Merge branch 'main' into propagations-september-2024

.Rbuildignore

@@ -41,3 +41,6 @@ pkgdown
 ^\.covrignore$
 ^cran-comments\.md$
 ^CRAN-SUBMISSION$
+
+# reverse dep cehcks
+^checked$

.github/workflows/recheck.yml

@@ -0,0 +1,19 @@
+on:
+  workflow_dispatch:
+    inputs:
+      which:
+        type: choice
+        description: Which dependents to check
+        options:
+          - strong
+          - most
+
+name: Reverse dependency check
+
+jobs:
+  revdep_check:
+    name: Reverse check ${{ inputs.which }} dependents
+    uses: r-devel/recheck/.github/workflows/recheck.yml@v1
+    with:
+      which: ${{ inputs.which }}
+      subdirectory: '' #if your package is in a git subdir

.gitignore

@@ -12,7 +12,9 @@ docs
 .DS_Store
 temp/
 
-
 .pre-commit-config.yaml
 tests/testthat/_snaps/**/*.new.md
 tests/testthat/_snaps/**/*.new.svg
+
+# reverse dep cehcks
+checked/

CRAN-SUBMISSION

@@ -1,3 +1,3 @@
-Version: 0.2.0
-Date: 2024-07-20 17:12:32 UTC
-SHA: 214cf55600df7d6a5037acbb88c135afba284c91
+Version: 0.2.1
+Date: 2024-09-03 01:03:13 UTC
+SHA: 1c9a44df460938bfc90d1833fd6410a0387935da

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: cardx
 Title: Extra Analysis Results Data Utilities
-Version: 0.2.0.9011
+Version: 0.2.1.9001
 Authors@R: c(
     person("Daniel", "Sjoberg", , "[email protected]", role = c("aut", "cre")),
     person("Abinaya", "Yogasekaram", , "[email protected]", role = "aut"),
@@ -19,32 +19,31 @@ BugReports: https://github.com/insightsengineering/cardx/issues
 Depends:
     R (>= 4.1)
 Imports:
-    cards (>= 0.2.1.9006),
+    cards (>= 0.2.2),
     cli (>= 3.6.1),
     dplyr (>= 1.1.2),
     glue (>= 1.6.2),
+    lifecycle (>= 1.0.3),
     rlang (>= 1.1.1),
     tidyr (>= 1.3.0)
 Suggests:
     aod (>= 1.3.3),
     broom (>= 1.0.5),
-    broom.helpers (>= 1.15.0),
+    broom.helpers (>= 1.17.0),
     broom.mixed (>= 0.2.9),
     car (>= 3.1-2),
     effectsize (>= 0.8.8),
     emmeans (>= 1.7.3),
     geepack (>= 1.3.2),
     ggsurvfit (>= 1.1.0),
-    lme4 (>= 1.1-35.1),
+    lme4 (>= 1.1-35.5),
     parameters (>= 0.20.2),
     smd (>= 0.6.6),
     spelling (>= 2.3.0),
     survey (>= 4.2),
     survival (>= 3.6-4),
     testthat (>= 3.2.0),
     withr (>= 2.5.0)
-Remotes: 
-    insightsengineering/cards
 Config/Needs/website: insightsengineering/nesttemplate
 Config/testthat/edition: 3
 Config/testthat/parallel: true

NEWS.md

@@ -1,13 +1,23 @@
-# cardx 0.2.0.9011
+# cardx 0.2.1.9001
 
-* Bug fix in `ard_categorical.survey.design()` where all unweighted statistics were returned, even in the case where they were explicitly not requested.
+# cardx 0.2.1
+
+## New Features and Updates
 
 * Added S3 method `ard_total_n.survey.design()` which returns an ARD with both the survey-weighted and unweighted total sample size.
 
