diff --git a/R/argument_convention.R b/R/argument_convention.R index 6c70ef260..d55ccf3e4 100644 --- a/R/argument_convention.R +++ b/R/argument_convention.R @@ -204,8 +204,8 @@ NULL #' @param worst_flag_var ([teal.transform::choices_selected()])\cr object #' with all available choices and preselected option for variable names that can be used as worst flag variable. #' @param decorators `r lifecycle::badge("experimental")` -#' " (`list` of `teal_transform_module`, named `list` of `teal_transform_module` or" `NULL`) optional, -#' if not `NULL`, decorator for tables or plots included in the module. +#' (`list` of `teal_transform_module`, named `list` of `teal_transform_module`) optional, +#' decorator for tables or plots included in the module output reported. #' When a named list of `teal_transform_module`, the decorators are applied to the respective output objects. #' #' Otherwise, the decorators are applied to all objects, which is equivalent as using the name `default`. diff --git a/R/tm_a_gee.R b/R/tm_a_gee.R index 3a4d354f4..0313dff61 100644 --- a/R/tm_a_gee.R +++ b/R/tm_a_gee.R @@ -129,6 +129,7 @@ template_a_gee <- function(output_table, #' This module produces an analysis table using Generalized Estimating Equations (GEE). #' #' @inheritParams module_arguments +#' @inheritParams teal::module #' @inheritParams template_arguments #' @inheritParams template_a_gee #' @@ -208,7 +209,8 @@ tm_a_gee <- function(label, pre_output = NULL, post_output = NULL, basic_table_args = teal.widgets::basic_table_args(), - decorators = NULL) { + transformators = list(), + decorators = list()) { message("Initializing tm_a_gee (prototype)") cov_var <- teal.transform::add_no_selected_choices(cov_var, multiple = TRUE) @@ -227,7 +229,7 @@ tm_a_gee <- function(label, checkmate::assert_class(post_output, classes = "shiny.tag", null.ok = TRUE) checkmate::assert_class(basic_table_args, "basic_table_args") decorators <- normalize_decorators(decorators) - assert_decorators(decorators, "table", null.ok = TRUE) + assert_decorators(decorators, "table") args <- as.list(environment()) @@ -257,6 +259,7 @@ tm_a_gee <- function(label, decorators = decorators ) ), + transformators = transformators, datanames = teal.transform::get_extract_datanames(data_extract_list) ) } diff --git a/R/tm_a_mmrm.R b/R/tm_a_mmrm.R index 63455af4f..3dbc5a7b6 100644 --- a/R/tm_a_mmrm.R +++ b/R/tm_a_mmrm.R @@ -440,6 +440,7 @@ template_mmrm_plots <- function(fit_name, #' This module produces analysis tables and plots for Mixed Model Repeated Measurements. #' #' @inheritParams module_arguments +#' @inheritParams teal::module #' @inheritParams template_mmrm_tables #' @inheritParams template_mmrm_plots #' @param method ([teal.transform::choices_selected()])\cr object with @@ -569,7 +570,8 @@ tm_a_mmrm <- function(label, post_output = NULL, basic_table_args = teal.widgets::basic_table_args(), ggplot2_args = teal.widgets::ggplot2_args(), - decorators = NULL) { + transformators = list(), + decorators = list()) { message("Initializing tm_a_mmrm") cov_var <- teal.transform::add_no_selected_choices(cov_var, multiple = TRUE) checkmate::assert_string(label) @@ -608,8 +610,7 @@ tm_a_mmrm <- function(label, "fixed_effects_table", "diagnostic_table", "diagnostic_plot" - ), - null.ok = TRUE + ) ) args <- as.list(environment()) @@ -644,6 +645,7 @@ tm_a_mmrm <- function(label, decorators = decorators ) ), + transformators = transformators, datanames = teal.transform::get_extract_datanames(data_extract_list) ) } diff --git a/R/tm_g_barchart_simple.R b/R/tm_g_barchart_simple.R index 107a2248d..6bfa5b655 100644 --- a/R/tm_g_barchart_simple.R +++ b/R/tm_g_barchart_simple.R @@ -6,6 +6,7 @@ #' `x_facet`, and `y_facet` parameters. Any parameters set to `NULL` (default) are ignored. #' #' @inheritParams module_arguments +#' @inheritParams teal::module #' @inheritParams template_arguments #' @param x (`data_extract_spec`)\cr variable on the x-axis. #' @param fill (`data_extract_spec`)\cr grouping variable to determine bar colors. @@ -155,7 +156,8 @@ tm_g_barchart_simple <- function(x = NULL, pre_output = NULL, post_output = NULL, ggplot2_args = teal.widgets::ggplot2_args(), - decorators = NULL) { + transformators = list(), + decorators = list()) { message("Initializing tm_g_barchart_simple") checkmate::assert_string(label) checkmate::assert_list(plot_options, null.ok = TRUE) @@ -181,7 +183,7 @@ tm_g_barchart_simple <- function(x = NULL, checkmate::assert_class(post_output, classes = "shiny.tag", null.ok = TRUE) checkmate::assert_class(ggplot2_args, "ggplot2_args") decorators <- normalize_decorators(decorators) - assert_decorators(decorators, names = "plot", null.ok = TRUE) + assert_decorators(decorators, names = "plot") plot_options <- utils::modifyList( list(stacked = FALSE), # default @@ -210,6 +212,7 @@ tm_g_barchart_simple <- function(x = NULL, ggplot2_args = ggplot2_args, decorators = decorators ), + transformators = transformators, datanames = teal.transform::get_extract_datanames(data_extract_list) ) } diff --git a/R/tm_g_ci.R b/R/tm_g_ci.R index 41e525af8..6e6f06df5 100644 --- a/R/tm_g_ci.R +++ b/R/tm_g_ci.R @@ -183,6 +183,7 @@ template_g_ci <- function(dataname, #' `CIG01` available [here](https://insightsengineering.github.io/tlg-catalog/stable/graphs/other/cig01.html). #' #' @inheritParams module_arguments +#' @inheritParams teal::module #' @inheritParams template_g_ci #' @param color (`data_extract_spec`)\cr the group variable used to determine the plot colors, shapes, and line types. #' @@ -283,7 +284,8 @@ tm_g_ci <- function(label, pre_output = NULL, post_output = NULL, ggplot2_args = teal.widgets::ggplot2_args(), - decorators = NULL) { + transformators = list(), + decorators = list()) { message("Initializing tm_g_ci") checkmate::assert_string(label) stat <- match.arg(stat) @@ -309,7 +311,7 @@ tm_g_ci <- function(label, checkmate::assert_class(post_output, classes = "shiny.tag", null.ok = TRUE) checkmate::assert_class(ggplot2_args, "ggplot2_args") decorators <- normalize_decorators(decorators) - assert_decorators(decorators, "plot", null.ok = TRUE) + assert_decorators(decorators, "plot") args <- as.list(environment()) @@ -328,6 +330,7 @@ tm_g_ci <- function(label, ggplot2_args = ggplot2_args, decorators = decorators ), + transformators = transformators, ui = ui_g_ci, ui_args = args, datanames = teal.transform::get_extract_datanames(data_extract_list) diff --git a/R/tm_g_forest_rsp.R b/R/tm_g_forest_rsp.R index bc9369bc1..46661e9da 100644 --- a/R/tm_g_forest_rsp.R +++ b/R/tm_g_forest_rsp.R @@ -239,6 +239,7 @@ template_forest_rsp <- function(dataname = "ANL", #' #' @inheritParams tern::g_forest #' @inheritParams module_arguments +#' @inheritParams teal::module #' @inheritParams template_forest_rsp #' #' @inherit module_arguments return seealso @@ -364,7 +365,8 @@ tm_g_forest_rsp <- function(label, pre_output = NULL, post_output = NULL, ggplot2_args = teal.widgets::ggplot2_args(), - decorators = NULL) { + transformators = list(), + decorators = list()) { message("Initializing tm_g_forest_rsp") checkmate::assert_string(label) checkmate::assert_string(dataname) @@ -391,7 +393,7 @@ tm_g_forest_rsp <- function(label, checkmate::assert_class(post_output, classes = "shiny.tag", null.ok = TRUE) checkmate::assert_class(ggplot2_args, "ggplot2_args") decorators <- normalize_decorators(decorators) - assert_decorators(decorators, "plot", null.ok = TRUE) + assert_decorators(decorators, "plot") args <- as.list(environment()) @@ -424,6 +426,7 @@ tm_g_forest_rsp <- function(label, decorators = decorators ) ), + transformators = transformators, datanames = teal.transform::get_extract_datanames(data_extract_list) ) } diff --git a/R/tm_g_forest_tte.R b/R/tm_g_forest_tte.R index f70b0cfbc..c1e086231 100644 --- a/R/tm_g_forest_tte.R +++ b/R/tm_g_forest_tte.R @@ -239,6 +239,7 @@ template_forest_tte <- function(dataname = "ANL", #' #' @inheritParams tern::g_forest #' @inheritParams module_arguments +#' @inheritParams teal::module #' @inheritParams template_forest_tte #' #' @inherit module_arguments return seealso @@ -348,7 +349,8 @@ tm_g_forest_tte <- function(label, pre_output = NULL, post_output = NULL, ggplot2_args = teal.widgets::ggplot2_args(), - decorators = NULL) { + transformators = list(), + decorators = list()) { message("Initializing tm_g_forest_tte") checkmate::assert_string(label) checkmate::assert_string(dataname) @@ -377,7 +379,7 @@ tm_g_forest_tte <- function(label, checkmate::assert_class(post_output, classes = "shiny.tag", null.ok = TRUE) checkmate::assert_class(ggplot2_args, "ggplot2_args") decorators <- normalize_decorators(decorators) - assert_decorators(decorators, "plot", null.ok = TRUE) + assert_decorators(decorators, "plot") args <- as.list(environment()) @@ -410,6 +412,7 @@ tm_g_forest_tte <- function(label, decorators = decorators ) ), + transformators = transformators, datanames = teal.transform::get_extract_datanames(data_extract_list) ) } diff --git a/R/tm_g_ipp.R b/R/tm_g_ipp.R index 3cd65e3b8..91fc5cafc 100644 --- a/R/tm_g_ipp.R +++ b/R/tm_g_ipp.R @@ -173,6 +173,7 @@ template_g_ipp <- function(dataname = "ANL", #' values over time for each patient, using data with ADaM structure. #' #' @inheritParams module_arguments +#' @inheritParams teal::module #' @inheritParams template_g_ipp #' @param arm_var ([teal.transform::choices_selected()])\cr object with #' all available choices and preselected option for variable values that can be used as arm variable. @@ -303,7 +304,8 @@ tm_g_ipp <- function(label, pre_output = NULL, post_output = NULL, ggplot2_args = teal.widgets::ggplot2_args(), - decorators = NULL) { + transformators = list(), + decorators = list()) { if (lifecycle::is_present(base_var)) { baseline_var <- base_var warning( @@ -340,7 +342,7 @@ tm_g_ipp <- function(label, checkmate::assert_class(post_output, classes = "shiny.tag", null.ok = TRUE) checkmate::assert_class(ggplot2_args, "ggplot2_args") decorators <- normalize_decorators(decorators) - assert_decorators(decorators, "plot", null.ok = TRUE) + assert_decorators(decorators, "plot") args <- as.list(environment()) data_extract_list <- list( @@ -370,6 +372,7 @@ tm_g_ipp <- function(label, decorators = decorators ) ), + transformators = transformators, datanames = teal.transform::get_extract_datanames(data_extract_list) ) } diff --git a/R/tm_g_km.R b/R/tm_g_km.R index e96d79aa1..9cca4e806 100644 --- a/R/tm_g_km.R +++ b/R/tm_g_km.R @@ -264,6 +264,7 @@ template_g_km <- function(dataname = "ANL", #' This module produces a `ggplot`-style Kaplan-Meier plot for data with ADaM structure. #' #' @inheritParams module_arguments +#' @inheritParams teal::module #' @inheritParams template_g_km #' @param facet_var ([teal.transform::choices_selected()])\cr object with #' all available choices and preselected option for names of variable that can be used for plot faceting. @@ -373,7 +374,8 @@ tm_g_km <- function(label, plot_width = NULL, pre_output = NULL, post_output = NULL, - decorators = NULL) { + transformators = list(), + decorators = list()) { message("Initializing tm_g_km") checkmate::assert_string(label) @@ -397,7 +399,7 @@ tm_g_km <- function(label, checkmate::assert_class(pre_output, classes = "shiny.tag", null.ok = TRUE) checkmate::assert_class(post_output, classes = "shiny.tag", null.ok = TRUE) decorators <- normalize_decorators(decorators) - assert_decorators(decorators, "plot", null.ok = TRUE) + assert_decorators(decorators, "plot") args <- as.list(environment()) data_extract_list <- list( @@ -430,6 +432,7 @@ tm_g_km <- function(label, decorators = decorators ) ), + transformators = transformators, datanames = teal.transform::get_extract_datanames(data_extract_list) ) } diff --git a/R/tm_g_lineplot.R b/R/tm_g_lineplot.R index 9cead8485..14a53dc00 100644 --- a/R/tm_g_lineplot.R +++ b/R/tm_g_lineplot.R @@ -210,6 +210,7 @@ template_g_lineplot <- function(dataname = "ANL", #' This module produces a [ggplot2::ggplot()] type line plot, with optional summary table, for standard ADaM data. #' #' @inheritParams module_arguments +#' @inheritParams teal::module #' @inheritParams template_g_lineplot #' #' @inherit module_arguments return seealso @@ -307,7 +308,8 @@ tm_g_lineplot <- function(label, pre_output = NULL, post_output = NULL, ggplot2_args = teal.widgets::ggplot2_args(), - decorators = NULL) { + transformators = list(), + decorators = list()) { if (lifecycle::is_present(strata)) { warning( "The `strata` argument of `tm_g_lineplot()` is deprecated as of teal.modules.clinical 0.9.1. ", @@ -348,7 +350,7 @@ tm_g_lineplot <- function(label, checkmate::assert_class(ggplot2_args, "ggplot2_args") decorators <- normalize_decorators(decorators) - assert_decorators(decorators, "plot", null.ok = TRUE) + assert_decorators(decorators, "plot") args <- as.list(environment()) data_extract_list <- list( @@ -377,6 +379,7 @@ tm_g_lineplot <- function(label, decorators = decorators ) ), + transformators = transformators, datanames = teal.transform::get_extract_datanames(data_extract_list) ) } diff --git a/R/tm_g_pp_adverse_events.R b/R/tm_g_pp_adverse_events.R index 674827b11..e60f6dc31 100644 --- a/R/tm_g_pp_adverse_events.R +++ b/R/tm_g_pp_adverse_events.R @@ -165,6 +165,7 @@ template_adverse_events <- function(dataname = "ANL", #' This module produces an adverse events table and [ggplot2::ggplot()] type plot using ADaM datasets. #' #' @inheritParams module_arguments +#' @inheritParams teal::module #' @inheritParams template_adverse_events #' @param aeterm ([teal.transform::choices_selected()])\cr object with all #' available choices and preselected option for the `AETERM` variable from `dataname`. @@ -287,7 +288,8 @@ tm_g_pp_adverse_events <- function(label, pre_output = NULL, post_output = NULL, ggplot2_args = teal.widgets::ggplot2_args(), - decorators = NULL) { + transformators = list(), + decorators = list()) { message("Initializing tm_g_pp_adverse_events") checkmate::assert_string(label) checkmate::assert_string(dataname) @@ -313,7 +315,7 @@ tm_g_pp_adverse_events <- function(label, checkmate::assert_class(post_output, classes = "shiny.tag", null.ok = TRUE) checkmate::assert_class(ggplot2_args, "ggplot2_args") decorators <- normalize_decorators(decorators) - assert_decorators(decorators, names = c("plot", "table"), null.ok = TRUE) + assert_decorators(decorators, names = c("plot", "table")) args <- as.list(environment()) data_extract_list <- list( @@ -344,6 +346,7 @@ tm_g_pp_adverse_events <- function(label, decorators = decorators ) ), + transformators = transformators, datanames = c(dataname, parentname) ) } diff --git a/R/tm_g_pp_patient_timeline.R b/R/tm_g_pp_patient_timeline.R index a451c3663..350344609 100644 --- a/R/tm_g_pp_patient_timeline.R +++ b/R/tm_g_pp_patient_timeline.R @@ -323,6 +323,7 @@ template_patient_timeline <- function(dataname = "ANL", #' #' @inheritParams tm_g_pp_adverse_events #' @inheritParams module_arguments +#' @inheritParams teal::module #' @inheritParams template_patient_timeline #' @param dataname_adcm (`character`)\cr name of `ADCM` dataset or equivalent. #' @param dataname_adae (`character`)\cr name of `ADAE` dataset or equivalent. @@ -471,7 +472,8 @@ tm_g_pp_patient_timeline <- function(label, pre_output = NULL, post_output = NULL, ggplot2_args = teal.widgets::ggplot2_args(), - decorators = NULL) { + transformators = list(), + decorators = list()) { message("Initializing tm_g_pp_patient_timeline") checkmate::assert_string(label) checkmate::assert_string(dataname_adcm) @@ -498,7 +500,7 @@ tm_g_pp_patient_timeline <- function(label, lower = plot_width[2], upper = plot_width[3], null.ok = TRUE, .var.name = "plot_width" ) decorators <- normalize_decorators(decorators) - assert_decorators(decorators, "plot", null.ok = TRUE) + assert_decorators(decorators, "plot") xor_error_string <- function(x, y) { paste( @@ -559,6 +561,7 @@ tm_g_pp_patient_timeline <- function(label, decorators = decorators ) ), + transformators = transformators, datanames = c(dataname_adcm, dataname_adae, parentname) ) } diff --git a/R/tm_g_pp_therapy.R b/R/tm_g_pp_therapy.R index 7a40b5088..c51de8ccd 100644 --- a/R/tm_g_pp_therapy.R +++ b/R/tm_g_pp_therapy.R @@ -228,6 +228,7 @@ template_therapy <- function(dataname = "ANL", #' This module produces a patient profile therapy table and [ggplot2::ggplot()] type plot using ADaM datasets. #' #' @inheritParams module_arguments +#' @inheritParams teal::module #' @inheritParams template_therapy #' @param cmdose ([teal.transform::choices_selected()])\cr object with all #' available choices and preselected option for the `CMDOSE` variable from `dataname`. @@ -370,7 +371,8 @@ tm_g_pp_therapy <- function(label, pre_output = NULL, post_output = NULL, ggplot2_args = teal.widgets::ggplot2_args(), - decorators = NULL) { + transformators = list(), + decorators = list()) { message("Initializing tm_g_pp_therapy") checkmate::assert_class(atirel, "choices_selected", null.ok = TRUE) checkmate::assert_class(cmdecod, "choices_selected", null.ok = TRUE) @@ -399,7 +401,7 @@ tm_g_pp_therapy <- function(label, checkmate::assert_class(post_output, classes = "shiny.tag", null.ok = TRUE) checkmate::assert_class(ggplot2_args, "ggplot2_args") decorators <- normalize_decorators(decorators) - assert_decorators(decorators, names = c("plot", "table"), null.ok = TRUE) + assert_decorators(decorators, names = c("plot", "table")) args <- as.list(environment()) data_extract_list <- list( @@ -433,6 +435,7 @@ tm_g_pp_therapy <- function(label, decorators = decorators ) ), + transformators = transformators, datanames = c(dataname, parentname) ) } diff --git a/R/tm_g_pp_vitals.R b/R/tm_g_pp_vitals.R index 9598cb633..02f918272 100644 --- a/R/tm_g_pp_vitals.R +++ b/R/tm_g_pp_vitals.R @@ -203,6 +203,7 @@ template_vitals <- function(dataname = "ANL", #' `"SYSBP"`, `"DIABP"`, `"TEMP"`, `"RESP"`, `"OXYSAT"`. #' #' @inheritParams module_arguments +#' @inheritParams teal::module #' @inheritParams template_vitals #' @param xaxis ([teal.transform::choices_selected()])\cr object with all #' available choices and preselected option for the time variable from `dataname` to be put on the plot x-axis. @@ -279,7 +280,8 @@ tm_g_pp_vitals <- function(label, pre_output = NULL, post_output = NULL, ggplot2_args = teal.widgets::ggplot2_args(), - decorators = NULL) { + transformators = list(), + decorators = list()) { if (lifecycle::is_present(aval)) { aval_var <- aval warning( @@ -315,7 +317,7 @@ tm_g_pp_vitals <- function(label, checkmate::assert_multi_class(aval_var, c("choices_selected", "data_extract_spec"), null.ok = TRUE) checkmate::assert_multi_class(xaxis, c("choices_selected", "data_extract_spec"), null.ok = TRUE) decorators <- normalize_decorators(decorators) - assert_decorators(decorators, null.ok = TRUE, "plot") + assert_decorators(decorators, "plot") args <- as.list(environment()) data_extract_list <- list( @@ -342,6 +344,7 @@ tm_g_pp_vitals <- function(label, decorators = decorators ) ), + transformators = transformators, datanames = c(dataname, parentname) ) } diff --git a/R/tm_t_abnormality.R b/R/tm_t_abnormality.R index 7874ca4df..d8b0debd5 100644 --- a/R/tm_t_abnormality.R +++ b/R/tm_t_abnormality.R @@ -225,6 +225,7 @@ template_abnormality <- function(parentname, #' This module produces a table to summarize abnormality. #' #' @inheritParams module_arguments +#' @inheritParams teal::module #' @inheritParams template_abnormality #' @param grade ([teal.transform::choices_selected()])\cr #' object with all available choices and preselected option for variable names that can be used to @@ -338,7 +339,8 @@ tm_t_abnormality <- function(label, post_output = NULL, na_level = default_na_str(), basic_table_args = teal.widgets::basic_table_args(), - decorators = NULL) { + transformators = list(), + decorators = list()) { message("Initializing tm_t_abnormality") checkmate::assert_string(label) checkmate::assert_string(dataname) @@ -360,7 +362,7 @@ tm_t_abnormality <- function(label, checkmate::assert_class(post_output, classes = "shiny.tag", null.ok = TRUE) checkmate::assert_class(basic_table_args, "basic_table_args") decorators <- normalize_decorators(decorators) - assert_decorators(decorators, "table", null.ok = TRUE) + assert_decorators(decorators, "table") data_extract_list <- list( arm_var = cs_to_des_select(arm_var, dataname = parentname), @@ -392,6 +394,7 @@ tm_t_abnormality <- function(label, decorators = decorators ) ), + transformators = transformators, datanames = teal.transform::get_extract_datanames(data_extract_list) ) } diff --git a/R/tm_t_abnormality_by_worst_grade.R b/R/tm_t_abnormality_by_worst_grade.R index 2caca1588..2aa6a2805 100644 --- a/R/tm_t_abnormality_by_worst_grade.R +++ b/R/tm_t_abnormality_by_worst_grade.R @@ -234,6 +234,7 @@ template_abnormality_by_worst_grade <- function(parentname, # nolint: object_len #' This module produces a table to summarize laboratory test results with highest grade post-baseline #' @inheritParams module_arguments +#' @inheritParams teal::module #' @inheritParams template_abnormality_by_worst_grade #' @param atoxgr_var ([teal.transform::choices_selected()])\cr #' object with all available choices and preselected option @@ -347,7 +348,8 @@ tm_t_abnormality_by_worst_grade <- function(label, # nolint: object_length. pre_output = NULL, post_output = NULL, basic_table_args = teal.widgets::basic_table_args(), - decorators = NULL) { + transformators = list(), + decorators = list()) { message("Initializing tm_t_abnormality_by_worst_grade") checkmate::assert_string(label) checkmate::assert_string(dataname) @@ -364,7 +366,7 @@ tm_t_abnormality_by_worst_grade <- function(label, # nolint: object_length. checkmate::assert_class(post_output, classes = "shiny.tag", null.ok = TRUE) checkmate::assert_class(basic_table_args, "basic_table_args") decorators <- normalize_decorators(decorators) - assert_decorators(decorators, null.ok = TRUE, "table") + assert_decorators(decorators, "table") data_extract_list <- list( arm_var = cs_to_des_select(arm_var, dataname = parentname), @@ -394,6 +396,7 @@ tm_t_abnormality_by_worst_grade <- function(label, # nolint: object_length. decorators = decorators ) ), + transformators = transformators, datanames = teal.transform::get_extract_datanames(data_extract_list) ) } diff --git a/R/tm_t_ancova.R b/R/tm_t_ancova.R index 16c4c56a9..a9051599b 100644 --- a/R/tm_t_ancova.R +++ b/R/tm_t_ancova.R @@ -420,6 +420,7 @@ template_ancova <- function(dataname = "ANL", #' endpoints are selected. #' #' @inheritParams module_arguments +#' @inheritParams teal::module #' @inheritParams template_ancova #' #' @inherit module_arguments return @@ -528,7 +529,8 @@ tm_t_ancova <- function(label, pre_output = NULL, post_output = NULL, basic_table_args = teal.widgets::basic_table_args(), - decorators = NULL) { + transformators = list(), + decorators = list()) { message("Initializing tm_t_ancova") checkmate::assert_string(label) checkmate::assert_string(dataname) @@ -543,7 +545,7 @@ tm_t_ancova <- function(label, checkmate::assert_class(post_output, classes = "shiny.tag", null.ok = TRUE) checkmate::assert_class(basic_table_args, "basic_table_args") decorators <- normalize_decorators(decorators) - assert_decorators(decorators, null.ok = TRUE, "table") + assert_decorators(decorators, "table") args <- c(as.list(environment())) @@ -580,6 +582,7 @@ tm_t_ancova <- function(label, decorators = decorators ) ), + transformators = transformators, datanames = teal.transform::get_extract_datanames(data_extract_list) ) } diff --git a/R/tm_t_binary_outcome.R b/R/tm_t_binary_outcome.R index f17f8d012..6b8fea079 100644 --- a/R/tm_t_binary_outcome.R +++ b/R/tm_t_binary_outcome.R @@ -328,6 +328,7 @@ template_binary_outcome <- function(dataname, #' https://insightsengineering.github.io/tlg-catalog/stable/tables/efficacy/rspt01.html). #' #' @inheritParams module_arguments +#' @inheritParams teal::module #' @inheritParams template_binary_outcome #' @param rsp_table (`logical`)\cr whether the initial set-up of the module should match `RSPT01`. Defaults to `FALSE`. #' @param control (named `list`)\cr named list containing 3 named lists as follows: @@ -472,7 +473,8 @@ tm_t_binary_outcome <- function(label, pre_output = NULL, post_output = NULL, basic_table_args = teal.widgets::basic_table_args(), - decorators = NULL) { + transformators = list(), + decorators = list()) { message("Initializing tm_t_binary_outcome") checkmate::assert_string(label) checkmate::assert_string(dataname) @@ -513,7 +515,7 @@ tm_t_binary_outcome <- function(label, ) checkmate::assert_subset(control$strat$method_test, c("cmh")) decorators <- normalize_decorators(decorators) - assert_decorators(decorators, "table", null.ok = TRUE) + assert_decorators(decorators, "table") args <- as.list(environment()) @@ -545,6 +547,7 @@ tm_t_binary_outcome <- function(label, decorators = decorators ) ), + transformators = transformators, datanames = teal.transform::get_extract_datanames(data_extract_list) ) } diff --git a/R/tm_t_coxreg.R b/R/tm_t_coxreg.R index 5ad7fd125..d42f1f3b8 100644 --- a/R/tm_t_coxreg.R +++ b/R/tm_t_coxreg.R @@ -332,6 +332,7 @@ template_coxreg_m <- function(dataname, #' and `COXT02` [here](https://insightsengineering.github.io/tlg-catalog/stable/tables/efficacy/coxt02.html). #' #' @inheritParams module_arguments +#' @inheritParams teal::module #' @inheritParams template_coxreg_u #' @inheritParams template_coxreg_m #' @param multivariate (`logical`)\cr if `FALSE`, the univariable approach is used instead of the @@ -528,7 +529,8 @@ tm_t_coxreg <- function(label, pre_output = NULL, post_output = NULL, basic_table_args = teal.widgets::basic_table_args(), - decorators = NULL) { + transformators = list(), + decorators = list()) { message("Initializing tm_t_coxreg") checkmate::assert_string(label) checkmate::assert_string(dataname) @@ -545,7 +547,7 @@ tm_t_coxreg <- function(label, checkmate::assert_class(post_output, classes = "shiny.tag", null.ok = TRUE) checkmate::assert_class(basic_table_args, "basic_table_args") decorators <- normalize_decorators(decorators) - assert_decorators(decorators, "table", null.ok = TRUE) + assert_decorators(decorators, "table") args <- as.list(environment()) @@ -575,6 +577,7 @@ tm_t_coxreg <- function(label, decorators = decorators ) ), + transformators = transformators, datanames = teal.transform::get_extract_datanames(data_extract_list) ) } diff --git a/R/tm_t_events.R b/R/tm_t_events.R index 496d9b338..2283a6f71 100644 --- a/R/tm_t_events.R +++ b/R/tm_t_events.R @@ -452,6 +452,7 @@ template_events <- function(dataname, #' This module produces a table of events by term. #' #' @inheritParams module_arguments +#' @inheritParams teal::module #' @inheritParams template_events #' @param arm_var ([teal.transform::choices_selected()])\cr object with all #' available choices and preselected option for variable names that can be used as `arm_var`. @@ -533,7 +534,8 @@ tm_t_events <- function(label, pre_output = NULL, post_output = NULL, basic_table_args = teal.widgets::basic_table_args(), - decorators = NULL) { + transformators = list(), + decorators = list()) { message("Initializing tm_t_events") checkmate::assert_string(label) checkmate::assert_string(dataname) @@ -555,7 +557,7 @@ tm_t_events <- function(label, checkmate::assert_class(post_output, classes = "shiny.tag", null.ok = TRUE) checkmate::assert_class(basic_table_args, "basic_table_args") decorators <- normalize_decorators(decorators) - assert_decorators(decorators, "table", null.ok = TRUE) + assert_decorators(decorators, "table") args <- as.list(environment()) @@ -585,6 +587,7 @@ tm_t_events <- function(label, decorators = decorators ) ), + transformators = transformators, datanames = teal.transform::get_extract_datanames(data_extract_list) ) } diff --git a/R/tm_t_events_by_grade.R b/R/tm_t_events_by_grade.R index 8e99ee1ac..d801f6f3a 100644 --- a/R/tm_t_events_by_grade.R +++ b/R/tm_t_events_by_grade.R @@ -773,6 +773,7 @@ template_events_col_by_grade <- function(dataname, #' This module produces a table to summarize events by grade. #' #' @inheritParams module_arguments +#' @inheritParams teal::module #' @inheritParams template_events_by_grade #' @inheritParams template_events_col_by_grade #' @param col_by_grade (`logical`)\cr whether to display