f5f03 100644 --- a/tests/testthat/test-smk-ds.unique.R +++ b/tests/testthat/test-smk-ds.unique.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.unique::smk::setup") +# context("ds.unique::smk::setup") connect.studies.dataset.cnsim(list("GENDER")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.unique::smk::simple test") +# context("ds.unique::smk::simple test") test_that("simple test", { original.newobj.length <- ds.length("D$GENDER") @@ -51,7 +52,7 @@ test_that("simple test", { # Done # -context("ds.unique::smk::shutdown") +# context("ds.unique::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "unique.newobj")) @@ -59,4 +60,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.unique::smk::done") +#context("ds.unique::smk::done") diff --git a/tests/testthat/test-smk-ds.var.R b/tests/testthat/test-smk-ds.var.R index bc2aceb6d..834ece232 100644 --- a/tests/testthat/test-smk-ds.var.R +++ b/tests/testthat/test-smk-ds.var.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.var::smk::setup") +# context("ds.var::smk::setup") connect.studies.dataset.cnsim(list("LAB_TSC")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.var::smk::split") +# context("ds.var::smk::split") test_that("simple var, split", { var.res <- ds.var(x = 'D$LAB_TSC', type='split') @@ -49,7 +50,7 @@ test_that("simple var, split", { expect_equal(var.res$ValidityMessage[3], "VALID ANALYSIS") }) -context("ds.var::smk::combine") +# context("ds.var::smk::combine") test_that("simple var, combine", { var.res <- ds.var(x = 'D$LAB_TSC', type='combine') @@ -66,7 +67,7 @@ test_that("simple var, combine", { expect_equal(var.res$ValidityMessage[3], "VALID ANALYSIS") }) -context("ds.var::smk::both") +# context("ds.var::smk::both") test_that("simple var, both", { var.res <- ds.var(x = 'D$LAB_TSC', type='both') @@ -100,7 +101,7 @@ test_that("simple var, both", { # Done # -context("ds.var::smk::shutdown") +# context("ds.var::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -108,4 +109,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.var::smk::done") +# context("ds.var::smk::done") diff --git a/tests/testthat/test-smk-ds.vectorCalc.R b/tests/testthat/test-smk-ds.vectorCalc.R index e318c7477..3c03191fe 100644 --- a/tests/testthat/test-smk-ds.vectorCalc.R +++ b/tests/testthat/test-smk-ds.vectorCalc.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.vectorCalc::smk::setup") +# context("ds.vectorCalc::smk::setup") connect.studies.dataset.cnsim(list('LAB_TSC', 'LAB_HDL')) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.vectorCalc::smk") +# context("ds.vectorCalc::smk") test_that("simple test", { vectors <- c('D$LAB_TSC', 'D$LAB_HDL') res <- expect_warning(ds.vectorCalc(x=vectors, calc='+'), "'ds.vectorCalc' is deprecated.\nUse 'ds.make' instead.", fixed = TRUE) @@ -58,7 +59,7 @@ test_that("simple test", { # Done # -context("ds.vectorCalc::smk::shutdown") +# context("ds.vectorCalc::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "vectorcalc.newobj")) @@ -66,4 +67,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.vectorCalc::smk::done") +# context("ds.vectorCalc::smk::done") diff --git a/tests/testthat/test-smk-isDefined.R b/tests/testthat/test-smk-isDefined.R index 5f37b0aa6..ab3f43b07 100644 --- a/tests/testthat/test-smk-isDefined.R +++ b/tests/testthat/test-smk-isDefined.R @@ -1,6 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. -# Copyright (c) 2022 