diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index a3ac618..562fe0f 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -4,9 +4,10 @@ on: push: branches: [main, master] pull_request: - branches: [main, master] -name: R-CMD-check +name: R-CMD-check.yaml + +permissions: read-all jobs: R-CMD-check: @@ -29,7 +30,7 @@ jobs: R_KEEP_PKG_SOURCE: yes steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - uses: r-lib/actions/setup-pandoc@v2 @@ -47,3 +48,4 @@ jobs: - uses: r-lib/actions/check-r-package@v2 with: upload-snapshots: true + build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")' diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml index 087f0b0..bfc9f4d 100644 --- a/.github/workflows/pkgdown.yaml +++ b/.github/workflows/pkgdown.yaml @@ -4,12 +4,13 @@ on: push: branches: [main, master] pull_request: - branches: [main, master] release: types: [published] workflow_dispatch: -name: pkgdown +name: pkgdown.yaml + +permissions: read-all jobs: pkgdown: @@ -19,8 +20,10 @@ jobs: group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }} env: GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} + permissions: + contents: write steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - uses: r-lib/actions/setup-pandoc@v2 @@ -39,7 +42,7 @@ jobs: - name: Deploy to GitHub pages 🚀 if: github.event_name != 'pull_request' - uses: JamesIves/github-pages-deploy-action@v4.4.1 + uses: JamesIves/github-pages-deploy-action@v4.5.0 with: clean: false branch: gh-pages diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml index 2c5bb50..e050312 100644 --- a/.github/workflows/test-coverage.yaml +++ b/.github/workflows/test-coverage.yaml @@ -4,9 +4,10 @@ on: push: branches: [main, master] pull_request: - branches: [main, master] -name: test-coverage +name: test-coverage.yaml + +permissions: read-all jobs: test-coverage: @@ -15,7 +16,7 @@ jobs: GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - uses: r-lib/actions/setup-r@v2 with: @@ -23,28 +24,38 @@ jobs: - uses: r-lib/actions/setup-r-dependencies@v2 with: - extra-packages: any::covr + extra-packages: any::covr, any::xml2 needs: coverage - name: Test coverage run: | - covr::codecov( + cov <- covr::package_coverage( quiet = FALSE, clean = FALSE, - install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package") + install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package") ) + covr::to_cobertura(cov) shell: Rscript {0} + - uses: codecov/codecov-action@v4 + with: + # Fail if error if not on PR, or if on PR and token is given + fail_ci_if_error: ${{ github.event_name != 'pull_request' || secrets.CODECOV_TOKEN }} + file: ./cobertura.xml + plugin: noop + disable_search: true + token: ${{ secrets.CODECOV_TOKEN }} + - name: Show testthat output if: always() run: | ## -------------------------------------------------------------------- - find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true + find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true shell: bash - name: Upload test results if: failure() - uses: actions/upload-artifact@v3 + uses: actions/upload-artifact@v4 with: name: coverage-test-failures path: ${{ runner.temp }}/package diff --git a/DESCRIPTION b/DESCRIPTION index 09de0f6..536f03c 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -23,10 +23,12 @@ Imports: Suggests: covr, scales, + spelling, testthat (>= 2.1.0), tibble License: AGPL-3 Encoding: UTF-8 LazyData: true -RoxygenNote: 7.2.1 -URL: https://billdenney.github.io/Rsdtm/ +RoxygenNote: 7.3.2 +URL: https://humanpred.github.io/Rsdtm/ +Language: en-US diff --git a/R/data.R b/R/data.R index 68259b7..95d2ab1 100644 --- a/R/data.R +++ b/R/data.R @@ -1,26 +1,26 @@ #' A data.frame with 4 columns and one row per valid SDTM version/IG/IG version #' combination -#' +#' #' @format #' \describe{ #' \item{SDTM}{The SDTM version} #' \item{IG_NAME}{The implementation guide (IG) name being used} -#' \item{IG_VERSION}{The implemetation guide (IG) version} +#' \item{IG_VERSION}{The implementation guide (IG) version} #' \item{archived}{The SDTM version/IG pair has been archived (and should not #' be used for current studies)} #' } "valid_versions" #' The current SDTM terminology -#' +#' #' SDTM terminology is used for reserved words and lists of codes that can be #' used for values in the SDTM standard. The version date from the download is #' available via \code{attr(sdtm_terminology, "version")}. -#' +#' #' The description of the columns draw from #' \url{https://evs.nci.nih.gov/ftp1/CDISC/SDTM/SDTM CDISC ReadMe.doc}, and #' the column names are modified slightly to work better in R. -#' +#' #' @format #' \describe{ #' \item{code}{Unique numeric code randomly generated by NCI Thesaurus (NCIt) and assigned to individual CDISC controlled terms.} @@ -32,4 +32,4 @@ #' \item{CDISC_definition}{This identifies the CDISC definition for a particular term. In many cases an existing NCI definition has been used. The source for a definition is noted in parentheses (e.g. NCI, CDISC glossary).} #' \item{NCI_preferred_term}{This identifies the NCI preferred name for a term as identified in NCIt. **NOTE - This column designates the human readable, fully specified preferred term corresponding to the NCI c-code, and is especially helpful for searching NCIt to get the entire concept with links to all instances of the term.} #' } -"sdtm_terminology" \ No newline at end of file +"sdtm_terminology" diff --git a/R/import_sdtm.R b/R/import_sdtm.R index be2ae9c..901d4aa 100644 --- a/R/import_sdtm.R +++ b/R/import_sdtm.R @@ -121,7 +121,7 @@ import_sdtm_file <- function(path, #' \code{values} #' @param x,values,after See \code{base::append} #' @param ignore_blank Ignore blank names? (Blank names \code{""} occur when an -#' unnamed vector is appeneded to a named vector.) +#' unnamed vector is appended to a named vector.) #' @param method Function to notify the user if a duplicate is provided? It is #' called with a message indicating the name of the duplicate. Typically this #' will be \code{stop} or \code{warning}. diff --git a/R/iso8601_regexp.R b/R/iso8601_regexp.R index dedeb71..bd8e2ca 100644 --- a/R/iso8601_regexp.R +++ b/R/iso8601_regexp.R @@ -587,7 +587,7 @@ pattern_ISO8601_time <- function(truncated=0, ret } -#' Generate a regular expression for ISO 8601 timezones. +#' Generate a regular expression for ISO 8601 time zones. #' #' @details Offsets are always multiples of 15 minutes, so if the minute part is #' provided, it must be 00, 15, 30, or 45. The range allowed by this function diff --git a/R/sdtm_example_dataverse.R b/R/sdtm_example_dataverse.R index 1f6a8dc..0260947 100644 --- a/R/sdtm_example_dataverse.R +++ b/R/sdtm_example_dataverse.R @@ -104,7 +104,7 @@ #' \item{LBSTRESU}{Standard Units, character} #' \item{LBSTNRLO}{Reference Range Lower Limit-Std Units, numeric} #' \item{LBSTNRHI}{Reference Range Upper Limit-Std Units, numeric} -#' \item{LBSTNRC}{Reference Range for Char Rslt-Std Units, character} +#' \item{LBSTNRC}{Reference Range for Char Result-Std Units, character} #' \item{LBNRIND}{Reference Range