Merge branch 'main' into 413_qtcat@main

.github/CONTRIBUTING.md

@@ -42,9 +42,9 @@ For new feature requests, please elaborate on the context and the benefit the fe
 
 ## Pull requests
 
-### Github Flow
+### GitHub Flow
 
-This repository uses the [Github Flow](https://docs.github.com/en/get-started/quickstart/github-flow) model for collaboration. To submit a pull request:
+This repository uses the [GitHub Flow](https://docs.github.com/en/get-started/quickstart/github-flow) model for collaboration. To submit a pull request:
 
 1. Create a branch
 

.github/workflows/check.yaml

@@ -37,10 +37,10 @@ jobs:
       additional-r-cmd-check-params: --as-cran
       enforce-note-blocklist: 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 dependencies in R code .* NOTE
+        checking R code for possible problems .* NOTE
+        checking examples .* NOTE
+        checking Rd line widths .* NOTE
       unit-test-report-brand: >-
         https://raw.githubusercontent.com/insightsengineering/hex-stickers/main/thumbs/chevron.png
   coverage:

.github/workflows/docs.yaml

@@ -7,7 +7,7 @@ on:
       - main
     paths:
       - inst/templates/**
-      - _pkgdown.yml
+      - _pkgdown.*
       - DESCRIPTION
       - '**.md'
       - man/**
@@ -23,7 +23,7 @@ on:
       - main
     paths:
       - inst/templates/**
-      - _pkgdown.yml
+      - _pkgdown.*
       - DESCRIPTION
       - '**.md'
       - man/**

.github/workflows/post-release.yaml

@@ -0,0 +1,15 @@
+---
+name: Post release ✨
+
+on:
+  release:
+    types: ["released"]
+
+jobs:
+  vbump:
+    name: Version Bump 🤜🤛
+    uses: insightsengineering/r.pkg.template/.github/workflows/version-bump.yaml@main
+    secrets:
+      REPO_GITHUB_TOKEN: ${{ secrets.REPO_GITHUB_TOKEN }}
+    with:
+      vbump-after-release: true

.github/workflows/release.yaml

@@ -34,8 +34,8 @@ jobs:
   release:
     name: Create release 🎉
     uses: insightsengineering/r.pkg.template/.github/workflows/release.yaml@main
-    permissions:
-      contents: write
+    secrets:
+      REPO_GITHUB_TOKEN: ${{ secrets.REPO_GITHUB_TOKEN }}
   r-cmd:
     name: R CMD Check 🧬
     needs: [release, docs]
@@ -48,10 +48,10 @@ jobs:
       additional-r-cmd-check-params: --as-cran
       enforce-note-blocklist: 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 dependencies in R code .* NOTE
+        checking R code for possible problems .* NOTE
+        checking examples .* NOTE
+        checking Rd line widths .* NOTE
       unit-test-report-brand: >-
         https://raw.githubusercontent.com/insightsengineering/hex-stickers/main/thumbs/chevron.png
   coverage:

.pre-commit-config.yaml

@@ -15,6 +15,8 @@ repos:
       - id: roxygenize
         name: Regenerate package documentation
         additional_dependencies:
+          - purrr
+          - vctrs
           - checkmate
           - dplyr
           - insightsengineering/dunlin

