Merge branch 'main' into 454-bug-null-report@main

insightsengineering · Oct 9, 2024 · ea6c504 · ea6c504
2 parents 840a182 + ea1b62f
commit ea6c504
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diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,7 +1,7 @@
 ---
 # All available hooks: https://pre-commit.com/hooks.html
 # R specific hooks: https://github.com/lorenzwalthert/precommit
-default_stages: [commit]
+default_stages: [pre-commit]
 default_language_version:
   python: python3
 repos:

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Type: Package
 Package: chevron
 Title: Standard TLGs for Clinical Trials Reporting
-Version: 0.2.6.9021
-Date: 2024-09-16
+Version: 0.2.7.9000
+Date: 2024-10-09
 Authors@R: c(
     person("Liming", "Li", , "liming.li@roche.com", role = c("aut", "cre")),
     person("Benoit", "Falquet", , "benoit.falquet@roche.com", role = "aut"),
@@ -31,7 +31,7 @@ Imports:
     dplyr (>= 1.1.0),
     dunlin (>= 0.1.7),
     forcats (>= 1.0.0),
-    formatters (>= 0.5.8),
+    formatters (>= 0.5.9),
     ggplot2 (>= 3.4.0),
     glue (>= 1.0.0),
     grid,
@@ -43,9 +43,9 @@ Imports:
     purrr (>= 0.3.0),
     rlang (>= 1.0.0),
     rlistings (>= 0.2.9),
-    rtables (>= 0.6.8),
+    rtables (>= 0.6.10),
     stringr (>= 1.4.1),
-    tern (>= 0.9.5),
+    tern (>= 0.9.6),
     tibble (>= 2.0.0),
     utils
 Suggests:

diff --git a/NEWS.md b/NEWS.md
@@ -1,8 +1,10 @@
-# chevron 0.2.6.9021
+# chevron 0.2.7.9000
 
-* Add `AEL02`, `AEL03`, `CML02A_gl` templates.
+# chevron 0.2.7
+
+* Add the `AEL02`, `AEL03` and `CML02A_gl` templates.
 * Modify the post processing of `MHT01` to allow multiple `row_split_var`.
-* Improve the `report_null` method to facilitate the creation of null reports
+* Improve the `report_null` method to facilitate the creation of null reports.
 * Export the `std_postprocessing` function to simplify post processing logic.
 * `AET01` can now additionally display the number of death and withdrawal using the `show_wd` argument.
 * `MNG01` line type can now be controlled with the `line_type` argument.

diff --git a/R/utils.R b/R/utils.R
@@ -424,8 +424,12 @@ listing_format_chevron <- function() {
 #' @export
 #' @examples
 #' format_date("%d%b%Y")(as.Date("2021-01-01"))
-#' format_date("%d%b%Y")(as.POSIXct("2021-01-01 00:00:01", tz = "NZ"))
-#' format_date("%d%b%Y")(as.POSIXct("2021-01-01 00:00:01", tz = "US/Pacific"))
+#' if ("NZ" %in% OlsonNames()) {
+#'   format_date("%d%b%Y")(as.POSIXct("2021-01-01 00:00:01", tz = "NZ"))
+#' }
+#' if ("US/Pacific" %in% OlsonNames()) {
+#'   format_date("%d%b%Y")(as.POSIXct("2021-01-01 00:00:01", tz = "US/Pacific"))
+#' }
 format_date <- function(date_format = "%d%b%Y") {
   function(x, ...) {
     toupper(

diff --git a/man/format_date.Rd b/man/format_date.Rd
diff --git a/tests/testthat/_snaps/vst01.md b/tests/testthat/_snaps/vst01.md
diff --git a/tests/testthat/test-ael01_nollt.R b/tests/testthat/test-ael01_nollt.R
@@ -9,6 +9,7 @@ test_that("ael01_nollt works with admh dataset", {
 
 
 test_that("ael01_nollt works with non-default label", {
+  skip_on_os("windows")
   proc_data <- syn_data
   attr(proc_data$adae$AETERM, "label") <- "Investigator-Specified\n Adverse Event Term"
   res <- expect_silent(
@@ -21,6 +22,7 @@ test_that("ael01_nollt works with non-default label", {
 })
 
 test_that("ael01_nollt can handle all missing values", {
+  skip_on_os("windows")
   proc_data <- syn_data
   proc_data$adae <- proc_data$adae %>%
     mutate(
@@ -34,6 +36,7 @@ test_that("ael01_nollt can handle all missing values", {
 })
 
 test_that("ael01_nollt can handle some missing values", {
+  skip_on_os("windows")
   new_aebodsys <- c(NA, "", as.character(syn_data$adae$AEBODSYS[-c(1, 2)]))
   new_aedecod <- c(NA, "", as.character(syn_data$adae$AEDECOD[-c(1, 2)]))
 
