From 4203d09e46a4b2728ff20b257ae71208568c9dbf Mon Sep 17 00:00:00 2001 From: Emily de la Rua <59304861+edelarua@users.noreply.github.com> Date: Fri, 26 May 2023 08:45:49 -0400 Subject: [PATCH] Remove mentions of STREAM from documentation (#772) Closes https://github.com/insightsengineering/sme-tasks/issues/175 --- NEWS.md | 9 ++++----- R/tm_t_ancova.R | 2 +- R/tm_t_binary_outcome.R | 3 +-- R/tm_t_events_by_grade.R | 1 - R/tm_t_logistic.R | 3 +-- R/tm_t_tte.R | 3 +-- inst/WORDLIST | 4 ++++ man/tm_t_ancova.Rd | 2 +- man/tm_t_binary_outcome.Rd | 3 +-- man/tm_t_logistic.Rd | 3 +-- man/tm_t_tte.Rd | 3 +-- tests/testthat/_snaps/tm_t_events_by_grade.md | 2 +- tests/testthat/test-tm_t_events_by_grade.R | 2 +- 13 files changed, 18 insertions(+), 22 deletions(-) diff --git a/NEWS.md b/NEWS.md index 480e1e2427..7191cea6b1 100644 --- a/NEWS.md +++ b/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. diff --git a/R/tm_t_ancova.R b/R/tm_t_ancova.R index 5a7f032805..39d6147c5b 100644 --- a/R/tm_t_ancova.R +++ b/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: diff --git a/R/tm_t_binary_outcome.R b/R/tm_t_binary_outcome.R index bb4c92a10b..9c0b2d2517 100644 --- a/R/tm_t_binary_outcome.R +++ b/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) diff --git a/R/tm_t_events_by_grade.R b/R/tm_t_events_by_grade.R index fb2f250cfc..c9f93cbf00 100644 --- a/R/tm_t_events_by_grade.R +++ b/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, diff --git a/R/tm_t_logistic.R b/R/tm_t_logistic.R index 676d95fb2b..54f07f6b43 100644 --- a/R/tm_t_logistic.R +++ b/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 diff --git a/R/tm_t_tte.R b/R/tm_t_tte.R index f482e7ae09..9cebc40e02 100644 --- a/R/tm_t_tte.R +++ b/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: #' diff --git a/inst/WORDLIST b/inst/WORDLIST index 83b852ab5d..103c703969 100644 --- a/inst/WORDLIST +++ b/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 diff --git a/man/tm_t_ancova.Rd b/man/tm_t_ancova.Rd index 1b843f339d..8097fd2c6e 100644 --- a/man/tm_t_ancova.Rd +++ b/man/tm_t_ancova.Rd @@ -96,7 +96,7 @@ Teal Module: ANCOVA Teal Module } \details{ This module produces an analysis of variance summary table that is -similar to STREAM template \code{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: diff --git a/man/tm_t_binary_outcome.Rd b/man/tm_t_binary_outcome.Rd index 7ca38f34ad..e613879178 100644 --- a/man/tm_t_binary_outcome.Rd +++ b/man/tm_t_binary_outcome.Rd @@ -72,8 +72,7 @@ and contain arrays, each name corresponding to a single value of \code{paramcd}. may contain default response values or named arrays \code{rsp} of default selected response values and \code{levels} of default level choices.} -\item{rsp_table}{(\code{logical})\cr should the initial set-up of the module match -the STREAM template \code{rspt01}. (default FALSE)} +\item{rsp_table}{(\code{logical})\cr should the initial set-up of the module match RSPT01. (default FALSE)} \item{add_total}{(\code{logical})\cr whether to include column with total number of patients.} diff --git a/man/tm_t_logistic.Rd b/man/tm_t_logistic.Rd index 45e361bad3..fbb5995209 100644 --- a/man/tm_t_logistic.Rd +++ b/man/tm_t_logistic.Rd @@ -76,8 +76,7 @@ The argument is merged with option \code{teal.basic_table_args} and with default For more details, see the vignette: \code{vignette("custom-basic-table-arguments", package = "teal.widgets")}.} } \description{ -This module produces a multi-variable logistic regression table that matches the -STREAM template \code{lgrt02}. +This module produces a multi-variable logistic regression table that matches LGRT02. } \examples{ adsl <- tmc_ex_adsl diff --git a/man/tm_t_tte.Rd b/man/tm_t_tte.Rd index 7d35aca4c6..a93798162d 100644 --- a/man/tm_t_tte.Rd +++ b/man/tm_t_tte.Rd @@ -109,8 +109,7 @@ For more details, see the vignette: \code{vignette("custom-basic-table-arguments Teal Module: Time To Event Table Teal Module } \details{ -This module produces a response summary table that is similar to -STREAM template \code{ttet01}. The core functionality is based on +This module produces a response summary table that is similar to TTET01. The core functionality is based on \code{\link[=coxph_pairwise]{coxph_pairwise()}}, \code{\link[=surv_timepoint]{surv_timepoint()}} and \code{\link[=surv_time]{surv_time()}} from package \code{tern}.\cr The following variables are used in the module: diff --git a/tests/testthat/_snaps/tm_t_events_by_grade.md b/tests/testthat/_snaps/tm_t_events_by_grade.md index be2854c319..e3a80e1b15 100644 --- a/tests/testthat/_snaps/tm_t_events_by_grade.md +++ b/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 diff --git a/tests/testthat/test-tm_t_events_by_grade.R b/tests/testthat/test-tm_t_events_by_grade.R index e9408621a7..e5288b2224 100644 --- a/tests/testthat/test-tm_t_events_by_grade.R +++ b/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",