standardize the notation for optional parameters (#698)

fixes
#674

R/tm_a_pca.R

@@ -8,8 +8,8 @@
 #' @inheritParams teal::module
 #' @inheritParams shared_params
 #' @param dat (`data_extract_spec` or `list` of multiple `data_extract_spec`)
-#'   specifying columns used to compute PCA.
-#' @param font_size (`numeric`, optional) Specifies font size.
+#' specifying columns used to compute PCA.
+#' @param font_size (`numeric`) optional, specifies font size.
 #' It controls the font size for plot titles, axis labels, and legends.
 #' - If vector of `length == 1` then the font sizes will have a fixed size.
 #' - while vector of `value`, `min`, and `max` allows dynamic adjustment.

R/tm_a_regression.R

@@ -14,8 +14,8 @@
 #' Regressor variables from an incoming dataset with filtering and selecting.
 #' @param response (`data_extract_spec` or `list` of multiple `data_extract_spec`)
 #' Response variables from an incoming dataset with filtering and selecting.
-#' @param default_outlier_label (`character`, optional) The default column selected to label outliers.
-#' @param default_plot_type (`numeric`, optional) Defaults to Response vs Regressor.
+#' @param default_outlier_label (`character`) optional, default column selected to label outliers.
+#' @param default_plot_type (`numeric`) optional, defaults to "Response vs Regressor".
 #' 1. Response vs Regressor
 #' 2. Residuals vs Fitted
 #' 3. Normal Q-Q

R/tm_g_association.R

@@ -15,9 +15,9 @@
 #' to ensure single selection option.
 #' @param vars (`data_extract_spec` or `list` of multiple `data_extract_spec`)
 #' Variables to be associated with the reference variable.
-#' @param show_association (`logical`) optional whether show association of `vars`
+#' @param show_association (`logical`) optional, whether show association of `vars`
 #' with reference variable. Defaults to `TRUE`.
-#' @param distribution_theme,association_theme (`character`) optional `ggplot2` themes to be used by default.
+#' @param distribution_theme,association_theme (`character`) optional, `ggplot2` themes to be used by default.
 #' Default to `"gray"`.
 #'
 #' @templateVar ggnames "Bivariate1", "Bivariate2"

