Merge branch 'develop' into visc_git_ignore_dataspec_html

.github/workflows/R-CMD-check.yaml

@@ -22,7 +22,6 @@ jobs:
           - {os: windows-latest, r: 'release'}
           - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
           - {os: ubuntu-latest,   r: 'release'}
-          - {os: ubuntu-latest,   r: 'oldrel-1'}
           - {os: ubuntu-latest,   r: '4.0.4', pandoc-version: '2.11.4'}
 
     env:

.github/workflows/test-coverage.yaml

@@ -0,0 +1,72 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master, develop]
+  pull_request:
+    branches: [main, master, develop]
+
+name: test-coverage.yaml
+
+permissions: read-all
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-tinytex@v2
+
+      - name: Preinstall required latex packages
+        run: >
+          tlmgr install
+          lastpage morefloats parskip pdflscape textpos multirow lipsum
+          fancyhdr colortbl soul setspace relsize makecell threeparttable
+          threeparttablex environ trimspaces
+
+      - 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, any::xml2
+          needs: coverage
+
+      - name: Test coverage
+        run: |
+          cov <- covr::package_coverage(
+            quiet = FALSE,
+            clean = FALSE,
+            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_ci_if_error: ${{ github.event_name != 'pull_request' && true || false }}
+          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
+        shell: bash
+
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v4
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: VISCtemplates
 Title: Tools for writing reproducible reports at VISC
-Version: 1.3.2
+Version: 1.3.2.9000
 Authors@R: 
     person(given = "Jimmy",
            family = "Fulp",

NEWS.md

@@ -1,3 +1,19 @@
+# VISCtemplates (development version)
+
+Bug fixes
+* Provide default CRAN mirror if missing in install_load_cran_packages(), e.g., in a child R session during knitting. Fixes 'trying to use CRAN without setting a mirror' error (#218)
+* Update template.tex so that flextable package can be used to create tables in PDF documents (#226)
+* Clean up invalid ORCID placeholder generated by usethis 3.0.0 that threw error on R version 4.5.x (#248)
+* Fix error when running skeleton.Rmd file interactively (#249)
+* Include pdata object name and data package name in visc_load_pdata() error message (#252)
+
+Other improvements
+* create_visc_project() now discards README.Rmd after knitting template to README.md (#223)
+* Update PT report naming practices to the format VDCnnn_assay_PTreport_interim/final_(un)blinded.Rmd (#202)
+* Add auxiliary files to template .gitignore (.aux, .toc, .lof, .lot, .out, cache files, and .smbdelete files) (#230)
+* Update names in template acknowledgements section (#234)
+* Include dataspec html in the files to ignore in use_visc_gitignore() (#254) 
+
 # VISCtemplates 1.3.2
 
 Bug Fix
@@ -50,7 +66,6 @@ Package Maintenance
 * Adjust dependencies in DESCRIPTION (#164)
 * Update package authors and maintainer (#190)
 * Clean up latex template code, removing commented-out code and reorganizing for better readability (#196)
-* Include dataspec html in the files to ignore in use_visc_gitignore() (#254) 
 
 # VISCtemplates 1.2.0
 

R/create_visc_project.R

@@ -33,7 +33,15 @@ create_visc_project <- function(path, interactive = TRUE){
   usethis::create_package(
     path = path,
     rstudio = TRUE,
-    open = interactive
+    open = interactive,
+    # fields override for usethis 3.0.0 ORCID placeholder that errored in R 4.5
+    # https://github.com/r-lib/usethis/issues/2059
+    fields = list(
+      `Authors@R` = paste0(
+        "person(\"First\", \"Last\", email = \"first.last",
+        "@example.com\", role = c(\"aut\", \"cre\"))"
+      )
+    )
   )
 
   # must set active project otherwise it is <no active project>

R/report_functions.R

@@ -15,7 +15,10 @@ install_load_cran_packages <- function(packages) {
         stop(paste0("The package ", package, " must be installed through GitHub:
                   https://github.com/FredHutch/", package, ".git"))
       } else {
-        utils::install.packages(package)
+        # provide a default CRAN mirror if missing (e.g. in knitr R session)
+        repos <- getOption("repos")
+        if ("@CRAN@" %in% repos) repos <- "https://cloud.r-project.org/"
+        utils::install.packages(package, repos = repos)
         # install.packages() installs packages from the repository identified in
         # options('repos'), which is CRAN by default. To change this
         # setting, edit your .Rprofile. To view a list of available CRAN

R/use_visc_gitignore.R

@@ -36,10 +36,19 @@ use_visc_gitignore <- function(directory = ".") {
       "Thumbs.db",
       # files from Latex
       "*.log",
+      "*.aux",
+      "*.toc",
+      "*.lof",
+      "*.lot",
+      "*.out",
       "**/figure-latex/*.pdf",
       "**/figure-docx/*.pdf",
       "*.zip",
       "*dataspec*.html"
+      # cache files
+      "*_cache/",
+      # other
+      ".smbdelete*"
     ),
     directory = directory
   )