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -13,7 +13,7 @@ # Set up # -context("isDefined::smk::setup") +# context("isDefined::smk::setup") connect.discordant.dataset.simple(list("A", "B", "C")) @@ -27,7 +27,7 @@ test_that("setup", { # default -context("isDefined::smk::default") +# context("isDefined::smk::default") test_that("default test, dataframe D", { res <- isDefined(ds.test_env$connections, "D") @@ -91,7 +91,7 @@ test_that("default test, dataframe columns D$A,D$B", { # error.message = FALSE -context("isDefined::smk::error.message=FALSE") +# context("isDefined::smk::error.message=FALSE") test_that("error.message=FALSE test, dataframe D", { res <- isDefined(ds.test_env$connections, "D", error.message = FALSE) @@ -197,7 +197,7 @@ test_that("error.message=FALSE test, dataframe columns D$A,D$B", { # error.message = TRUE -context("isDefined::smk::error.message=TRUE") +# context("isDefined::smk::error.message=TRUE") test_that("error.message=TRUE test, dataframe D", { res <- isDefined(ds.test_env$connections, "D", error.message = TRUE) @@ -263,7 +263,7 @@ test_that("error.message=TRUE test, dataframe columns D$A,D$B", { # Done # -context("isDefined::smk::shutdown") +# context("isDefined::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -271,4 +271,4 @@ test_that("shutdown", { disconnect.discordant.dataset.simple() -context("isDefined::smk::done") +# context("isDefined::smk::done") diff --git a/tests/testthat/test-smk_bug-ds.listOpals.R b/tests/testthat/test-smk_bug-ds.listOpals.R index d6b35ff6f..72b28ccdb 100644 --- a/tests/testthat/test-smk_bug-ds.listOpals.R +++ b/tests/testthat/test-smk_bug-ds.listOpals.R @@ -1,6 +1,7 @@ #------------------------------------------------------------------------------- # Copyright (c) 2014 OBiBa, # 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -19,7 +20,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC", "LAB_HDL")) # Tests # -context("ds.listOpals::smk::check results") +# context("ds.listOpals::smk::check results") test_that("check results", { message <- "\n* This function lists all Opal objects in the R analysis environment\n\n\n* There is only one set of opals available,\n that is: 'ds.test_env$connections'\n\n\n\n* This set of Opals has been copied to create 'default.opals',\n which all DataSHIELD functions will now use by default.\n If you want to change the default Opal object,\n please run the function ds.setDefaultOpals() again. \n\n\n\n" diff --git a/tests/testthat/test-smk_dgr-ds.asCharacter.R b/tests/testthat/test-smk_dgr-ds.asCharacter.R index 7f9e7c45a..48a2fbd12 100644 --- a/tests/testthat/test-smk_dgr-ds.asCharacter.R +++ b/tests/testthat/test-smk_dgr-ds.asCharacter.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.asCharacter::smk_dgr::setup") +# context("ds.asCharacter::smk_dgr::setup") require(dsDangerClient) @@ -26,7 +27,7 @@ test_that("setup", { # Tests # -context("ds.asCharacter::smk_dgr::simple test") +# context("ds.asCharacter::smk_dgr::simple test") test_that("simple test", { res <- ds.asCharacter("D$LAB_TSC") @@ -39,7 +40,7 @@ test_that("simple test", { # Shutdown # -context("ds.asCharacter::smk_dgr::stutdown") +# context("ds.asCharacter::smk_dgr::stutdown") test_that("setup", { ds_expect_variables(c("D", "ascharacter.newobj")) @@ -51,4 +52,4 @@ disconnect.studies.dataset.cnsim() # Done # -context("ds.asCharacter::smk_dgr::done") +# context("ds.asCharacter::smk_dgr::done") diff --git a/tests/testthat/test-smk_dgr-ds.listClientsideFunctions.R b/tests/testthat/test-smk_dgr-ds.listClientsideFunctions.R index 52807e3be..64399ac1b 100644 --- a/tests/testthat/test-smk_dgr-ds.listClientsideFunctions.R +++ b/tests/testthat/test-smk_dgr-ds.listClientsideFunctions.