 * Added `warning` and `error` columns to `ard_regression()` output. (#148)
 
 * Implemented `cards::as_card()` where needed in the package to convert data frames to class 'card'. (#200)
 
+## Bug Fixes
+
+* Bug fix in `ard_categorical.survey.design()` where all unweighted statistics were returned, even in the case where they were explicitly not requested.
+
+## Lifecycle Changes
+
+* The `bt(pattern)`, `reformulate2(pattern_term)`, `reformulate2(pattern_response)` arguments have been deprecated and are now ignored. We now use `make.names()` to determine whether a column name needs to be wrapped in backticks. (#192)
+
 # cardx 0.2.0
 
 ### Breaking Changes

R/construction_helpers.R

@@ -34,11 +34,7 @@
 #' @param package (`string`)\cr
 #'   string of package name that will be temporarily loaded when function
 #'   specified in `method` is executed.
-#' @param pattern (`string`)\cr
-#'   regular expression string. If the regex matches, backticks are added
-#'   to the string. When `NULL`, backticks are not added.
-#' @param pattern_term,pattern_response passed to `bt(pattern)` for arguments
-#'   `stats::reformulate(termlabels, response)`.
+#' @param pattern,pattern_term,pattern_response DEPRECATED
 #' @inheritParams rlang::eval_tidy
 #' @inheritParams stats::reformulate
 #' @inheritParams rlang::args_dots_empty
@@ -172,27 +168,32 @@ construct_model.survey.design <- function(data, formula, method, method.args = l
 #' @rdname construction_helpers
 #' @export
 reformulate2 <- function(termlabels, response = NULL, intercept = TRUE,
-                         pattern_term = "[ \n\r]", pattern_response = "[ \n\r]",
-                         env = parent.frame()) {
+                         env = parent.frame(),
+                         pattern_term = NULL, pattern_response = NULL) {
+  # deprecated argument --------------------------------------------------------
+  if (!missing(pattern_term)) lifecycle::deprecate_warn("0.2.1", what = "cardx::reformulate2(pattern_term)", details = "Argument has been ignored.") # styler: off
+  if (!missing(pattern_response)) lifecycle::deprecate_warn("0.2.1", what = "cardx::reformulate2(pattern_response)", details = "Argument has been ignored.") # styler: off
+
   stats::reformulate(
-    termlabels = bt(termlabels, pattern_term),
-    response = bt(response, pattern_response),
+    termlabels = bt(termlabels),
+    response = bt(response),
     intercept = intercept,
     env = env
   )
 }
 
 #' @rdname construction_helpers
 #' @export
-bt <- function(x, pattern = "[ \n\r]") {
+bt <- function(x, pattern = NULL) {
+  # deprecated argument --------------------------------------------------------
+  if (!missing(pattern)) lifecycle::deprecate_warn("0.2.1", what = "cardx::bt(pattern)", details = "Argument has been ignored.") # styler: off
+
   if (is_empty(x)) {
     return(x)
   }
-  if (is_empty(pattern)) {
-    return(x)
-  }
+
   ifelse(
-    str_detect(x, pattern = pattern) & !str_detect(x, "^`.*`$"),
+    make.names(x) != x & !str_detect(x, "^`.*`$"),
     paste0("`", x, "`"),
     x
   )

cran-comments.md

@@ -8,6 +8,13 @@
 
 0 errors ✔ | 0 warnings ✔ | 0 notes ✔
 
+## revdepcheck results
+
+We checked 4 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package.
+
+ * We saw 0 new problems
+ * We failed to check 0 packages
+
 ## Additional Comments
 
 * Thank you for your time!

revdep/README.md

@@ -0,0 +1,28 @@
+# Platform
+
+|field    |value                                                                                               |
+|:--------|:---------------------------------------------------------------------------------------------------|
+|version  |R version 4.3.3 (2024-02-29)                                                                        |
+|os       |macOS Ventura 13.4.1                                                                                |
+|system   |aarch64, darwin20                                                                                   |
+|ui       |RStudio                                                                                             |
+|language |(EN)                                                                                                |
+|collate  |en_US.UTF-8                                                                                         |
+|ctype    |en_US.UTF-8                                                                                         |
+|tz       |America/Los_Angeles                                                                                 |
+|date     |2024-09-02                                                                                          |
+|rstudio  |2024.04.2+764.pro1 Chocolate Cosmos (desktop)                                                       |
+|pandoc   |3.1.11 @ /Applications/RStudio.app/Contents/Resources/app/quarto/bin/tools/aarch64/ (via rmarkdown) |
+
+# Dependencies
+
+|package |old   |new        |Δ  |
+|:-------|:-----|:----------|:--|
+|cardx   |0.2.0 |0.2.0.9015 |*  |
+|cards   |0.2.2 |0.2.2      |   |
+|cli     |NA    |3.6.3      |*  |
+|cpp11   |NA    |0.4.7      |*  |
+|withr   |NA    |3.0.1      |*  |
+
+# Revdeps
+

