Devel

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

@@ -1,85 +1,59 @@
-# For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag.
-# https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions
+# 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
-      - devel
-  pull_request:
-    branches:
-      - main
-      - master
-      - devel
+    push:
+      branches:
+        - main
+        - master
+        - devel
+    pull_request:
+      branches:
+        - main
+        - master
+        - devel
 
-name: R-CMD-check
+name: R-CMD-check.yaml
 
-jobs:
-  R-CMD-check:
-    runs-on: ${{ matrix.config.os }}
-
-    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
-
-    strategy:
-      fail-fast: false
-      matrix:
-        config:
-          - {os: windows-latest, r: 'release'}
-          - {os: macOS-latest, r: 'release'}
-          - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
-          - {os: ubuntu-20.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
-
-    env:
-      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
-      RSPM: ${{ matrix.config.rspm }}
-
-    steps:
-      - uses: actions/checkout@v2
-
-      - uses: r-lib/actions/setup-r@v2
-        with:
-          r-version: ${{ matrix.config.r }}
-
-      - uses: r-lib/actions/setup-pandoc@v2
+permissions: read-all
 
-      - name: Query dependencies
-        run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
-        shell: Rscript {0}
-
-      - name: Cache R packages
-        if: runner.os != 'Windows'
-        uses: actions/cache@v2
-        with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
-
-      - name: Install system dependencies
-        if: runner.os == 'Linux'
-        run: |
-          while read -r cmd
-          do
-            eval sudo $cmd
-          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
-
-      - name: Install dependencies
-        run: |
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("rcmdcheck")
-        shell: Rscript {0}
-
-      - name: Check
-        env:
-          _R_CHECK_CRAN_INCOMING_REMOTE_: false
-        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
-        shell: Rscript {0}
-
-      - name: Upload check results
-        if: failure()
-        uses: actions/upload-artifact@main
-        with:
-          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
-          path: check
+jobs:
+    R-CMD-check:
+      runs-on: ${{ matrix.config.os }}
+
+      name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+      strategy:
+        fail-fast: false
+        matrix:
+          config:
+            - {os: windows-latest, r: 'release'}
+            - {os: macOS-latest, r: 'release'}
+            - {os: ubuntu-22.04, r: 'release', rspm: "https://packagemanager.posit.co/cran/__linux__/jammy/latest"}
+            - {os: ubuntu-22.04, r: 'devel', rspm: "https://packagemanager.posit.co/cran/__linux__/jammy/latest"}
+            - {os: ubuntu-latest,  r: 'devel', http-user-agent: 'release'}
+            - {os: ubuntu-latest,  r: 'release'}
+
+      env:
+        GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+        R_KEEP_PKG_SOURCE: yes
+
+      steps:
+        - uses: actions/checkout@v4
+
+        - uses: r-lib/actions/setup-pandoc@v2
+
+        - uses: r-lib/actions/setup-r@v2
+          with:
+            r-version: ${{ matrix.config.r }}
+            http-user-agent: ${{ matrix.config.http-user-agent }}
+            use-public-rspm: true
+
+        - uses: r-lib/actions/setup-r-dependencies@v2
+          with:
+            extra-packages: any::rcmdcheck
+            needs: check
+
+        - uses: r-lib/actions/check-r-package@v2
+          with:
+            upload-snapshots: true
+            build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

.github/workflows/rhub.yaml

@@ -0,0 +1,95 @@
+# R-hub's generic GitHub Actions workflow file. It's canonical location is at
+# https://github.com/r-hub/actions/blob/v1/workflows/rhub.yaml
+# You can update this file to a newer version using the rhub2 package:
+#
+# rhub::rhub_setup()
+#
+# It is unlikely that you need to modify this file manually.
+
+name: R-hub
+run-name: "${{ github.event.inputs.id }}: ${{ github.event.inputs.name || format('Manually run by {0}', github.triggering_actor) }}"
+
+on:
+  workflow_dispatch:
+    inputs:
+      config:
+        description: 'A comma separated list of R-hub platforms to use.'
+        type: string
+        default: 'linux,windows,macos'
+      name:
+        description: 'Run name. You can leave this empty now.'
+        type: string
+      id:
+        description: 'Unique ID. You can leave this empty now.'
+        type: string
+
+jobs:
+
+  setup:
+    runs-on: ubuntu-latest
+    outputs:
+      containers: ${{ steps.rhub-setup.outputs.containers }}
+      platforms: ${{ steps.rhub-setup.outputs.platforms }}
+
+    steps:
+    # NO NEED TO CHECKOUT HERE
+    - uses: r-hub/actions/setup@v1
+      with:
+        config: ${{ github.event.inputs.config }}
+      id: rhub-setup
+
+  linux-containers:
+    needs: setup
+    if: ${{ needs.setup.outputs.containers != '[]' }}
+    runs-on: ubuntu-latest
+    name: ${{ matrix.config.label }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config: ${{ fromJson(needs.setup.outputs.containers) }}
+    container:
+      image: ${{ matrix.config.container }}
+
+    steps:
+      - uses: r-hub/actions/checkout@v1
+      - uses: r-hub/actions/platform-info@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/setup-deps@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/run-check@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+
+  other-platforms:
+    needs: setup
+    if: ${{ needs.setup.outputs.platforms != '[]' }}
+    runs-on: ${{ matrix.config.os }}
+    name: ${{ matrix.config.label }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config: ${{ fromJson(needs.setup.outputs.platforms) }}
+
+    steps:
+      - uses: r-hub/actions/checkout@v1
+      - uses: r-hub/actions/setup-r@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}
+      - uses: r-hub/actions/platform-info@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/setup-deps@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}
+      - uses: r-hub/actions/run-check@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: Tplyr
 Title: A Traceability Focused Grammar of Clinical Data Summary
-Version: 1.2.1
+Version: 1.2.1.9000
 Authors@R: 
     c(
     person(given = "Eli",
@@ -43,7 +43,7 @@ Authors@R:
     )
 Description: A traceability focused tool created to simplify the data manipulation necessary to create clinical summaries.
 License: MIT + file LICENSE
-URL: https://github.com/atorus-research/Tplyr
+URL: https://atorus-research.github.io/Tplyr/, https://github.com/atorus-research/Tplyr
 BugReports: https://github.com/atorus-research/Tplyr/issues
 Encoding: UTF-8
 Depends: R (>= 3.5.0)
@@ -71,7 +71,7 @@ Suggests:
     pharmaRTF,
     withr
 VignetteBuilder: knitr
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.2
 RdMacros: lifecycle
 Config/testthat/edition: 3
 LazyData: true