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.listClientsideFunctions::smk_dgr::setup") +# context("ds.listClientsideFunctions::smk_dgr::setup") require(dsDangerClient) @@ -26,7 +27,7 @@ test_that("setup", { # Tests # -context("ds.listClientsideFunctions::smk_dgr::check results") +# context("ds.listClientsideFunctions::smk_dgr::check results") test_that("check results", { output <- list( "ds.DANGERc2sMATDF", @@ -51,7 +52,7 @@ test_that("check results", { # Shutdown # -context("ds.listClientsideFunctions::smk_dgr::shutdown") +# context("ds.listClientsideFunctions::smk_dgr::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -63,4 +64,4 @@ disconnect.studies.dataset.cnsim() # Done # -context("ds.listClientsideFunctions::smk_dgr::done") +# context("ds.listClientsideFunctions::smk_dgr::done") diff --git a/tests/testthat/test-smk_dgr-ds.listServersideFunctions.R b/tests/testthat/test-smk_dgr-ds.listServersideFunctions.R index 27d2e297c..9ed962278 100644 --- a/tests/testthat/test-smk_dgr-ds.listServersideFunctions.R +++ b/tests/testthat/test-smk_dgr-ds.listServersideFunctions.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.listServersideFunctions::smk_dgr::setup") +# context("ds.listServersideFunctions::smk_dgr::setup") require(dsDangerClient) @@ -26,7 +27,7 @@ test_that("setup", { # Tests # -context("ds.listServersideFunctions::smk_dgr::check results") +# context("ds.listServersideFunctions::smk_dgr::check results") test_that("check results", { assign.functions <- factor(c( )) @@ -73,7 +74,7 @@ test_that("check results", { # Done # -context("ds.listServersideFunctions::smk_dgr::shtudown") +# context("ds.listServersideFunctions::smk_dgr::shtudown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -85,4 +86,4 @@ disconnect.studies.dataset.cnsim() # Done # -context("ds.listServersideFunctions::smk_dgr::done") +# context("ds.listServersideFunctions::smk_dgr::done") diff --git a/tests/testthat/test-smk_dgr-ds.recodeValues-factor.R b/tests/testthat/test-smk_dgr-ds.recodeValues-factor.R index 840276726..180278c93 100644 --- a/tests/testthat/test-smk_dgr-ds.recodeValues-factor.R +++ b/tests/testthat/test-smk_dgr-ds.recodeValues-factor.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.recodeValues::smk_dgr::factor::setup") +# context("ds.recodeValues::smk_dgr::factor::setup") connect.studies.dataset.cnsim(list("GENDER", "PM_BMI_CATEGORICAL")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.recodeValues::smk_dgr::factor::simple factor 1") +# context("ds.recodeValues::smk_dgr::factor::simple factor 1") test_that("simple factor 1", { res <- ds.recodeValues("D$GENDER", values2replace.vector=c('0'), new.values.vector=c('2'), newobj="GENDER") @@ -79,7 +80,7 @@ test_that("simple factor 1", { expect_length((subset(ndf.sim3, GENDER == 2))$GENDER, 2091) }) -context("ds.recodeValues::smk_dgr::factor::simple factor 2") +# context("ds.recodeValues::smk_dgr::factor::simple factor 2") test_that("simple factor 2", { res <- ds.recodeValues("D$GENDER", values2replace.vector=c(0), new.values.vector=c(2), newobj="GENDER") @@ -134,7 +135,7 @@ test_that("simple factor 2", { expect_length((subset(ndf.sim3, GENDER == 2))$GENDER, 2091) }) -context("ds.recodeValues::smk_dgr::factor::simple factor 3") +# context("ds.recodeValues::smk_dgr::factor::simple factor 3") test_that("simple factor 3", { res <- ds.recodeValues("D$GENDER", values2replace.vector=c(0), new.values.vector=c(2), missing='3', newobj="GENDER") @@ -195,7 +196,7 @@ test_that("simple factor 3", { expect_length((subset(ndf.sim3, GENDER == 3))$GENDER, 0) }) -context("ds.recodeValues::smk_dgr::factor::simple factor 4") +# context("ds.recodeValues::smk_dgr::factor::simple factor 4") test_that("simple factor 4", { res <- ds.recodeValues("D$GENDER", values2replace.vector=c(0,1), new.values.vector=c(10,20), newobj="GENDER") @@ -259,7 +260,7 @@ test_that("simple factor 4", { # # Done # -context("ds.recodeValues::smk_dgr::factor::shutdown") +# context("ds.recodeValues::smk_dgr::factor::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "GENDER", "odf_1", "ndf_1", "odf_2", "ndf_2", "odf_3", "ndf_3", "odf_4", "ndf_4")) @@ -267,4 +268,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.recodeValues::smk_dgr::factor::done") +# context("ds.recodeValues::smk_dgr::factor::done") diff --git a/tests/testthat/test-smk_dgr-ds.recodeValues-factor_missing.R b/tests/testthat/test-smk_dgr-ds.recodeValues-factor_missing.R index c6cc808b3..2172c27fd 100644 --- a/tests/testthat/test-smk_dgr-ds.recodeValues-factor_missing.R +++ b/tests/testthat/test-smk_dgr-ds.recodeValues-factor_missing.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.recodeValues::smk_dgr::factor_missing::setup") +# context("ds.recodeValues::smk_dgr::factor_missing::setup") connect.studies.dataset.cnsim(list("GENDER", "PM_BMI_CATEGORICAL")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.recodeValues::smk_dgr::factor_missing::simple missing factor 1") +# context("ds.recodeValues::smk_dgr::factor_missing::simple missing factor 1") test_that("simple missing factor 1", { res <- ds.recodeValues("D$PM_BMI_CATEGORICAL", values2replace.vector=c(1,2,3), new.values.vector=c(10,20,30), missing='999', newobj="PM_BMI_CATEGORICAL") @@ -109,7 +110,7 @@ test_that("simple missing factor 1", { expect_length((subset(ndf.sim3, PM_BMI_CATEGORICAL == 999))$PM_BMI_CATEGORICAL, 205) }) -context("ds.recodeValues::smk_dgr::factor_missing::simple missing factor 2") +# context("ds.recodeValues::smk_dgr::factor_missing::simple missing factor 2") test_that("simple missing factor 2", { res <- ds.recodeValues("D$PM_BMI_CATEGORICAL", values2replace.vector=c(1,2), new.values.vector=c(1,2), missing=99, newobj="PM_BMI_CATEGORICAL") @@ -176,7 +177,7 @@ test_that("simple missing factor 2", { expect_length((subset(ndf.sim3, PM_BMI_CATEGORICAL == 99))$PM_BMI_CATEGORICAL, 205) }) -context("ds.recodeValues::smk_dgr::factor_missing::simple missing factor 3") +# context("ds.recodeValues::smk_dgr::factor_missing::simple missing factor 3") test_that("simple missing factor 3", { res <- ds.recodeValues("D$PM_BMI_CATEGORICAL", values2replace.vector=c(1,2,3), new.values.vector=c('low','medium','high'), newobj="PM_BMI_CATEGORICAL") @@ -252,7 +253,7 @@ test_that("simple missing factor 3", { # # Done # -context("ds.recodeValues::smk_dgr::factor_missing::shutdown") +# context("ds.recodeValues::smk_dgr::factor_missing::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "PM_BMI_CATEGORICAL", "odf_1", "ndf_1", "odf_2", "ndf_2", "odf_3", "ndf_3")) @@ -260,4 +261,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.recodeValues::smk_dgr::factor_missing::done") +# context("ds.recodeValues::smk_dgr::factor_missing::done") diff --git a/tests/testthat/test-smk_dgr-ds.recodeValues.R b/tests/testthat/test-smk_dgr-ds.recodeValues.R index a7f798210..a7bf78805 100644 --- a/tests/testthat/test-smk_dgr-ds.recodeValues.R +++ b/tests/testthat/test-smk_dgr-ds.recodeValues.