DESCRIPTION

@@ -1,17 +1,14 @@
 Type: Package
 Package: chevron
 Title: Standard TLGs for Clinical Trials Reporting
-Version: 0.2.0.9004
-Date: 2023-06-08
+Version: 0.2.0.9024
+Date: 2023-07-10
 Authors@R: c(
     person("Benoit", "Falquet", , "benoit.falquet@roche.com", role = c("aut", "cre")),
     person("Liming", "Li", , "liming.li@roche.com", role = "aut"),
-    person("Adrian", "Waddell", , "adrian.waddell@gene.com", role = "aut"),
-    person("Emily", "de la Rua", , "emily.de_la_rua@contractors.roche.com", role = "aut"),
-    person("Joe", "Zhu", , "joe.zhu@roche.com", role = "aut"),
-    person("Tim", "Barnett", , "timothy.barnett@roche.com", role = "aut"),
-    person("Lena", "Wang", , "wang.xinyue@gene.com", role = "aut"),
-    person("Heng", "Wang", , "wang.heng@gene.com", role = "aut"),
+    person("Xiaoli", "Duan", , "xiaoli.duan@roche.com", role = "aut"),
+    person("Tim", "Barnett", , "timothy.barnett@roche.com", role = "ctb"),
+    person("Tian", "Fang", , "tian.fang@roche.com", role = "ctb"),
     person("F. Hoffmann-La Roche AG", role = c("cph", "fnd"))
   )
 Description: Standard Table, Listings, and Graphs (TLG) library used in
@@ -35,7 +32,7 @@ Imports:
     rlistings (>= 0.2.2),
     rtables (>= 0.6.1),
     stringr,
-    tern (>= 0.8.2),
+    tern (>= 0.8.4),
     tibble,
     utils
 Suggests:
@@ -55,6 +52,7 @@ Remotes:
 Config/Needs/website: insightsengineering/nesttemplate
 Config/testthat/edition: 3
 Encoding: UTF-8
+Language: en-US
 LazyData: true
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.2.3
@@ -67,13 +65,16 @@ Collate:
     'aet02.R'
     'aet03.R'
     'aet04.R'
+    'aet05.R'
+    'aet05_all.R'
     'aet10.R'
     'assertions.R'
     'cfbt01.R'
     'checks.R'
     'chevron_tlg-S4methods.R'
     'cmt01a.R'
     'cmt02_pt.R'
+    'coxt01.R'
     'coxt02.R'
     'data.R'
     'dmt01.R'
@@ -100,6 +101,9 @@ Collate:
     'pdt02.R'
     'reexports.R'
     'rmpt01.R'
+    'rmpt03.R'
+    'rmpt04.R'
+    'rmpt05.R'
     'rspt01.R'
     'rtables_utils.R'
     'standard_rules.R'

NAMESPACE

@@ -11,7 +11,6 @@ S3method(empty_as_na,factor)
 S3method(lvls,character)
 S3method(lvls,default)
 S3method(lvls,factor)
-export("datasets<-")
 export("main<-")
 export("postprocess<-")
 export("preprocess<-")
@@ -38,6 +37,12 @@ export(aet04)
 export(aet04_main)
 export(aet04_post)
 export(aet04_pre)
+export(aet05)
+export(aet05_all)
+export(aet05_all_pre)
+export(aet05_main)
+export(aet05_post)
+export(aet05_pre)
 export(aet10)
 export(aet10_main)
 export(aet10_post)
@@ -62,11 +67,12 @@ export(cmt02_pt)
 export(cmt02_pt_main)
 export(cmt02_pt_post)
 export(cmt02_pt_pre)
+export(coxt01)
+export(coxt01_main)
+export(coxt01_post)
+export(coxt01_pre)
 export(coxt02)
 export(coxt02_main)
-export(coxt02_post)
-export(coxt02_pre)
-export(datasets)
 export(dmt01)
 export(dmt01_main)
 export(dmt01_post)
@@ -166,6 +172,15 @@ export(rmpt01)
 export(rmpt01_main)
 export(rmpt01_post)
 export(rmpt01_pre)
+export(rmpt03)
+export(rmpt03_main)
+export(rmpt03_pre)
+export(rmpt04)
+export(rmpt04_main)
+export(rmpt04_pre)
+export(rmpt05)
+export(rmpt05_main)
+export(rmpt05_pre)
 export(rspt01)
 export(rspt01_main)
 export(rspt01_post)
@@ -192,12 +207,10 @@ exportClasses(chevron_g)
 exportClasses(chevron_l)
 exportClasses(chevron_t)
 exportClasses(chevron_tlg)
-exportMethods("datasets<-")
 exportMethods("main<-")
 exportMethods("postprocess<-")
 exportMethods("preprocess<-")
 exportMethods(args_ls)
-exportMethods(datasets)
 exportMethods(main)
 exportMethods(postprocess)
 exportMethods(preprocess)
@@ -210,6 +223,7 @@ import(rtables)
 import(tern)
 importFrom(checkmate,check_class)
 importFrom(dunlin,reformat)
+importFrom(dunlin,render_safe)
 importFrom(dunlin,rule)
 importFrom(forcats,fct_relevel)
 importFrom(formatters,with_label)

