Merge branch '1187_decorate_output@main' into tm_a_mmrm@1187_decorate…

…_output@main
insightsengineering · Dec 12, 2024 · d428aae · d428aae
2 parents 68011c5 + 00c8c0b
commit d428aae
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Showing 24 changed files with 243 additions and 33 deletions.
diff --git a/.github/workflows/check.yaml b/.github/workflows/check.yaml
@@ -41,6 +41,25 @@ jobs:
         checking top-level files .* NOTE
       unit-test-report-brand: >-
         https://raw.githubusercontent.com/insightsengineering/hex-stickers/main/thumbs/teal.png
+      deps-installation-method: setup-r-dependencies
+      lookup-refs: |
+        insightsengineering/teal
+        insightsengineering/teal.transform
+        insightsengineering/tern
+        insightsengineering/rlistings
+        insightsengineering/formatters
+        insightsengineering/rtables
+        insightsengineering/rtables.officer
+        insightsengineering/teal.code
+        insightsengineering/teal.data
+        insightsengineering/teal.logger
+        insightsengineering/teal.reporter
+        insightsengineering/teal.widgets
+        insightsengineering/teal.slice
+        insightsengineering/tern.gee
+        insightsengineering/tern.mmrm
+        insightsengineering/nestcolor
+        insightsengineering/roxy.shinylive
   r-cmd-non-cran:
     name: R CMD Check (non-CRAN) 🧬
     uses: insightsengineering/r.pkg.template/.github/workflows/build-check-install.yaml@main
@@ -61,6 +80,25 @@ jobs:
         checking Rd .usage sections .* NOTE
         checking for unstated dependencies in vignettes .* NOTE
         checking top-level files .* NOTE
+      deps-installation-method: setup-r-dependencies
+      lookup-refs: |
+        insightsengineering/teal
+        insightsengineering/teal.transform
+        insightsengineering/tern
+        insightsengineering/rlistings
+        insightsengineering/formatters
+        insightsengineering/rtables
+        insightsengineering/rtables.officer
+        insightsengineering/teal.code
+        insightsengineering/teal.data
+        insightsengineering/teal.logger
+        insightsengineering/teal.reporter
+        insightsengineering/teal.widgets
+        insightsengineering/teal.slice
+        insightsengineering/tern.gee
+        insightsengineering/tern.mmrm
+        insightsengineering/nestcolor
+        insightsengineering/roxy.shinylive
   coverage:
     name: Coverage 📔
     uses: insightsengineering/r.pkg.template/.github/workflows/test-coverage.yaml@main
@@ -69,6 +107,25 @@ jobs:
     with:
       additional-env-vars: |
         NOT_CRAN=true
+      deps-installation-method: setup-r-dependencies
+      lookup-refs: |
+        insightsengineering/teal
+        insightsengineering/teal.transform
+        insightsengineering/tern
+        insightsengineering/rlistings
+        insightsengineering/formatters
+        insightsengineering/rtables
+        insightsengineering/rtables.officer
+        insightsengineering/teal.code
+        insightsengineering/teal.data
+        insightsengineering/teal.logger
+        insightsengineering/teal.reporter
+        insightsengineering/teal.widgets
+        insightsengineering/teal.slice
+        insightsengineering/tern.gee
+        insightsengineering/tern.mmrm
+        insightsengineering/nestcolor
+        insightsengineering/roxy.shinylive
   linter:
     if: github.event_name != 'push'
     name: SuperLinter 🦸‍♀️
@@ -80,6 +137,25 @@ jobs:
       REPO_GITHUB_TOKEN: ${{ secrets.REPO_GITHUB_TOKEN }}
     with:
       auto-update: true
+      deps-installation-method: setup-r-dependencies
+      lookup-refs: |
+        insightsengineering/teal
+        insightsengineering/teal.transform
+        insightsengineering/tern
+        insightsengineering/rlistings
+        insightsengineering/formatters
+        insightsengineering/rtables
+        insightsengineering/rtables.officer
+        insightsengineering/teal.code
+        insightsengineering/teal.data
+        insightsengineering/teal.logger
+        insightsengineering/teal.reporter
+        insightsengineering/teal.widgets
+        insightsengineering/teal.slice
+        insightsengineering/tern.gee
+        insightsengineering/tern.mmrm
+        insightsengineering/nestcolor
+        insightsengineering/roxy.shinylive
   gitleaks:
     name: gitleaks 💧
     uses: insightsengineering/r.pkg.template/.github/workflows/gitleaks.yaml@main