R/tm_g_bivariate.R

@@ -18,31 +18,31 @@
 #' @param y (`data_extract_spec` or `list` of multiple `data_extract_spec`)
 #' Variable names selected to plot along the y-axis by default.
 #' Can be numeric, factor or character.
-#' @param use_density (`logical`, optional) Indicates whether to plot density (`TRUE`) or frequency (`FALSE`).
+#' @param use_density (`logical`) optional, indicates whether to plot density (`TRUE`) or frequency (`FALSE`).
 #' Defaults to frequency (`FALSE`).
-#' @param row_facet (`data_extract_spec` or `list` of multiple `data_extract_spec`, optional)
-#' Variables for row facetting.
-#' @param col_facet (`data_extract_spec` or `list` of multiple `data_extract_spec`, optional)
-#' Variables for column facetting.
-#' @param facet (`logical`, optional) to specify whether the facet encodings `ui` elements are toggled
+#' @param row_facet (`data_extract_spec` or `list` of multiple `data_extract_spec`) optional,
+#' specification of the data variable(s) to use for faceting rows.
+#' @param col_facet (`data_extract_spec` or `list` of multiple `data_extract_spec`) optional,
+#' specification of the data variable(s) to use for faceting columns.
+#' @param facet (`logical`) optional, specifies whether the facet encodings `ui` elements are toggled
 #' on and shown to the user by default. Defaults to `TRUE` if either `row_facet` or `column_facet`
 #' are supplied.
 #' @param color_settings (`logical`) Whether coloring, filling and size should be applied
 #' and `UI` tool offered to the user.
-#' @param color (`data_extract_spec` or `list` of multiple `data_extract_spec`, optional)
-#' Variables selected for the outline color inside the coloring settings.
+#' @param color (`data_extract_spec` or `list` of multiple `data_extract_spec`) optional,
+#' specification of the data variable(s) selected for the outline color inside the coloring settings.
 #' It will be applied when `color_settings` is set to `TRUE`.
-#' @param fill (`data_extract_spec` or `list` of multiple `data_extract_spec`, optional)
-#' Variables selected for the fill color inside the coloring settings.
+#' @param fill (`data_extract_spec` or `list` of multiple `data_extract_spec`) optional,
+#' specification of the data variable(s) selected for the fill color inside the coloring settings.
 #' It will be applied when `color_settings` is set to `TRUE`.
-#' @param size (`data_extract_spec` or `list` of multiple `data_extract_spec`, optional)
-#' Variables selected for the size of `geom_point` plots inside the coloring settings.
+#' @param size (`data_extract_spec` or `list` of multiple `data_extract_spec`) optional,
+#' specification of the data variable(s) selected for the size of `geom_point` plots inside the coloring settings.
 #' It will be applied when `color_settings` is set to `TRUE`.
-#' @param free_x_scales (`logical`, optional) Whether X scaling shall be changeable.
+#' @param free_x_scales (`logical`) optional, whether X scaling shall be changeable.
 #' Does not allow scaling to be changed by default (`FALSE`).
-#' @param free_y_scales (`logical`, optional) Whether Y scaling shall be changeable.
+#' @param free_y_scales (`logical`) optional, whether Y scaling shall be changeable.
 #' Does not allow scaling to be changed by default (`FALSE`).
-#' @param swap_axes (`logical`, optional) Whether to swap X and Y axes. Defaults to `FALSE`.
+#' @param swap_axes (`logical`) optional, whether to swap X and Y axes. Defaults to `FALSE`.
 #'
 #' @inherit shared_params return
 #'

R/tm_g_distribution.R

@@ -14,9 +14,9 @@
 #' Categorical variable used to split the distribution analysis.
 #' @param group_var (`data_extract_spec` or `list` of multiple `data_extract_spec`)
 #' Variable used for faceting plot into multiple panels.
-#' @param freq (`logical`, optional) Whether to display frequency (`TRUE`) or density (`FALSE`).
+#' @param freq (`logical`) optional, whether to display frequency (`TRUE`) or density (`FALSE`).
 #' Defaults to density (`FALSE`).
-#' @param bins (`integer(1)` or `integer(3)`, optional)  Determines the number of bins for the histogram.
+#' @param bins (`integer(1)` or `integer(3)`) optional,  specifies the number of bins for the histogram.
 #' - When the length of `bins` is one: The histogram bins will have a fixed size based on the `bins` provided.
 #' - When the length of `bins` is three: The histogram bins are dynamically adjusted based on vector of `value`, `min`,
 #' and `max`.

