Merge c525a64 into 25b6ad0

R/string_ops.R

@@ -47,26 +47,26 @@ as_num.character <- function(str) {
   y <- lapply(y, as.numeric)
   y[unlist(lapply(y, length) == 0)] <- NA
 
-  return(y)
+  y
 }
 
 #' @export
 #' @rdname as_num
 as_num.numeric <- function(str) {
-  return(str)
+  str
 }
 
 #' @export
 #' @rdname as_num
 as_num.factor <- function(str) {
   y <- as.character(str)
   y <- as_num(y)
-  return(y)
+  y
 }
 
 #' @export
 #' @rdname as_num
 as_num.logical <- function(str) {
   y <- as.numeric(str)
-  return(y)
+  y
 }

R/tm_a_gee.R

@@ -140,8 +140,21 @@ template_a_gee <- function(output_table,
 #' This module generates the following objects, which can be modified in place using decorators:
 #' - `table` (`ElementaryTable` - output of `rtables::build_table`)
 #'
+#' A Decorator is applied to the specific output using a named list of `teal_transform_module` objects.
+#' The name of this list corresponds to the name of the output to which the decorator is applied.
+#' See code snippet below:
+#'
+#' ```
+#' tm_a_gee(
+#'    ..., # arguments for module
+#'    decorators = list(
+#'      table = teal_transform_module(...) # applied to the `table` output
+#'    )
+#' )
+#' ```
+#'
 #' For additional details and examples of decorators, refer to the vignette
-#' `vignette("decorate-modules-output", package = "teal")` or the [`teal_transform_module()`] documentation.
+#' `vignette("transform-module-output", package = "teal")` or the [`teal::teal_transform_module()`] documentation.
 #'
 #' @examplesShinylive
 #' library(teal.modules.clinical)
@@ -228,7 +241,6 @@ tm_a_gee <- function(label,
   checkmate::assert_class(pre_output, classes = "shiny.tag", null.ok = TRUE)
   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")
 
   args <- as.list(environment())

R/tm_a_mmrm.R

@@ -462,32 +462,34 @@ template_mmrm_plots <- function(fit_name,
 #' @section Decorating Module:
 #'
 #' This module generates the following objects, which can be modified in place using decorators:
-#' - `lsmeans_plot` (`ggplot2`)
-#' - `diagnostic_plot` (`TableTree`- output from `rtables::build_table`)
+#' - `lsmeans_plot` (`ggplot`)
+#' - `diagnostic_plot` (`ggplot`)
 #' - `lsmeans_table` (`TableTree`- output from `rtables::build_table`)
-#' - `covariance_table` (`TableTree`- output from `rtables::build_table`)
-#' - `fixed_effects_table` (`TableTree`- output from `rtables::build_table`)
-#' - `diagnostic_table` (`TableTree`- output from `rtables::build_table`)
+#' - `covariance_table` (`ElementaryTable`- output from `rtables::build_table`)
+#' - `fixed_effects_table` (`ElementaryTable`- output from `rtables::build_table`)
+#' - `diagnostic_table` (`ElementaryTable`- output from `rtables::build_table`)
 #'
-#' Decorators can be applied to all outputs or only to specific objects using a
-#' named list of `teal_transform_module` objects.
-#' The `"default"` name is reserved for decorators that are applied to all outputs.
+#' A Decorator is applied to the specific output using a named list of `teal_transform_module` objects.
+#' The name of this list corresponds to the name of the output to which the decorator is applied.
 #' See code snippet below:
 #'
 #' ```
 #' tm_a_mrmm(
 #'    ..., # arguments for module
 #'    decorators = list(
-#'      default = list(teal_transform_module(...)), # applied to all outputs
-#'      lsmeans_plot = list(teal_transform_module(...)) # applied only to `lsmeans_plot` output
-#'      diagnostic_plot = list(teal_transform_module(...)) # applied only to `diagnostic_plot` output
-#'      lsmeans_table = list(teal_transform_module(...)) # applied only to `lsmeans_table` output
-#'      covariance_table = list(teal_transform_module(...)) # applied only to `covariance_table` output
-#'      fixed_effects_table = list(teal_transform_module(...)) # applied only to `fixed_effects_table` output
-#'      diagnostic_table = list(teal_transform_module(...)) # applied only to `diagnostic_table` output
+#'      lsmeans_plot = teal_transform_module(...), # applied only to `lsmeans_plot` output
+#'      diagnostic_plot = teal_transform_module(...), # applied only to `diagnostic_plot` output
+#'      lsmeans_table = teal_transform_module(...), # applied only to `lsmeans_table` output
+#'      covariance_table = teal_transform_module(...), # applied only to `covariance_table` output
+#'      fixed_effects_table = teal_transform_module(...), # applied only to `fixed_effects_table` output
+#'      diagnostic_table = teal_transform_module(...) # applied only to `diagnostic_table` output
 #'    )
 #' )
 #' ```
+#'
+#' For additional details and examples of decorators, refer to the vignette
+#' `vignette("transform-module-output", package = "teal")` or the [`teal::teal_transform_module()`] documentation.
+#'
 #' @examplesShinylive
 #' library(teal.modules.clinical)
 #' interactive <- function() TRUE
@@ -600,7 +602,6 @@ tm_a_mmrm <- function(label,
   checkmate::assert_list(ggplot2_args, types = "ggplot2_args")
   checkmate::assert_subset(names(ggplot2_args), c("default", plot_choices))
 