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.recodeValues::smk_dgr::setup") +# context("ds.recodeValues::smk_dgr::setup") connect.studies.dataset.survival(list("time.id")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.recodeValues::smk_dgr::simple numeric") +# context("ds.recodeValues::smk_dgr::simple numeric") test_that("simple test", { res <- ds.recodeValues("D$time.id", values2replace.vector=c(1,2), new.values.vector=c(10,20), newobj="time.id") @@ -88,7 +89,7 @@ test_that("simple test", { # # Done # -context("ds.recodeValues::smk_dgr::shutdown") +# context("ds.recodeValues::smk_dgr::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "time.id", "odf", "ndf")) @@ -96,4 +97,4 @@ test_that("shutdown", { disconnect.studies.dataset.survival() -context("ds.recodeValues::smk_dgr::done") +# context("ds.recodeValues::smk_dgr::done") diff --git a/tests/testthat/test-smk_expt-ds.mean.R b/tests/testthat/test-smk_expt-ds.mean.R index 3d1d22fa3..c2682730d 100644 --- a/tests/testthat/test-smk_expt-ds.mean.R +++ b/tests/testthat/test-smk_expt-ds.mean.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -18,112 +19,112 @@ connect.studies.dataset.cnsim(list("LAB_TSC", "LAB_TRIG", "LAB_HDL", "LAB_GLUC_A # Tests # -context("ds.mean::smk_expt::type=combine") +# context("ds.mean::smk_expt::type=combine") test_that("mean values [combine]", { stat.mean <- ds.mean(x='D$LAB_TSC',type='combine') expect_equal_to_reference(stat.mean, 'smk_expt-results/ds.mean-LAB_TSC-combine.rds') }) -context("ds.mean::smk_expt::type=split") +# context("ds.mean::smk_expt::type=split") test_that("mean values [split]", { stat.mean <- ds.mean(x='D$LAB_TSC', type='split') expect_equal_to_reference(stat.mean, 'smk_expt-results/ds.mean-LAB_TSC-split.rds') }) -context("ds.mean::smk_expt::type=both") +# context("ds.mean::smk_expt::type=both") test_that("mean values [both]", { stat.mean <- ds.mean(x='D$LAB_TSC', type='both') expect_equal_to_reference(stat.mean, 'smk_expt-results/ds.mean-LAB_TSC-both.rds') }) -context("ds.mean::smk_expt::type=combine") +# context("ds.mean::smk_expt::type=combine") test_that("mean values [combine]", { # stat.mean <- ds.mean(x='D$LAB_TRIG',type='combine') # expect_equal_to_reference(stat.mean, 'smk_expt-results/ds.mean-LAB_TRIG-combine.rds') }) -context("ds.mean::smk_expt::type=split") +# context("ds.mean::smk_expt::type=split") test_that("mean values [split]", { # stat.mean <- ds.mean(x='D$LAB_TRIG', type='split') # expect_equal_to_reference(stat.mean, 'smk_expt-results/ds.mean-LAB_TRIG-split.rds') }) -context("ds.mean::smk_expt::type=both") +# context("ds.mean::smk_expt::type=both") test_that("mean values [both]", { # stat.mean <- ds.mean(x='D$LAB_TRIG', type='both') # expect_equal_to_reference(stat.mean, 'smk_expt-results/ds.mean-LAB_TRIG-both.rds') }) -context("ds.mean::smk_expt::type=combine") +# context("ds.mean::smk_expt::type=combine") test_that("mean values [combine]", { stat.mean <- ds.mean(x='D$LAB_HDL',type='combine') expect_equal_to_reference(stat.mean, 