R/tm_g_scatterplot.R

@@ -14,19 +14,19 @@
 #' variable names selected to plot along the x-axis by default.
 #' @param y (`data_extract_spec` or `list` of multiple `data_extract_spec`) Specifies
 #' variable names selected to plot along the y-axis by default.
-#' @param color_by (`data_extract_spec` or `list` of multiple `data_extract_spec`, optional)
-#' Defines the color encoding. If `NULL` then no color encoding option will be displayed.
-#' @param size_by (`data_extract_spec` or `list` of multiple `data_extract_spec`, optional)
-#' Defines the point size encoding. If `NULL` then no size encoding option will be displayed.
-#' @param row_facet (`data_extract_spec` or `list` of multiple `data_extract_spec`, optional)
-#' Specifies the variable(s) for faceting rows.
-#' @param col_facet (`data_extract_spec` or `list` of multiple `data_extract_spec`, optional)
-#' Specifies the variable(s) for faceting columns.
-#' @param shape (`character`, optional) A character vector with the names of the
+#' @param color_by (`data_extract_spec` or `list` of multiple `data_extract_spec`) optional,
+#' defines the color encoding. If `NULL` then no color encoding option will be displayed.
+#' @param size_by (`data_extract_spec` or `list` of multiple `data_extract_spec`) optional,
+#' defines the point size encoding. If `NULL` then no size encoding option will be displayed.
+#' @param row_facet (`data_extract_spec` or `list` of multiple `data_extract_spec`) optional,
+#' specifies the variable(s) for faceting rows.
+#' @param col_facet (`data_extract_spec` or `list` of multiple `data_extract_spec`) optional,
+#' specifies the variable(s) for faceting columns.
+#' @param shape (`character`) optional, character vector with the names of the
 #' shape, e.g. `c("triangle", "square", "circle")`. It defaults to `shape_names`. This is a complete list from
 #' `vignette("ggplot2-specs", package="ggplot2")`.
-#' @param max_deg (`integer`, optional) The maximum degree for the polynomial trend line. Must not be less than 1.
-#' @param table_dec (`integer`, optional) Number of decimal places used to round numeric values in the table.
+#' @param max_deg (`integer`) optional, maximum degree for the polynomial trend line. Must not be less than 1.
+#' @param table_dec (`integer`) optional, number of decimal places used to round numeric values in the table.
 #'
 #' @inherit shared_params return
 #'

R/tm_g_scatterplotmatrix.R

@@ -484,8 +484,8 @@ srv_g_scatterplotmatrix <- function(id, data, reporter, filter_panel_api, variab
 #' @param .f (`function`) function that accepts x and y as formula input `~ x + y`.
 #' Default `stats::cor.test`.
 #' @param .f_args (`list`) of arguments to be passed to `.f`.
-#' @param round_stat (`integer(1)`) optional. Number of decimal places to use when rounding the estimate.
-#' @param round_pval (`integer(1)`) optional. Number of decimal places to use when rounding the p-value.
+#' @param round_stat (`integer(1)`) optional, number of decimal places to use when rounding the estimate.
+#' @param round_pval (`integer(1)`) optional, number of decimal places to use when rounding the p-value.
 #'
 #' @return Character with stats. For [stats::cor.test()] correlation coefficient and p-value.
 #'

R/tm_missing_data.R

@@ -10,7 +10,7 @@
 #' @param parent_dataname (`character(1)`) Specifies the parent dataset name. Default is `ADSL` for `CDISC` data.
 #' If provided and exists, enables additional analysis "by subject". For non-`CDISC` data, this parameter can be
 #' ignored.
-#' @param ggtheme (`character`, optional) Specifies the default `ggplot2` theme for plots. Defaults to `classic`.
+#' @param ggtheme (`character`) optional, specifies the default `ggplot2` theme for plots. Defaults to `classic`.
 #'
 #' @templateVar ggnames "Summary Obs", "Summary Patients", "Combinations Main", "Combinations Hist", "By Subject"
 #' @template ggplot2_args_multi

R/tm_outliers.R

@@ -9,8 +9,8 @@
 #'
 #' @param outlier_var (`data_extract_spec` or `list` of multiple `data_extract_spec`)
 #' Specifies variable(s) to be analyzed for outliers.
-#' @param categorical_var (`data_extract_spec` or `list` of multiple `data_extract_spec`, optional)
-#' Specifies the categorical variable(s) to split the selected outlier variables on.
+#' @param categorical_var (`data_extract_spec` or `list` of multiple `data_extract_spec`) optional,
+#' specifies the categorical variable(s) to split the selected outlier variables on.
 #'
 #' @templateVar ggnames "Boxplot","Density Plot","Cumulative Distribution Plot"
 #' @template ggplot2_args_multi