diff --git a/.github/workflows/docs.yaml b/.github/workflows/docs.yaml
@@ -42,3 +42,22 @@ jobs:
     with:
       default-landing-page: latest-tag
       additional-unit-test-report-directories: unit-test-report-non-cran
+      deps-installation-method: setup-r-dependencies
+      lookup-refs: |
+        insightsengineering/teal
+        insightsengineering/teal.transform
+        insightsengineering/tern
+        insightsengineering/rlistings
+        insightsengineering/formatters
+        insightsengineering/rtables
+        insightsengineering/rtables.officer
+        insightsengineering/teal.code
+        insightsengineering/teal.data
+        insightsengineering/teal.logger
+        insightsengineering/teal.reporter
+        insightsengineering/teal.widgets
+        insightsengineering/teal.slice
+        insightsengineering/tern.gee
+        insightsengineering/tern.mmrm
+        insightsengineering/nestcolor
+        insightsengineering/roxy.shinylive
diff --git a/.github/workflows/release.yaml b/.github/workflows/release.yaml
@@ -16,12 +16,51 @@ jobs:
       REPO_GITHUB_TOKEN: ${{ secrets.REPO_GITHUB_TOKEN }}
     with:
       default-landing-page: latest-tag
+      deps-installation-method: setup-r-dependencies
+      lookup-refs: |
+        insightsengineering/teal
+        insightsengineering/teal.transform
+        insightsengineering/tern
+        insightsengineering/rlistings
+        insightsengineering/formatters
+        insightsengineering/rtables
+        insightsengineering/rtables.officer
+        insightsengineering/teal.code
+        insightsengineering/teal.data
+        insightsengineering/teal.logger
+        insightsengineering/teal.reporter
+        insightsengineering/teal.widgets
+        insightsengineering/teal.slice
+        insightsengineering/tern.gee
+        insightsengineering/tern.mmrm
+        insightsengineering/nestcolor
+        insightsengineering/roxy.shinylive
   validation:
     name: R Package Validation report 📃
     needs: release
     uses: insightsengineering/r.pkg.template/.github/workflows/validation.yaml@main
     secrets:
       REPO_GITHUB_TOKEN: ${{ secrets.REPO_GITHUB_TOKEN }}
+    with:
+      deps-installation-method: setup-r-dependencies
+      lookup-refs: |
+        insightsengineering/teal
+        insightsengineering/teal.transform
+        insightsengineering/tern
+        insightsengineering/rlistings
+        insightsengineering/formatters
+        insightsengineering/rtables
+        insightsengineering/rtables.officer
+        insightsengineering/teal.code
+        insightsengineering/teal.data
+        insightsengineering/teal.logger
+        insightsengineering/teal.reporter
+        insightsengineering/teal.widgets
+        insightsengineering/teal.slice
+        insightsengineering/tern.gee
+        insightsengineering/tern.mmrm
+        insightsengineering/nestcolor
+        insightsengineering/roxy.shinylive
   release:
     name: Create release 🎉
     uses: insightsengineering/r.pkg.template/.github/workflows/release.yaml@main
@@ -46,6 +85,25 @@ jobs:
         checking top-level files .* NOTE
       unit-test-report-brand: >-
         https://raw.githubusercontent.com/insightsengineering/hex-stickers/main/thumbs/teal.png
+      deps-installation-method: setup-r-dependencies
+      lookup-refs: |
+        insightsengineering/teal
+        insightsengineering/teal.transform
+        insightsengineering/tern
+        insightsengineering/rlistings
+        insightsengineering/formatters
+        insightsengineering/rtables
+        insightsengineering/rtables.officer
+        insightsengineering/teal.code
+        insightsengineering/teal.data
+        insightsengineering/teal.logger
+        insightsengineering/teal.reporter
+        insightsengineering/teal.widgets
+        insightsengineering/teal.slice
+        insightsengineering/tern.gee
+        insightsengineering/tern.mmrm
+        insightsengineering/nestcolor
+        insightsengineering/roxy.shinylive
   coverage:
     name: Coverage 📔
     needs: [release, docs]
@@ -55,6 +113,25 @@ jobs:
     with:
       additional-env-vars: |
         NOT_CRAN=true
+      deps-installation-method: setup-r-dependencies
+      lookup-refs: |
+        insightsengineering/teal
+        insightsengineering/teal.transform
+        insightsengineering/tern
+        insightsengineering/rlistings
+        insightsengineering/formatters
+        insightsengineering/rtables
+        insightsengineering/rtables.officer
+        insightsengineering/teal.code
+        insightsengineering/teal.data
+        insightsengineering/teal.logger
+        insightsengineering/teal.reporter
+        insightsengineering/teal.widgets
+        insightsengineering/teal.slice
+        insightsengineering/tern.gee
+        insightsengineering/tern.mmrm
+        insightsengineering/nestcolor
+        insightsengineering/roxy.shinylive
   wasm:
     name: Build WASM packages 🧑‍🏭
     needs: release