@@ -49,6 +52,7 @@ test_that("ael01_nollt can handle some missing values", {
 })
 
 test_that("ael01_nollt listing can be split by an additional variable", {
+  skip_on_os("windows")
   res <- expect_silent(
     run(
       ael01_nollt,
@@ -64,6 +68,7 @@ test_that("ael01_nollt listing can be split by an additional variable", {
 })
 
 test_that("split ael01_nollt listing do not display missing values", {
+  skip_on_os("windows")
   proc_data <- syn_data
   proc_data$admh <- proc_data$admh[proc_data$admh$SEX == "F", ]
 

diff --git a/tests/testthat/test-ael02.R b/tests/testthat/test-ael02.R
@@ -10,6 +10,7 @@ test_that("ael02 works with adae dataset", {
 })
 
 test_that("ael02 can handle all missing values", {
+  skip_on_os("windows")
   proc_data <- syn_data
   proc_data$adae <- proc_data$adae %>%
     mutate(
@@ -27,6 +28,7 @@ test_that("ael02 can handle all missing values", {
 
 
 test_that("ael02 functions work as expected", {
+  skip_on_os("windows")
   res <- expect_silent(
     ael02_pre(syn_data) %>%
       ael02_main()

diff --git a/tests/testthat/test-ael03.R b/tests/testthat/test-ael03.R
@@ -10,6 +10,7 @@ test_that("ael03 works with adae dataset", {
 })
 
 test_that("ael03 can handle all missing values", {
+  skip_on_os("windows")
   proc_data <- syn_data
   proc_data$adae <- proc_data$adae %>%
     mutate(
@@ -27,6 +28,7 @@ test_that("ael03 can handle all missing values", {
 # ael03 functions ----
 
 test_that("ael03 functions work as expected", {
+  skip_on_os("windows")
   res <- expect_silent(
     ael03_pre(syn_data) %>%
       ael03_main()

diff --git a/tests/testthat/test-aet01.R b/tests/testthat/test-aet01.R
@@ -15,6 +15,7 @@ test_that("aet01 can handle all NA values", {
 })
 
 test_that("aet01 can handle some NA values", {
+  skip_on_os("windows")
   new_aesdth <- c(NA, "", as.character(syn_data$adae$AESDTH[-c(1, 2)]))
   new_aeser <- c(NA, "", as.character(syn_data$adae$AESER[-c(1, 2)]))
 
@@ -30,12 +31,14 @@ test_that("aet01 can handle some NA values", {
 })
 
 test_that("aet01 can use custom anl_vars", {
+  skip_on_os("windows")
   proc_data <- syn_data
   res <- expect_silent(run(aet01, proc_data, anl_vars = list(safety_var = "FATAL")))
   expect_snapshot(cat(export_as_txt(res, lpp = 100)))
 })
 
 test_that("aet01 fails on incomplete data input", {
+  skip_on_os("windows")
   proc_data <- syn_data
   proc_data$adae <- proc_data$adae %>%
     mutate(AESER = NULL)
@@ -48,6 +51,7 @@ test_that("aet01 fails on incomplete data input", {
 })
 
 test_that("aet01 can use custom medconcept_var", {
+  skip_on_os("windows")
   proc_data <- syn_data
   proc_data$adae$SMQ01 <- with_label(proc_data$adae$SMQ01NAM != "", "SMQ 01")
   res <- expect_silent(
@@ -66,6 +70,7 @@ test_that("aet01 can use custom medconcept_var", {
 })
 
 test_that("aet01 can conditionally show the number of withdrawal", {
+  skip_on_os("windows")
   expect_silent(res <- run(aet01, syn_data, arm_var = "ARM", show_wd = FALSE))
   expect_snapshot(cat(export_as_txt(res, lpp = 100)))
 })
diff --git a/tests/testthat/test-aet01_aesi.R b/tests/testthat/test-aet01_aesi.R
@@ -20,6 +20,7 @@ test_that("aet01_aesi can handle all NA values", {
 })
 
 test_that("aet01_aesi can handle some NA values", {
+  skip_on_os("windows")
   proc_data <- syn_data
   proc_data$adae <- proc_data$adae %>%
     mutate(
@@ -31,12 +32,14 @@ test_that("aet01_aesi can handle some NA values", {
 })
 
 test_that("aet01_aesi works with `ALL` argument", {
+  skip_on_os("windows")
   proc_data <- syn_data
   res <- expect_silent(run(aet01_aesi, proc_data, aesi_vars = c("ALL")))
   expect_snapshot(cat(export_as_txt(res, lpp = 100, cpp = 200)))
 })
 