NEWS.md

@@ -1,9 +1,15 @@
-# chevron 0.2.0.9004
+# chevron 0.2.0.9024
 
+* Add `row_split_var` and `page_var` as argument for some template.
 * Update `LBT06` template to use `PARAM` as row split.
 * Convert `AVISIT` to factor according to `AVISITN` as order in preprocessing.
 * Add `CFBT01` template. `VST01`, `EGT01` and `LBT01` are now all following `CFBT01`. By default parameters are by page displayed.
+* Add `RMPT04` and `RMPT05` which follow `RMPT01`.
+* Add `RMPT03` template.
 * Update `EGT03` to use `ACTARMCD` as default arm variable, and remove the preprocessing of filtering to "HR".
+* Update `EXT01` to allow it to be displayed by `PARCAT2`.
+* Add `COXT01` template. `COXT02` is based on `COXT01` now.
+* Add `AET05` and `AET05_ALL` template.
 
 # chevron 0.2.0
 
@@ -12,7 +18,7 @@
 * Remove deprecated `getter` functions `get_main`, `get_preprocess` and `get_postprocess`.
 * Simplify `pre` function and add more data checks in `main` function.
 * Remove redundant assertion functions.
-* Add more templates: `AET10`, `KMG01`, `RSPT01`, `RMPT01`, `COXT02`, `FSTG01`, `LBT06`.
+* Add more templates: `AET10`, `KMG01`, `RSPT01`, `RMPT01`, `COXT02`, `FSTG01`, and `LBT06`.
 
 # chevron 0.1.4
 

R/aet01.R

@@ -24,12 +24,13 @@ aet01_main <- function(adam_db,
                            "RELSER", "WD", "DSM", "REL", "RELWD", "RELDSM", "SEV"
                          )
                        ),
-                       anl_lbls = "Total number of patients with at least one",
+                       anl_lbls = "Total number of {patient_label} with at least one",
                        ...) {
   assert_all_tablenames(adam_db, "adsl", "adae")
   checkmate::assert_string(arm_var)
   checkmate::assert_list(anl_vars, types = "character", names = "unique")
   checkmate::assert_character(anl_lbls, min.chars = 1L)
+  lbl_overall <- render_safe(lbl_overall)
   checkmate::assert_string(lbl_overall, null.ok = TRUE)
   assert_valid_variable(adam_db$adsl, c("USUBJID", arm_var), types = list(c("character", "factor")))
   assert_valid_variable(adam_db$adsl, c("DTHFL", "DCSREAS"), types = list(c("character", "factor")), min_chars = 0L)
@@ -42,6 +43,7 @@ aet01_main <- function(adam_db,
     var_labels_for,
     df = adam_db$adae
   )
+  anl_lbls <- render_safe(anl_lbls)
   if (length(anl_lbls) == 1) {
     anl_lbls <- rep(anl_lbls, length(anl_vars))
   }
@@ -81,7 +83,7 @@ aet01_lyt <- function(arm_var,
       vars = "USUBJID",
       .stats = c("unique", "nonunique"),
       .labels = c(
-        unique = "Total number of patients with at least one AE",
+        unique = render_safe("Total number of {patient_label} with at least one AE"),
         nonunique = "Total number of AEs"
       ),
       .formats = list(unique = format_count_fraction_fixed_dp, nonunique = "xx"),
@@ -99,7 +101,7 @@ aet01_lyt <- function(arm_var,
       "USUBJID",
       filters = c("DCSREAS" = "ADVERSE EVENT"),
       denom = "N_col",
-      .labels = c(count_fraction = "Total number of patients withdrawn from study due to an AE"),
+      .labels = c(count_fraction = render_safe("Total number of {patient_label} withdrawn from study due to an AE")),
       table_names = "TotWithdrawal"
     )
 
@@ -168,6 +170,5 @@ aet01_post <- function(tlg, prune_0 = FALSE, ...) {
 aet01 <- chevron_t(
   main = aet01_main,
   preprocess = aet01_pre,
-  postprocess = aet01_post,
-  adam_datasets = c("adsl", "adae")
+  postprocess = aet01_post
 )