diff --git a/.github/workflows/scheduled.yaml b/.github/workflows/scheduled.yaml
@@ -3,7 +3,7 @@ name: Scheduled 🕰️
 
 on:
   schedule:
-    - cron: '45 3 * * 0'
+    - cron: "45 3 * * 0"
   workflow_dispatch:
     inputs:
       chosen-workflow:
@@ -56,6 +56,23 @@ jobs:
       )
     name: revdepcheck ↩️
     uses: insightsengineering/r.pkg.template/.github/workflows/revdepcheck.yaml@main
+    with:
+      lookup-refs: |
+        insightsengineering/teal
+        insightsengineering/teal.transform
+        insightsengineering/tern
+        insightsengineering/rlistings
+        insightsengineering/formatters
+        insightsengineering/rtables
+        insightsengineering/rtables.officer
+        insightsengineering/teal.code
+        insightsengineering/teal.data
+        insightsengineering/teal.logger
+        insightsengineering/teal.reporter
+        insightsengineering/teal.widgets
+        insightsengineering/teal.slice
+        insightsengineering/tern.gee
+        insightsengineering/tern.mmrm
   rhub:
     if: >
       github.event_name == 'schedule' || (
@@ -70,12 +87,14 @@ jobs:
         insightsengineering/teal.transform
         insightsengineering/tern
         insightsengineering/rlistings
+        insightsengineering/formatters
         insightsengineering/rtables
+        insightsengineering/rtables.officer
         insightsengineering/teal.code
         insightsengineering/teal.data
         insightsengineering/teal.logger
         insightsengineering/teal.reporter
-        insightsengineering/teal.slice
         insightsengineering/teal.widgets
+        insightsengineering/teal.slice
         insightsengineering/tern.gee
         insightsengineering/tern.mmrm
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: teal.modules.clinical
 Title: 'teal' Modules for Standard Clinical Outputs
-Version: 0.9.1.9038
-Date: 2024-12-10
+Version: 0.9.1.9040
+Date: 2024-12-11
 Authors@R: c(
     person("Joe", "Zhu", , "[email protected]", role = c("aut", "cre")),
     person("Jana", "Stoilova", , "[email protected]", role = "aut"),

diff --git a/NEWS.md b/NEWS.md
@@ -1,4 +1,4 @@
-# teal.modules.clinical 0.9.1.9038
+# teal.modules.clinical 0.9.1.9040
 
 ### Enhancements
 * Added `teal.logger` functionality for logging changes in shiny inputs in all modules.

diff --git a/R/tm_g_forest_rsp.R b/R/tm_g_forest_rsp.R
@@ -14,7 +14,7 @@
 #'   * `pval`: p-value of the effect.
 #'   Note, the statistics `n_tot`, `or`, and `ci` are required.
 #' @param riskdiff (`list`)\cr if a risk (proportion) difference column should be added, a list of settings to apply
-#'   within the column. See [control_riskdiff()] for details. If `NULL`, no risk difference column will be added.
+#'   within the column. See [tern::control_riskdiff()] for details. If `NULL`, no risk difference column will be added.
 #' @param obj_var_name (`character`)\cr additional text to append to the table title.
 #' @param responders (`character`)\cr values of `aval_var` that are considered to be responders.
 #' @param col_symbol_size (`integer` or `NULL`)\cr column index to be used to determine relative size for