-  decorators <- normalize_decorators(decorators)
   assert_decorators(
     decorators,
     c(

R/tm_g_barchart_simple.R

@@ -19,10 +19,23 @@
 #' @section Decorating Module:
 #'
 #' This module generates the following objects, which can be modified in place using decorators:
-#' - `plot` (`ggplot2`)
+#' - `plot` (`ggplot`)
+#'
+#' A Decorator is applied to the specific output using a named list of `teal_transform_module` objects.
+#' The name of this list corresponds to the name of the output to which the decorator is applied.
+#' See code snippet below:
+#'
+#' ```
+#' tm_g_barchart_simple(
+#'    ..., # arguments for module
+#'    decorators = list(
+#'      plot = teal_transform_module(...) # applied only to `plot` output
+#'    )
+#' )
+#' ```
 #'
 #' For additional details and examples of decorators, refer to the vignette
-#' `vignette("decorate-modules-output", package = "teal")` or the [`teal_transform_module()`] documentation.
+#' `vignette("transform-module-output", package = "teal")` or the [`teal::teal_transform_module()`] documentation.
 #'
 #' @examplesShinylive
 #' library(teal.modules.clinical)
@@ -182,7 +195,6 @@ tm_g_barchart_simple <- function(x = NULL,
   checkmate::assert_class(pre_output, classes = "shiny.tag", null.ok = TRUE)
   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")
 
   plot_options <- utils::modifyList(

R/tm_g_ci.R

@@ -192,10 +192,23 @@ template_g_ci <- function(dataname,
 #' @section Decorating Module:
 #'
 #' This module generates the following objects, which can be modified in place using decorators:
-#' - `plot` (`ggplot2`)
+#' - `plot` (`ggplot`)
+#'
+#' A Decorator is applied to the specific output using a named list of `teal_transform_module` objects.
+#' The name of this list corresponds to the name of the output to which the decorator is applied.
+#' See code snippet below:
+#'
+#' ```
+#' tm_g_ci(
+#'    ..., # arguments for module
+#'    decorators = list(
+#'      plot = teal_transform_module(...) # applied only to `plot` output
+#'    )
+#' )
+#' ```
 #'
 #' For additional details and examples of decorators, refer to the vignette
-#' `vignette("decorate-modules-output", package = "teal")` or the [`teal_transform_module()`] documentation.
+#' `vignette("transform-module-output", package = "teal")` or the [`teal::teal_transform_module()`] documentation.
 #'
 #' @examplesShinylive
 #' library(teal.modules.clinical)
@@ -310,7 +323,6 @@ tm_g_ci <- function(label,
   checkmate::assert_class(pre_output, classes = "shiny.tag", null.ok = TRUE)
   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")
 
   args <- as.list(environment())

R/tm_g_forest_rsp.R

@@ -247,10 +247,23 @@ template_forest_rsp <- function(dataname = "ANL",
 #' @section Decorating Module:
 #'
 #' This module generates the following objects, which can be modified in place using decorators:
-#' - `plot` (`ggplot2`)
+#' - `plot` (`ggplot`)
+#'
+#' A Decorator is applied to the specific output using a named list of `teal_transform_module` objects.
+#' The name of this list corresponds to the name of the output to which the decorator is applied.
+#' See code snippet below:
+#'
+#' ```
+#' tm_g_forest_rsp(
+#'    ..., # arguments for module
+#'    decorators = list(
+#'      plot = teal_transform_module(...) # applied only to `plot` output
+#'    )
+#' )
+#' ```
 #'
 #' For additional details and examples of decorators, refer to the vignette
-#' `vignette("decorate-modules-output", package = "teal")` or the [`teal_transform_module()`] documentation.
+#' `vignette("transform-module-output", package = "teal")` or the [`teal::teal_transform_module()`] documentation.
 #'
 #' @examplesShinylive
 #' library(teal.modules.clinical)
@@ -392,7 +405,6 @@ tm_g_forest_rsp <- function(label,
   checkmate::assert_class(pre_output, classes = "shiny.tag", null.ok = TRUE)
   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")
 
   args <- as.list(environment())