'smk_expt-results/ds.mean-LAB_HDL-combine.rds') }) -context("ds.mean::smk_expt::type=split") +# context("ds.mean::smk_expt::type=split") test_that("mean values [split]", { stat.mean <- ds.mean(x='D$LAB_HDL', type='split') expect_equal_to_reference(stat.mean, 'smk_expt-results/ds.mean-LAB_HDL-split.rds') }) -context("ds.mean::smk_expt::type=both") +# context("ds.mean::smk_expt::type=both") test_that("mean values [both]", { stat.mean <- ds.mean(x='D$LAB_HDL', type='both') expect_equal_to_reference(stat.mean, 'smk_expt-results/ds.mean-LAB_HDL-both.rds') }) -context("ds.mean::smk_expt::type=combine") +# context("ds.mean::smk_expt::type=combine") test_that("mean values [combine]", { stat.mean <- ds.mean(x='D$LAB_GLUC_ADJUSTED',type='combine') expect_equal_to_reference(stat.mean, 'smk_expt-results/ds.mean-LAB_GLUC_ADJUSTED-combine.rds') }) -context("ds.mean::smk_expt::type=split") +# context("ds.mean::smk_expt::type=split") test_that("mean values [split]", { stat.mean <- ds.mean(x='D$LAB_GLUC_ADJUSTED', type='split') expect_equal_to_reference(stat.mean, 'smk_expt-results/ds.mean-LAB_GLUC_ADJUSTED-split.rds') }) -context("ds.mean::smk_expt::type=both") +# context("ds.mean::smk_expt::type=both") test_that("mean values [both]", { stat.mean <- ds.mean(x='D$LAB_GLUC_ADJUSTED', type='both') expect_equal_to_reference(stat.mean, 'smk_expt-results/ds.mean-LAB_GLUC_ADJUSTED-both.rds') }) -context("ds.mean::smk_expt::type=combine") +# context("ds.mean::smk_expt::type=combine") test_that("mean values [combine]", { stat.mean <- ds.mean(x='D$PM_BMI_CONTINUOUS',type='combine') expect_equal_to_reference(stat.mean, 'smk_expt-results/ds.mean-PM_BMI_CONTINUOUS-combine.rds') }) -context("ds.mean::smk_expt::type=split") +# context("ds.mean::smk_expt::type=split") test_that("mean values [split]", { stat.mean <- ds.mean(x='D$PM_BMI_CONTINUOUS', type='split') expect_equal_to_reference(stat.mean, 'smk_expt-results/ds.mean-PM_BMI_CONTINUOUS-split.rds') }) -context("ds.mean::smk_expt::type=both") +# context("ds.mean::smk_expt::type=both") test_that("mean values [both]", { stat.mean <- ds.mean(x='D$PM_BMI_CONTINUOUS', type='both') expect_equal_to_reference(stat.mean, 'smk_expt-results/ds.mean-PM_BMI_CONTINUOUS-both.rds') }) -context("ds.mean::smk_expt::type=combine") +# context("ds.mean::smk_expt::type=combine") test_that("mean values [combine]", { ds.asNumeric(x.name="D$DIS_CVA", newobj="DIS_CVA") @@ -132,7 +133,7 @@ test_that("mean values [combine]", { expect_equal_to_reference(stat.mean, 'smk_expt-results/ds.mean-DIS_CVA-combine.rds') }) -context("ds.mean::smk_expt::type=split") +# context("ds.mean::smk_expt::type=split") test_that("mean values [split]", { ds.asNumeric(x.name="D$DIS_CVA", newobj="DIS_CVA") @@ -141,7 +142,7 @@ test_that("mean values [split]", { expect_equal_to_reference(stat.mean, 'smk_expt-results/ds.mean-DIS_CVA-split.rds') }) -context("ds.mean::smk_expt::type=both") +# context("ds.mean::smk_expt::type=both") test_that("mean values [both]", { ds.asNumeric(x.name="D$DIS_CVA", newobj="DIS_CVA") @@ -150,7 +151,7 @@ test_that("mean values [both]", { expect_equal_to_reference(stat.mean, 'smk_expt-results/ds.mean-DIS_CVA-both.rds') }) -context("ds.mean::smk_expt::type=combine") +# context("ds.mean::smk_expt::type=combine") test_that("mean values [combine]", { ds.asNumeric(x.name="D$MEDI_LPD", newobj="MEDI_LPD") @@ -159,7 +160,7 @@ test_that("mean values [combine]", { expect_equal_to_reference(stat.mean, 