R/utils.R

@@ -3,13 +3,13 @@
 #' Defines common arguments shared across multiple functions in the package
 #' to avoid repetition by using `inheritParams`.
 #'
-#' @param plot_height optional, (`numeric`) Specifies the plot height as a three-element vector of
+#' @param plot_height (`numeric`) optional, specifies the plot height as a three-element vector of
 #' `value`, `min`, and `max` intended for use with a slider UI element.
-#' @param plot_width optional, (`numeric`) Specifies the plot width as a three-element vector of
+#' @param plot_width (`numeric`) optional, specifies the plot width as a three-element vector of
 #' `value`, `min`, and `max` for a slider encoding the plot width.
-#' @param rotate_xaxis_labels optional, (`logical`) Whether to rotate plot X axis labels. Does not
+#' @param rotate_xaxis_labels (`logical`) optional, whether to rotate plot X axis labels. Does not
 #' rotate by default (`FALSE`).
-#' @param ggtheme optional, (`character`) `ggplot2` theme to be used by default. Defaults to `"gray"`.
+#' @param ggtheme (`character`) optional, `ggplot2` theme to be used by default. Defaults to `"gray"`.
 #' @param ggplot2_args (`ggplot2_args`) object created by [teal.widgets::ggplot2_args()]
 #' with settings for the module plot.
 #' The argument is merged with options variable `teal.ggplot2_args` and default module setup.
@@ -20,17 +20,17 @@
 #' The argument is merged with options variable `teal.basic_table_args` and default module setup.
 #'
 #' For more details see the vignette: `vignette("custom-basic-table-arguments", package = "teal.widgets")`
-#' @param pre_output (`shiny.tag`, optional) Text or UI element to be displayed before the module's output,
+#' @param pre_output (`shiny.tag`) optional, text or UI element to be displayed before the module's output,
 #' providing context or a title.
 #'  with text placed before the output to put the output into context. For example a title.
-#' @param post_output (`shiny.tag`, optional) Text or UI element to be displayed after the module's output,
+#' @param post_output (`shiny.tag`) optional, text or UI element to be displayed after the module's output,
 #' adding context or further instructions. Elements like `shiny::helpText()` are useful.
 #'
-#' @param alpha (`integer(1)` or `integer(3)`, optional) Specifies point opacity.
+#' @param alpha (`integer(1)` or `integer(3)`) optional, specifies point opacity.
 #' - When the length of `alpha` is one: the plot points will have a fixed opacity.
 #' - When the length of `alpha` is three: the plot points opacity are dynamically adjusted based on
 #' vector of `value`, `min`, and `max`.
-#' @param size (`integer(1)` or `integer(3)`, optional) Specifies point size.
+#' @param size (`integer(1)` or `integer(3)`) optional, specifies point size.
 #' - When the length of `size` is one: the plot point sizes will have a fixed size.
 #' - When the length of `size` is three: the plot points size are dynamically adjusted based on
 #' vector of `value`, `min`, and `max`.
@@ -235,7 +235,7 @@ variable_type_icons <- function(var_type) {
 #' not work with `devtools`. Therefore, we redefine this method in each package
 #' as needed. Thus, we do not export this method
 #'
-#' @param pattern (`character`) optional regular expression to match the file names to be included.
+#' @param pattern (`character`) optional, regular expression to match the file names to be included.
 #'
 #' @return HTML code that includes `CSS` files.
 #' @keywords internal

man-roxygen/ggplot2_args_multi.R

@@ -0,0 +1,7 @@
+#' @param ggplot2_args (`ggplot2_args`) optional, object created by [`teal.widgets::ggplot2_args()`]
+#'  with settings for all the plots or named list of `ggplot2_args` objects for plot-specific settings.
+#'  The argument is merged with options variable `teal.ggplot2_args` and default module setup.
+#'
+#'  List names should match the following: `c("default", <%=ggnames%>)`.
+#'
+#'  For more details see the vignette: `vignette("custom-ggplot2-arguments", package = "teal.widgets")`.