the grading groups in nested columns. @@ -863,7 +864,8 @@ tm_t_events_by_grade <- function(label, pre_output = NULL, post_output = NULL, basic_table_args = teal.widgets::basic_table_args(), - decorators = NULL) { + transformators = list(), + decorators = list()) { message("Initializing tm_t_events_by_grade") checkmate::assert_string(label) checkmate::assert_string(dataname) @@ -882,7 +884,7 @@ tm_t_events_by_grade <- function(label, checkmate::assert_class(post_output, classes = "shiny.tag", null.ok = TRUE) checkmate::assert_class(basic_table_args, "basic_table_args") decorators <- normalize_decorators(decorators) - assert_decorators(decorators, "table", null.ok = TRUE) + assert_decorators(decorators, "table") args <- as.list(environment()) @@ -911,6 +913,7 @@ tm_t_events_by_grade <- function(label, decorators = decorators ) ), + transformators = transformators, datanames = teal.transform::get_extract_datanames(data_extract_list) ) } diff --git a/R/tm_t_events_patyear.R b/R/tm_t_events_patyear.R index b42e92313..620b0f8da 100644 --- a/R/tm_t_events_patyear.R +++ b/R/tm_t_events_patyear.R @@ -181,6 +181,7 @@ template_events_patyear <- function(dataname, #' This module produces a table of event rates adjusted for patient-years. #' #' @inheritParams module_arguments +#' @inheritParams teal::module #' @inheritParams template_events_patyear #' @param arm_var ([teal.transform::choices_selected()])\cr object with all #' available choices and preselected option for variable names that can be used as `arm_var`. @@ -319,7 +320,8 @@ tm_t_events_patyear <- function(label, pre_output = NULL, post_output = NULL, basic_table_args = teal.widgets::basic_table_args(), - decorators = NULL) { + transformators = list(), + decorators = list()) { message("Initializing tm_t_events_patyear") checkmate::assert_string(label) checkmate::assert_string(dataname) @@ -338,7 +340,7 @@ tm_t_events_patyear <- function(label, checkmate::assert_class(post_output, classes = "shiny.tag", null.ok = TRUE) checkmate::assert_class(basic_table_args, "basic_table_args") decorators <- normalize_decorators(decorators) - assert_decorators(decorators, "table", null.ok = TRUE) + assert_decorators(decorators, "table") args <- c(as.list(environment())) @@ -367,6 +369,7 @@ tm_t_events_patyear <- function(label, decorators = decorators ) ), + transformators = transformators, datanames = teal.transform::get_extract_datanames(data_extract_list) ) } diff --git a/R/tm_t_events_summary.R b/R/tm_t_events_summary.R index 3ffa8b6f0..5de732c9a 100644 --- a/R/tm_t_events_summary.R +++ b/R/tm_t_events_summary.R @@ -497,6 +497,7 @@ template_events_summary <- function(anl_name, #' This module produces an adverse events summary table. #' #' @inheritParams module_arguments +#' @inheritParams teal::module #' @inheritParams template_arguments #' @inheritParams template_events_summary #' @param arm_var ([teal.transform::choices_selected()])\cr object with all @@ -647,7 +648,8 @@ tm_t_events_summary <- function(label, pre_output = NULL, post_output = NULL, basic_table_args = teal.widgets::basic_table_args(), - decorators = NULL) { + transformators = list(), + decorators = list()) { message("Initializing tm_t_events_summary") checkmate::assert_string(label) checkmate::assert_string(dataname) @@ -671,7 +673,7 @@ tm_t_events_summary <- function(label, checkmate::assert_class(post_output, classes = "shiny.tag", null.ok = TRUE) checkmate::assert_class(basic_table_args, "basic_table_args") decorators <- normalize_decorators(decorators) - assert_decorators(decorators, "table", null.ok = TRUE) + assert_decorators(decorators, "table") args <- c(as.list(environment())) @@ -710,6 +712,7 @@ tm_t_events_summary <- function(label, decorators = decorators ) ), + transformators = transformators, datanames = teal.transform::get_extract_datanames(data_extract_list) ) } diff --git a/R/tm_t_exposure.R b/R/tm_t_exposure.R index 0ac3a4d93..35b28ccb5 100644 --- a/R/tm_t_exposure.R +++ b/R/tm_t_exposure.R @@ -211,6 +211,7 @@ template_exposure <- function(parentname, #' The module produces an exposure table for risk management plan. #' #' @inheritParams module_arguments +#' @inheritParams teal::module #' @inheritParams template_exposure #' @param row_by_var ([teal.transform::choices_selected()])\cr #' object with all available choices and preselected option for @@ -332,7 +333,8 @@ tm_t_exposure <- function(label, pre_output = NULL, post_output = NULL, basic_table_args = teal.widgets::basic_table_args(), - decorators = NULL) { + transformators = list(), + decorators = list()) { message("Initializing tm_t_exposure") checkmate::assert_string(label) checkmate::assert_string(dataname) @@ -353,7 +355,7 @@ tm_t_exposure <- function(label, checkmate::assert_class(post_output, classes = "shiny.tag", null.ok = TRUE) checkmate::assert_class(basic_table_args, "basic_table_args") decorators <- normalize_decorators(decorators) - assert_decorators(decorators, "table", null.ok = TRUE) + assert_decorators(decorators, "table") data_extract_list <- list( paramcd = cs_to_des_filter(paramcd, dataname = dataname), @@ -385,6 +387,7 @@ tm_t_exposure <- function(label, decorators = decorators ) ), + transformators = transformators, datanames = teal.transform::get_extract_datanames(data_extract_list) ) } diff --git a/R/tm_t_logistic.R b/R/tm_t_logistic.R index 40563a000..d7ac1a23f 100644 --- a/R/tm_t_logistic.R +++ b/R/tm_t_logistic.R @@ -210,6 +210,7 @@ template_logistic <- function(dataname, #' `LGRT02` available [here](https://insightsengineering.github.io/tlg-catalog/stable/tables/efficacy/lgrt02.html). #' #' @inheritParams module_arguments +#' @inheritParams teal::module #' @inheritParams template_logistic #' @param arm_var ([teal.transform::choices_selected()] or `NULL`)\cr object #' with all available choices and preselected option for variable names that can be used as `arm_var`. This defines @@ -305,7 +306,8 @@ tm_t_logistic <- function(label, pre_output = NULL, post_output = NULL, basic_table_args = teal.widgets::basic_table_args(), - decorators = NULL) { + transformators = list(), + decorators = list()) { message("Initializing tm_t_logistic") checkmate::assert_string(label) checkmate::assert_string(dataname) @@ -320,7 +322,7 @@ tm_t_logistic <- function(label, checkmate::assert_class(post_output, classes = "shiny.tag", null.ok = TRUE) checkmate::assert_class(basic_table_args, "basic_table_args") decorators <- normalize_decorators(decorators) - assert_decorators(decorators, null.ok = TRUE, "table") + assert_decorators(decorators, "table") args <- as.list(environment()) @@ -347,6 +349,7 @@ tm_t_logistic <- function(label, decorators = decorators ) ), + transformators = transformators, datanames = teal.transform::get_extract_datanames(data_extract_list) ) } diff --git a/R/tm_t_mult_events.R b/R/tm_t_mult_events.R index 4ba2dacb5..96a00fd0b 100644 --- a/R/tm_t_mult_events.R +++ b/R/tm_t_mult_events.R @@ -275,6 +275,7 @@ template_mult_events <- function(dataname, #' This module produces a table of multiple events by term. #' #' @inheritParams module_arguments +#' @inheritParams teal::module #' @inheritParams template_mult_events #' @param seq_var ([teal.transform::choices_selected()])\cr object with #' all available choices and preselected option for variable names that can be used as analysis sequence number @@ -353,7 +354,8 @@ tm_t_mult_events <- function(label, pre_output = NULL, post_output = NULL, basic_table_args = teal.widgets::basic_table_args(), - decorators = NULL) { + transformators = list(), + decorators = list()) { message("Initializing tm_t_mult_events") checkmate::assert_string(label) checkmate::assert_string(dataname) @@ -371,7 +373,7 @@ tm_t_mult_events <- function(label, checkmate::assert_class(post_output, classes = "shiny.tag", null.ok = TRUE) checkmate::assert_class(basic_table_args, "basic_table_args") decorators <- normalize_decorators(decorators) - assert_decorators(decorators, null.ok = TRUE, "table") + assert_decorators(decorators, "table") args <- as.list(environment()) @@ -400,6 +402,7 @@ tm_t_mult_events <- function(label, decorators = decorators ) ), + transformators = transformators, datanames = teal.transform::get_extract_datanames(data_extract_list) ) } diff --git a/R/tm_t_pp_basic_info.R b/R/tm_t_pp_basic_info.R index 609caddb1..3d8ff9cb9 100644 --- a/R/tm_t_pp_basic_info.R +++ b/R/tm_t_pp_basic_info.R @@ -58,6 +58,7 @@ template_basic_info <- function(dataname = "ANL", #' This module produces a patient profile basic info report using ADaM datasets. #' #' @inheritParams module_arguments +#' @inheritParams teal::module #' @inheritParams template_basic_info #' @param vars ([teal.transform::choices_selected()])\cr object with all #' available choices and preselected option for variables from `dataname` to show in the table. @@ -111,7 +112,8 @@ tm_t_pp_basic_info <- function(label, vars = NULL, pre_output = NULL, post_output = NULL, - decorators = NULL) { + transformators = list(), + decorators = list()) { message("Initializing tm_t_pp_basic_info") checkmate::assert_string(label) checkmate::assert_string(dataname) @@ -120,7 +122,7 @@ tm_t_pp_basic_info <- function(label, checkmate::assert_class(pre_output, classes = "shiny.tag", null.ok = TRUE) checkmate::assert_class(post_output, classes = "shiny.tag", null.ok = TRUE) decorators <- normalize_decorators(decorators) - assert_decorators(decorators, null.ok = TRUE, "table") + assert_decorators(decorators, "table") args <- as.list(environment()) data_extract_list <- list( @@ -141,6 +143,7 @@ tm_t_pp_basic_info <- function(label, decorators = decorators ) ), + transformators = transformators, datanames = dataname ) } diff --git a/R/tm_t_pp_laboratory.R b/R/tm_t_pp_laboratory.R index c0a268e8a..8ff251a27 100644 --- a/R/tm_t_pp_laboratory.R +++ b/R/tm_t_pp_laboratory.R @@ -142,6 +142,7 @@ template_laboratory <- function(dataname = "ANL", #' This module produces a patient profile laboratory table using ADaM datasets. #' #' @inheritParams module_arguments +#' @inheritParams teal::module #' @inheritParams template_laboratory #' @param param ([teal.transform::choices_selected()])\cr object with all #' available choices and preselected option for the `PARAM` variable from `dataname`. @@ -230,7 +231,8 @@ tm_t_pp_laboratory <- function(label, anrind = NULL, pre_output = NULL, post_output = NULL, - decorators = NULL) { + transformators = list(), + decorators = list()) { if (lifecycle::is_present(aval)) { aval_var <- aval warning( @@ -267,7 +269,7 @@ tm_t_pp_laboratory <- function(label, checkmate::assert_class(pre_output, classes = "shiny.tag", null.ok = TRUE) checkmate::assert_class(post_output, classes = "shiny.tag", null.ok = TRUE) decorators <- normalize_decorators(decorators) - assert_decorators(decorators, null.ok = TRUE, "table") + assert_decorators(decorators, "table") args <- as.list(environment()) data_extract_list <- list( @@ -294,6 +296,7 @@ tm_t_pp_laboratory <- function(label, decorators = decorators ) ), + transformators = transformators, datanames = c(dataname, parentname) ) } diff --git a/R/tm_t_pp_medical_history.R b/R/tm_t_pp_medical_history.R index 881e77725..243e25273 100644 --- a/R/tm_t_pp_medical_history.R +++ b/R/tm_t_pp_medical_history.R @@ -77,6 +77,7 @@ template_medical_history <- function(dataname = "ANL", #' This module produces a patient profile medical history report using ADaM datasets. #' #' @inheritParams module_arguments +#' @inheritParams teal::module #' @inheritParams template_medical_history #' @param mhterm ([teal.transform::choices_selected()])\cr object with all #' available choices and preselected option for the `MHTERM` variable from `dataname`. @@ -147,7 +148,8 @@ tm_t_pp_medical_history <- function(label, mhdistat = NULL, pre_output = NULL, post_output = NULL, - decorators = NULL) { + transformators = list(), + decorators = list()) { message("Initializing tm_t_pp_medical_history") checkmate::assert_string(label) checkmate::assert_string(dataname) @@ -159,7 +161,7 @@ tm_t_pp_medical_history <- function(label, checkmate::assert_class(pre_output, classes = "shiny.tag", null.ok = TRUE) checkmate::assert_class(post_output, classes = "shiny.tag", null.ok = TRUE) decorators <- normalize_decorators(decorators) - assert_decorators(decorators, null.ok = TRUE, "table") + assert_decorators(decorators, "table") args <- as.list(environment()) data_extract_list <- list( @@ -183,6 +185,7 @@ tm_t_pp_medical_history <- function(label, decorators = decorators ) ), + transformators = transformators, datanames = c(dataname, parentname) ) } diff --git a/R/tm_t_pp_prior_medication.R b/R/tm_t_pp_prior_medication.R index ee502da99..b7bcb573e 100644 --- a/R/tm_t_pp_prior_medication.R +++ b/R/tm_t_pp_prior_medication.R @@ -64,6 +64,7 @@ template_prior_medication <- function(dataname = "ANL", #' This module produces a patient profile prior medication report using ADaM datasets. #' #' @inheritParams module_arguments +#' @inheritParams teal::module #' @inheritParams template_prior_medication #' #' @inherit module_arguments return @@ -139,7 +140,8 @@ tm_t_pp_prior_medication <- function(label, cmstdy = NULL, pre_output = NULL, post_output = NULL, - decorators = NULL) { + transformators = list(), + decorators = list()) { message("Initializing tm_t_pp_prior_medication") checkmate::assert_string(label) checkmate::assert_string(dataname) @@ -152,7 +154,7 @@ tm_t_pp_prior_medication <- function(label, checkmate::assert_class(pre_output, classes = "shiny.tag", null.ok = TRUE) checkmate::assert_class(post_output, classes = "shiny.tag", null.ok = TRUE) decorators <- normalize_decorators(decorators) - assert_decorators(decorators, null.ok = TRUE, "table") + assert_decorators(decorators, "table") args <- as.list(environment()) data_extract_list <- list( @@ -177,6 +179,7 @@ tm_t_pp_prior_medication <- function(label, decorators = decorators ) ), + transformators = transformators, datanames = c(dataname, parentname) ) } diff --git a/R/tm_t_shift_by_arm.R b/R/tm_t_shift_by_arm.R index 678bb81d0..92119e942 100644 --- a/R/tm_t_shift_by_arm.R +++ b/R/tm_t_shift_by_arm.R @@ -186,6 +186,7 @@ template_shift_by_arm <- function(dataname, #' This module produces a summary table of analysis indicator levels by arm. #' #' @inheritParams module_arguments +#' @inheritParams teal::module #' @inheritParams template_shift_by_arm #' #' @inherit module_arguments return seealso @@ -276,7 +277,8 @@ tm_t_shift_by_arm <- function(label, pre_output = NULL, post_output = NULL, basic_table_args = teal.widgets::basic_table_args(), - decorators = NULL) { + transformators = list(), + decorators = list()) { if (lifecycle::is_present(base_var)) { baseline_var <- base_var warning( @@ -306,7 +308,7 @@ tm_t_shift_by_arm <- function(label, checkmate::assert_class(post_output, classes = "shiny.tag", null.ok = TRUE) checkmate::assert_class(basic_table_args, "basic_table_args") decorators <- normalize_decorators(decorators) - assert_decorators(decorators, null.ok = TRUE, "table") + assert_decorators(decorators, "table") args <- as.list(environment()) @@ -337,6 +339,7 @@ tm_t_shift_by_arm <- function(label, decorators = decorators ) ), + transformators = transformators, datanames = teal.transform::get_extract_datanames(data_extract_list) ) } diff --git a/R/tm_t_shift_by_arm_by_worst.R b/R/tm_t_shift_by_arm_by_worst.R index 005d86bd0..ea2be9bcc 100644 --- a/R/tm_t_shift_by_arm_by_worst.R +++ b/R/tm_t_shift_by_arm_by_worst.R @@ -192,6 +192,7 @@ template_shift_by_arm_by_worst <- function(dataname, #' This module produces a summary table of worst analysis indicator variable level per subject by arm. #' #' @inheritParams module_arguments +#' @inheritParams teal::module #' @inheritParams template_shift_by_arm_by_worst #' #' @inherit module_arguments return @@ -286,7 +287,8 @@ tm_t_shift_by_arm_by_worst <- function(label, pre_output = NULL, post_output = NULL, basic_table_args = teal.widgets::basic_table_args(), - decorators = NULL) { + transformators = list(), + decorators = list()) { if (lifecycle::is_present(base_var)) { baseline_var <- base_var warning( @@ -316,7 +318,7 @@ tm_t_shift_by_arm_by_worst <- function(label, checkmate::assert_class(post_output, classes = "shiny.tag", null.ok = TRUE) checkmate::assert_class(basic_table_args, "basic_table_args") decorators <- normalize_decorators(decorators) - assert_decorators(decorators, null.ok = TRUE, "table") + assert_decorators(decorators, "table") args <- as.list(environment()) @@ -348,6 +350,7 @@ tm_t_shift_by_arm_by_worst <- function(label, decorators = decorators ) ), + transformators = transformators, datanames = teal.transform::get_extract_datanames(data_extract_list) ) } diff --git a/R/tm_t_shift_by_grade.R b/R/tm_t_shift_by_grade.R index 97256f3f6..b8512dfcb 100644 --- a/R/tm_t_shift_by_grade.R +++ b/R/tm_t_shift_by_grade.R @@ -463,6 +463,7 @@ template_shift_by_grade <- function(parentname, #' This module produces a summary table of worst grades per subject by visit and parameter. #' #' @inheritParams module_arguments +#' @inheritParams teal::module #' @inheritParams template_shift_by_grade #' @param anl_toxgrade_var ([teal.transform::choices_selected()])\cr #' variable for analysis toxicity grade. @@ -580,7 +581,8 @@ tm_t_shift_by_grade <- function(label, na_level = default_na_str(), code_missing_baseline = FALSE, basic_table_args = teal.widgets::basic_table_args(), - decorators = NULL) { + transformators = list(), + decorators = list()) { message("Initializing tm_t_shift_by_grade") checkmate::assert_string(label) checkmate::assert_string(dataname) @@ -602,7 +604,7 @@ tm_t_shift_by_grade <- function(label, checkmate::assert_class(post_output, classes = "shiny.tag", null.ok = TRUE) checkmate::assert_class(basic_table_args, "basic_table_args") decorators <- normalize_decorators(decorators) - assert_decorators(decorators, null.ok = TRUE, "table") + assert_decorators(decorators, "table") args <- as.list(environment()) @@ -633,6 +635,7 @@ tm_t_shift_by_grade <- function(label, decorators = decorators ) ), + transformators = transformators, datanames = teal.transform::get_extract_datanames(data_extract_list) ) } diff --git a/R/tm_t_smq.R b/R/tm_t_smq.R index b79251aca..9b4a9aeca 100644 --- a/R/tm_t_smq.R +++ b/R/tm_t_smq.R @@ -302,6 +302,7 @@ template_smq <- function(dataname, #' This module produces an adverse events table by Standardized MedDRA Query. #' #' @inheritParams module_arguments +#' @inheritParams teal::module #' @inheritParams template_smq #' @param arm_var ([teal.transform::choices_selected()])\cr object with all #' available choices and preselected option for variable names that can be used as `arm_var`. @@ -399,7 +400,8 @@ tm_t_smq <- function(label, pre_output = NULL, post_output = NULL, basic_table_args = teal.widgets::basic_table_args(), - decorators = NULL) { + transformators = list(), + decorators = list()) { message("Initializing tm_t_smq") checkmate::assert_string(label) checkmate::assert_string(dataname) @@ -417,7 +419,7 @@ tm_t_smq <- function(label, checkmate::assert_class(post_output, classes = "shiny.tag", null.ok = TRUE) checkmate::assert_class(basic_table_args, "basic_table_args") decorators <- normalize_decorators(decorators) - assert_decorators(decorators, null.ok = TRUE, "table") + assert_decorators(decorators, "table") args <- as.list(environment()) @@ -446,6 +448,7 @@ tm_t_smq <- function(label, decorators = decorators ) ), + transformators = transformators, datanames = teal.transform::get_extract_datanames(data_extract_list) ) } diff --git a/R/tm_t_summary.R b/R/tm_t_summary.R index c1f7b9f7d..b92cfdaa6 100644 --- a/R/tm_t_summary.R +++ b/R/tm_t_summary.R @@ -212,6 +212,7 @@ template_summary <- function(dataname, #' This module produces a table to summarize variables. #' #' @inheritParams module_arguments +#' @inheritParams teal::module #' @inheritParams template_summary #' @param arm_var ([teal.transform::choices_selected()])\cr object with all #' available choices and preselected option for variable names that can be used as `arm_var`. @@ -289,7 +290,8 @@ tm_t_summary <- function(label, pre_output = NULL, post_output = NULL, basic_table_args = teal.widgets::basic_table_args(), - decorators = NULL) { + transformators = list(), + decorators = list()) { message("Initializing tm_t_summary") checkmate::assert_string(label) checkmate::assert_string(dataname) @@ -306,7 +308,7 @@ tm_t_summary <- function(label, checkmate::assert_flag(show_arm_var_labels) checkmate::assert_string(total_label) decorators <- normalize_decorators(decorators) - assert_decorators(decorators, null.ok = TRUE, "table") + assert_decorators(decorators, "table") useNA <- match.arg(useNA) # nolint: object_name. denominator <- match.arg(denominator) @@ -337,6 +339,7 @@ tm_t_summary <- function(label, decorators = decorators ) ), + transformators = transformators, datanames = c(dataname, parentname) ) } diff --git a/R/tm_t_summary_by.R b/R/tm_t_summary_by.R index 49d1df798..ba17f3098 100644 --- a/R/tm_t_summary_by.R +++ b/R/tm_t_summary_by.R @@ -310,6 +310,7 @@ template_summary_by <- function(parentname, #' This module produces a table to summarize variables by row groups. #' #' @inheritParams module_arguments +#' @inheritParams teal::module #' @inheritParams template_summary_by #' @param arm_var ([teal.transform::choices_selected()])\cr object with all #' available choices and preselected option for variable names that can be used as `arm_var`. @@ -403,7 +404,8 @@ tm_t_summary_by <- function(label, pre_output = NULL, post_output = NULL, basic_table_args = teal.widgets::basic_table_args(), - decorators = NULL) { + transformators = list(), + decorators = list()) { message("Initializing tm_t_summary_by") checkmate::assert_string(label) checkmate::assert_string(dataname) @@ -432,7 +434,7 @@ tm_t_summary_by <- function(label, numeric_stats <- match.arg(numeric_stats, numeric_stats_choices, several.ok = TRUE) decorators <- normalize_decorators(decorators) - assert_decorators(decorators, null.ok = TRUE, "table") + assert_decorators(decorators, "table") args <- c(as.list(environment())) @@ -465,6 +467,7 @@ tm_t_summary_by <- function(label, decorators = decorators ) ), + transformators = transformators, datanames = teal.transform::get_extract_datanames(data_extract_list) ) } diff --git a/R/tm_t_tte.R b/R/tm_t_tte.R index dd63cde12..3c1944257 100644 --- a/R/tm_t_tte.R +++ b/R/tm_t_tte.R @@ -379,6 +379,7 @@ template_tte <- function(dataname = "ANL", #' https://insightsengineering.github.io/tlg-catalog/stable/tables/efficacy/ttet01.html). #' #' @inheritParams module_arguments +#' @inheritParams teal::module #' @inheritParams template_tte #' @param conf_level_coxph ([teal.transform::choices_selected()])\cr object with all available choices and #' pre-selected option for confidence level, each within range of (0, 1). @@ -501,7 +502,8 @@ tm_t_tte <- function(label, pre_output = NULL, post_output = NULL, basic_table_args = teal.widgets::basic_table_args(), - decorators = NULL) { + transformators = list(), + decorators = list()) { message("Initializing tm_t_tte") checkmate::assert_string(label) checkmate::assert_string(dataname) @@ -522,7 +524,7 @@ tm_t_tte <- function(label, checkmate::assert_class(post_output, classes = "shiny.tag", null.ok = TRUE) checkmate::assert_class(basic_table_args, "basic_table_args") decorators <- normalize_decorators(decorators) - assert_decorators(decorators, null.ok = TRUE, "table") + assert_decorators(decorators, "table") args <- as.list(environment()) @@ -554,6 +556,7 @@ tm_t_tte <- function(label, decorators = decorators ) ), + transformators = transformators, datanames = teal.transform::get_extract_datanames(data_extract_list) ) } diff --git a/R/utils.R b/R/utils.R index be2e38125..e92ef63bb 100644 --- a/R/utils.R +++ b/R/utils.R @@ -1003,18 +1003,22 @@ ui_decorate_teal_data <- function(id, decorators, ...) { #' Internal function to check if decorators is a valid object #' @noRd -check_decorators <- function(x, names = NULL, null.ok = FALSE) { # nolint: object_name. - checkmate::qassert(null.ok, "B1") +check_decorators <- function(x, names = NULL) { # nolint: object_name. - check_message <- checkmate::check_list( - x, - null.ok = null.ok, - names = "named" - ) + check_message <- checkmate::check_list(x, names = "named") if (!is.null(names)) { check_message <- if (isTRUE(check_message)) { out_message <- checkmate::check_names(names(x), subset.of = c("default", names)) + if (length(names(x)) != length(unique(names(x)))) { + unique_message <- "Non-unique names in decorators" + if (isTRUE(out_message)) { + out_message <- unique_message + } else { + out_message <- paste0(out_message, ". Also, ", tolower(unique_message)) + } + } + # see https://github.com/insightsengineering/teal.logger/issues/101 if (isTRUE(out_message)) { out_message @@ -1034,7 +1038,6 @@ check_decorators <- function(x, names = NULL, null.ok = FALSE) { # nolint: objec x, checkmate::test_list, types = "teal_transform_module", - null.ok = TRUE, FUN.VALUE = logical(1L) ) @@ -1072,7 +1075,7 @@ select_decorators <- function(decorators, scope) { #' @return A named list of lists with `teal_transform_module` objects. #' @keywords internal normalize_decorators <- function(decorators) { - if (checkmate::test_list(decorators, "teal_transform_module", null.ok = TRUE)) { + if (checkmate::test_list(decorators, "teal_transform_module")) { if (checkmate::test_names(names(decorators))) { lapply(decorators, list) } else { diff --git a/man/module_arguments.Rd b/man/module_arguments.Rd index d21b1100b..bd7e6165c 100644 --- a/man/module_arguments.Rd +++ b/man/module_arguments.Rd @@ -135,8 +135,8 @@ value indicating worst grade.} with all available choices and preselected option for variable names that can be used as worst flag variable.} \item{decorators}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#experimental}{\figure{lifecycle-experimental.svg}{options: alt='[Experimental]'}}}{\strong{[Experimental]}} -" (\code{list} of \code{teal_transform_module}, named \code{list} of \code{teal_transform_module} or" \code{NULL}) optional, -if not \code{NULL}, decorator for tables or plots included in the module. +(\code{list} of \code{teal_transform_module}, named \code{list} of \code{teal_transform_module}) optional, +decorator for tables or plots included in the module output reported. When a named list of \code{teal_transform_module}, the decorators are applied to the respective output objects. Otherwise, the decorators are applied to all objects, which is equivalent as using the name \code{default}. diff --git a/man/tm_a_gee.Rd b/man/tm_a_gee.Rd index 1ddd4d6b8..9f5cb2df2 100644 --- a/man/tm_a_gee.Rd +++ b/man/tm_a_gee.Rd @@ -21,7 +21,8 @@ tm_a_gee( pre_output = NULL, post_output = NULL, basic_table_args = teal.widgets::basic_table_args(), - decorators = NULL + transformators = list(), + decorators = list() ) } \arguments{ @@ -71,9 +72,12 @@ with settings for the module table. The argument is merged with option \code{tea module arguments (hard coded in the module body). For more details, see the vignette: \code{vignette("custom-basic-table-arguments", package = "teal.widgets")}.} +\item{transformators}{(\code{list} of \code{teal_transform_module}) that will be applied to transform module's data input. +To learn more check \code{vignette("data-transform-as-shiny-module", package = "teal")}.} + \item{decorators}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#experimental}{\figure{lifecycle-experimental.svg}{options: alt='[Experimental]'}}}{\strong{[Experimental]}} -" (\code{list} of \code{teal_transform_module}, named \code{list} of \code{teal_transform_module} or" \code{NULL}) optional, -if not \code{NULL}, decorator for tables or plots included in the module. +(\code{list} of \code{teal_transform_module}, named \code{list} of \code{teal_transform_module}) optional, +decorator for tables or plots included in the module output reported. When a named list of \code{teal_transform_module}, the decorators are applied to the respective output objects. Otherwise, the decorators are applied to all objects, which is equivalent as using the name \code{default}. diff --git a/man/tm_a_mmrm.Rd b/man/tm_a_mmrm.Rd index 24a9ba960..a4601bb43 100644 --- a/man/tm_a_mmrm.Rd +++ b/man/tm_a_mmrm.Rd @@ -27,7 +27,8 @@ tm_a_mmrm( post_output = NULL, basic_table_args = teal.widgets::basic_table_args(), ggplot2_args = teal.widgets::ggplot2_args(), - decorators = NULL + transformators = list(), + decorators = list() ) } \arguments{ @@ -96,9 +97,12 @@ List names should match the following: \code{c("default", "lsmeans", "diagnostic with option \code{teal.ggplot2_args} and with default module arguments (hard coded in the module body). For more details, see the help vignette: \code{vignette("custom-ggplot2-arguments", package = "teal.widgets")}.