'smk_expt-results/ds.mean-MEDI_LPD-combine.rds') }) -context("ds.mean::smk_expt::type=split") +# context("ds.mean::smk_expt::type=split") test_that("mean values [split]", { ds.asNumeric(x.name="D$MEDI_LPD", newobj="MEDI_LPD") @@ -168,7 +169,7 @@ test_that("mean values [split]", { expect_equal_to_reference(stat.mean, 'smk_expt-results/ds.mean-MEDI_LPD-split.rds') }) -context("ds.mean::smk_expt::type=both") +# context("ds.mean::smk_expt::type=both") test_that("mean values [both]", { ds.asNumeric(x.name="D$MEDI_LPD", newobj="MEDI_LPD") @@ -177,7 +178,7 @@ test_that("mean values [both]", { expect_equal_to_reference(stat.mean, 'smk_expt-results/ds.mean-MEDI_LPD-both.rds') }) -context("ds.mean::smk_expt::type=combine") +# context("ds.mean::smk_expt::type=combine") test_that("mean values [combine]", { ds.asNumeric(x.name="D$DIS_DIAB", newobj="DIS_DIAB") @@ -186,7 +187,7 @@ test_that("mean values [combine]", { expect_equal_to_reference(stat.mean, 'smk_expt-results/ds.mean-DIS_DIAB-combine.rds') }) -context("ds.mean::smk_expt::type=split") +# context("ds.mean::smk_expt::type=split") test_that("mean values [split]", { ds.asNumeric(x.name="D$DIS_DIAB", newobj="DIS_DIAB") @@ -195,7 +196,7 @@ test_that("mean values [split]", { expect_equal_to_reference(stat.mean, 'smk_expt-results/ds.mean-DIS_DIAB-split.rds') }) -context("ds.mean::smk_expt::type=both") +# context("ds.mean::smk_expt::type=both") test_that("mean values [both]", { ds.asNumeric(x.name="D$DIS_DIAB", newobj="DIS_DIAB") @@ -204,7 +205,7 @@ test_that("mean values [both]", { expect_equal_to_reference(stat.mean, 'smk_expt-results/ds.mean-DIS_DIAB-both.rds') }) -context("ds.mean::smk_expt::type=combine") +# context("ds.mean::smk_expt::type=combine") test_that("mean values [combine]", { ds.asNumeric(x.name="D$DIS_AMI", newobj="DIS_AMI") @@ -213,7 +214,7 @@ test_that("mean values [combine]", { expect_equal_to_reference(stat.mean, 'smk_expt-results/ds.mean-DIS_AMI-combine.rds') }) -context("ds.mean::smk_expt::type=split") +# context("ds.mean::smk_expt::type=split") test_that("mean values [split]", { ds.asNumeric(x.name="D$DIS_AMI", newobj="DIS_AMI") @@ -222,7 +223,7 @@ test_that("mean values [split]", { expect_equal_to_reference(stat.mean, 'smk_expt-results/ds.mean-DIS_AMI-split.rds') }) -context("ds.mean::smk_expt::type=both") +# context("ds.mean::smk_expt::type=both") test_that("mean values [both]", { ds.asNumeric(x.name="D$DIS_AMI", newobj="DIS_AMI") @@ -231,7 +232,7 @@ test_that("mean values [both]", { expect_equal_to_reference(stat.mean, 'smk_expt-results/ds.mean-DIS_AMI-both.rds') }) -context("ds.mean::smk_expt::type=combine") +# context("ds.mean::smk_expt::type=combine") test_that("mean values [combine]", { ds.asNumeric(x.name="D$GENDER", newobj="GENDER") @@ -240,7 +241,7 @@ test_that("mean values [combine]", { expect_equal_to_reference(stat.mean, 'smk_expt-results/ds.mean-GENDER-combine.rds') }) -context("ds.mean::smk_expt::type=split") +# context("ds.mean::smk_expt::type=split") test_that("mean values [split]", { ds.asNumeric(x.name="D$GENDER", newobj="GENDER") @@ -249,7 +250,7 @@ test_that("mean values [split]", { expect_equal_to_reference(stat.mean, 'smk_expt-results/ds.mean-GENDER-split.rds') }) -context("ds.mean::smk_expt::type=both") +# context("ds.mean::smk_expt::type=both") test_that("mean values [both]", { ds.asNumeric(x.name="D$GENDER", newobj="GENDER") @@ -258,7 +259,7 @@ test_that("mean values [both]", { expect_equal_to_reference(stat.mean, 