Remove mentions of STREAM from documentation (#772)

Closes insightsengineering/sme-tasks#175

NEWS.md

@@ -8,8 +8,8 @@
 * Replaced `synthetic_cdisc_data` with refactored `synthetic_cdisc_dataset` function to speed up dataset loading in tests/examples.
 * Added new GEE module `tm_a_gee`.
 * Added interface for selecting an interaction term to `tm_t_ancova`.
-* Updated encodings input checks to use `shinyvalidate::InputValidator` instead of `shiny::validate` for better UI experience.   
-* Added adjustment method choice to `tm_a_mmrm` to allow for Kenward-Roger adjustment of standard errors and p-values.
+* Updated encodings input checks to use `shinyvalidate::InputValidator` for better UI experience. Previously used `shiny::validate`.
+* Added option to `tm_a_mmrm` to allow for Kenward-Roger adjustments of standard errors and p-values.
 * Added option to choose facet scale options in `tm_g_barchart_simple`.
 * Added `label` parameter to `cs_to_select_spec`/`cs_to_des_select` and `cs_to_filter_spec`/`cs_to_des_filter` to allow the user to customize the label printed over the selection field.
 * Updated `tm_t_coxreg` module after refactoring `summarize_coxreg` in `tern` to fix indentation.
@@ -18,8 +18,7 @@
 ### Miscellaneous
 * Package now uses `scda.2022` rather than `scda.2021` in SUGGESTS.
 * Removed unused argument `param` from `tm_g_pp_vitals`.
-* Removed optimizer choice from `tm_a_mmrm` since we can just always use the 
-  automatically determined optimizer.
+* Removed optimizer choice from `tm_a_mmrm` since we can always use the automatically determined optimizer.
 * Creation of internal data for `adsl`, `adae`, `adaette`, `adcm`, `adeg`, `adex`, `adlb`, `admh`, `adqs`, `adrs`, `adtte`, and `advs`. 
   They are accessible via `tmc_ex_*` prefix.
 * Updated all examples and tests to use datasets from the `teal.modules.clinical` package instead of `scda` datasets.
@@ -52,7 +51,7 @@
 
 ### Bug fixes
 
-* Fixed bug in `tm_g_barchart_simple` which prevented graph from being shown.
+* Fixed bug in `tm_g_barchart_simple` which prevented display of graph.
 * Fixed broken example for `tm_t_abnormality_by_worst_grade`.
 * Fixed bug in `tm_a_mmrm` which prevented table headers from displaying.
 * Fixed bug in `tm_g_forest_rsp` when deselecting endpoint.

R/tm_t_ancova.R

@@ -414,7 +414,7 @@ template_ancova <- function(dataname = "ANL",
 #' @inheritParams module_arguments
 #'
 #' @details This module produces an analysis of variance summary table that is
-#' similar to STREAM template `aovt01` when multiple endpoints are selected.
+#' similar to AOVT01 when multiple endpoints are selected.
 #' When a single endpoint is selected, both unadjusted and adjusted comparison
 #' would be provided. This modules expects that the analysis data has the
 #' following variables:

R/tm_t_binary_outcome.R

@@ -365,8 +365,7 @@ template_binary_outcome <- function(dataname,
 #'   may contain default response values or named arrays `rsp` of default selected response
 #'   values and `levels` of default level choices.
 #'
-#' @param rsp_table (`logical`)\cr should the initial set-up of the module match
-#'   the STREAM template `rspt01`. (default FALSE)
+#' @param rsp_table (`logical`)\cr should the initial set-up of the module match RSPT01. (default FALSE)
 #'
 #' @details Additional standard UI inputs include `responders`,
 #'   `ref_arm`, `comp_arm` and `combine_comp_arms` (default FALSE)

R/tm_t_events_by_grade.R

@@ -550,7 +550,6 @@ template_events_col_by_grade <- function(dataname,
     )
   )
 
-  # for variant 8 in STREAM manual
   if (!is.null(hlt)) {
     layout_list <- add_expr(
       layout_list,

R/tm_t_logistic.R

@@ -214,8 +214,7 @@ template_logistic <- function(dataname,
 
 #' Teal Module: Logistic Regression
 #'
-#' @description This module produces a multi-variable logistic regression table that matches the
-#'   STREAM template `lgrt02`.
+#' @description This module produces a multi-variable logistic regression table that matches LGRT02.
 #'
 #' @inheritParams module_arguments
 #' @param arm_var ([teal.transform::choices_selected()] or [teal.transform::data_extract_spec()]) or `NULL`\cr

R/tm_t_tte.R

@@ -363,8 +363,7 @@ template_tte <- function(dataname = "ANL",
 #' @param event_desc_var (`character` or [data_extract_spec()])\cr variable name with the event description
 #'   information, optional.
 #'
-#' @details This module produces a response summary table that is similar to
-#'   STREAM template `ttet01`. The core functionality is based on
+#' @details This module produces a response summary table that is similar to TTET01. The core functionality is based on
 #'   [coxph_pairwise()], [surv_timepoint()] and [surv_time()] from package `tern`.\cr
 #'   The following variables are used in the module:
 #'

inst/WORDLIST

@@ -14,6 +14,7 @@ ADaM
 AE
 AETOXGR
 ANCOVA
+AOVT
 CDISC
 CMH
 CoxPH
@@ -24,14 +25,17 @@ GDSR
 Github
 Kaplan
 Kenward
+LGRT
 MMRM
 NSE
 Newcombe
 PARAMCD
+RSPT
 Repo
 Rua
 SREPs
 TLG
+TTET
 UI
 USUBJID
 Univariable

tests/testthat/_snaps/tm_t_events_by_grade.md

@@ -280,7 +280,7 @@
       }
       
 
-# template_events_col_by_grade generates STREAM variant 8
+# template_events_col_by_grade works with custom values
 
     Code
       res

tests/testthat/test-tm_t_events_by_grade.R

@@ -95,7 +95,7 @@ testthat::test_that("template_events_col_by_grade generates standard expressions
   testthat::expect_snapshot(res)
 })
 
-testthat::test_that("template_events_col_by_grade generates STREAM variant 8", {
+testthat::test_that("template_events_col_by_grade works with custom values", {
   result <- template_events_col_by_grade(
     dataname = "adae",
     parentname = "adsl",