} +\item{transformators}{(\code{list} of \code{teal_transform_module}) that will be applied to transform module's data input. +To learn more check \code{vignette("data-transform-as-shiny-module", package = "teal")}.} + \item{decorators}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#experimental}{\figure{lifecycle-experimental.svg}{options: alt='[Experimental]'}}}{\strong{[Experimental]}} -" (\code{list} of \code{teal_transform_module}, named \code{list} of \code{teal_transform_module} or" \code{NULL}) optional, -if not \code{NULL}, decorator for tables or plots included in the module. +(\code{list} of \code{teal_transform_module}, named \code{list} of \code{teal_transform_module}) optional, +decorator for tables or plots included in the module output reported. When a named list of \code{teal_transform_module}, the decorators are applied to the respective output objects. Otherwise, the decorators are applied to all objects, which is equivalent as using the name \code{default}. diff --git a/man/tm_g_barchart_simple.Rd b/man/tm_g_barchart_simple.Rd index 3cf410fcf..c72dbceac 100644 --- a/man/tm_g_barchart_simple.Rd +++ b/man/tm_g_barchart_simple.Rd @@ -16,7 +16,8 @@ tm_g_barchart_simple( pre_output = NULL, post_output = NULL, ggplot2_args = teal.widgets::ggplot2_args(), - decorators = NULL + transformators = list(), + decorators = list() ) } \arguments{ @@ -49,9 +50,12 @@ for the module plot. The argument is merged with option \code{teal.ggplot2_args} (hard coded in the module body). For more details, see the vignette: \code{vignette("custom-ggplot2-arguments", package = "teal.widgets")}.} +\item{transformators}{(\code{list} of \code{teal_transform_module}) that will be applied to transform module's data input. +To learn more check \code{vignette("data-transform-as-shiny-module", package = "teal")}.} + \item{decorators}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#experimental}{\figure{lifecycle-experimental.svg}{options: alt='[Experimental]'}}}{\strong{[Experimental]}} -" (\code{list} of \code{teal_transform_module}, named \code{list} of \code{teal_transform_module} or" \code{NULL}) optional, -if not \code{NULL}, decorator for tables or plots included in the module. +(\code{list} of \code{teal_transform_module}, named \code{list} of \code{teal_transform_module}) optional, +decorator for tables or plots included in the module output reported. When a named list of \code{teal_transform_module}, the decorators are applied to the respective output objects. Otherwise, the decorators are applied to all objects, which is equivalent as using the name \code{default}. diff --git a/man/tm_g_ci.Rd b/man/tm_g_ci.Rd index 6d9f6ef3b..1c8ef2a5f 100644 --- a/man/tm_g_ci.Rd +++ b/man/tm_g_ci.Rd @@ -17,7 +17,8 @@ tm_g_ci( pre_output = NULL, post_output = NULL, ggplot2_args = teal.widgets::ggplot2_args(), - decorators = NULL + transformators = list(), + decorators = list() ) } \arguments{ @@ -51,9 +52,12 @@ for the module plot. The argument is merged with option \code{teal.ggplot2_args} (hard coded in the module body). For more details, see the vignette: \code{vignette("custom-ggplot2-arguments", package = "teal.widgets")}.} +\item{transformators}{(\code{list} of \code{teal_transform_module}) that will be applied to transform module's data input. +To learn more check \code{vignette("data-transform-as-shiny-module", package = "teal")}.} + \item{decorators}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#experimental}{\figure{lifecycle-experimental.svg}{options: alt='[Experimental]'}}}{\strong{[Experimental]}} -" (\code{list} of \code{teal_transform_module}, named \code{list} of \code{teal_transform_module} or" \code{NULL}) optional, -if not \code{NULL}, decorator for tables or plots included in the module. +(\code{list} of \code{teal_transform_module}, named \code{list} of \code{teal_transform_module}) optional, +decorator for tables or plots included in the module output reported. When a named list of \code{teal_transform_module}, the decorators are applied to the respective output objects. Otherwise, the decorators are applied to all objects, which is equivalent as using the name \code{default}. diff --git a/man/tm_g_forest_rsp.Rd b/man/tm_g_forest_rsp.Rd index 3812c351a..a02fe8e68 100644 --- a/man/tm_g_forest_rsp.Rd +++ b/man/tm_g_forest_rsp.Rd @@ -30,7 +30,8 @@ tm_g_forest_rsp( pre_output = NULL, post_output = NULL, ggplot2_args = teal.widgets::ggplot2_args(), - decorators = NULL + transformators = list(), + decorators = list() ) } \arguments{ @@ -115,9 +116,12 @@ merged with option \code{teal.ggplot2_args} and with default module arguments (h For more details, see the vignette: \code{vignette("custom-ggplot2-arguments", package = "teal.widgets")}.} +\item{transformators}{(\code{list} of \code{teal_transform_module}) that will be applied to transform module's data input. +To learn more check \code{vignette("data-transform-as-shiny-module", package = "teal")}.} + \item{decorators}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#experimental}{\figure{lifecycle-experimental.svg}{options: alt='[Experimental]'}}}{\strong{[Experimental]}} -" (\code{list} of \code{teal_transform_module}, named \code{list} of \code{teal_transform_module} or" \code{NULL}) optional, -if not \code{NULL}, decorator for tables or plots included in the module. +(\code{list} of \code{teal_transform_module}, named \code{list} of \code{teal_transform_module}) optional, +decorator for tables or plots included in the module output reported. When a named list of \code{teal_transform_module}, the decorators are applied to the respective output objects. Otherwise, the decorators are applied to all objects, which is equivalent as using the name \code{default}. diff --git a/man/tm_g_forest_tte.Rd b/man/tm_g_forest_tte.Rd index 6a63e6fd9..9de5a65b1 100644 --- a/man/tm_g_forest_tte.Rd +++ b/man/tm_g_forest_tte.Rd @@ -33,7 +33,8 @@ tm_g_forest_tte( pre_output = NULL, post_output = NULL, ggplot2_args = teal.widgets::ggplot2_args(), - decorators = NULL + transformators = list(), + decorators = list() ) } \arguments{ @@ -116,9 +117,12 @@ for the module plot. The argument is merged with option \code{teal.ggplot2_args} (hard coded in the module body). For more details, see the vignette: \code{vignette("custom-ggplot2-arguments", package = "teal.widgets")}.} +\item{transformators}{(\code{list} of \code{teal_transform_module}) that will be applied to transform module's data input. +To learn more check \code{vignette("data-transform-as-shiny-module", package = "teal")}.} + \item{decorators}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#experimental}{\figure{lifecycle-experimental.svg}{options: alt='[Experimental]'}}}{\strong{[Experimental]}} -" (\code{list} of \code{teal_transform_module}, named \code{list} of \code{teal_transform_module} or" \code{NULL}) optional, -if not \code{NULL}, decorator for tables or plots included in the module. +(\code{list} of \code{teal_transform_module}, named \code{list} of \code{teal_transform_module}) optional, +decorator for tables or plots included in the module output reported. When a named list of \code{teal_transform_module}, the decorators are applied to the respective output objects. Otherwise, the decorators are applied to all objects, which is equivalent as using the name \code{default}. diff --git a/man/tm_g_ipp.Rd b/man/tm_g_ipp.Rd index e0bdd6f36..e15c4557e 100644 --- a/man/tm_g_ipp.Rd +++ b/man/tm_g_ipp.Rd @@ -32,7 +32,8 @@ tm_g_ipp( pre_output = NULL, post_output = NULL, ggplot2_args = teal.widgets::ggplot2_args(), - decorators = NULL + transformators = list(), + decorators = list() ) } \arguments{ @@ -94,9 +95,12 @@ body). For more details, see the vignette: \code{vignette("custom-ggplot2-arguments", package = "teal.widgets")}.} +\item{transformators}{(\code{list} of \code{teal_transform_module}) that will be applied to transform module's data input. +To learn more check \code{vignette("data-transform-as-shiny-module", package = "teal")}.} + \item{decorators}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#experimental}{\figure{lifecycle-experimental.svg}{options: alt='[Experimental]'}}}{\strong{[Experimental]}} -" (\code{list} of \code{teal_transform_module}, named \code{list} of \code{teal_transform_module} or" \code{NULL}) optional, -if not \code{NULL}, decorator for tables or plots included in the module. +(\code{list} of \code{teal_transform_module}, named \code{list} of \code{teal_transform_module}) optional, +decorator for tables or plots included in the module output reported. When a named list of \code{teal_transform_module}, the decorators are applied to the respective output objects. Otherwise, the decorators are applied to all objects, which is equivalent as using the name \code{default}. diff --git a/man/tm_g_km.Rd b/man/tm_g_km.Rd index 3ba6fe9c3..92864cbcf 100644 --- a/man/tm_g_km.Rd +++ b/man/tm_g_km.Rd @@ -32,7 +32,8 @@ tm_g_km( plot_width = NULL, pre_output = NULL, post_output = NULL, - decorators = NULL + transformators = list(), + decorators = list() ) } \arguments{ @@ -103,9 +104,12 @@ For example a title.} \item{post_output}{(\code{shiny.tag}) optional,\cr with text placed after the output to put the output into context. For example the \code{\link[shiny:helpText]{shiny::helpText()}} elements are useful.} +\item{transformators}{(\code{list} of \code{teal_transform_module}) that will be applied to transform module's data input. +To learn more check \code{vignette("data-transform-as-shiny-module", package = "teal")}.} + \item{decorators}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#experimental}{\figure{lifecycle-experimental.svg}{options: alt='[Experimental]'}}}{\strong{[Experimental]}} -" (\code{list} of \code{teal_transform_module}, named \code{list} of \code{teal_transform_module} or" \code{NULL}) optional, -if not \code{NULL}, decorator for tables or plots included in the module. +(\code{list} of \code{teal_transform_module}, named \code{list} of \code{teal_transform_module}) optional, +decorator for tables or plots included in the module output reported. When a named list of \code{teal_transform_module}, the decorators are applied to the respective output objects. Otherwise, the decorators are applied to all objects, which is equivalent as using the name \code{default}. diff --git a/man/tm_g_lineplot.Rd b/man/tm_g_lineplot.Rd index 653edf00e..d759357d8 100644 --- a/man/tm_g_lineplot.Rd +++ b/man/tm_g_lineplot.Rd @@ -36,7 +36,8 @@ tm_g_lineplot( pre_output = NULL, post_output = NULL, ggplot2_args = teal.widgets::ggplot2_args(), - decorators = NULL + transformators = list(), + decorators = list() ) } \arguments{ @@ -50,7 +51,7 @@ tm_g_lineplot( \item{group_var}{(\code{string} or \code{NA})\cr group variable name.} -\item{x}{(\code{string})\cr x-variable name.} +\item{x}{(\code{teal_module} or \code{teal_modules}) Object to format/print.} \item{y}{(\code{string})\cr y-variable name.} @@ -108,9 +109,12 @@ the module body). For more details, see the vignette: \code{vignette("custom-ggplot2-arguments", package = "teal.widgets")}.} +\item{transformators}{(\code{list} of \code{teal_transform_module}) that will be applied to transform module's data input. +To learn more check \code{vignette("data-transform-as-shiny-module", package = "teal")}.} + \item{decorators}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#experimental}{\figure{lifecycle-experimental.svg}{options: alt='[Experimental]'}}}{\strong{[Experimental]}} -" (\code{list} of \code{teal_transform_module}, named \code{list} of \code{teal_transform_module} or" \code{NULL}) optional, -if not \code{NULL}, decorator for tables or plots included in the module. +(\code{list} of \code{teal_transform_module}, named \code{list} of \code{teal_transform_module}) optional, +decorator for tables or plots included in the module output reported. When a named list of \code{teal_transform_module}, the decorators are applied to the respective output objects. Otherwise, the decorators are applied to all objects, which is equivalent as using the name \code{default}. diff --git a/man/tm_g_pp_adverse_events.Rd b/man/tm_g_pp_adverse_events.Rd index 3c5f45e4b..1395fa2b5 100644 --- a/man/tm_g_pp_adverse_events.Rd +++ b/man/tm_g_pp_adverse_events.Rd @@ -22,7 +22,8 @@ tm_g_pp_adverse_events( pre_output = NULL, post_output = NULL, ggplot2_args = teal.widgets::ggplot2_args(), - decorators = NULL + transformators = list(), + decorators = list() ) } \arguments{ @@ -74,9 +75,12 @@ for the module plot. The argument is merged with option \code{teal.ggplot2_args} (hard coded in the module body). For more details, see the vignette: \code{vignette("custom-ggplot2-arguments", package = "teal.widgets")}.} +\item{transformators}{(\code{list} of \code{teal_transform_module}) that will be applied to transform module's data input. +To learn more check \code{vignette("data-transform-as-shiny-module", package = "teal")}.