revdep/cran.md

@@ -0,0 +1,7 @@
+## revdepcheck results
+
+We checked 4 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package.
+
+ * We saw 0 new problems
+ * We failed to check 0 packages
+

revdep/failures.md

@@ -0,0 +1 @@
+*Wow, no problems at all. :)*

revdep/problems.md

@@ -0,0 +1 @@
+*Wow, no problems at all. :)*

tests/testthat/_snaps/construction_helpers.md

@@ -2,16 +2,15 @@
 
     Code
       dplyr::filter(as.data.frame(ard_regression(construct_model(data = dplyr::rename(
-        mtcars, `M P G` = mpg), formula = reformulate2(c("M P G", "cyl"), response = "hp"),
-      method = "lm"))), stat_name %in% c("term", "estimate", "p.value"))
+        mtcars, `M P G` = mpg, `c/yl` = cyl), formula = reformulate2(c("M P G",
+        "c/yl"), response = "hp"), method = "lm"))), stat_name %in% c("term",
+        "estimate"))
     Output
-        variable    context stat_name  stat_label        stat fmt_fn warning error
-      1    M P G regression      term        term     `M P G`   NULL    NULL  NULL
-      2    M P G regression  estimate Coefficient   -2.774769      1    NULL  NULL
-      3    M P G regression   p.value     p-value   0.2125285      1    NULL  NULL
-      4      cyl regression      term        term         cyl   NULL    NULL  NULL
-      5      cyl regression  estimate Coefficient    23.97863      1    NULL  NULL
-      6      cyl regression   p.value     p-value 0.002814958      1    NULL  NULL
+        variable    context stat_name  stat_label      stat fmt_fn warning error
+      1    M P G regression      term        term   `M P G`   NULL    NULL  NULL
+      2    M P G regression  estimate Coefficient -2.774769      1    NULL  NULL
+      3     c/yl regression      term        term    `c/yl`   NULL    NULL  NULL
+      4     c/yl regression  estimate Coefficient  23.97863      1    NULL  NULL
 
 # construct_model() messaging
 

tests/testthat/test-ard_stats_chisq_test.R

@@ -30,26 +30,6 @@ test_that("ard_stats_chisq_test() works", {
   )
 })
 
-test_that("shuffle_ard fills missing group levels if the group is meaningful", {
-  adsl_sub <- cards::ADSL |> dplyr::filter(ARM %in% unique(ARM)[1:2])
-
-  expect_snapshot(
-    cards::bind_ard(
-      ard_stats_chisq_test(
-        data = adsl_sub,
-        by = "ARM",
-        variables = "AGEGR1"
-      ),
-      ard_stats_chisq_test(
-        data = adsl_sub,
-        by = "SEX",
-        variables = "AGEGR1"
-      )
-    ) |>
-      cards::shuffle_ard() |>
-      as.data.frame()
-  )
-})
 
 test_that("ard_stats_chisq_test() follows ard structure", {
   expect_silent(

tests/testthat/test-construction_helpers.R

@@ -3,13 +3,13 @@ skip_if_not(is_pkg_installed(c("broom.helpers", "withr", "survey", "survival"),
 test_that("construct_model() works", {
   expect_snapshot(
     construct_model(
-      data = mtcars |> dplyr::rename(`M P G` = mpg),
-      formula = reformulate2(c("M P G", "cyl"), response = "hp"),
+      data = mtcars |> dplyr::rename(`M P G` = mpg, `c/yl` = cyl),
+      formula = reformulate2(c("M P G", "c/yl"), response = "hp"),
       method = "lm"
     ) |>
       ard_regression() |>
       as.data.frame() |>
-      dplyr::filter(stat_name %in% c("term", "estimate", "p.value"))
+      dplyr::filter(stat_name %in% c("term", "estimate"))
   )
 
   expect_equal(
@@ -26,7 +26,7 @@ test_that("construct_model() works", {
   )
 
   expect_equal(
-    cardx::bt("`a b`"),
+    bt("`a b`"),
     "`a b`"
   )