Update CI; update URLs

.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")'

.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

.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:
@@ -15,36 +16,46 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true
 
       - 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

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

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"
+"sdtm_terminology"

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}.

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

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}

README.md

@@ -1,8 +1,8 @@
 # Rsdtm
 
 <!-- badges: start -->
-[![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)
 <!-- badges: end -->
 
@@ -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")
 ```

_pkgdown.yml

@@ -1,4 +1,4 @@
-url: https://billdenney.github.io/Rsdtm/
+url: https://humanpred.github.io/Rsdtm/
 template:
   bootstrap: 5
 

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