R/use_visc_report.R

@@ -16,6 +16,21 @@ use_visc_readme <- function(study_name, save_as = "README.Rmd") {
     data = list(study_name = study_name),
     package = "VISCtemplates"
   )
+  # knit the md from the Rmd on request of SRA team
+  rmarkdown::render(
+    usethis::proj_path('README.Rmd'),
+    quiet = TRUE
+  )
+  # remove Rmd at request of SRA team; they just manually edit the *.md
+  # so the Rmd file merely clutters their working directory
+  unlink(
+    usethis::proj_path(
+      paste0(
+        'README',
+        c('.Rmd', '.html')
+      )
+    )
+  )
 }
 
 #' Create a VISC docs directory with template files
@@ -105,7 +120,7 @@ use_bib <- function(study_name) {
 #'
 #' @param report_name name of the file (character)
 #' @param path path of the file within the active project
-#' @param report_type "empty", "generic", "bama", or "nab"
+#' @param report_type "empty", "generic", "bama", "nab", or "adcc"
 #' @param interactive TRUE by default. FALSE is for non-interactive unit testing
 #'   only.
 #'
@@ -119,20 +134,20 @@ use_bib <- function(study_name) {
 #'   report_type = "bama"
 #'   )
 #' }
-use_visc_report <- function(report_name = "PT-Report",
+use_visc_report <- function(report_name = "PTreport",
                             path = ".",
-                            report_type = c("empty", "generic", "bama", "nab"),
+                            report_type = c("empty", "generic", "bama", "nab", "adcc"),
                             interactive = TRUE) {
 
-  stopifnot(report_type %in% c("empty", "generic", "bama", "nab"))
+  stopifnot(report_type %in% c("empty", "generic", "bama", "nab", "adcc"))
 
   # suppress usethis output when non-interactive
   old_usethis_quiet <- getOption('usethis.quiet')
   on.exit(options(usethis.quiet = old_usethis_quiet))
-  options(usethis.quiet = ! interactive)
+  options(usethis.quiet = !interactive)
 
   if (report_type != 'empty') challenge_visc_report(report_name, interactive)
-  if (! dir.exists(path)) dir.create(path, recursive = TRUE)
+  if (!dir.exists(path)) dir.create(path, recursive = TRUE)
   use_template <- paste0(
     'visc', '_', if (report_type == 'empty') 'empty' else 'report'
   )
@@ -145,7 +160,7 @@ use_visc_report <- function(report_name = "PT-Report",
   usethis::ui_done(
     glue::glue("Creating {{report_type}} VISC report at '{{file.path(path, report_name)}}'")
   )
-  if (report_type != 'empty'){
+  if (report_type != 'empty') {
     use_visc_methods(path = file.path(path, report_name), assay = report_type,
                      interactive = interactive)
   }
@@ -154,15 +169,15 @@ use_visc_report <- function(report_name = "PT-Report",
 }
 
 challenge_visc_report <- function(report_name, interactive = TRUE) {
-  if (! interactive) return(invisible(NULL))
+  if (!interactive) return(invisible(NULL))
 
   continue <- usethis::ui_yeah("
     Creating a new VISC PT Report called {report_name}.
     At VISC, we use a naming convention for PT reports:
-    'VDCnnn_assay_PT_Report_statusifapplicable'
-    where 'statusifapplicable' distinguishes blinded reports,
-    HIV status, or something that distinguishes a type/subset
-    of a report.
+    'VDCnnn_assay_PTreport_status_blindingifapplicable'
+    where 'status' should be either 'interim' or 'final'
+    and 'blindingifapplicable' should be either 'blinded'
+    or 'unblinded' (applicable to interim reports only).
     'VDC' is the PI name and 'nnn' is the study number.
     Would you like to continue?")
 
@@ -177,7 +192,7 @@ challenge_visc_report <- function(report_name, interactive = TRUE) {
 #'  used in PT reports: statistical-methods.Rmd, lab-methods.Rmd,
 #'  and biological-endpoints.Rmd
 #'
-#' @param assay "bama" or "generic"
+#' @param assay "generic", "bama", "nab" or "adcc"
 #' @param path path within the active project
 #' @param interactive TRUE by default. FALSE is for non-interactive unit testing
 #'   only.
@@ -188,13 +203,13 @@ challenge_visc_report <- function(report_name, interactive = TRUE) {
 #' \dontrun{
 #' use_visc_methods(path = "bama/BAMA-PT-Report", assay = "bama")
 #' }
-use_visc_methods <- function(path = ".", assay = c("generic", "bama", "nab"),
+use_visc_methods <- function(path = ".", assay = c("generic", "bama", "nab", "adcc"),
                              interactive = TRUE) {
 
   # suppress usethis output when non-interactive
   old_usethis_quiet <- getOption('usethis.quiet')
   on.exit(options(usethis.quiet = old_usethis_quiet))
-  options(usethis.quiet = ! interactive)
+  options(usethis.quiet = !interactive)
 
   pkg_ver <- utils::packageVersion("VISCtemplates")
 