'smk_expt-results/ds.mean-GENDER-both.rds') }) -context("ds.mean::smk_expt::type=combine") +# context("ds.mean::smk_expt::type=combine") test_that("mean values [combine]", { ds.asNumeric(x.name="D$PM_BMI_CATEGORICAL", newobj="PM_BMI_CATEGORICAL") @@ -267,7 +268,7 @@ test_that("mean values [combine]", { expect_equal_to_reference(stat.mean, 'smk_expt-results/ds.mean-PM_BMI_CATEGORICAL-combine.rds') }) -context("ds.mean::smk_expt::type=split") +# context("ds.mean::smk_expt::type=split") test_that("mean values [split]", { ds.asNumeric(x.name="D$PM_BMI_CATEGORICAL", newobj="PM_BMI_CATEGORICAL") @@ -276,7 +277,7 @@ test_that("mean values [split]", { expect_equal_to_reference(stat.mean, 'smk_expt-results/ds.mean-PM_BMI_CATEGORICAL-split.rds') }) -context("ds.mean::smk_expt::type=both") +# context("ds.mean::smk_expt::type=both") test_that("mean values [both]", { ds.asNumeric(x.name="D$PM_BMI_CATEGORICAL", newobj="PM_BMI_CATEGORICAL") diff --git a/tests/testthat/test-smk_expt-ds.ranksSecure.R b/tests/testthat/test-smk_expt-ds.ranksSecure.R index 0061df2ce..edb86cd2e 100644 --- a/tests/testthat/test-smk_expt-ds.ranksSecure.R +++ b/tests/testthat/test-smk_expt-ds.ranksSecure.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.ranksSecure::smk_expt::setup") +# context("ds.ranksSecure::smk_expt::setup") connect.studies.dataset.cnsim(list("LAB_TRIG", "LAB_TSC")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.ranksSecure::smk_expt::continous, without NAs, all positive") +# context("ds.ranksSecure::smk_expt::continous, without NAs, all positive") test_that("continous, without NAs, all positive", { res.cc <- ds.completeCases("D$LAB_TSC", newobj="CC_LAB_TSC") expect_equal(res.cc$validity.check, " appears valid in all sources") @@ -40,7 +41,7 @@ test_that("continous, without NAs, all positive", { expect_equal_to_reference(res, 'smk_expt-results/ds.ranksSecure-cont.rds') }) -context("ds.ranksSecure::smk_expt::continous, without NAs, with negative") +# context("ds.ranksSecure::smk_expt::continous, without NAs, with negative") test_that("continous, without NAs, with negative", { res.cc <- ds.completeCases("D$LAB_TRIG", newobj="CC_LAB_TRIG") expect_equal(res.cc$validity.check, " appears valid in all sources") @@ -56,14 +57,14 @@ test_that("continous, without NAs, with negative", { expect_equal_to_reference(res, 'smk_expt-results/ds.ranksSecure-cont_neg.rds') }) -context("ds.ranksSecure::smk_expt::continous, with NAs, all positive") +# context("ds.ranksSecure::smk_expt::continous, with NAs, all positive") test_that("continous, with NAs, all positive", { res <- ds.ranksSecure("D$LAB_TSC") expect_equal_to_reference(res, 'smk_expt-results/ds.ranksSecure-cont_nas.rds') }) -context("ds.ranksSecure::smk_expt::continous, with NAs, with negative") +# context("ds.ranksSecure::smk_expt::continous, with NAs, with negative") test_that("continous, with NAs, with negative", { res <- ds.ranksSecure("D$LAB_TRIG") @@ -74,7 +75,7 @@ test_that("continous, with NAs, with negative", { # Done # -context("ds.ranksSecure::smk_expt::shutdown") +# context("ds.ranksSecure::smk_expt::shutdown") test_that("setup", { ds_expect_variables(c("D", "CC_LAB_TSC", "CC_LAB_TRIG", "final.quantile.df", "summary.ranks.df", "testvar.ranks")) @@ -82,4 +83,4 @@ test_that("setup", { disconnect.studies.dataset.cnsim() -context("ds.ranksSecure::smk_expt::done") +# context("ds.ranksSecure::smk_expt::done")