} + \item{decorators}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#experimental}{\figure{lifecycle-experimental.svg}{options: alt='[Experimental]'}}}{\strong{[Experimental]}} -" (\code{list} of \code{teal_transform_module}, named \code{list} of \code{teal_transform_module} or" \code{NULL}) optional, -if not \code{NULL}, decorator for tables or plots included in the module. +(\code{list} of \code{teal_transform_module}, named \code{list} of \code{teal_transform_module}) optional, +decorator for tables or plots included in the module output reported. When a named list of \code{teal_transform_module}, the decorators are applied to the respective output objects. Otherwise, the decorators are applied to all objects, which is equivalent as using the name \code{default}. diff --git a/man/tm_g_pp_patient_timeline.Rd b/man/tm_g_pp_patient_timeline.Rd index 45175ce25..cac30859d 100644 --- a/man/tm_g_pp_patient_timeline.Rd +++ b/man/tm_g_pp_patient_timeline.Rd @@ -26,7 +26,8 @@ tm_g_pp_patient_timeline( pre_output = NULL, post_output = NULL, ggplot2_args = teal.widgets::ggplot2_args(), - decorators = NULL + transformators = list(), + decorators = list() ) } \arguments{ @@ -89,9 +90,12 @@ for the module plot. The argument is merged with option \code{teal.ggplot2_args} (hard coded in the module body). For more details, see the vignette: \code{vignette("custom-ggplot2-arguments", package = "teal.widgets")}.} +\item{transformators}{(\code{list} of \code{teal_transform_module}) that will be applied to transform module's data input. +To learn more check \code{vignette("data-transform-as-shiny-module", package = "teal")}.} + \item{decorators}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#experimental}{\figure{lifecycle-experimental.svg}{options: alt='[Experimental]'}}}{\strong{[Experimental]}} -" (\code{list} of \code{teal_transform_module}, named \code{list} of \code{teal_transform_module} or" \code{NULL}) optional, -if not \code{NULL}, decorator for tables or plots included in the module. +(\code{list} of \code{teal_transform_module}, named \code{list} of \code{teal_transform_module}) optional, +decorator for tables or plots included in the module output reported. When a named list of \code{teal_transform_module}, the decorators are applied to the respective output objects. Otherwise, the decorators are applied to all objects, which is equivalent as using the name \code{default}. diff --git a/man/tm_g_pp_therapy.Rd b/man/tm_g_pp_therapy.Rd index f30946520..cce5e7c2d 100644 --- a/man/tm_g_pp_therapy.Rd +++ b/man/tm_g_pp_therapy.Rd @@ -25,7 +25,8 @@ tm_g_pp_therapy( pre_output = NULL, post_output = NULL, ggplot2_args = teal.widgets::ggplot2_args(), - decorators = NULL + transformators = list(), + decorators = list() ) } \arguments{ @@ -86,9 +87,12 @@ for the module plot. The argument is merged with option \code{teal.ggplot2_args} (hard coded in the module body). For more details, see the vignette: \code{vignette("custom-ggplot2-arguments", package = "teal.widgets")}.} +\item{transformators}{(\code{list} of \code{teal_transform_module}) that will be applied to transform module's data input. +To learn more check \code{vignette("data-transform-as-shiny-module", package = "teal")}.} + \item{decorators}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#experimental}{\figure{lifecycle-experimental.svg}{options: alt='[Experimental]'}}}{\strong{[Experimental]}} -" (\code{list} of \code{teal_transform_module}, named \code{list} of \code{teal_transform_module} or" \code{NULL}) optional, -if not \code{NULL}, decorator for tables or plots included in the module. +(\code{list} of \code{teal_transform_module}, named \code{list} of \code{teal_transform_module}) optional, +decorator for tables or plots included in the module output reported. When a named list of \code{teal_transform_module}, the decorators are applied to the respective output objects. Otherwise, the decorators are applied to all objects, which is equivalent as using the name \code{default}. diff --git a/man/tm_g_pp_vitals.Rd b/man/tm_g_pp_vitals.Rd index 1989d7327..71fb6c4fd 100644 --- a/man/tm_g_pp_vitals.Rd +++ b/man/tm_g_pp_vitals.Rd @@ -19,7 +19,8 @@ tm_g_pp_vitals( pre_output = NULL, post_output = NULL, ggplot2_args = teal.widgets::ggplot2_args(), - decorators = NULL + transformators = list(), + decorators = list() ) } \arguments{ @@ -61,9 +62,12 @@ for the module plot. The argument is merged with option \code{teal.ggplot2_args} (hard coded in the module body). For more details, see the vignette: \code{vignette("custom-ggplot2-arguments", package = "teal.widgets")}.} +\item{transformators}{(\code{list} of \code{teal_transform_module}) that will be applied to transform module's data input. +To learn more check \code{vignette("data-transform-as-shiny-module", package = "teal")}.} + \item{decorators}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#experimental}{\figure{lifecycle-experimental.svg}{options: alt='[Experimental]'}}}{\strong{[Experimental]}} -" (\code{list} of \code{teal_transform_module}, named \code{list} of \code{teal_transform_module} or" \code{NULL}) optional, -if not \code{NULL}, decorator for tables or plots included in the module. +(\code{list} of \code{teal_transform_module}, named \code{list} of \code{teal_transform_module}) optional, +decorator for tables or plots included in the module output reported. When a named list of \code{teal_transform_module}, the decorators are applied to the respective output objects. Otherwise, the decorators are applied to all objects, which is equivalent as using the name \code{default}. diff --git a/man/tm_t_abnormality.Rd b/man/tm_t_abnormality.Rd index b6f09ce0e..063fd9f28 100644 --- a/man/tm_t_abnormality.Rd +++ b/man/tm_t_abnormality.Rd @@ -30,7 +30,8 @@ tm_t_abnormality( post_output = NULL, na_level = default_na_str(), basic_table_args = teal.widgets::basic_table_args(), - decorators = NULL + transformators = list(), + decorators = list() ) } \arguments{ @@ -91,9 +92,12 @@ with settings for the module table. The argument is merged with option \code{tea module arguments (hard coded in the module body). For more details, see the vignette: \code{vignette("custom-basic-table-arguments", package = "teal.widgets")}.} +\item{transformators}{(\code{list} of \code{teal_transform_module}) that will be applied to transform module's data input. +To learn more check \code{vignette("data-transform-as-shiny-module", package = "teal")}.} + \item{decorators}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#experimental}{\figure{lifecycle-experimental.svg}{options: alt='[Experimental]'}}}{\strong{[Experimental]}} -" (\code{list} of \code{teal_transform_module}, named \code{list} of \code{teal_transform_module} or" \code{NULL}) optional, -if not \code{NULL}, decorator for tables or plots included in the module. +(\code{list} of \code{teal_transform_module}, named \code{list} of \code{teal_transform_module}) optional, +decorator for tables or plots included in the module output reported. When a named list of \code{teal_transform_module}, the decorators are applied to the respective output objects. Otherwise, the decorators are applied to all objects, which is equivalent as using the name \code{default}. diff --git a/man/tm_t_abnormality_by_worst_grade.Rd b/man/tm_t_abnormality_by_worst_grade.Rd index f0349e611..77f01639a 100644 --- a/man/tm_t_abnormality_by_worst_grade.Rd +++ b/man/tm_t_abnormality_by_worst_grade.Rd @@ -29,7 +29,8 @@ tm_t_abnormality_by_worst_grade( pre_output = NULL, post_output = NULL, basic_table_args = teal.widgets::basic_table_args(), - decorators = NULL + transformators = list(), + decorators = list() ) } \arguments{ @@ -85,9 +86,12 @@ with settings for the module table. The argument is merged with option \code{tea module arguments (hard coded in the module body). For more details, see the vignette: \code{vignette("custom-basic-table-arguments", package = "teal.widgets")}.} +\item{transformators}{(\code{list} of \code{teal_transform_module}) that will be applied to transform module's data input. +To learn more check \code{vignette("data-transform-as-shiny-module", package = "teal")}.} + \item{decorators}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#experimental}{\figure{lifecycle-experimental.svg}{options: alt='[Experimental]'}}}{\strong{[Experimental]}} -" (\code{list} of \code{teal_transform_module}, named \code{list} of \code{teal_transform_module} or" \code{NULL}) optional, -if not \code{NULL}, decorator for tables or plots included in the module. +(\code{list} of \code{teal_transform_module}, named \code{list} of \code{teal_transform_module}) optional, +decorator for tables or plots included in the module output reported. When a named list of \code{teal_transform_module}, the decorators are applied to the respective output objects. Otherwise, the decorators are applied to all objects, which is equivalent as using the name \code{default}. diff --git a/man/tm_t_ancova.Rd b/man/tm_t_ancova.Rd index b2826c42e..e2b33cbf8 100644 --- a/man/tm_t_ancova.Rd +++ b/man/tm_t_ancova.Rd @@ -23,7 +23,8 @@ tm_t_ancova( pre_output = NULL, post_output = NULL, basic_table_args = teal.widgets::basic_table_args(), - decorators = NULL + transformators = list(), + decorators = list() ) } \arguments{ @@ -78,9 +79,12 @@ with settings for the module table. The argument is merged with option \code{tea module arguments (hard coded in the module body). For more details, see the vignette: \code{vignette("custom-basic-table-arguments", package = "teal.widgets")}.} +\item{transformators}{(\code{list} of \code{teal_transform_module}) that will be applied to transform module's data input. +To learn more check \code{vignette("data-transform-as-shiny-module", package = "teal")}.} + \item{decorators}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#experimental}{\figure{lifecycle-experimental.svg}{options: alt='[Experimental]'}}}{\strong{[Experimental]}} -" (\code{list} of \code{teal_transform_module}, named \code{list} of \code{teal_transform_module} or" \code{NULL}) optional, -if not \code{NULL}, decorator for tables or plots included in the module. +(\code{list} of \code{teal_transform_module}, named \code{list} of \code{teal_transform_module}) optional, +decorator for tables or plots included in the module output reported. When a named list of \code{teal_transform_module}, the decorators are applied to the respective output objects. Otherwise, the decorators are applied to all objects, which is equivalent as using the name \code{default}. diff --git a/man/tm_t_binary_outcome.Rd b/man/tm_t_binary_outcome.Rd index b942d9d98..ef34ec49d 100644 --- a/man/tm_t_binary_outcome.Rd +++ b/man/tm_t_binary_outcome.Rd @@ -31,7 +31,8 @@ tm_t_binary_outcome( pre_output = NULL, post_output = NULL, basic_table_args = teal.widgets::basic_table_args(), - decorators = NULL + transformators = list(), + decorators = list() ) } \arguments{ @@ -105,9 +106,12 @@ with settings for the module table. The argument is merged with option \code{tea module arguments (hard coded in the module body). For more details, see the vignette: \code{vignette("custom-basic-table-arguments", package = "teal.widgets")}.} +\item{transformators}{(\code{list} of \code{teal_transform_module}) that will be applied to transform module's data input. +To learn more check \code{vignette("data-transform-as-shiny-module", package = "teal")}.} + \item{decorators}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#experimental}{\figure{lifecycle-experimental.svg}{options: alt='[Experimental]'}}}{\strong{[Experimental]}} -" (\code{list} of \code{teal_transform_module}, named \code{list} of \code{teal_transform_module} or" \code{NULL}) optional, -if not \code{NULL}, decorator for tables or plots included in the module. +(\code{list} of \code{teal_transform_module}, named \code{list} of \code{teal_transform_module}) optional, +decorator for tables or plots included in the module output reported. When a named list of \code{teal_transform_module}, the decorators are applied to the respective output objects. Otherwise, the decorators are applied to all objects, which is equivalent as using the name \code{default}. diff --git a/man/tm_t_coxreg.Rd b/man/tm_t_coxreg.Rd index 623cbcd20..e7da41115 100644 --- a/man/tm_t_coxreg.Rd +++ b/man/tm_t_coxreg.Rd @@ -25,7 +25,8 @@ tm_t_coxreg( pre_output = NULL, post_output = NULL, basic_table_args = teal.widgets::basic_table_args(), - decorators = NULL + transformators = list(), + decorators = list() ) } \arguments{ @@ -81,9 +82,12 @@ with settings for the module table. The argument is merged with option \code{tea module arguments (hard coded in the module body). For more details, see the vignette: \code{vignette("custom-basic-table-arguments", package = "teal.widgets")}.} +\item{transformators}{(\code{list} of \code{teal_transform_module}) that will be applied to transform module's data input. +To learn more check \code{vignette("data-transform-as-shiny-module", package = "teal")}.} + \item{decorators}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#experimental}{\figure{lifecycle-experimental.svg}{options: alt='[Experimental]'}}}{\strong{[Experimental]}} -" (\code{list} of \code{teal_transform_module}, named \code{list} of \code{teal_transform_module} or" \code{NULL}) optional, -if not \code{NULL}, decorator for tables or plots included in the module. +(\code{list} of \code{teal_transform_module}, named \code{list} of \code{teal_transform_module}) optional, +decorator for tables or plots included in the module output reported. When a named list of \code{teal_transform_module}, the decorators are applied to the respective output objects. Otherwise, the decorators are applied to all objects, which is equivalent as using the name \code{default}. diff --git a/man/tm_t_events.Rd b/man/tm_t_events.Rd index 271a58efd..59ba5d269 100644 --- a/man/tm_t_events.Rd +++ b/man/tm_t_events.Rd @@ -25,7 +25,8 @@ tm_t_events( pre_output = NULL, post_output = NULL, basic_table_args = teal.widgets::basic_table_args(), - decorators = NULL + transformators = list(), + decorators = list() ) } \arguments{ @@ -90,9 +91,12 @@ with settings for the module table. The argument is merged with option \code{tea module arguments (hard coded in the module body). For more details, see the vignette: \code{vignette("custom-basic-table-arguments", package = "teal.widgets")}.} +\item{transformators}{(\code{list} of \code{teal_transform_module}) that will be applied to transform module's data input. +To learn more check \code{vignette("data-transform-as-shiny-module", package = "teal")}.} + \item{decorators}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#experimental}{\figure{lifecycle-experimental.svg}{options: alt='[Experimental]'}}}{\strong{[Experimental]}} -" (\code{list} of \code{teal_transform_module}, named \code{list} of \code{teal_transform_module} or" \code{NULL}) optional, -if not \code{NULL}, decorator for tables or plots included in the module. +(\code{list} of \code{teal_transform_module}, named \code{list} of \code{teal_transform_module}) optional, +decorator for tables or plots included in the module output reported. When a named list of \code{teal_transform_module}, the decorators are applied to the respective output objects. Otherwise, the decorators are applied to all objects, which is equivalent as using the name \code{default}. diff --git a/man/tm_t_events_by_grade.Rd b/man/tm_t_events_by_grade.Rd index ab31a139b..6c5a50cbb 100644 --- a/man/tm_t_events_by_grade.Rd +++ b/man/tm_t_events_by_grade.Rd @@ -25,7 +25,8 @@ tm_t_events_by_grade( pre_output = NULL, post_output = NULL, basic_table_args = teal.widgets::basic_table_args(), - decorators = NULL + transformators = list(), + decorators = list() ) } \arguments{ @@ -82,9 +83,12 @@ with settings for the module table. The argument is merged with option \code{tea module arguments (hard coded in the module body). For more details, see the vignette: \code{vignette("custom-basic-table-arguments", package = "teal.widgets")}.} +\item{transformators}{(\code{list} of \code{teal_transform_module}) that will be applied to transform module's data input. +To learn more check \code{vignette("data-transform-as-shiny-module", package = "teal")}.} + \item{decorators}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#experimental}{\figure{lifecycle-experimental.svg}{options: alt='[Experimental]'}}}{\strong{[Experimental]}} -" (\code{list} of \code{teal_transform_module}, named \code{list} of \code{teal_transform_module} or" \code{NULL}) optional, -if not \code{NULL}, decorator for tables or plots included in the module. +(\code{list} of \code{teal_transform_module}, named \code{list} of \code{teal_transform_module}) optional, +decorator for tables or plots included in the module output reported. When a named list of \code{teal_transform_module}, the decorators are applied to the respective output objects. Otherwise, the decorators are applied to all objects, which is equivalent as using the name \code{default}. diff --git a/man/tm_t_events_patyear.Rd b/man/tm_t_events_patyear.Rd index 354a2b091..1b0a86670 100644 --- a/man/tm_t_events_patyear.Rd +++ b/man/tm_t_events_patyear.Rd @@ -25,7 +25,8 @@ tm_t_events_patyear( pre_output = NULL, post_output = NULL, basic_table_args = teal.widgets::basic_table_args(), - decorators = NULL + transformators = list(), + decorators = list() ) } \arguments{ @@ -82,9 +83,12 @@ with settings for the module table. The argument is merged with option \code{tea module arguments (hard coded in the module body). For more details, see the vignette: \code{vignette("custom-basic-table-arguments", package = "teal.widgets")}.} +\item{transformators}{(\code{list} of \code{teal_transform_module}) that will be applied to transform module's data input. +To learn more check \code{vignette("data-transform-as-shiny-module", package = "teal")}.} + \item{decorators}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#experimental}{\figure{lifecycle-experimental.svg}{options: alt='[Experimental]'}}}{\strong{[Experimental]}} -" (\code{list} of \code{teal_transform_module}, named \code{list} of \code{teal_transform_module} or" \code{NULL}) optional, -if not \code{NULL}, decorator for tables or plots included in the module. +(\code{list} of \code{teal_transform_module}, named \code{list} of \code{teal_transform_module}) optional, +decorator for tables or plots included in the module output reported. When a named list of \code{teal_transform_module}, the decorators are applied to the respective output objects. Otherwise, the decorators are applied to all objects, which is equivalent as using the name \code{default}. diff --git a/man/tm_t_events_summary.Rd b/man/tm_t_events_summary.Rd index 47fc8eb87..8b33ea36b 100644 --- a/man/tm_t_events_summary.Rd +++ b/man/tm_t_events_summary.Rd @@ -33,7 +33,8 @@ tm_t_events_summary( pre_output = NULL, post_output = NULL, basic_table_args = teal.widgets::basic_table_args(), - decorators = NULL + transformators = list(), + decorators = list() ) } \arguments{ @@ -107,9 +108,12 @@ with settings for the module table. The argument is merged with option \code{tea module arguments (hard coded in the module body). For more details, see the vignette: \code{vignette("custom-basic-table-arguments", package = "teal.widgets")}.} +\item{transformators}{(\code{list} of \code{teal_transform_module}) that will be applied to transform module's data input. +To learn more check \code{vignette("data-transform-as-shiny-module", package = "teal")}.} + \item{decorators}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#experimental}{\figure{lifecycle-experimental.svg}{options: alt='[Experimental]'}}}{\strong{[Experimental]}} -" (\code{list} of \code{teal_transform_module}, named \code{list} of \code{teal_transform_module} or" \code{NULL}) optional, -if not \code{NULL}, decorator for tables or plots included in the module. +(\code{list} of \code{teal_transform_module}, named \code{list} of \code{teal_transform_module}) optional, +decorator for tables or plots included in the module output reported. When a named list of \code{teal_transform_module}, the decorators are applied to the respective output objects. Otherwise, the decorators are applied to all objects, which is equivalent as using the name \code{default}. diff --git a/man/tm_t_exposure.Rd b/man/tm_t_exposure.Rd index 1899db3c0..e2f09da75 100644 --- a/man/tm_t_exposure.Rd +++ b/man/tm_t_exposure.Rd @@ -29,7 +29,8 @@ tm_t_exposure( pre_output = NULL, post_output = NULL, basic_table_args = teal.widgets::basic_table_args(), - decorators = NULL + transformators = list(), + decorators = list() ) } \arguments{ @@ -93,9 +94,12 @@ with settings for the module table. The argument is merged with option \code{tea module arguments (hard coded in the module body). For more details, see the vignette: \code{vignette("custom-basic-table-arguments", package = "teal.widgets")}.} +\item{transformators}{(\code{list} of \code{teal_transform_module}) that will be applied to transform module's data input. +To learn more check \code{vignette("data-transform-as-shiny-module", package = "teal")}.} + \item{decorators}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#experimental}{\figure{lifecycle-experimental.svg}{options: alt='[Experimental]'}}}{\strong{[Experimental]}} -" (\code{list} of \code{teal_transform_module}, named \code{list} of \code{teal_transform_module} or" \code{NULL}) optional, -if not \code{NULL}, decorator for tables or plots included in the module. +(\code{list} of \code{teal_transform_module}, named \code{list} of \code{teal_transform_module}) optional, +decorator for tables or plots included in the module output reported. When a named list of \code{teal_transform_module}, the decorators are applied to the respective output objects. Otherwise, the decorators are applied to all objects, which is equivalent as using the name \code{default}. diff --git a/man/tm_t_logistic.Rd b/man/tm_t_logistic.Rd index a40e45660..dae959c3a 100644 --- a/man/tm_t_logistic.Rd +++ b/man/tm_t_logistic.Rd @@ -20,7 +20,8 @@ tm_t_logistic( pre_output = NULL, post_output = NULL, basic_table_args = teal.widgets::basic_table_args(), - decorators = NULL + transformators = list(), + decorators = list() ) } \arguments{ @@ -65,9 +66,12 @@ with settings for the module table. The argument is merged with option \code{tea module arguments (hard coded in the module body). For more details, see the vignette: \code{vignette("custom-basic-table-arguments", package = "teal.widgets")}.} +\item{transformators}{(\code{list} of \code{teal_transform_module}) that will be applied to transform module's data input. +To learn more check \code{vignette("data-transform-as-shiny-module", package = "teal")}.} + \item{decorators}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#experimental}{\figure{lifecycle-experimental.svg}{options: alt='[Experimental]'}}}{\strong{[Experimental]}} -" (\code{list} of \code{teal_transform_module}, named \code{list} of \code{teal_transform_module} or" \code{NULL}) optional, -if not \code{NULL}, decorator for tables or plots included in the module. +(\code{list} of \code{teal_transform_module}, named \code{list} of \code{teal_transform_module}) optional, +decorator for tables or plots included in the module output reported. When a named list of \code{teal_transform_module}, the decorators are applied to the respective output objects. Otherwise, the decorators are applied to all objects, which is equivalent as using the name \code{default}. diff --git a/man/tm_t_mult_events.Rd b/man/tm_t_mult_events.Rd index 029f8663a..0fc0303ad 100644 --- a/man/tm_t_mult_events.Rd +++ b/man/tm_t_mult_events.Rd @@ -21,7 +21,8 @@ tm_t_mult_events( pre_output = NULL, post_output = NULL, basic_table_args = teal.widgets::basic_table_args(), - decorators = NULL + transformators = list(), + decorators = list() ) } \arguments{ @@ -74,9 +75,12 @@ with settings for the module table. The argument is merged with option \code{tea module arguments (hard coded in the module body). For more details, see the vignette: \code{vignette("custom-basic-table-arguments", package = "teal.widgets")}.} +\item{transformators}{(\code{list} of \code{teal_transform_module}) that will be applied to transform module's data input. +To learn more check \code{vignette("data-transform-as-shiny-module", package = "teal")}.} + \item{decorators}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#experimental}{\figure{lifecycle-experimental.svg}{options: alt='[Experimental]'}}}{\strong{[Experimental]}} -" (\code{list} of \code{teal_transform_module}, named \code{list} of \code{teal_transform_module} or" \code{NULL}) optional, -if not \code{NULL}, decorator for tables or plots included in the module. +(\code{list} of \code{teal_transform_module}, named \code{list} of \code{teal_transform_module}) optional, +decorator for tables or plots included in the module output reported. When a named list of \code{teal_transform_module}, the decorators are applied to the respective output objects. Otherwise, the decorators are applied to all objects, which is equivalent as using the name \code{default}. diff --git a/man/tm_t_pp_basic_info.Rd b/man/tm_t_pp_basic_info.Rd index 817a27fdd..758d30700 100644 --- a/man/tm_t_pp_basic_info.Rd +++ b/man/tm_t_pp_basic_info.Rd @@ -11,7 +11,8 @@ tm_t_pp_basic_info( vars = NULL, pre_output = NULL, post_output = NULL, - decorators = NULL + transformators = list(), + decorators = list() ) } \arguments{ @@ -30,9 +31,12 @@ For example a title.} \item{post_output}{(\code{shiny.tag}) optional,\cr with text placed after the output to put the output into context. For example the \code{\link[shiny:helpText]{shiny::helpText()}} elements are useful.} +\item{transformators}{(\code{list} of \code{teal_transform_module}) that will be applied to transform module's data input. +To learn more check \code{vignette("data-transform-as-shiny-module", package = "teal")}.} + \item{decorators}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#experimental}{\figure{lifecycle-experimental.svg}{options: alt='[Experimental]'}}}{\strong{[Experimental]}} -" (\code{list} of \code{teal_transform_module}, named \code{list} of \code{teal_transform_module} or" \code{NULL}) optional, -if not \code{NULL}, decorator for tables or plots included in the module. +(\code{list} of \code{teal_transform_module}, named \code{list} of \code{teal_transform_module}) optional, +decorator for tables or plots included in the module output reported. When a named list of \code{teal_transform_module}, the decorators are applied to the respective output objects. Otherwise, the decorators are applied to all objects, which is equivalent as using the name \code{default}. diff --git a/man/tm_t_pp_laboratory.Rd b/man/tm_t_pp_laboratory.Rd index c2d32a50f..d7aff7672 100644 --- a/man/tm_t_pp_laboratory.Rd +++ b/man/tm_t_pp_laboratory.Rd @@ -19,7 +19,8 @@ tm_t_pp_laboratory( anrind = NULL, pre_output = NULL, post_output = NULL, - decorators = NULL + transformators = list(), + decorators = list() ) } \arguments{ @@ -60,9 +61,12 @@ For example a title.} \item{post_output}{(\code{shiny.tag}) optional,\cr with text placed after the output to put the output into context. For example the \code{\link[shiny:helpText]{shiny::helpText()}} elements are useful.} +\item{transformators}{(\code{list} of \code{teal_transform_module}) that will be applied to transform module's data input. +To learn more check \code{vignette("data-transform-as-shiny-module", package = "teal")}.} + \item{decorators}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#experimental}{\figure{lifecycle-experimental.svg}{options: alt='[Experimental]'}}}{\strong{[Experimental]}} -" (\code{list} of \code{teal_transform_module}, named \code{list} of \code{teal_transform_module} or" \code{NULL}) optional, -if not \code{NULL}, decorator for tables or plots included in the module. +(\code{list} of \code{teal_transform_module}, named \code{list} of \code{teal_transform_module}) optional, +decorator for tables or plots included in the module output reported. When a named list of \code{teal_transform_module}, the decorators are applied to the respective output objects. Otherwise, the decorators are applied to all objects, which is equivalent as using the name \code{default}. diff --git a/man/tm_t_pp_medical_history.Rd b/man/tm_t_pp_medical_history.Rd index 6e6dc2ce9..09bb54771 100644 --- a/man/tm_t_pp_medical_history.Rd +++ b/man/tm_t_pp_medical_history.Rd @@ -14,7 +14,8 @@ tm_t_pp_medical_history( mhdistat = NULL, pre_output = NULL, post_output = NULL, - decorators = NULL + transformators = list(), + decorators = list() ) } \arguments{ @@ -41,9 +42,12 @@ For example a title.} \item{post_output}{(\code{shiny.tag}) optional,\cr with text placed after the output to put the output into context. For example the \code{\link[shiny:helpText]{shiny::helpText()}} elements are useful.} +\item{transformators}{(\code{list} of \code{teal_transform_module}) that will be applied to transform module's data input. +To learn more check \code{vignette("data-transform-as-shiny-module", package = "teal")}.} + \item{decorators}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#experimental}{\figure{lifecycle-experimental.svg}{options: alt='[Experimental]'}}}{\strong{[Experimental]}} -" (\code{list} of \code{teal_transform_module}, named \code{list} of \code{teal_transform_module} or" \code{NULL}) optional, -if not \code{NULL}, decorator for tables or plots included in the module. +(\code{list} of \code{teal_transform_module}, named \code{list} of \code{teal_transform_module}) optional, +decorator for tables or plots included in the module output reported. When a named list of \code{teal_transform_module}, the decorators are applied to the respective output objects. Otherwise, the decorators are applied to all objects, which is equivalent as using the name \code{default}. diff --git a/man/tm_t_pp_prior_medication.Rd b/man/tm_t_pp_prior_medication.Rd index 0dff80898..f704572c0 100644 --- a/man/tm_t_pp_prior_medication.Rd +++ b/man/tm_t_pp_prior_medication.Rd @@ -15,7 +15,8 @@ tm_t_pp_prior_medication( cmstdy = NULL, pre_output = NULL, post_output = NULL, - decorators = NULL + transformators = list(), + decorators = list() ) } \arguments{ @@ -45,9 +46,12 @@ For example a title.} \item{post_output}{(\code{shiny.tag}) optional,\cr with text placed after the output to put the output into context. For example the \code{\link[shiny:helpText]{shiny::helpText()}} elements are useful.} +\item{transformators}{(\code{list} of \code{teal_transform_module}) that will be applied to transform module's data input. +To learn more check \code{vignette("data-transform-as-shiny-module", package = "teal")}.} + \item{decorators}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#experimental}{\figure{lifecycle-experimental.svg}{options: alt='[Experimental]'}}}{\strong{[Experimental]}} -" (\code{list} of \code{teal_transform_module}, named \code{list} of \code{teal_transform_module} or" \code{NULL}) optional, -if not \code{NULL}, decorator for tables or plots included in the module. +(\code{list} of \code{teal_transform_module}, named \code{list} of \code{teal_transform_module}) optional, +decorator for tables or plots included in the module output reported. When a named list of \code{teal_transform_module}, the decorators are applied to the respective output objects. Otherwise, the decorators are applied to all objects, which is equivalent as using the name \code{default}. diff --git a/man/tm_t_shift_by_arm.Rd b/man/tm_t_shift_by_arm.Rd index d3123be14..2a5135b02 100644 --- a/man/tm_t_shift_by_arm.Rd +++ b/man/tm_t_shift_by_arm.Rd @@ -26,7 +26,8 @@ tm_t_shift_by_arm( pre_output = NULL, post_output = NULL, basic_table_args = teal.widgets::basic_table_args(), - decorators = NULL + transformators = list(), + decorators = list() ) } \arguments{ @@ -84,9 +85,12 @@ with settings for the module table. The argument is merged with option \code{tea module arguments (hard coded in the module body). For more details, see the vignette: \code{vignette("custom-basic-table-arguments", package = "teal.widgets")}.} +\item{transformators}{(\code{list} of \code{teal_transform_module}) that will be applied to transform module's data input. +To learn more check \code{vignette("data-transform-as-shiny-module", package = "teal")}.} + \item{decorators}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#experimental}{\figure{lifecycle-experimental.svg}{options: alt='[Experimental]'}}}{\strong{[Experimental]}} -" (\code{list} of \code{teal_transform_module}, named \code{list} of \code{teal_transform_module} or" \code{NULL}) optional, -if not \code{NULL}, decorator for tables or plots included in the module. +(\code{list} of \code{teal_transform_module}, named \code{list} of \code{teal_transform_module}) optional, +decorator for tables or plots included in the module output reported. When a named list of \code{teal_transform_module}, the decorators are applied to the respective output objects. Otherwise, the decorators are applied to all objects, which is equivalent as using the name \code{default}. diff --git a/man/tm_t_shift_by_arm_by_worst.Rd b/man/tm_t_shift_by_arm_by_worst.Rd index 6d7823f39..9cf37ca16 100644 --- a/man/tm_t_shift_by_arm_by_worst.Rd +++ b/man/tm_t_shift_by_arm_by_worst.Rd @@ -26,7 +26,8 @@ tm_t_shift_by_arm_by_worst( pre_output = NULL, post_output = NULL, basic_table_args = teal.widgets::basic_table_args(), - decorators = NULL + transformators = list(), + decorators = list() ) } \arguments{ @@ -85,9 +86,12 @@ with settings for the module table. The argument is merged with option \code{tea module arguments (hard coded in the module body). For more details, see the vignette: \code{vignette("custom-basic-table-arguments", package = "teal.widgets")}.} +\item{transformators}{(\code{list} of \code{teal_transform_module}) that will be applied to transform module's data input. +To learn more check \code{vignette("data-transform-as-shiny-module", package = "teal")}.} + \item{decorators}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#experimental}{\figure{lifecycle-experimental.svg}{options: alt='[Experimental]'}}}{\strong{[Experimental]}} -" (\code{list} of \code{teal_transform_module}, named \code{list} of \code{teal_transform_module} or" \code{NULL}) optional, -if not \code{NULL}, decorator for tables or plots included in the module. +(\code{list} of \code{teal_transform_module}, named \code{list} of \code{teal_transform_module}) optional, +decorator for tables or plots included in the module output reported. When a named list of \code{teal_transform_module}, the decorators are applied to the respective output objects. Otherwise, the decorators are applied to all objects, which is equivalent as using the name \code{default}. diff --git a/man/tm_t_shift_by_grade.Rd b/man/tm_t_shift_by_grade.Rd index 059adb022..d22b2ee27 100644 --- a/man/tm_t_shift_by_grade.Rd +++ b/man/tm_t_shift_by_grade.Rd @@ -35,7 +35,8 @@ tm_t_shift_by_grade( na_level = default_na_str(), code_missing_baseline = FALSE, basic_table_args = teal.widgets::basic_table_args(), - decorators = NULL + transformators = list(), + decorators = list() ) } \arguments{ @@ -99,9 +100,12 @@ with settings for the module table. The argument is merged with option \code{tea module arguments (hard coded in the module body). For more details, see the vignette: \code{vignette("custom-basic-table-arguments", package = "teal.widgets")}.} +\item{transformators}{(\code{list} of \code{teal_transform_module}) that will be applied to transform module's data input. +To learn more check \code{vignette("data-transform-as-shiny-module", package = "teal")}.} + \item{decorators}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#experimental}{\figure{lifecycle-experimental.svg}{options: alt='[Experimental]'}}}{\strong{[Experimental]}} -" (\code{list} of \code{teal_transform_module}, named \code{list} of \code{teal_transform_module} or" \code{NULL}) optional, -if not \code{NULL}, decorator for tables or plots included in the module. +(\code{list} of \code{teal_transform_module}, named \code{list} of \code{teal_transform_module}) optional, +decorator for tables or plots included in the module output reported. When a named list of \code{teal_transform_module}, the decorators are applied to the respective output objects. Otherwise, the decorators are applied to all objects, which is equivalent as using the name \code{default}. diff --git a/man/tm_t_smq.Rd b/man/tm_t_smq.Rd index 5169323c1..df75bf2e4 100644 --- a/man/tm_t_smq.Rd +++ b/man/tm_t_smq.Rd @@ -24,7 +24,8 @@ tm_t_smq( pre_output = NULL, post_output = NULL, basic_table_args = teal.widgets::basic_table_args(), - decorators = NULL + transformators = list(), + decorators = list() ) } \arguments{ @@ -84,9 +85,12 @@ with settings for the module table. The argument is merged with option \code{tea module arguments (hard coded in the module body). For more details, see the vignette: \code{vignette("custom-basic-table-arguments", package = "teal.widgets")}.} +\item{transformators}{(\code{list} of \code{teal_transform_module}) that will be applied to transform module's data input. +To learn more check \code{vignette("data-transform-as-shiny-module", package = "teal")}.} + \item{decorators}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#experimental}{\figure{lifecycle-experimental.svg}{options: alt='[Experimental]'}}}{\strong{[Experimental]}} -" (\code{list} of \code{teal_transform_module}, named \code{list} of \code{teal_transform_module} or" \code{NULL}) optional, -if not \code{NULL}, decorator for tables or plots included in the module. +(\code{list} of \code{teal_transform_module}, named \code{list} of \code{teal_transform_module}) optional, +decorator for tables or plots included in the module output reported. When a named list of \code{teal_transform_module}, the decorators are applied to the respective output objects. Otherwise, the decorators are applied to all objects, which is equivalent as using the name \code{default}. diff --git a/man/tm_t_summary.Rd b/man/tm_t_summary.Rd index 912584a41..87cbb1298 100644 --- a/man/tm_t_summary.Rd +++ b/man/tm_t_summary.Rd @@ -23,7 +23,8 @@ tm_t_summary( pre_output = NULL, post_output = NULL, basic_table_args = teal.widgets::basic_table_args(), - decorators = NULL + transformators = list(), + decorators = list() ) } \arguments{ @@ -80,9 +81,12 @@ with settings for the module table. The argument is merged with option \code{tea module arguments (hard coded in the module body). For more details, see the vignette: \code{vignette("custom-basic-table-arguments", package = "teal.widgets")}.} +\item{transformators}{(\code{list} of \code{teal_transform_module}) that will be applied to transform module's data input. +To learn more check \code{vignette("data-transform-as-shiny-module", package = "teal")}.} + \item{decorators}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#experimental}{\figure{lifecycle-experimental.svg}{options: alt='[Experimental]'}}}{\strong{[Experimental]}} -" (\code{list} of \code{teal_transform_module}, named \code{list} of \code{teal_transform_module} or" \code{NULL}) optional, -if not \code{NULL}, decorator for tables or plots included in the module. +(\code{list} of \code{teal_transform_module}, named \code{list} of \code{teal_transform_module}) optional, +decorator for tables or plots included in the module output reported. When a named list of \code{teal_transform_module}, the decorators are applied to the respective output objects. Otherwise, the decorators are applied to all objects, which is equivalent as using the name \code{default}. diff --git a/man/tm_t_summary_by.Rd b/man/tm_t_summary_by.Rd index 44bf42ceb..24a7f0253 100644 --- a/man/tm_t_summary_by.Rd +++ b/man/tm_t_summary_by.Rd @@ -29,7 +29,8 @@ tm_t_summary_by( pre_output = NULL, post_output = NULL, basic_table_args = teal.widgets::basic_table_args(), - decorators = NULL + transformators = list(), + decorators = list() ) } \arguments{ @@ -100,9 +101,12 @@ with settings for the module table. The argument is merged with option \code{tea module arguments (hard coded in the module body). For more details, see the vignette: \code{vignette("custom-basic-table-arguments", package = "teal.widgets")}.} +\item{transformators}{(\code{list} of \code{teal_transform_module}) that will be applied to transform module's data input. +To learn more check \code{vignette("data-transform-as-shiny-module", package = "teal")}.} + \item{decorators}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#experimental}{\figure{lifecycle-experimental.svg}{options: alt='[Experimental]'}}}{\strong{[Experimental]}} -" (\code{list} of \code{teal_transform_module}, named \code{list} of \code{teal_transform_module} or" \code{NULL}) optional, -if not \code{NULL}, decorator for tables or plots included in the module. +(\code{list} of \code{teal_transform_module}, named \code{list} of \code{teal_transform_module}) optional, +decorator for tables or plots included in the module output reported. When a named list of \code{teal_transform_module}, the decorators are applied to the respective output objects. Otherwise, the decorators are applied to all objects, which is equivalent as using the name \code{default}. diff --git a/man/tm_t_tte.Rd b/man/tm_t_tte.Rd index 3fb8d1828..0b24ea46c 100644 --- a/man/tm_t_tte.Rd +++ b/man/tm_t_tte.Rd @@ -32,7 +32,8 @@ tm_t_tte( pre_output = NULL, post_output = NULL, basic_table_args = teal.widgets::basic_table_args(), - decorators = NULL + transformators = list(), + decorators = list() ) } \arguments{ @@ -100,9 +101,12 @@ with settings for the module table. The argument is merged with option \code{tea module arguments (hard coded in the module body). For more details, see the vignette: \code{vignette("custom-basic-table-arguments", package = "teal.widgets")}.} +\item{transformators}{(\code{list} of \code{teal_transform_module}) that will be applied to transform module's data input. +To learn more check \code{vignette("data-transform-as-shiny-module", package = "teal")}.} + \item{decorators}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#experimental}{\figure{lifecycle-experimental.svg}{options: alt='[Experimental]'}}}{\strong{[Experimental]}} -" (\code{list} of \code{teal_transform_module}, named \code{list} of \code{teal_transform_module} or" \code{NULL}) optional, -if not \code{NULL}, decorator for tables or plots included in the module. +(\code{list} of \code{teal_transform_module}, named \code{list} of \code{teal_transform_module}) optional, +decorator for tables or plots included in the module output reported. When a named list of \code{teal_transform_module}, the decorators are applied to the respective output objects. Otherwise, the decorators are applied to all objects, which is equivalent as using the name \code{default}.