 test_that("aet01_aesi_check fails on incomplete data input", {
+  skip_on_os("windows")
   proc_data <- syn_data
   proc_data$adae <- proc_data$adae %>%
     mutate(AEOUT = NULL)

diff --git a/tests/testthat/test-aet02.R b/tests/testthat/test-aet02.R
@@ -15,6 +15,7 @@ test_that("aet02 fails on incomplete data input", {
 })
 
 test_that("aet02 handle empty data input", {
+  skip_on_os("windows")
   proc_data <- syn_data
   proc_data$adae <- proc_data$adae %>%
     filter(
@@ -25,6 +26,7 @@ test_that("aet02 handle empty data input", {
 })
 
 test_that("aet02 can have different levels of row_split", {
+  skip_on_os("windows")
   res1 <- run(aet02, syn_data, row_split_var = NULL)
   res2 <- run(aet02, syn_data, row_split_var = c("AEBODSYS", "AEDECOD"))
   expect_snapshot(cat(export_as_txt(res1, lpp = 100)))

diff --git a/tests/testthat/test-aet03.R b/tests/testthat/test-aet03.R
@@ -11,6 +11,7 @@ test_that("aet03 can handle NA values", {
 })
 
 test_that("aet03 can handle some NA values", {
+  skip_on_os("windows")
   new_aebodsys <- c(NA, "", as.character(syn_data$adae$AEBODSYS[-c(1, 2)]))
   new_aedecod <- c(NA, "", as.character(syn_data$adae$AEDECOD[-c(1, 2)]))
   new_asev <- c(NA, "", as.character(syn_data$adae$ASEV[-c(1, 2)]))

diff --git a/tests/testthat/test-aet04.R b/tests/testthat/test-aet04.R
@@ -8,7 +8,7 @@ test_that("aet04 can handle NA values", {
 
   res1 <- expect_silent(run(aet04, proc_data))
   expect_snapshot(cat(export_as_txt(res1, lpp = 100)))
-
+  skip_on_os("windows")
   grade_groups <- list(
     "Grade 1-2" = c("1", "2"),
     "Grade 3-4" = c("3", "4"),
@@ -26,6 +26,7 @@ test_that("aet04 can handle NA values", {
 })
 
 test_that("aet04 can handle some NA values", {
+  skip_on_os("windows")
   proc_data <- syn_data
   proc_data$adae[1:2, c("AEBODSYS", "AEDECOD")] <- NA
   res1 <- expect_silent(run(aet04, proc_data))

diff --git a/tests/testthat/test-aet05.R b/tests/testthat/test-aet05.R
@@ -8,6 +8,7 @@ test_that("aet05 can handle NA values", {
 })
 
 test_that("aet05 can handle some NA values", {
+  skip_on_os("windows")
   new_paramcd <- c(
     as.character(syn_data$adsaftte$PARAMCD[1:4]), NA, "",
     as.character(syn_data$adsaftte$PARAMCD[-rep(1:6)])

diff --git a/tests/testthat/test-aet05_all.R b/tests/testthat/test-aet05_all.R
@@ -8,6 +8,7 @@ test_that("aet05_all can handle NA values", {
 })
 
 test_that("aet05_all can handle some NA values", {
+  skip_on_os("windows")
   new_paramcd <- c(NA, "", as.character(syn_data$adsaftte$PARAMCD[-c(1, 2)]))
 
   proc_data <- syn_data

diff --git a/tests/testthat/test-aet10.R b/tests/testthat/test-aet10.R
@@ -11,6 +11,7 @@ test_that("aet10 can handle NA values", {
 })
 
 test_that("aet10 can handle some NA values", {
+  skip_on_os("windows")
   new_aedecod <- c(NA, "", as.character(syn_data$adae$AEDECOD[-c(1, 2)]))
 
   proc_data <- syn_data

diff --git a/tests/testthat/test-cfbt01.R b/tests/testthat/test-cfbt01.R
@@ -1,6 +1,7 @@
 # cfbt01 functions ----
 
 test_that("cfbt01 functions with default argument value return expected result with test data", {
+  skip_on_os("windows")
   pre_data <- cfbt01_pre(syn_data, dataset = "advs")
   raw_res <- cfbt01_main(pre_data, dataset = "advs")
   res <- cfbt01_post(raw_res)
@@ -10,6 +11,7 @@ test_that("cfbt01 functions with default argument value return expected result w
 # cfbt01 ----
 
 test_that("cfbt01 can handle n = 0 and outputs NE instead of infs and NAs", {
+  skip_on_os("windows")
   proc_data <- dunlin::log_filter(
     syn_data,
     PARAMCD %in% c("DIABP", "SYSBP"), "advs"