R/tm_g_forest_tte.R

@@ -247,10 +247,23 @@ template_forest_tte <- function(dataname = "ANL",
 #' @section Decorating Module:
 #'
 #' This module generates the following objects, which can be modified in place using decorators:
-#' - `plot` (`ggplot2`)
+#' - `plot` (`ggplot`)
+#'
+#' A Decorator is applied to the specific output using a named list of `teal_transform_module` objects.
+#' The name of this list corresponds to the name of the output to which the decorator is applied.
+#' See code snippet below:
+#'
+#' ```
+#' tm_g_forest_tte(
+#'    ..., # arguments for module
+#'    decorators = list(
+#'      plot = teal_transform_module(...) # applied only to `plot` output
+#'    )
+#' )
+#' ```
 #'
 #' For additional details and examples of decorators, refer to the vignette
-#' `vignette("decorate-modules-output", package = "teal")` or the [`teal_transform_module()`] documentation.
+#' `vignette("transform-module-output", package = "teal")` or the [`teal::teal_transform_module()`] documentation.
 #'
 #' @examplesShinylive
 #' library(teal.modules.clinical)
@@ -378,7 +391,6 @@ tm_g_forest_tte <- function(label,
   checkmate::assert_class(pre_output, classes = "shiny.tag", null.ok = TRUE)
   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")
 
   args <- as.list(environment())

R/tm_g_ipp.R

@@ -183,10 +183,23 @@ template_g_ipp <- function(dataname = "ANL",
 #' @section Decorating Module:
 #'
 #' This module generates the following objects, which can be modified in place using decorators:
-#' - `plot` (`ggplot2`)
+#' - `plot` (`ggplot`)
+#'
+#' A Decorator is applied to the specific output using a named list of `teal_transform_module` objects.
+#' The name of this list corresponds to the name of the output to which the decorator is applied.
+#' See code snippet below:
+#'
+#' ```
+#' tm_g_ipp(
+#'    ..., # arguments for module
+#'    decorators = list(
+#'      plot = teal_transform_module(...) # applied only to `plot` output
+#'    )
+#' )
+#' ```
 #'
 #' For additional details and examples of decorators, refer to the vignette
-#' `vignette("decorate-modules-output", package = "teal")` or the [`teal_transform_module()`] documentation.
+#' `vignette("transform-module-output", package = "teal")` or the [`teal::teal_transform_module()`] documentation.
 #'
 #'
 #' @examplesShinylive
@@ -341,7 +354,6 @@ tm_g_ipp <- function(label,
   checkmate::assert_class(pre_output, classes = "shiny.tag", null.ok = TRUE)
   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")
 
   args <- as.list(environment())

R/tm_g_km.R

@@ -274,10 +274,23 @@ template_g_km <- function(dataname = "ANL",
 #' @section Decorating Module:
 #'
 #' This module generates the following objects, which can be modified in place using decorators:
-#' - `plot` (`ggplot2`)
+#' - `plot` (`ggplot`)
+#'
+#' A Decorator is applied to the specific output using a named list of `teal_transform_module` objects.
+#' The name of this list corresponds to the name of the output to which the decorator is applied.
+#' See code snippet below:
+#'
+#' ```
+#' tm_g_km(
+#'    ..., # arguments for module
+#'    decorators = list(
+#'      plot = teal_transform_module(...) # applied only to `plot` output
+#'    )
+#' )
+#' ```
 #'
 #' For additional details and examples of decorators, refer to the vignette
-#' `vignette("decorate-modules-output", package = "teal")` or the [`teal_transform_module()`] documentation.
+#' `vignette("transform-module-output", package = "teal")` or the [`teal::teal_transform_module()`] documentation.
 #'
 #'
 #' @examplesShinylive
@@ -398,7 +411,6 @@ 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")
 
   args <- as.list(environment())

R/tm_g_lineplot.R

@@ -218,10 +218,23 @@ template_g_lineplot <- function(dataname = "ANL",
 #' @section Decorating Module:
 #'
 #' This module generates the following objects, which can be modified in place using decorators:
-#' - `plot` (`ggplot2`)
+#' - `plot` (`ggplot`)
+#'
+#' A Decorator is applied to the specific output using a named list of `teal_transform_module` objects.
+#' The name of this list corresponds to the name of the output to which the decorator is applied.
+#' See code snippet below:
+#'
+#' ```
+#' tm_g_lineplot(
+#'    ..., # arguments for module
+#'    decorators = list(
+#'      plot = teal_transform_module(...) # applied only to `plot` output
+#'    )
+#' )
+#' ```
 #'
 #' For additional details and examples of decorators, refer to the vignette
-#' `vignette("decorate-modules-output", package = "teal")` or the [`teal_transform_module()`] documentation.
+#' `vignette("transform-module-output", package = "teal")` or the [`teal::teal_transform_module()`] documentation.
 #'
 #' @examplesShinylive
 #' library(teal.modules.clinical)
@@ -349,7 +362,6 @@ tm_g_lineplot <- 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")
 
   args <- as.list(environment())