R/visc_load_pdata.R

@@ -75,7 +75,13 @@ visc_load_pdata <- function(.data,
       lazyLoad(filebase = system.file(file.path('data', 'Rdata'),
                  package = pkg_name), envir = pdata_env)
     } else {
-      stop('Unable to find data object file')
+      stop(
+        sprintf(
+          "Unable to find data object '%s' in package '%s'",
+          pdata_name,
+          pkg_name
+        )
+      )
     }
   }
 

README.Rmd

@@ -13,6 +13,11 @@ knitr::opts_chunk$set(
 )
 ```
 
+<!-- badges: start -->
+[![R-CMD-check](https://github.com/FredHutch/VISCtemplates/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/FredHutch/VISCtemplates/actions/workflows/R-CMD-check.yaml)
+[![Codecov test coverage](https://codecov.io/gh/FredHutch/VISCtemplates/graph/badge.svg)](https://app.codecov.io/gh/FredHutch/VISCtemplates)
+<!-- badges: end -->
+
 # VISCtemplates
 
 The goal of VISCtemplates is to: 
@@ -76,7 +81,7 @@ Use a VISC Report:
 
 ```{r eval=FALSE}
 use_visc_report(
-  report_name = "VDCnnn_BAMA_PT_Report_statusifapplicable", # the name of the report file
+  report_name = "VDCnnn_BAMA_PTreport_interim_blinded", # the name of the report file
   path = "BAMA", # the path within the active directory, usually the name of the assay
   report_type = "bama" # "empty", "generic", "bama", or "nab"
 )

README.md

@@ -1,5 +1,11 @@
 
 <!-- README.md is generated from README.Rmd. Please edit that file -->
+<!-- badges: start -->
+
+[![R-CMD-check](https://github.com/FredHutch/VISCtemplates/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/FredHutch/VISCtemplates/actions/workflows/R-CMD-check.yaml)
+[![Codecov test
+coverage](https://codecov.io/gh/FredHutch/VISCtemplates/graph/badge.svg)](https://app.codecov.io/gh/FredHutch/VISCtemplates)
+<!-- badges: end -->
 
 # VISCtemplates
 
@@ -66,7 +72,7 @@ Use a VISC Report:
 
 ``` r
 use_visc_report(
-  report_name = "VDCnnn_BAMA_PT_Report_statusifapplicable", # the name of the report file
+  report_name = "VDCnnn_BAMA_PTreport_interim_blinded", # the name of the report file
   path = "BAMA", # the path within the active directory, usually the name of the assay
   report_type = "bama" # "empty", "generic", "bama", or "nab"
 )

inst/rmarkdown/templates/visc_empty/skeleton/skeleton.Rmd

@@ -61,7 +61,7 @@ opts_chunk$set(cache = FALSE,
                out.extra = "",
                fig.pos = "H")
 # fig.align argument is not supported in Word (align in template docx)
-if (knitr::opts_knit$get('rmarkdown.pandoc.to') == 'latex'){
+if (get_output_type() == 'latex'){
   opts_chunk$set(fig.align = "center")
 }
 

inst/rmarkdown/templates/visc_report/resources/template.tex

@@ -20,6 +20,11 @@
 \usepackage{threeparttable} % provides a scheme for tables that have a structured (foot)note section, after the caption
 \usepackage{threeparttablex} % provides the functionality of the threeparttable package to tables created using the longtable package
 
+% needed for flextable to work
+\usepackage{hhline}
+\newlength\Oldarrayrulewidth
+\newlength\Oldtabcolsep
+
 % being able to set emphasis for entire table row
 \newcommand\setrow[1]{\gdef\rowmac{#1}#1\ignorespaces}
 \newcommand\clearrow{\global\let\rowmac\relax}

inst/rmarkdown/templates/visc_report/skeleton/skeleton.Rmd

@@ -65,7 +65,7 @@ opts_chunk$set(cache = FALSE,
                out.extra = "",
                fig.pos = "H")
 # fig.align argument is not supported in Word (align in template docx)
-if (knitr::opts_knit$get('rmarkdown.pandoc.to') == 'latex'){
+if (get_output_type() == 'latex'){
   opts_chunk$set(fig.align = "center")
 }
 
@@ -398,7 +398,7 @@ kable(
 
 The authors thank the following individuals for their invaluable contributions to this report.
 From [insert group name or affiliation, for example: the CAVIMC/Duke team] we thank [insert individual names, and roles here, for example: Kelli Greene and Hongmei Gao (Experimental Design, Data Interpretation, Study Management); Nicole Yates (Scientific Research Laboratory Manager) and Sheetal Sawant (Biostatistician)].
-From Fred Hutch Cancer Center, we also thank [insert names and roles here, for example: Ratana Som (SCHARP Lab Data Manager); Marie Vendettuoli and Valeria Duran (SCHARP Statistical Programmers); and Lindsey Mwoga and Drienna Holman (VISC Project Management)].
+From Fred Hutch Cancer Center, we also thank [insert names and roles here, for example: Ratana Som (SCHARP Lab Data Manager); Valeria Duran (SCHARP Statistical Programmer); and Lindsey Mwoga and Drienna Holman (VISC Project Management)].
 
 Note: names may be listed in bullet point format instead of paragraph format if that helps with 
 readability, for example: