Merge branch 'main' into 126-ard_survfit_diff

.Rbuildignore

@@ -35,3 +35,6 @@ pkgdown
 # others
 ^renv$
 ^renv\.lock$
+^.revdeprefs\.yaml$
+^revdep$
+^\.covrignore$

.github/workflows/check.yaml

@@ -35,6 +35,27 @@ jobs:
         checking Rd .usage sections .* NOTE
         checking for unstated dependencies in vignettes .* NOTE
         checking top-level files .* NOTE
+  r-cmd-non-cran:
+    name: R CMD Check (non-CRAN) 🧬
+    uses: insightsengineering/r.pkg.template/.github/workflows/build-check-install.yaml@main
+    secrets:
+      REPO_GITHUB_TOKEN: ${{ secrets.REPO_GITHUB_TOKEN }}
+    with:
+      enforce-note-blocklist: true
+      publish-unit-test-report-gh-pages: false
+      junit-xml-comparison: false
+      concurrency-group: non-cran
+      disable-unit-test-reports: true
+      skip-r-cmd-install: true
+      note-blocklist: |
+        checking dependencies in R code .* NOTE
+        checking R code for possible problems .* NOTE
+        checking examples .* NOTE
+        checking Rd line widths .* NOTE
+        checking S3 generic/method consistency .* NOTE
+        checking Rd .usage sections .* NOTE
+        checking for unstated dependencies in vignettes .* NOTE
+        checking top-level files .* NOTE
   coverage:
     name: Coverage 📔
     uses: insightsengineering/r.pkg.template/.github/workflows/test-coverage.yaml@main
@@ -77,6 +98,8 @@ jobs:
     uses: insightsengineering/r.pkg.template/.github/workflows/style.yaml@main
     with:
       auto-update: false
+    secrets:
+      REPO_GITHUB_TOKEN: ${{ secrets.REPO_GITHUB_TOKEN }}
   grammar:
     if: github.event_name != 'push'
     name: Grammar Check 🔤

.github/workflows/cla.yaml

@@ -0,0 +1,18 @@
+name: CLA 🔏
+
+on:
+  issue_comment:
+    types:
+      - created
+  # For PRs that originate from forks
+  pull_request_target:
+    types:
+      - opened
+      - closed
+      - synchronize
+
+jobs:
+  CLA:
+    name: CLA 📝
+    uses: insightsengineering/.github/.github/workflows/cla.yaml@main
+    secrets: inherit

.github/workflows/on-demand.yaml

@@ -0,0 +1,12 @@
+---
+name: On-demand 🧑‍🔬
+
+on:
+  schedule:
+    - cron: '45 3 * * 0'
+  workflow_dispatch:
+
+jobs:
+  revdepcheck:
+    name: revdepcheck ↩️
+    uses: insightsengineering/r.pkg.template/.github/workflows/revdepcheck.yaml@main

.github/workflows/release.yaml

@@ -8,15 +8,6 @@ on:
   workflow_dispatch:
 
 jobs:
-  build:
-    name: Build package 🎁
-    needs: release
-    uses: insightsengineering/r.pkg.template/.github/workflows/build-check-install.yaml@main
-    secrets:
-      REPO_GITHUB_TOKEN: ${{ secrets.REPO_GITHUB_TOKEN }}
-    with:
-      skip-r-cmd-check: true
-      skip-r-cmd-install: true
   docs:
     name: Pkgdown Docs 📚
     needs: release
@@ -36,8 +27,8 @@ jobs:
     uses: insightsengineering/r.pkg.template/.github/workflows/release.yaml@main
     secrets:
       REPO_GITHUB_TOKEN: ${{ secrets.REPO_GITHUB_TOKEN }}
-  r-cmd:
-    name: R CMD Check 🧬
+  build:
+    name: Build package and reports 🎁
     needs: [release, docs]
     uses: insightsengineering/r.pkg.template/.github/workflows/build-check-install.yaml@main
     secrets:

.gitignore

@@ -14,3 +14,5 @@ temp/
 
 
 .pre-commit-config.yaml
+tests/testthat/_snaps/**/*.new.md
+tests/testthat/_snaps/**/*.new.svg

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: cardx
 Title: Extra Analysis Results Data Utilities
-Version: 0.1.0.9028
+Version: 0.1.0.9031
 Authors@R: c(
     person("Daniel", "Sjoberg", , "[email protected]", role = c("aut", "cre")),
     person("Abinaya", "Yogasekaram", , "[email protected]", role = "aut"),
@@ -28,6 +28,7 @@ Suggests:
     aod (>= 1.3.3),
     broom (>= 1.0.5),
     broom.helpers (>= 1.15.0),
+    broom.mixed (>= 0.2.9),
     car (>= 3.0-11),
     effectsize (>= 0.6.0),
     emmeans (>= 1.7.3),

NEWS.md

@@ -1,4 +1,4 @@
-# cardx 0.1.0.9028
+# cardx 0.1.0.9031
 
 ### Breaking Changes
 

R/ard_survey_svycontinuous.R

@@ -213,7 +213,7 @@ accepted_svy_stats <- function(expand_quantiles = TRUE) {
 
   # if no by variable, calculate univariate statistics
   if (is_empty(by)) {
-    args$x <- stats::reformulate(variable)
+    args$x <- reformulate2(variable)
     # calculate statistic (and remove FUN from the argument list)
     stat <-
       cards::eval_capture_conditions(
@@ -244,8 +244,8 @@ accepted_svy_stats <- function(expand_quantiles = TRUE) {
 
   # if there is by variable(s), calculate statistics for the combinations
   else {
-    args$formula <- stats::reformulate(variable)
-    args$by <- stats::reformulate(by)
+    args$formula <- reformulate2(variable)
+    args$by <- reformulate2(by)
     stat <-
       if (stat_name %in% c("median", paste0("p", 0:100))) {
         cards::eval_capture_conditions(

R/ard_survey_svyranktest.R

@@ -48,7 +48,7 @@ ard_survey_svyranktest <- function(data, by, variables, test, ...) {
         variable = variable,
         lst_tidy =
           cards::eval_capture_conditions(
-            survey::svyranktest(stats::reformulate(by, response = variable), design = data, test = test, ...) |>
+            survey::svyranktest(reformulate2(termlabels = by, response = variable), design = data, test = test, ...) |>
               broom::tidy()
           )
       )

R/ard_survey_svyttest.R

@@ -46,7 +46,7 @@ ard_survey_svyttest <- function(data, by, variables, conf.level = 0.95, ...) {
         variable = variable,
         lst_tidy =
           cards::eval_capture_conditions(
-            survey::svyttest(stats::reformulate(by, response = variable), design = data, ...) %>%
+            survey::svyttest(reformulate2(termlabels = by, response = variable), design = data, ...) %>%
               # a slightly enhanced tidier that allows us to specify the conf.level
               {
                 dplyr::bind_cols(

revdep/.gitignore

@@ -0,0 +1,7 @@
+checks
+library
+checks.noindex
+library.noindex
+cloud.noindex
+data.sqlite
+*.html

tests/testthat/test-ard_regression.R

@@ -1,4 +1,4 @@
-skip_if_not(do.call(asNamespace("cardx")$is_pkg_installed, list(pkg = "broom.helpers", reference_pkg = "cardx")))
+skip_if_not(is_pkg_installed(pkg = "broom.helpers", reference_pkg = "cardx"))
 
 test_that("ard_regression() works", {
   expect_snapshot(
@@ -21,6 +21,20 @@ test_that("ard_regression() works", {
   )
 })
 
+test_that("ard_regression() works specifying custom tidier", {
+  skip_if_not(is_pkg_installed(pkg = c("lme4", "broom.mixed"), reference_pkg = "cardx"))
+  expect_snapshot(
+   lme4::lmer(mpg ~ hp + (1 | cyl), data = mtcars) |>
+      ard_regression(tidy_fun = broom.mixed::tidy) |>
+      as.data.frame() |>
+      dplyr::select(-context, -stat_label, -fmt_fn) |>
+      dplyr::filter(map_lgl(stat, is.numeric)) |>
+      dplyr::mutate(
+        stat = lapply(stat, function(x) ifelse(is.numeric(x), cards::round5(x, 3), x))
+      )
+  )
+})
+
 test_that("ard_regression() does not produce `variable_level` column where not applicable", {
   expect_true(!"variable_level" %in% names(lm(mpg ~ hp, mtcars) |> ard_regression()))
 })