diff --git a/R/tm_g_pp_adverse_events.R b/R/tm_g_pp_adverse_events.R
@@ -180,11 +180,10 @@ template_adverse_events <- function(dataname = "ANL",
 #'   available choices and preselected option for the `ASTDY` variable from `dataname`.
 #' @param decod ([teal.transform::choices_selected()])\cr object with all
 #'   available choices and preselected option for the `AEDECOD` variable from `dataname`.
-#' @param decorators `r roxygen_decorators_param("tm_g_pp_adverse_events")`
 #'
 #' @inherit module_arguments return
 #'
-#' @section Decorating `tm_g_pp_adverse_events`:
+#' @section Decorating Modules:
 #'
 #' This module generates the following objects, which can be modified in place using decorators::
 #' - `plot` (`ggplot2`)

diff --git a/R/tm_t_coxreg.R b/R/tm_t_coxreg.R
@@ -3,7 +3,7 @@
 #' Creates a valid expression to generate a univariable Cox regression analysis.
 #'
 #' @inheritParams template_arguments
-#' @param control (`list`)\cr list of settings for the analysis (see [control_coxreg()]).
+#' @param control (`list`)\cr list of settings for the analysis (see [tern::control_coxreg()]).
 #' @param at (`list` of `numeric`)\cr when the candidate covariate is a `numeric` type variable, use `at`
 #'   to specify the value of the covariate at which the effect should be estimated.
 #' @param append (`logical`)\cr whether the result should be appended to the previous one.

diff --git a/R/tm_t_events_by_grade.R b/R/tm_t_events_by_grade.R
@@ -1207,7 +1207,7 @@ srv_t_events_by_grade <- function(id,
 
 
     table_renamed_q <- reactive({
-      within(table_q(), {table <- pruned_and_sorted_result})
+      within(table_q(), table <- pruned_and_sorted_result)
     })
 
     decorated_table_q <- srv_decorate_teal_data(

diff --git a/R/tm_t_exposure.R b/R/tm_t_exposure.R
@@ -223,11 +223,10 @@ template_exposure <- function(parentname,
 #'   parameter category values.
 #' @param paramcd_label (`character`)\cr the column from the dataset where the value will be used to
 #'   label the argument `paramcd`.
-#' @param decorators `r roxygen_decorators_param("tm_t_exposure")`
 #'
 #' @inherit module_arguments return seealso
 #'
-#' @section Decorating `tm_t_exposure`:
+#' @section Decorating Modules:
 #'
 #' This module generates the following objects, which can be modified in place using decorators:
 #' - `table` (`TableTree` as created from `rtables::build_table`)

diff --git a/R/tm_t_tte.R b/R/tm_t_tte.R
@@ -384,8 +384,8 @@ template_tte <- function(dataname = "ANL",
 #'   pre-selected option for confidence level, each within range of (0, 1).
 #' @param conf_level_survfit ([teal.transform::choices_selected()])\cr object with all available choices and
 #'   pre-selected option for confidence level, each within range of (0, 1).
-#' @param event_desc_var (`character` or [data_extract_spec()])\cr variable name with the event description
-#'   information, optional.
+#' @param event_desc_var (`character` or [teal.transform::data_extract_spec()])\cr variable name with the
+#'   event description information, optional.
 #'
 #' @section Decorating Module:
 #'
@@ -396,8 +396,8 @@ template_tte <- function(dataname = "ANL",
 #' `vignette("decorate-modules-output", package = "teal")` or the [`teal_transform_module()`] documentation.
 #'
 #' @details
-#' * The core functionality of this module is based on [coxph_pairwise()], [surv_timepoint()], and [surv_time()] from
-#' the `tern` package.
+#' * The core functionality of this module is based on [tern::coxph_pairwise()], [tern::surv_timepoint()],
+#'   and [tern::surv_time()] from the `tern` package.
 #' * The arm and stratification variables are taken from the `parentname` data.
 #' * The following variables are used in the module:
 #'

diff --git a/R/utils.R b/R/utils.R
@@ -434,7 +434,7 @@ split_col_expr <- function(compare, combine, ref, arm_var) {
 #'
 #' @note uses the regex `\\*|:` to perform the split.
 #'
-#' @return  a [choices_selected()] object.
+#' @return  a [teal.transform::choices_selected()] object.
 #'
 #' @examples
 #' split_choices(choices_selected(choices = c("x:y", "a*b"), selected = all_choices()))

diff --git a/man/split_choices.Rd b/man/split_choices.Rd
diff --git a/man/template_coxreg_m.Rd b/man/template_coxreg_m.Rd