R/regex.R

@@ -3,15 +3,16 @@
 #' This function allows you to extract important regular expressions used inside
 #' Tplyr.
 #'
-#' There are two important regular expressions used within Tplyr. The
+#' There are three important regular expressions used within Tplyr. The
 #' format_string expression is the expression to parse format strings. This is
 #' what is used to make sense out of strings like 'xx (XX.x%)' or 'a+1 (A.a+2)'
 #' by inferring what the user is specifying about number formatting.
 #'
 #' The 'format_group' regex is the opposite of this, and when given a string of
 #' numbers, such as ' 5 (34%) \[9]' will return the separate segments of numbers
 #' broken into their format groups, which in this example would be ' 5',
-#' '(34%)', and '\[9]'.
+#' '(34%)', and '\[9]'. Lastly, the 'number_group' regex has a similar application
+#' to the 'format_group' regex, but targets only numbers
 #'
 #' @param rx A character string with either the value 'format_string' or
 #'   'format_group'
@@ -25,14 +26,17 @@
 #' get_tplyr_regex('format_string')
 #'
 #' get_tplyr_regex('format_group')
+#' 
+#' get_tplyr_regex('number_group')
 #'
-get_tplyr_regex <- function(rx=c("format_string", "format_group")) {
+get_tplyr_regex <- function(rx=c("format_string", "format_group", "number_group")) {
   rx <- match.arg(rx)
 
   switch(
     rx,
     'format_string' = get_format_string_regex(),
-    'format_group' = get_format_group_regex()
+    'format_group' = get_format_group_regex(),
+    'number_group' = get_numeric_group_regex()
   )
 }
 
@@ -110,3 +114,17 @@ get_format_group_regex <- function() {
   regex(paste0(nwsd, ws, num, nws))
 
 }
+
+#' Return the regex for identifying numbers within an output string
+#'
+#' This regex targets the individual numbers within the string
+#'
+#' @return A regular expression
+#' @noRd
+get_numeric_group_regex <- function() {
+	#`-?` - Matches an optional negative sign
+	# `(?:\d*\.\d+|\d+)` - A non-capturing group with two alternatives:
+	#	`\d*\.\d+` - Matches decimals like `.75`, `0.56`, or `123.45`
+	#	`\d+` - Matches integers like `1`, `523`, `56`
+  regex("-?(?:\\d*\\.\\d+|\\d+)")
+}

R/riskdiff.R

@@ -176,7 +176,21 @@ prep_two_way <- function(comp) {
                 msg = paste0("There are no records for the following groups within the variable ", as_name(treat_var),
                              ": ", paste(invalid_groups, collapse=", ")))
 
-    two_way <- numeric_data
+    # create the merge columns
+    mrg <- as_label(pop_treat_var)
+    names(mrg) <- as_label(treat_var)
+    mrg_cols <- append(mrg, map_chr(cols, as_label))
+
+    two_way <- numeric_data %>%
+      left_join(
+        select(header_n, everything(), tot_fill = n), 
+        by = mrg_cols
+      ) %>%
+      mutate(
+        distinct_total = if_else(is.na(distinct_total), tot_fill, distinct_total)
+      )
+
+    rm(mrg, mrg_cols)
 
     # Nested layers need to plug the NAs left over - needs revision in the future
     if (is_built_nest && quo_is_symbol(by[[1]])) {
@@ -188,7 +202,6 @@ prep_two_way <- function(comp) {
         )
     }
 
-
     # If distinct is set and distinct values are there, use them
     if (comp_distinct && !is.null(distinct_by)) {
       two_way <- two_way %>%