Indicator, character} #' \item{LBSPEC}{Specimen Type, character} #' \item{LBMETHOD}{Method of Test or Examination, character} diff --git a/README.md b/README.md index ec0bc81..55c5da7 100644 --- a/README.md +++ b/README.md @@ -1,8 +1,8 @@ # Rsdtm -[![R-CMD-check](https://github.com/billdenney/Rsdtm/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/billdenney/Rsdtm/actions/workflows/R-CMD-check.yaml) -[![Codecov test coverage](https://codecov.io/gh/billdenney/Rsdtm/branch/main/graph/badge.svg)](https://app.codecov.io/gh/billdenney/Rsdtm?branch=main) +[![R-CMD-check](https://github.com/humanpred/Rsdtm/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/humanpred/Rsdtm/actions/workflows/R-CMD-check.yaml) +[![Codecov test coverage](https://codecov.io/gh/humanpred/Rsdtm/graph/badge.svg)](https://app.codecov.io/gh/humanpred/Rsdtm) [![CRAN status](https://www.r-pkg.org/badges/version/Rsdtm)](https://CRAN.R-project.org/package=Rsdtm) @@ -15,7 +15,7 @@ The goal of Rsdtm is to simplify SDTM data management and file creation for R. To install the development version, run the following: ``` r -devtools::install_github("billdenney/Rsdtm") +devtools::install_github("humanpred/Rsdtm") ``` ### CRAN (someday) @@ -32,5 +32,5 @@ This is a basic example which shows you how to solve a common problem: ``` r library(Rsdtm) -d <- import_sdtm("/director/to/data") +d <- import_sdtm("/directory/to/data") ``` diff --git a/_pkgdown.yml b/_pkgdown.yml index 0e63e8a..5948789 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -1,4 +1,4 @@ -url: https://billdenney.github.io/Rsdtm/ +url: https://humanpred.github.io/Rsdtm/ template: bootstrap: 5 diff --git a/inst/WORDLIST b/inst/WORDLIST new file mode 100644 index 0000000..885171f --- /dev/null +++ b/inst/WORDLIST @@ -0,0 +1,31 @@ +ADaM +CDISC +CMD +Codecov +Codelist +DDD +DTC +IG +NCI +NCIt +POSIXct +POSIXt +Pharmacokinetic +Pharmacokinetics +Pre +SDTM +STUDYID +SUBJID +USUBJID +Www +YYYY +codelist +codelists +datetime +ddd +difftime +ggplots +https +trimws +wikipedia +yyyy diff --git a/man/append_no_duplicate_names.Rd b/man/append_no_duplicate_names.Rd index 0b7eeee..fba0f55 100644 --- a/man/append_no_duplicate_names.Rd +++ b/man/append_no_duplicate_names.Rd @@ -17,7 +17,7 @@ append_no_duplicate_names( \item{x, values, after}{See \code{base::append}} \item{ignore_blank}{Ignore blank names? (Blank names \code{""} occur when an -unnamed vector is appeneded to a named vector.)} +unnamed vector is appended to a named vector.)} \item{method}{Function to notify the user if a duplicate is provided? It is called with a message indicating the name of the duplicate. Typically this diff --git a/man/dateany_to_date.Rd b/man/dateany_to_date.Rd index 9b2224b..5473702 100644 --- a/man/dateany_to_date.Rd +++ b/man/dateany_to_date.Rd @@ -28,24 +28,24 @@ dateany_to_date(as.POSIXct("2022-01-02T03:04")) # the time part is still gone \seealso{ Other Date management and conversion: \code{\link{generate_dtc}()}, -\code{\link{is_ISO8601_calendar_datetime}()}, \code{\link{is_ISO8601_calendar_date}()}, +\code{\link{is_ISO8601_calendar_datetime}()}, \code{\link{is_ISO8601_ordinal_datetime}()}, -\code{\link{is_ISO8601_timezone}()}, \code{\link{is_ISO8601_time}()}, +\code{\link{is_ISO8601_timezone}()}, \code{\link{is_ISO8601_week_datetime}()}, \code{\link{make_dy}()}, -\code{\link{pattern_ISO8601_any_datetime}()}, \code{\link{pattern_ISO8601_any_date}()}, -\code{\link{pattern_ISO8601_calendar_datetime}()}, +\code{\link{pattern_ISO8601_any_datetime}()}, \code{\link{pattern_ISO8601_calendar_date}()}, +\code{\link{pattern_ISO8601_calendar_datetime}()}, \code{\link{pattern_ISO8601_calendar_year}()}, -\code{\link{pattern_ISO8601_ordinal_datetime}()}, \code{\link{pattern_ISO8601_ordinal_date}()}, -\code{\link{pattern_ISO8601_timezone}()}, +\code{\link{pattern_ISO8601_ordinal_datetime}()}, \code{\link{pattern_ISO8601_time}()}, -\code{\link{pattern_ISO8601_week_datetime}()}, +\code{\link{pattern_ISO8601_timezone}()}, \code{\link{pattern_ISO8601_week_date}()}, +\code{\link{pattern_ISO8601_week_datetime}()}, \code{\link{sdtm_dtc_to_datetime}()}, \code{\link{sdtm_first_dose}()}, \code{\link{sdtm_time_actual}()} diff --git a/man/generate_dtc.Rd b/man/generate_dtc.Rd index 8f78a43..33c59f4 100644 --- a/man/generate_dtc.Rd +++ b/man/generate_dtc.Rd @@ -51,24 +51,24 @@ When times are not zero-padded (for example, "5:12" instead of \seealso{ Other Date management and conversion: \code{\link{dateany_to_date}()}, -\code{\link{is_ISO8601_calendar_datetime}()}, \code{\link{is_ISO8601_calendar_date}()}, +\code{\link{is_ISO8601_calendar_datetime}()}, \code{\link{is_ISO8601_ordinal_datetime}()}, -\code{\link{is_ISO8601_timezone}()}, \code{\link{is_ISO8601_time}()}, +\code{\link{is_ISO8601_timezone}()}, \code{\link{is_ISO8601_week_datetime}()}, \code{\link{make_dy}()}, -\code{\link{pattern_ISO8601_any_datetime}()}, \code{\link{pattern_ISO8601_any_date}()}, -\code{\link{pattern_ISO8601_calendar_datetime}()}, +\code{\link{pattern_ISO8601_any_datetime}()}, \code{\link{pattern_ISO8601_calendar_date}()}, +\code{\link{pattern_ISO8601_calendar_datetime}()}, \code{\link{pattern_ISO8601_calendar_year}()}, -\code{\link{pattern_ISO8601_ordinal_datetime}()}, \code{\link{pattern_ISO8601_ordinal_date}()}, -\code{\link{pattern_ISO8601_timezone}()}, +\code{\link{pattern_ISO8601_ordinal_datetime}()}, \code{\link{pattern_ISO8601_time}()}, -\code{\link{pattern_ISO8601_week_datetime}()}, +\code{\link{pattern_ISO8601_timezone}()}, \code{\link{pattern_ISO8601_week_date}()}, +\code{\link{pattern_ISO8601_week_datetime}()}, \code{\link{sdtm_dtc_to_datetime}()}, \code{\link{sdtm_first_dose}()}, \code{\link{sdtm_time_actual}()} diff --git a/man/is_ISO8601_calendar_date.Rd b/man/is_ISO8601_calendar_date.Rd index 3aebbab..85baf59 100644 --- a/man/is_ISO8601_calendar_date.Rd +++ b/man/is_ISO8601_calendar_date.Rd @@ -43,8 +43,8 @@ ordinal date Other ISO8601 String checking: \code{\link{is_ISO8601_calendar_datetime}()}, \code{\link{is_ISO8601_ordinal_datetime}()}, -\code{\link{is_ISO8601_timezone}()}, \code{\link{is_ISO8601_time}()}, +\code{\link{is_ISO8601_timezone}()}, \code{\link{is_ISO8601_week_datetime}()} Other Date management and conversion: @@ -52,21 +52,21 @@ Other Date management and conversion: \code{\link{generate_dtc}()}, \code{\link{is_ISO8601_calendar_datetime}()}, \code{\link{is_ISO8601_ordinal_datetime}()}, -\code{\link{is_ISO8601_timezone}()}, \code{\link{is_ISO8601_time}()}, +\code{\link{is_ISO8601_timezone}()}, \code{\link{is_ISO8601_week_datetime}()}, \code{\link{make_dy}()}, -\code{\link{pattern_ISO8601_any_datetime}()}, \code{\link{pattern_ISO8601_any_date}()}, -\code{\link{pattern_ISO8601_calendar_datetime}()}, +\code{\link{pattern_ISO8601_any_datetime}()}, \code{\link{pattern_ISO8601_calendar_date}()}, +\code{\link{pattern_ISO8601_calendar_datetime}()}, \code{\link{pattern_ISO8601_calendar_year}()}, -\code{\link{pattern_ISO8601_ordinal_datetime}()}, \code{\link{pattern_ISO8601_ordinal_date}()}, -\code{\link{pattern_ISO8601_timezone}()}, +\code{\link{pattern_ISO8601_ordinal_datetime}()}, \code{\link{pattern_ISO8601_time}()}, -\code{\link{pattern_ISO8601_week_datetime}()}, +\code{\link{pattern_ISO8601_timezone}()}, \code{\link{pattern_ISO8601_week_date}()}, +\code{\link{pattern_ISO8601_week_datetime}()}, \code{\link{sdtm_dtc_to_datetime}()}, \code{\link{sdtm_first_dose}()}, \code{\link{sdtm_time_actual}()} diff --git a/man/is_ISO8601_calendar_datetime.Rd b/man/is_ISO8601_calendar_datetime.Rd index 6036a46..7b53633 100644 --- a/man/is_ISO8601_calendar_datetime.Rd +++ b/man/is_ISO8601_calendar_datetime.Rd @@ -27,8 +27,8 @@ notation Other ISO8601 String checking: \code{\link{is_ISO8601_calendar_date}()}, \code{\link{is_ISO8601_ordinal_datetime}()}, -\code{\link{is_ISO8601_timezone}()}, \code{\link{is_ISO8601_time}()}, +\code{\link{is_ISO8601_timezone}()}, \code{\link{is_ISO8601_week_datetime}()} Other Date management and conversion: @@ -36,21 +36,21 @@ Other Date management and conversion: \code{\link{generate_dtc}()}, \code{\link{is_ISO8601_calendar_date}()}, \code{\link{is_ISO8601_ordinal_datetime}()}, -\code{\link{is_ISO8601_timezone}()}, \code{\link{is_ISO8601_time}()}, +\code{\link{is_ISO8601_timezone}()}, \code{\link{is_ISO8601_week_datetime}()}, \code{\link{make_dy}()}, -\code{\link{pattern_ISO8601_any_datetime}()}, \code{\link{pattern_ISO8601_any_date}()}, -\code{\link{pattern_ISO8601_calendar_datetime}()}, +\code{\link{pattern_ISO8601_any_datetime}()}, \code{\link{pattern_ISO8601_calendar_date}()}, +\code{\link{pattern_ISO8601_calendar_datetime}()}, \code{\link{pattern_ISO8601_calendar_year}()}, -\code{\link{pattern_ISO8601_ordinal_datetime}()}, \code{\link{pattern_ISO8601_ordinal_date}()}, -\code{\link{pattern_ISO8601_timezone}()}, +\code{\link{pattern_ISO8601_ordinal_datetime}()}, \code{\link{pattern_ISO8601_time}()}, -\code{\link{pattern_ISO8601_week_datetime}()}, +\code{\link{pattern_ISO8601_timezone}()}, \code{\link{pattern_ISO8601_week_date}()}, +\code{\link{pattern_ISO8601_week_datetime}()}, \code{\link{sdtm_dtc_to_datetime}()}, \code{\link{sdtm_first_dose}()}, \code{\link{sdtm_time_actual}()} diff --git a/man/is_ISO8601_ordinal_datetime.Rd b/man/is_ISO8601_ordinal_datetime.Rd index 2f18ee6..b063716 100644 --- a/man/is_ISO8601_ordinal_datetime.Rd +++ b/man/is_ISO8601_ordinal_datetime.Rd @@ -23,32 +23,32 @@ Determine if a string matches an ISO 8601 date/time using ordinal date notation } \seealso{ Other ISO8601 String checking: -\code{\link{is_ISO8601_calendar_datetime}()}, \code{\link{is_ISO8601_calendar_date}()}, -\code{\link{is_ISO8601_timezone}()}, +\code{\link{is_ISO8601_calendar_datetime}()}, \code{\link{is_ISO8601_time}()}, +\code{\link{is_ISO8601_timezone}()}, \code{\link{is_ISO8601_week_datetime}()} Other Date management and conversion: \code{\link{dateany_to_date}()}, \code{\link{generate_dtc}()}, -\code{\link{is_ISO8601_calendar_datetime}()}, \code{\link{is_ISO8601_calendar_date}()}, -\code{\link{is_ISO8601_timezone}()}, +\code{\link{is_ISO8601_calendar_datetime}()}, \code{\link{is_ISO8601_time}()}, +\code{\link{is_ISO8601_timezone}()}, \code{\link{is_ISO8601_week_datetime}()}, \code{\link{make_dy}()}, -\code{\link{pattern_ISO8601_any_datetime}()}, \code{\link{pattern_ISO8601_any_date}()}, -\code{\link{pattern_ISO8601_calendar_datetime}()}, +\code{\link{pattern_ISO8601_any_datetime}()}, \code{\link{pattern_ISO8601_calendar_date}()}, +\code{\link{pattern_ISO8601_calendar_datetime}()}, \code{\link{pattern_ISO8601_calendar_year}()}, -\code{\link{pattern_ISO8601_ordinal_datetime}()}, \code{\link{pattern_ISO8601_ordinal_date}()}, -\code{\link{pattern_ISO8601_timezone}()}, +\code{\link{pattern_ISO8601_ordinal_datetime}()}, \code{\link{pattern_ISO8601_time}()}, -\code{\link{pattern_ISO8601_week_datetime}()}, +\code{\link{pattern_ISO8601_timezone}()}, \code{\link{pattern_ISO8601_week_date}()}, +\code{\link{pattern_ISO8601_week_datetime}()}, \code{\link{sdtm_dtc_to_datetime}()}, \code{\link{sdtm_first_dose}()}, \code{\link{sdtm_time_actual}()} diff --git a/man/is_ISO8601_time.Rd b/man/is_ISO8601_time.Rd index 2168bb7..0108df1 100644 --- a/man/is_ISO8601_time.Rd +++ b/man/is_ISO8601_time.Rd @@ -36,8 +36,8 @@ Determine if a string is an ISO 8601 time } \seealso{ Other ISO8601 String checking: -\code{\link{is_ISO8601_calendar_datetime}()}, \code{\link{is_ISO8601_calendar_date}()}, +\code{\link{is_ISO8601_calendar_datetime}()}, \code{\link{is_ISO8601_ordinal_datetime}()}, \code{\link{is_ISO8601_timezone}()}, \code{\link{is_ISO8601_week_datetime}()} @@ -45,23 +45,23 @@ Other ISO8601 String checking: Other Date management and conversion: \code{\link{dateany_to_date}()}, \code{\link{generate_dtc}()}, -\code{\link{is_ISO8601_calendar_datetime}()}, \code{\link{is_ISO8601_calendar_date}()}, +\code{\link{is_ISO8601_calendar_datetime}()}, \code{\link{is_ISO8601_ordinal_datetime}()}, \code{\link{is_ISO8601_timezone}()}, \code{\link{is_ISO8601_week_datetime}()}, \code{\link{make_dy}()}, -\code{\link{pattern_ISO8601_any_datetime}()}, \code{\link{pattern_ISO8601_any_date}()}, -\code{\link{pattern_ISO8601_calendar_datetime}()}, +\code{\link{pattern_ISO8601_any_datetime}()}, \code{\link{pattern_ISO8601_calendar_date}()}, +\code{\link{pattern_ISO8601_calendar_datetime}()}, \code{\link{pattern_ISO8601_calendar_year}()}, -\code{\link{pattern_ISO8601_ordinal_datetime}()}, \code{\link{pattern_ISO8601_ordinal_date}()}, -\code{\link{pattern_ISO8601_timezone}()}, +\code{\link{pattern_ISO8601_ordinal_datetime}()}, \code{\link{pattern_ISO8601_time}()}, -\code{\link{pattern_ISO8601_week_datetime}()}, +\code{\link{pattern_ISO8601_timezone}()}, \code{\link{pattern_ISO8601_week_date}()}, +\code{\link{pattern_ISO8601_week_datetime}()}, \code{\link{sdtm_dtc_to_datetime}()}, \code{\link{sdtm_first_dose}()}, \code{\link{sdtm_time_actual}()} diff --git a/man/is_ISO8601_timezone.Rd b/man/is_ISO8601_timezone.Rd index 1e7dd2d..72369f9 100644 --- a/man/is_ISO8601_timezone.Rd +++ b/man/is_ISO8601_timezone.Rd @@ -14,8 +14,8 @@ Determine if a string is an ISO 8601 timezone } \seealso{ Other ISO8601 String checking: -\code{\link{is_ISO8601_calendar_datetime}()}, \code{\link{is_ISO8601_calendar_date}()}, +\code{\link{is_ISO8601_calendar_datetime}()}, \code{\link{is_ISO8601_ordinal_datetime}()}, \code{\link{is_ISO8601_time}()}, \code{\link{is_ISO8601_week_datetime}()} @@ -23,23 +23,23 @@ Other ISO8601 String checking: Other Date management and conversion: \code{\link{dateany_to_date}()}, \code{\link{generate_dtc}()}, -\code{\link{is_ISO8601_calendar_datetime}()}, \code{\link{is_ISO8601_calendar_date}()}, +\code{\link{is_ISO8601_calendar_datetime}()}, \code{\link{is_ISO8601_ordinal_datetime}()}, \code{\link{is_ISO8601_time}()}, \code{\link{is_ISO8601_week_datetime}()}, \code{\link{make_dy}()}, -\code{\link{pattern_ISO8601_any_datetime}()}, \code{\link{pattern_ISO8601_any_date}()}, -\code{\link{pattern_ISO8601_calendar_datetime}()}, +\code{\link{pattern_ISO8601_any_datetime}()}, \code{\link{pattern_ISO8601_calendar_date}()}, +\code{\link{pattern_ISO8601_calendar_datetime}()}, \code{\link{pattern_ISO8601_calendar_year}()}, -\code{\link{pattern_ISO8601_ordinal_datetime}()}, \code{\link{pattern_ISO8601_ordinal_date}()}, -\code{\link{pattern_ISO8601_timezone}()}, +\code{\link{pattern_ISO8601_ordinal_datetime}()}, \code{\link{pattern_ISO8601_time}()}, -\code{\link{pattern_ISO8601_week_datetime}()}, +\code{\link{pattern_ISO8601_timezone}()}, \code{\link{pattern_ISO8601_week_date}()}, +\code{\link{pattern_ISO8601_week_datetime}()}, \code{\link{sdtm_dtc_to_datetime}()}, \code{\link{sdtm_first_dose}()}, \code{\link{sdtm_time_actual}()} diff --git a/man/is_ISO8601_week_datetime.Rd b/man/is_ISO8601_week_datetime.Rd index 20d63b4..d7a96e8 100644 --- a/man/is_ISO8601_week_datetime.Rd +++ b/man/is_ISO8601_week_datetime.Rd @@ -23,32 +23,32 @@ Determine if a string matches an ISO 8601 date/time using week date notation } \seealso{ Other ISO8601 String checking: -\code{\link{is_ISO8601_calendar_datetime}()}, \code{\link{is_ISO8601_calendar_date}()}, +\code{\link{is_ISO8601_calendar_datetime}()}, \code{\link{is_ISO8601_ordinal_datetime}()}, -\code{\link{is_ISO8601_timezone}()}, -\code{\link{is_ISO8601_time}()} +\code{\link{is_ISO8601_time}()}, +\code{\link{is_ISO8601_timezone}()} Other Date management and conversion: \code{\link{dateany_to_date}()}, \code{\link{generate_dtc}()}, -\code{\link{is_ISO8601_calendar_datetime}()}, \code{\link{is_ISO8601_calendar_date}()}, +\code{\link{is_ISO8601_calendar_datetime}()}, \code{\link{is_ISO8601_ordinal_datetime}()}, -\code{\link{is_ISO8601_timezone}()}, \code{\link{is_ISO8601_time}()}, +\code{\link{is_ISO8601_timezone}()}, \code{\link{make_dy}()}, -\code{\link{pattern_ISO8601_any_datetime}()}, \code{\link{pattern_ISO8601_any_date}()}, -\code{\link{pattern_ISO8601_calendar_datetime}()}, +\code{\link{pattern_ISO8601_any_datetime}()}, \code{\link{pattern_ISO8601_calendar_date}()}, +\code{\link{pattern_ISO8601_calendar_datetime}()}, \code{\link{pattern_ISO8601_calendar_year}()}, -\code{\link{pattern_ISO8601_ordinal_datetime}()}, \code{\link{pattern_ISO8601_ordinal_date}()}, -\code{\link{pattern_ISO8601_timezone}()}, +\code{\link{pattern_ISO8601_ordinal_datetime}()}, \code{\link{pattern_ISO8601_time}()}, -\code{\link{pattern_ISO8601_week_datetime}()}, +\code{\link{pattern_ISO8601_timezone}()}, \code{\link{pattern_ISO8601_week_date}()}, +\code{\link{pattern_ISO8601_week_datetime}()}, \code{\link{sdtm_dtc_to_datetime}()}, \code{\link{sdtm_first_dose}()}, \code{\link{sdtm_time_actual}()} diff --git a/man/make_dy.Rd b/man/make_dy.Rd index 7909239..ffc180c 100644 --- a/man/make_dy.Rd +++ b/man/make_dy.Rd @@ -30,23 +30,23 @@ make_dy(c("2022-01-02", "2022-01-03", "2022-01-04"), "2022-01-03") Other Date management and conversion: \code{\link{dateany_to_date}()}, \code{\link{generate_dtc}()}, -\code{\link{is_ISO8601_calendar_datetime}()}, \code{\link{is_ISO8601_calendar_date}()}, +\code{\link{is_ISO8601_calendar_datetime}()}, \code{\link{is_ISO8601_ordinal_datetime}()}, -\code{\link{is_ISO8601_timezone}()}, \code{\link{is_ISO8601_time}()}, +\code{\link{is_ISO8601_timezone}()}, \code{\link{is_ISO8601_week_datetime}()}, -\code{\link{pattern_ISO8601_any_datetime}()}, \code{\link{pattern_ISO8601_any_date}()}, -\code{\link{pattern_ISO8601_calendar_datetime}()}, +\code{\link{pattern_ISO8601_any_datetime}()}, \code{\link{pattern_ISO8601_calendar_date}()}, +\code{\link{pattern_ISO8601_calendar_datetime}()}, \code{\link{pattern_ISO8601_calendar_year}()}, -\code{\link{pattern_ISO8601_ordinal_datetime}()}, \code{\link{pattern_ISO8601_ordinal_date}()}, -\code{\link{pattern_ISO8601_timezone}()}, +\code{\link{pattern_ISO8601_ordinal_datetime}()}, \code{\link{pattern_ISO8601_time}()}, -\code{\link{pattern_ISO8601_week_datetime}()}, +\code{\link{pattern_ISO8601_timezone}()}, \code{\link{pattern_ISO8601_week_date}()}, +\code{\link{pattern_ISO8601_week_datetime}()}, \code{\link{sdtm_dtc_to_datetime}()}, \code{\link{sdtm_first_dose}()}, \code{\link{sdtm_time_actual}()} diff --git a/man/pattern_ISO8601_any_date.Rd b/man/pattern_ISO8601_any_date.Rd index 1a37684..c858a4e 100644 --- a/man/pattern_ISO8601_any_date.Rd +++ b/man/pattern_ISO8601_any_date.Rd @@ -37,36 +37,36 @@ https://en.wikipedia.org/wiki/ISO_8601 \seealso{ Other ISO8601 patterns: \code{\link{pattern_ISO8601_any_datetime}()}, -\code{\link{pattern_ISO8601_calendar_datetime}()}, \code{\link{pattern_ISO8601_calendar_date}()}, +\code{\link{pattern_ISO8601_calendar_datetime}()}, \code{\link{pattern_ISO8601_calendar_year}()}, -\code{\link{pattern_ISO8601_ordinal_datetime}()}, \code{\link{pattern_ISO8601_ordinal_date}()}, -\code{\link{pattern_ISO8601_timezone}()}, +\code{\link{pattern_ISO8601_ordinal_datetime}()}, \code{\link{pattern_ISO8601_time}()}, -\code{\link{pattern_ISO8601_week_datetime}()}, -\code{\link{pattern_ISO8601_week_date}()} +\code{\link{pattern_ISO8601_timezone}()}, +\code{\link{pattern_ISO8601_week_date}()}, +\code{\link{pattern_ISO8601_week_datetime}()} Other Date management and conversion: \code{\link{dateany_to_date}()}, \code{\link{generate_dtc}()}, -\code{\link{is_ISO8601_calendar_datetime}()}, \code{\link{is_ISO8601_calendar_date}()}, +\code{\link{is_ISO8601_calendar_datetime}()}, \code{\link{is_ISO8601_ordinal_datetime}()}, -\code{\link{is_ISO8601_timezone}()}, \code{\link{is_ISO8601_time}()}, +\code{\link{is_ISO8601_timezone}()}, \code{\link{is_ISO8601_week_datetime}()}, \code{\link{make_dy}()}, \code{\link{pattern_ISO8601_any_datetime}()}, -\code{\link{pattern_ISO8601_calendar_datetime}()}, \code{\link{pattern_ISO8601_calendar_date}()}, +\code{\link{pattern_ISO8601_calendar_datetime}()}, \code{\link{pattern_ISO8601_calendar_year}()}, -\code{\link{pattern_ISO8601_ordinal_datetime}()}, \code{\link{pattern_ISO8601_ordinal_date}()}, -\code{\link{pattern_ISO8601_timezone}()}, +\code{\link{pattern_ISO8601_ordinal_datetime}()}, \code{\link{pattern_ISO8601_time}()}, -\code{\link{pattern_ISO8601_week_datetime}()}, +\code{\link{pattern_ISO8601_timezone}()}, \code{\link{pattern_ISO8601_week_date}()}, +\code{\link{pattern_ISO8601_week_datetime}()}, \code{\link{sdtm_dtc_to_datetime}()}, \code{\link{sdtm_first_dose}()}, \code{\link{sdtm_time_actual}()} diff --git a/man/pattern_ISO8601_any_datetime.Rd b/man/pattern_ISO8601_any_datetime.Rd index d807683..e675232 100644 --- a/man/pattern_ISO8601_any_datetime.Rd +++ b/man/pattern_ISO8601_any_datetime.Rd @@ -21,36 +21,36 @@ Generate a regular expression matching any ISO8601 date format with time \seealso{ Other ISO8601 patterns: \code{\link{pattern_ISO8601_any_date}()}, -\code{\link{pattern_ISO8601_calendar_datetime}()}, \code{\link{pattern_ISO8601_calendar_date}()}, +\code{\link{pattern_ISO8601_calendar_datetime}()}, \code{\link{pattern_ISO8601_calendar_year}()}, -\code{\link{pattern_ISO8601_ordinal_datetime}()}, \code{\link{pattern_ISO8601_ordinal_date}()}, -\code{\link{pattern_ISO8601_timezone}()}, +\code{\link{pattern_ISO8601_ordinal_datetime}()}, \code{\link{pattern_ISO8601_time}()}, -\code{\link{pattern_ISO8601_week_datetime}()}, -\code{\link{pattern_ISO8601_week_date}()} +\code{\link{pattern_ISO8601_timezone}()}, +\code{\link{pattern_ISO8601_week_date}()}, +\code{\link{pattern_ISO8601_week_datetime}()} Other Date management and conversion: \code{\link{dateany_to_date}()}, \code{\link{generate_dtc}()}, -\code{\link{is_ISO8601_calendar_datetime}()}, \code{\link{is_ISO8601_calendar_date}()}, +\code{\link{is_ISO8601_calendar_datetime}()}, \code{\link{is_ISO8601_ordinal_datetime}()}, -\code{\link{is_ISO8601_timezone}()}, \code{\link{is_ISO8601_time}()}, +\code{\link{is_ISO8601_timezone}()}, \code{\link{is_ISO8601_week_datetime}()}, \code{\link{make_dy}()}, \code{\link{pattern_ISO8601_any_date}()}, -\code{\link{pattern_ISO8601_calendar_datetime}()}, \code{\link{pattern_ISO8601_calendar_date}()}, +\code{\link{pattern_ISO8601_calendar_datetime}()}, \code{\link{pattern_ISO8601_calendar_year}()}, -\code{\link{pattern_ISO8601_ordinal_datetime}()}, \code{\link{pattern_ISO8601_ordinal_date}()}, -\code{\link{pattern_ISO8601_timezone}()}, +\code{\link{pattern_ISO8601_ordinal_datetime}()}, \code{\link{pattern_ISO8601_time}()}, -\code{\link{pattern_ISO8601_week_datetime}()}, +\code{\link{pattern_ISO8601_timezone}()}, \code{\link{pattern_ISO8601_week_date}()}, +\code{\link{pattern_ISO8601_week_datetime}()}, \code{\link{sdtm_dtc_to_datetime}()}, \code{\link{sdtm_first_dose}()}, \code{\link{sdtm_time_actual}()} diff --git a/man/pattern_ISO8601_calendar_date.Rd b/man/pattern_ISO8601_calendar_date.Rd index dd7aaf4..cbdd9a4 100644 --- a/man/pattern_ISO8601_calendar_date.Rd +++ b/man/pattern_ISO8601_calendar_date.Rd @@ -36,37 +36,37 @@ https://en.wikipedia.org/wiki/ISO_8601 } \seealso{ Other ISO8601 patterns: -\code{\link{pattern_ISO8601_any_datetime}()}, \code{\link{pattern_ISO8601_any_date}()}, +\code{\link{pattern_ISO8601_any_datetime}()}, \code{\link{pattern_ISO8601_calendar_datetime}()}, \code{\link{pattern_ISO8601_calendar_year}()}, -\code{\link{pattern_ISO8601_ordinal_datetime}()}, \code{\link{pattern_ISO8601_ordinal_date}()}, -\code{\link{pattern_ISO8601_timezone}()}, +\code{\link{pattern_ISO8601_ordinal_datetime}()}, \code{\link{pattern_ISO8601_time}()}, -\code{\link{pattern_ISO8601_week_datetime}()}, -\code{\link{pattern_ISO8601_week_date}()} +\code{\link{pattern_ISO8601_timezone}()}, +\code{\link{pattern_ISO8601_week_date}()}, +\code{\link{pattern_ISO8601_week_datetime}()} Other Date management and conversion: \code{\link{dateany_to_date}()}, \code{\link{generate_dtc}()}, -\code{\link{is_ISO8601_calendar_datetime}()}, \code{\link{is_ISO8601_calendar_date}()}, +\code{\link{is_ISO8601_calendar_datetime}()}, \code{\link{is_ISO8601_ordinal_datetime}()}, -\code{\link{is_ISO8601_timezone}()}, \code{\link{is_ISO8601_time}()}, +\code{\link{is_ISO8601_timezone}()}, \code{\link{is_ISO8601_week_datetime}()}, \code{\link{make_dy}()}, -\code{\link{pattern_ISO8601_any_datetime}()}, \code{\link{pattern_ISO8601_any_date}()}, +\code{\link{pattern_ISO8601_any_datetime}()}, \code{\link{pattern_ISO8601_calendar_datetime}()}, \code{\link{pattern_ISO8601_calendar_year}()}, -\code{\link{pattern_ISO8601_ordinal_datetime}()}, \code{\link{pattern_ISO8601_ordinal_date}()}, -\code{\link{pattern_ISO8601_timezone}()}, +\code{\link{pattern_ISO8601_ordinal_datetime}()}, \code{\link{pattern_ISO8601_time}()}, -\code{\link{pattern_ISO8601_week_datetime}()}, +\code{\link{pattern_ISO8601_timezone}()}, \code{\link{pattern_ISO8601_week_date}()}, +\code{\link{pattern_ISO8601_week_datetime}()}, \code{\link{sdtm_dtc_to_datetime}()}, \code{\link{sdtm_first_dose}()}, \code{\link{sdtm_time_actual}()} diff --git a/man/pattern_ISO8601_calendar_datetime.Rd b/man/pattern_ISO8601_calendar_datetime.Rd index d6ae746..472d048 100644 --- a/man/pattern_ISO8601_calendar_datetime.Rd +++ b/man/pattern_ISO8601_calendar_datetime.Rd @@ -20,37 +20,37 @@ Generate a regular expression matching an ISO8601 calendar date with time } \seealso{ Other ISO8601 patterns: -\code{\link{pattern_ISO8601_any_datetime}()}, \code{\link{pattern_ISO8601_any_date}()}, +\code{\link{pattern_ISO8601_any_datetime}()}, \code{\link{pattern_ISO8601_calendar_date}()}, \code{\link{pattern_ISO8601_calendar_year}()}, -\code{\link{pattern_ISO8601_ordinal_datetime}()}, \code{\link{pattern_ISO8601_ordinal_date}()}, -\code{\link{pattern_ISO8601_timezone}()}, +\code{\link{pattern_ISO8601_ordinal_datetime}()}, \code{\link{pattern_ISO8601_time}()}, -\code{\link{pattern_ISO8601_week_datetime}()}, -\code{\link{pattern_ISO8601_week_date}()} +\code{\link{pattern_ISO8601_timezone}()}, +\code{\link{pattern_ISO8601_week_date}()}, +\code{\link{pattern_ISO8601_week_datetime}()} Other Date management and conversion: \code{\link{dateany_to_date}()}, \code{\link{generate_dtc}()}, -\code{\link{is_ISO8601_calendar_datetime}()}, \code{\link{is_ISO8601_calendar_date}()}, +\code{\link{is_ISO8601_calendar_datetime}()}, \code{\link{is_ISO8601_ordinal_datetime}()}, -\code{\link{is_ISO8601_timezone}()}, \code{\link{is_ISO8601_time}()}, +\code{\link{is_ISO8601_timezone}()}, \code{\link{is_ISO8601_week_datetime}()}, \code{\link{make_dy}()}, -\code{\link{pattern_ISO8601_any_datetime}()}, \code{\link{pattern_ISO8601_any_date}()}, +\code{\link{pattern_ISO8601_any_datetime}()}, \code{\link{pattern_ISO8601_calendar_date}()}, \code{\link{pattern_ISO8601_calendar_year}()}, -\code{\link{pattern_ISO8601_ordinal_datetime}()}, \code{\link{pattern_ISO8601_ordinal_date}()}, -\code{\link{pattern_ISO8601_timezone}()}, +\code{\link{pattern_ISO8601_ordinal_datetime}()}, \code{\link{pattern_ISO8601_time}()}, -\code{\link{pattern_ISO8601_week_datetime}()}, +\code{\link{pattern_ISO8601_timezone}()}, \code{\link{pattern_ISO8601_week_date}()}, +\code{\link{pattern_ISO8601_week_datetime}()}, \code{\link{sdtm_dtc_to_datetime}()}, \code{\link{sdtm_first_dose}()}, \code{\link{sdtm_time_actual}()} diff --git a/man/pattern_ISO8601_calendar_year.Rd b/man/pattern_ISO8601_calendar_year.Rd index ad1b005..5198935 100644 --- a/man/pattern_ISO8601_calendar_year.Rd +++ b/man/pattern_ISO8601_calendar_year.Rd @@ -22,37 +22,37 @@ https://en.wikipedia.org/wiki/ISO_8601 } \seealso{ Other ISO8601 patterns: -\code{\link{pattern_ISO8601_any_datetime}()}, \code{\link{pattern_ISO8601_any_date}()}, -\code{\link{pattern_ISO8601_calendar_datetime}()}, +\code{\link{pattern_ISO8601_any_datetime}()}, \code{\link{pattern_ISO8601_calendar_date}()}, -\code{\link{pattern_ISO8601_ordinal_datetime}()}, +\code{\link{pattern_ISO8601_calendar_datetime}()}, \code{\link{pattern_ISO8601_ordinal_date}()}, -\code{\link{pattern_ISO8601_timezone}()}, +\code{\link{pattern_ISO8601_ordinal_datetime}()}, \code{\link{pattern_ISO8601_time}()}, -\code{\link{pattern_ISO8601_week_datetime}()}, -\code{\link{pattern_ISO8601_week_date}()} +\code{\link{pattern_ISO8601_timezone}()}, +\code{\link{pattern_ISO8601_week_date}()}, +\code{\link{pattern_ISO8601_week_datetime}()} Other Date management and conversion: \code{\link{dateany_to_date}()}, \code{\link{generate_dtc}()}, -\code{\link{is_ISO8601_calendar_datetime}()}, \code{\link{is_ISO8601_calendar_date}()}, +\code{\link{is_ISO8601_calendar_datetime}()}, \code{\link{is_ISO8601_ordinal_datetime}()}, -\code{\link{is_ISO8601_timezone}()}, \code{\link{is_ISO8601_time}()}, +\code{\link{is_ISO8601_timezone}()}, \code{\link{is_ISO8601_week_datetime}()}, \code{\link{make_dy}()}, -\code{\link{pattern_ISO8601_any_datetime}()}, \code{\link{pattern_ISO8601_any_date}()}, -\code{\link{pattern_ISO8601_calendar_datetime}()}, +\code{\link{pattern_ISO8601_any_datetime}()}, \code{\link{pattern_ISO8601_calendar_date}()}, -\code{\link{pattern_ISO8601_ordinal_datetime}()}, +\code{\link{pattern_ISO8601_calendar_datetime}()}, \code{\link{pattern_ISO8601_ordinal_date}()}, -\code{\link{pattern_ISO8601_timezone}()}, +\code{\link{pattern_ISO8601_ordinal_datetime}()}, \code{\link{pattern_ISO8601_time}()}, -\code{\link{pattern_ISO8601_week_datetime}()}, +\code{\link{pattern_ISO8601_timezone}()}, \code{\link{pattern_ISO8601_week_date}()}, +\code{\link{pattern_ISO8601_week_datetime}()}, \code{\link{sdtm_dtc_to_datetime}()}, \code{\link{sdtm_first_dose}()}, \code{\link{sdtm_time_actual}()} diff --git a/man/pattern_ISO8601_ordinal_date.Rd b/man/pattern_ISO8601_ordinal_date.Rd index 3665ace..8bffe0c 100644 --- a/man/pattern_ISO8601_ordinal_date.Rd +++ b/man/pattern_ISO8601_ordinal_date.Rd @@ -37,37 +37,37 @@ https://en.wikipedia.org/wiki/ISO_8601 } \seealso{ Other ISO8601 patterns: -\code{\link{pattern_ISO8601_any_datetime}()}, \code{\link{pattern_ISO8601_any_date}()}, -\code{\link{pattern_ISO8601_calendar_datetime}()}, +\code{\link{pattern_ISO8601_any_datetime}()}, \code{\link{pattern_ISO8601_calendar_date}()}, +\code{\link{pattern_ISO8601_calendar_datetime}()}, \code{\link{pattern_ISO8601_calendar_year}()}, \code{\link{pattern_ISO8601_ordinal_datetime}()}, -\code{\link{pattern_ISO8601_timezone}()}, \code{\link{pattern_ISO8601_time}()}, -\code{\link{pattern_ISO8601_week_datetime}()}, -\code{\link{pattern_ISO8601_week_date}()} +\code{\link{pattern_ISO8601_timezone}()}, +\code{\link{pattern_ISO8601_week_date}()}, +\code{\link{pattern_ISO8601_week_datetime}()} Other Date management and conversion: \code{\link{dateany_to_date}()}, \code{\link{generate_dtc}()}, -\code{\link{is_ISO8601_calendar_datetime}()}, \code{\link{is_ISO8601_calendar_date}()}, +\code{\link{is_ISO8601_calendar_datetime}()}, \code{\link{is_ISO8601_ordinal_datetime}()}, -\code{\link{is_ISO8601_timezone}()}, \code{\link{is_ISO8601_time}()}, +\code{\link{is_ISO8601_timezone}()}, \code{\link{is_ISO8601_week_datetime}()}, \code{\link{make_dy}()}, -\code{\link{pattern_ISO8601_any_datetime}()}, \code{\link{pattern_ISO8601_any_date}()}, -\code{\link{pattern_ISO8601_calendar_datetime}()}, +\code{\link{pattern_ISO8601_any_datetime}()}, \code{\link{pattern_ISO8601_calendar_date}()}, +\code{\link{pattern_ISO8601_calendar_datetime}()}, \code{\link{pattern_ISO8601_calendar_year}()}, \code{\link{pattern_ISO8601_ordinal_datetime}()}, -\code{\link{pattern_ISO8601_timezone}()}, \code{\link{pattern_ISO8601_time}()}, -\code{\link{pattern_ISO8601_week_datetime}()}, +\code{\link{pattern_ISO8601_timezone}()}, \code{\link{pattern_ISO8601_week_date}()}, +\code{\link{pattern_ISO8601_week_datetime}()}, \code{\link{sdtm_dtc_to_datetime}()}, \code{\link{sdtm_first_dose}()}, \code{\link{sdtm_time_actual}()} diff --git a/man/pattern_ISO8601_ordinal_datetime.Rd b/man/pattern_ISO8601_ordinal_datetime.Rd index 0ee5b71..102592b 100644 --- a/man/pattern_ISO8601_ordinal_datetime.Rd +++ b/man/pattern_ISO8601_ordinal_datetime.Rd @@ -20,37 +20,37 @@ Generate a regular expression matching an ISO8601 ordinal date with time } \seealso{ Other ISO8601 patterns: -\code{\link{pattern_ISO8601_any_datetime}()}, \code{\link{pattern_ISO8601_any_date}()}, -\code{\link{pattern_ISO8601_calendar_datetime}()}, +\code{\link{pattern_ISO8601_any_datetime}()}, \code{\link{pattern_ISO8601_calendar_date}()}, +\code{\link{pattern_ISO8601_calendar_datetime}()}, \code{\link{pattern_ISO8601_calendar_year}()}, \code{\link{pattern_ISO8601_ordinal_date}()}, -\code{\link{pattern_ISO8601_timezone}()}, \code{\link{pattern_ISO8601_time}()}, -\code{\link{pattern_ISO8601_week_datetime}()}, -\code{\link{pattern_ISO8601_week_date}()} +\code{\link{pattern_ISO8601_timezone}()}, +\code{\link{pattern_ISO8601_week_date}()}, +\code{\link{pattern_ISO8601_week_datetime}()} Other Date management and conversion: \code{\link{dateany_to_date}()}, \code{\link{generate_dtc}()}, -\code{\link{is_ISO8601_calendar_datetime}()}, \code{\link{is_ISO8601_calendar_date}()}, +\code{\link{is_ISO8601_calendar_datetime}()}, \code{\link{is_ISO8601_ordinal_datetime}()}, -\code{\link{is_ISO8601_timezone}()}, \code{\link{is_ISO8601_time}()}, +\code{\link{is_ISO8601_timezone}()}, \code{\link{is_ISO8601_week_datetime}()}, \code{\link{make_dy}()}, -\code{\link{pattern_ISO8601_any_datetime}()}, \code{\link{pattern_ISO8601_any_date}()}, -\code{\link{pattern_ISO8601_calendar_datetime}()}, +\code{\link{pattern_ISO8601_any_datetime}()}, \code{\link{pattern_ISO8601_calendar_date}()}, +\code{\link{pattern_ISO8601_calendar_datetime}()}, \code{\link{pattern_ISO8601_calendar_year}()}, \code{\link{pattern_ISO8601_ordinal_date}()}, -\code{\link{pattern_ISO8601_timezone}()}, \code{\link{pattern_ISO8601_time}()}, -\code{\link{pattern_ISO8601_week_datetime}()}, +\code{\link{pattern_ISO8601_timezone}()}, \code{\link{pattern_ISO8601_week_date}()}, +\code{\link{pattern_ISO8601_week_datetime}()}, \code{\link{sdtm_dtc_to_datetime}()}, \code{\link{sdtm_first_dose}()}, \code{\link{sdtm_time_actual}()} diff --git a/man/pattern_ISO8601_time.Rd b/man/pattern_ISO8601_time.Rd index 3ec24c9..5c2d845 100644 --- a/man/pattern_ISO8601_time.Rd +++ b/man/pattern_ISO8601_time.Rd @@ -57,37 +57,37 @@ differences which could occur on different hours and at the end of any } \seealso{ Other ISO8601 patterns: -\code{\link{pattern_ISO8601_any_datetime}()}, \code{\link{pattern_ISO8601_any_date}()}, -\code{\link{pattern_ISO8601_calendar_datetime}()}, +\code{\link{pattern_ISO8601_any_datetime}()}, \code{\link{pattern_ISO8601_calendar_date}()}, +\code{\link{pattern_ISO8601_calendar_datetime}()}, \code{\link{pattern_ISO8601_calendar_year}()}, -\code{\link{pattern_ISO8601_ordinal_datetime}()}, \code{\link{pattern_ISO8601_ordinal_date}()}, +\code{\link{pattern_ISO8601_ordinal_datetime}()}, \code{\link{pattern_ISO8601_timezone}()}, -\code{\link{pattern_ISO8601_week_datetime}()}, -\code{\link{pattern_ISO8601_week_date}()} +\code{\link{pattern_ISO8601_week_date}()}, +\code{\link{pattern_ISO8601_week_datetime}()} Other Date management and conversion: \code{\link{dateany_to_date}()}, \code{\link{generate_dtc}()}, -\code{\link{is_ISO8601_calendar_datetime}()}, \code{\link{is_ISO8601_calendar_date}()}, +\code{\link{is_ISO8601_calendar_datetime}()}, \code{\link{is_ISO8601_ordinal_datetime}()}, -\code{\link{is_ISO8601_timezone}()}, \code{\link{is_ISO8601_time}()}, +\code{\link{is_ISO8601_timezone}()}, \code{\link{is_ISO8601_week_datetime}()}, \code{\link{make_dy}()}, -\code{\link{pattern_ISO8601_any_datetime}()}, \code{\link{pattern_ISO8601_any_date}()}, -\code{\link{pattern_ISO8601_calendar_datetime}()}, +\code{\link{pattern_ISO8601_any_datetime}()}, \code{\link{pattern_ISO8601_calendar_date}()}, +\code{\link{pattern_ISO8601_calendar_datetime}()}, \code{\link{pattern_ISO8601_calendar_year}()}, -\code{\link{pattern_ISO8601_ordinal_datetime}()}, \code{\link{pattern_ISO8601_ordinal_date}()}, +\code{\link{pattern_ISO8601_ordinal_datetime}()}, \code{\link{pattern_ISO8601_timezone}()}, -\code{\link{pattern_ISO8601_week_datetime}()}, \code{\link{pattern_ISO8601_week_date}()}, +\code{\link{pattern_ISO8601_week_datetime}()}, \code{\link{sdtm_dtc_to_datetime}()}, \code{\link{sdtm_first_dose}()}, \code{\link{sdtm_time_actual}()} diff --git a/man/pattern_ISO8601_timezone.Rd b/man/pattern_ISO8601_timezone.Rd index 316c03e..4284dda 100644 --- a/man/pattern_ISO8601_timezone.Rd +++ b/man/pattern_ISO8601_timezone.Rd @@ -2,12 +2,12 @@ % Please edit documentation in R/iso8601_regexp.R \name{pattern_ISO8601_timezone} \alias{pattern_ISO8601_timezone} -\title{Generate a regular expression for ISO 8601 timezones.} +\title{Generate a regular expression for ISO 8601 time zones.} \usage{ pattern_ISO8601_timezone() } \description{ -Generate a regular expression for ISO 8601 timezones. +Generate a regular expression for ISO 8601 time zones. } \details{ Offsets are always multiples of 15 minutes, so if the minute part is @@ -24,37 +24,37 @@ https://en.wikipedia.org/wiki/UTC_offset } \seealso{ Other ISO8601 patterns: -\code{\link{pattern_ISO8601_any_datetime}()}, \code{\link{pattern_ISO8601_any_date}()}, -\code{\link{pattern_ISO8601_calendar_datetime}()}, +\code{\link{pattern_ISO8601_any_datetime}()}, \code{\link{pattern_ISO8601_calendar_date}()}, +\code{\link{pattern_ISO8601_calendar_datetime}()}, \code{\link{pattern_ISO8601_calendar_year}()}, -\code{\link{pattern_ISO8601_ordinal_datetime}()}, \code{\link{pattern_ISO8601_ordinal_date}()}, +\code{\link{pattern_ISO8601_ordinal_datetime}()}, \code{\link{pattern_ISO8601_time}()}, -\code{\link{pattern_ISO8601_week_datetime}()}, -\code{\link{pattern_ISO8601_week_date}()} +\code{\link{pattern_ISO8601_week_date}()}, +\code{\link{pattern_ISO8601_week_datetime}()} Other Date management and conversion: \code{\link{dateany_to_date}()}, \code{\link{generate_dtc}()}, -\code{\link{is_ISO8601_calendar_datetime}()}, \code{\link{is_ISO8601_calendar_date}()}, +\code{\link{is_ISO8601_calendar_datetime}()}, \code{\link{is_ISO8601_ordinal_datetime}()}, -\code{\link{is_ISO8601_timezone}()}, \code{\link{is_ISO8601_time}()}, +\code{\link{is_ISO8601_timezone}()}, \code{\link{is_ISO8601_week_datetime}()}, \code{\link{make_dy}()}, -\code{\link{pattern_ISO8601_any_datetime}()}, \code{\link{pattern_ISO8601_any_date}()}, -\code{\link{pattern_ISO8601_calendar_datetime}()}, +\code{\link{pattern_ISO8601_any_datetime}()}, \code{\link{pattern_ISO8601_calendar_date}()}, +\code{\link{pattern_ISO8601_calendar_datetime}()}, \code{\link{pattern_ISO8601_calendar_year}()}, -\code{\link{pattern_ISO8601_ordinal_datetime}()}, \code{\link{pattern_ISO8601_ordinal_date}()}, +\code{\link{pattern_ISO8601_ordinal_datetime}()}, \code{\link{pattern_ISO8601_time}()}, -\code{\link{pattern_ISO8601_week_datetime}()}, \code{\link{pattern_ISO8601_week_date}()}, +\code{\link{pattern_ISO8601_week_datetime}()}, \code{\link{sdtm_dtc_to_datetime}()}, \code{\link{sdtm_first_dose}()}, \code{\link{sdtm_time_actual}()} diff --git a/man/pattern_ISO8601_week_date.Rd b/man/pattern_ISO8601_week_date.Rd index cb278fe..6f61d38 100644 --- a/man/pattern_ISO8601_week_date.Rd +++ b/man/pattern_ISO8601_week_date.Rd @@ -36,36 +36,36 @@ https://en.wikipedia.org/wiki/ISO_8601 } \seealso{ Other ISO8601 patterns: -\code{\link{pattern_ISO8601_any_datetime}()}, \code{\link{pattern_ISO8601_any_date}()}, -\code{\link{pattern_ISO8601_calendar_datetime}()}, +\code{\link{pattern_ISO8601_any_datetime}()}, \code{\link{pattern_ISO8601_calendar_date}()}, +\code{\link{pattern_ISO8601_calendar_datetime}()}, \code{\link{pattern_ISO8601_calendar_year}()}, -\code{\link{pattern_ISO8601_ordinal_datetime}()}, \code{\link{pattern_ISO8601_ordinal_date}()}, -\code{\link{pattern_ISO8601_timezone}()}, +\code{\link{pattern_ISO8601_ordinal_datetime}()}, \code{\link{pattern_ISO8601_time}()}, +\code{\link{pattern_ISO8601_timezone}()}, \code{\link{pattern_ISO8601_week_datetime}()} Other Date management and conversion: \code{\link{dateany_to_date}()}, \code{\link{generate_dtc}()}, -\code{\link{is_ISO8601_calendar_datetime}()}, \code{\link{is_ISO8601_calendar_date}()}, +\code{\link{is_ISO8601_calendar_datetime}()}, \code{\link{is_ISO8601_ordinal_datetime}()}, -\code{\link{is_ISO8601_timezone}()}, \code{\link{is_ISO8601_time}()}, +\code{\link{is_ISO8601_timezone}()}, \code{\link{is_ISO8601_week_datetime}()}, \code{\link{make_dy}()}, -\code{\link{pattern_ISO8601_any_datetime}()}, \code{\link{pattern_ISO8601_any_date}()}, -\code{\link{pattern_ISO8601_calendar_datetime}()}, +\code{\link{pattern_ISO8601_any_datetime}()}, \code{\link{pattern_ISO8601_calendar_date}()}, +\code{\link{pattern_ISO8601_calendar_datetime}()}, \code{\link{pattern_ISO8601_calendar_year}()}, -\code{\link{pattern_ISO8601_ordinal_datetime}()}, \code{\link{pattern_ISO8601_ordinal_date}()}, -\code{\link{pattern_ISO8601_timezone}()}, +\code{\link{pattern_ISO8601_ordinal_datetime}()}, \code{\link{pattern_ISO8601_time}()}, +\code{\link{pattern_ISO8601_timezone}()}, \code{\link{pattern_ISO8601_week_datetime}()}, \code{\link{sdtm_dtc_to_datetime}()}, \code{\link{sdtm_first_dose}()}, diff --git a/man/pattern_ISO8601_week_datetime.Rd b/man/pattern_ISO8601_week_datetime.Rd index 0261837..2254b21 100644 --- a/man/pattern_ISO8601_week_datetime.Rd +++ b/man/pattern_ISO8601_week_datetime.Rd @@ -20,36 +20,36 @@ Generate a regular expression matching an ISO8601 week date with time } \seealso{ Other ISO8601 patterns: -\code{\link{pattern_ISO8601_any_datetime}()}, \code{\link{pattern_ISO8601_any_date}()}, -\code{\link{pattern_ISO8601_calendar_datetime}()}, +\code{\link{pattern_ISO8601_any_datetime}()}, \code{\link{pattern_ISO8601_calendar_date}()}, +\code{\link{pattern_ISO8601_calendar_datetime}()}, \code{\link{pattern_ISO8601_calendar_year}()}, -\code{\link{pattern_ISO8601_ordinal_datetime}()}, \code{\link{pattern_ISO8601_ordinal_date}()}, -\code{\link{pattern_ISO8601_timezone}()}, +\code{\link{pattern_ISO8601_ordinal_datetime}()}, \code{\link{pattern_ISO8601_time}()}, +\code{\link{pattern_ISO8601_timezone}()}, \code{\link{pattern_ISO8601_week_date}()} Other Date management and conversion: \code{\link{dateany_to_date}()}, \code{\link{generate_dtc}()}, -\code{\link{is_ISO8601_calendar_datetime}()}, \code{\link{is_ISO8601_calendar_date}()}, +\code{\link{is_ISO8601_calendar_datetime}()}, \code{\link{is_ISO8601_ordinal_datetime}()}, -\code{\link{is_ISO8601_timezone}()}, \code{\link{is_ISO8601_time}()}, +\code{\link{is_ISO8601_timezone}()}, \code{\link{is_ISO8601_week_datetime}()}, \code{\link{make_dy}()}, -\code{\link{pattern_ISO8601_any_datetime}()}, \code{\link{pattern_ISO8601_any_date}()}, -\code{\link{pattern_ISO8601_calendar_datetime}()}, +\code{\link{pattern_ISO8601_any_datetime}()}, \code{\link{pattern_ISO8601_calendar_date}()}, +\code{\link{pattern_ISO8601_calendar_datetime}()}, \code{\link{pattern_ISO8601_calendar_year}()}, -\code{\link{pattern_ISO8601_ordinal_datetime}()}, \code{\link{pattern_ISO8601_ordinal_date}()}, -\code{\link{pattern_ISO8601_timezone}()}, +\code{\link{pattern_ISO8601_ordinal_datetime}()}, \code{\link{pattern_ISO8601_time}()}, +\code{\link{pattern_ISO8601_timezone}()}, \code{\link{pattern_ISO8601_week_date}()}, \code{\link{sdtm_dtc_to_datetime}()}, \code{\link{sdtm_first_dose}()}, diff --git a/man/sdtm_dtc_to_datetime.Rd b/man/sdtm_dtc_to_datetime.Rd index 2bf7e84..21ccd4d 100644 --- a/man/sdtm_dtc_to_datetime.Rd +++ b/man/sdtm_dtc_to_datetime.Rd @@ -34,24 +34,24 @@ to a POSIXct object. Other Date management and conversion: \code{\link{dateany_to_date}()}, \code{\link{generate_dtc}()}, -\code{\link{is_ISO8601_calendar_datetime}()}, \code{\link{is_ISO8601_calendar_date}()}, +\code{\link{is_ISO8601_calendar_datetime}()}, \code{\link{is_ISO8601_ordinal_datetime}()}, -\code{\link{is_ISO8601_timezone}()}, \code{\link{is_ISO8601_time}()}, +\code{\link{is_ISO8601_timezone}()}, \code{\link{is_ISO8601_week_datetime}()}, \code{\link{make_dy}()}, -\code{\link{pattern_ISO8601_any_datetime}()}, \code{\link{pattern_ISO8601_any_date}()}, -\code{\link{pattern_ISO8601_calendar_datetime}()}, +\code{\link{pattern_ISO8601_any_datetime}()}, \code{\link{pattern_ISO8601_calendar_date}()}, +\code{\link{pattern_ISO8601_calendar_datetime}()}, \code{\link{pattern_ISO8601_calendar_year}()}, -\code{\link{pattern_ISO8601_ordinal_datetime}()}, \code{\link{pattern_ISO8601_ordinal_date}()}, -\code{\link{pattern_ISO8601_timezone}()}, +\code{\link{pattern_ISO8601_ordinal_datetime}()}, \code{\link{pattern_ISO8601_time}()}, -\code{\link{pattern_ISO8601_week_datetime}()}, +\code{\link{pattern_ISO8601_timezone}()}, \code{\link{pattern_ISO8601_week_date}()}, +\code{\link{pattern_ISO8601_week_datetime}()}, \code{\link{sdtm_first_dose}()}, \code{\link{sdtm_time_actual}()} } diff --git a/man/sdtm_example_dataverse_lb.Rd b/man/sdtm_example_dataverse_lb.Rd index 75b03ef..bdb59ec 100644 --- a/man/sdtm_example_dataverse_lb.Rd +++ b/man/sdtm_example_dataverse_lb.Rd @@ -25,7 +25,7 @@ A data frame with 29 variables and 83 observations: \item{LBSTRESU}{Standard Units, character} \item{LBSTNRLO}{Reference Range Lower Limit-Std Units, numeric} \item{LBSTNRHI}{Reference Range Upper Limit-Std Units, numeric} - \item{LBSTNRC}{Reference Range for Char Rslt-Std Units, character} + \item{LBSTNRC}{Reference Range for Char Result-Std Units, character} \item{LBNRIND}{Reference Range Indicator, character} \item{LBSPEC}{Specimen Type, character} \item{LBMETHOD}{Method of Test or Examination, character} diff --git a/man/sdtm_first_dose.Rd b/man/sdtm_first_dose.Rd index 3007a00..62b310f 100644 --- a/man/sdtm_first_dose.Rd +++ b/man/sdtm_first_dose.Rd @@ -46,24 +46,24 @@ Find the time of the first dose Other Date management and conversion: \code{\link{dateany_to_date}()}, \code{\link{generate_dtc}()}, -\code{\link{is_ISO8601_calendar_datetime}()}, \code{\link{is_ISO8601_calendar_date}()}, +\code{\link{is_ISO8601_calendar_datetime}()}, \code{\link{is_ISO8601_ordinal_datetime}()}, -\code{\link{is_ISO8601_timezone}()}, \code{\link{is_ISO8601_time}()}, +\code{\link{is_ISO8601_timezone}()}, \code{\link{is_ISO8601_week_datetime}()}, \code{\link{make_dy}()}, -\code{\link{pattern_ISO8601_any_datetime}()}, \code{\link{pattern_ISO8601_any_date}()}, -\code{\link{pattern_ISO8601_calendar_datetime}()}, +\code{\link{pattern_ISO8601_any_datetime}()}, \code{\link{pattern_ISO8601_calendar_date}()}, +\code{\link{pattern_ISO8601_calendar_datetime}()}, \code{\link{pattern_ISO8601_calendar_year}()}, -\code{\link{pattern_ISO8601_ordinal_datetime}()}, \code{\link{pattern_ISO8601_ordinal_date}()}, -\code{\link{pattern_ISO8601_timezone}()}, +\code{\link{pattern_ISO8601_ordinal_datetime}()}, \code{\link{pattern_ISO8601_time}()}, -\code{\link{pattern_ISO8601_week_datetime}()}, +\code{\link{pattern_ISO8601_timezone}()}, \code{\link{pattern_ISO8601_week_date}()}, +\code{\link{pattern_ISO8601_week_datetime}()}, \code{\link{sdtm_dtc_to_datetime}()}, \code{\link{sdtm_time_actual}()} } diff --git a/man/sdtm_time_actual.Rd b/man/sdtm_time_actual.Rd index 2a0cd7a..94d7fa5 100644 --- a/man/sdtm_time_actual.Rd +++ b/man/sdtm_time_actual.Rd @@ -47,24 +47,24 @@ Generate actual times from dates and times Other Date management and conversion: \code{\link{dateany_to_date}()}, \code{\link{generate_dtc}()}, -\code{\link{is_ISO8601_calendar_datetime}()}, \code{\link{is_ISO8601_calendar_date}()}, +\code{\link{is_ISO8601_calendar_datetime}()}, \code{\link{is_ISO8601_ordinal_datetime}()}, -\code{\link{is_ISO8601_timezone}()}, \code{\link{is_ISO8601_time}()}, +\code{\link{is_ISO8601_timezone}()}, \code{\link{is_ISO8601_week_datetime}()}, \code{\link{make_dy}()}, -\code{\link{pattern_ISO8601_any_datetime}()}, \code{\link{pattern_ISO8601_any_date}()}, -\code{\link{pattern_ISO8601_calendar_datetime}()}, +\code{\link{pattern_ISO8601_any_datetime}()}, \code{\link{pattern_ISO8601_calendar_date}()}, +\code{\link{pattern_ISO8601_calendar_datetime}()}, \code{\link{pattern_ISO8601_calendar_year}()}, -\code{\link{pattern_ISO8601_ordinal_datetime}()}, \code{\link{pattern_ISO8601_ordinal_date}()}, -\code{\link{pattern_ISO8601_timezone}()}, +\code{\link{pattern_ISO8601_ordinal_datetime}()}, \code{\link{pattern_ISO8601_time}()}, -\code{\link{pattern_ISO8601_week_datetime}()}, +\code{\link{pattern_ISO8601_timezone}()}, \code{\link{pattern_ISO8601_week_date}()}, +\code{\link{pattern_ISO8601_week_datetime}()}, \code{\link{sdtm_dtc_to_datetime}()}, \code{\link{sdtm_first_dose}()} } diff --git a/man/valid_versions.Rd b/man/valid_versions.Rd index 49a8488..3f3b761 100644 --- a/man/valid_versions.Rd +++ b/man/valid_versions.Rd @@ -9,7 +9,7 @@ combination} \describe{ \item{SDTM}{The SDTM version} \item{IG_NAME}{The implementation guide (IG) name being used} - \item{IG_VERSION}{The implemetation guide (IG) version} + \item{IG_VERSION}{The implementation guide (IG) version} \item{archived}{The SDTM version/IG pair has been archived (and should not be used for current studies)} } diff --git a/tests/spelling.R b/tests/spelling.R new file mode 100644 index 0000000..6713838 --- /dev/null +++ b/tests/spelling.R @@ -0,0 +1,3 @@ +if(requireNamespace('spelling', quietly = TRUE)) + spelling::spell_check_test(vignettes = TRUE, error = FALSE, + skip_on_cran = TRUE) diff --git a/tests/testthat/test-scale_x_VISITDY.R b/tests/testthat/test-scale_x_VISITDY.R index 55af13e..1094a5b 100644 --- a/tests/testthat/test-scale_x_VISITDY.R +++ b/tests/testthat/test-scale_x_VISITDY.R @@ -28,8 +28,13 @@ test_that("VISITDY_minor_breaks", { }) test_that("scale_x_VISITDY", { - expect_equal( - scale_x_VISITDY(), - ggplot2::scale_x_continuous(trans=VISITDY_trans) + # expect_equal( + # scale_x_VISITDY(), + # ggplot2::scale_x_continuous(trans=VISITDY_trans) + # ) + expect_error( + scale_x_VISITDY(trans = "A"), + regexp = "Cannot set 'trans' (just use scale_x_continuous())", + fixed = TRUE ) })