From f7ecb9ae3c7fb4a4a49df91912852086b8f4297c Mon Sep 17 00:00:00 2001 From: unknown Date: Wed, 28 Feb 2024 16:20:17 +0530 Subject: [PATCH 1/3] consistent otpional notation --- R/tm_a_pca.R | 4 ++-- R/tm_a_regression.R | 4 ++-- R/tm_g_bivariate.R | 30 +++++++++++++------------- R/tm_g_distribution.R | 4 ++-- R/tm_g_scatterplot.R | 22 +++++++++---------- R/tm_g_scatterplotmatrix.R | 4 ++-- R/tm_missing_data.R | 2 +- R/tm_outliers.R | 4 ++-- R/utils.R | 16 +++++++------- man-roxygen/ggplot2_args_multi.R | 2 +- man/get_scatterplotmatrix_stats.Rd | 4 ++-- man/shared_params.Rd | 8 +++---- man/tm_a_pca.Rd | 10 ++++----- man/tm_a_regression.Rd | 12 +++++------ man/tm_data_table.Rd | 4 ++-- man/tm_g_association.Rd | 4 ++-- man/tm_g_bivariate.Rd | 34 +++++++++++++++--------------- man/tm_g_distribution.Rd | 4 ++-- man/tm_g_response.Rd | 4 ++-- man/tm_g_scatterplot.Rd | 30 +++++++++++++------------- man/tm_g_scatterplotmatrix.Rd | 4 ++-- man/tm_missing_data.Rd | 6 +++--- man/tm_outliers.Rd | 8 +++---- man/tm_t_crosstable.Rd | 4 ++-- man/tm_variable_browser.Rd | 4 ++-- 25 files changed, 116 insertions(+), 116 deletions(-) diff --git a/R/tm_a_pca.R b/R/tm_a_pca.R index 5177ca2ca..d8f7e1872 100644 --- a/R/tm_a_pca.R +++ b/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. diff --git a/R/tm_a_regression.R b/R/tm_a_regression.R index c53ad2373..ecd2b16c6 100644 --- a/R/tm_a_regression.R +++ b/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 diff --git a/R/tm_g_bivariate.R b/R/tm_g_bivariate.R index f982bf57a..08bc83101 100644 --- a/R/tm_g_bivariate.R +++ b/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 #' diff --git a/R/tm_g_distribution.R b/R/tm_g_distribution.R index bf77345a9..88afa18f1 100644 --- a/R/tm_g_distribution.R +++ b/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`. diff --git a/R/tm_g_scatterplot.R b/R/tm_g_scatterplot.R index d2369364c..82f1edf8c 100644 --- a/R/tm_g_scatterplot.R +++ b/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 #' diff --git a/R/tm_g_scatterplotmatrix.R b/R/tm_g_scatterplotmatrix.R index e528c00a5..586bd8d83 100644 --- a/R/tm_g_scatterplotmatrix.R +++ b/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. #' diff --git a/R/tm_missing_data.R b/R/tm_missing_data.R index 311a64e44..9c995865b 100644 --- a/R/tm_missing_data.R +++ b/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 diff --git a/R/tm_outliers.R b/R/tm_outliers.R index 488d2b9d1..7f5903165 100644 --- a/R/tm_outliers.R +++ b/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 diff --git a/R/utils.R b/R/utils.R index b1b1661d5..dab35e748 100644 --- a/R/utils.R +++ b/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`. diff --git a/man-roxygen/ggplot2_args_multi.R b/man-roxygen/ggplot2_args_multi.R index 332f0084d..f8f2b39c3 100644 --- a/man-roxygen/ggplot2_args_multi.R +++ b/man-roxygen/ggplot2_args_multi.R @@ -1,4 +1,4 @@ -#' @param ggplot2_args optional, (`ggplot2_args`) object created by [`teal.widgets::ggplot2_args()`] +#' @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. #' diff --git a/man/get_scatterplotmatrix_stats.Rd b/man/get_scatterplotmatrix_stats.Rd index f50928b5c..7cfe9dd2b 100644 --- a/man/get_scatterplotmatrix_stats.Rd +++ b/man/get_scatterplotmatrix_stats.Rd @@ -21,9 +21,9 @@ Default \code{stats::cor.test}.} \item{.f_args}{(\code{list}) of arguments to be passed to \code{.f}.} -\item{round_stat}{(\code{integer(1)}) optional. Number of decimal places to use when rounding the estimate.} +\item{round_stat}{(\code{integer(1)}) optional number of decimal places to use when rounding the estimate.} -\item{round_pval}{(\code{integer(1)}) optional. Number of decimal places to use when rounding the p-value.} +\item{round_pval}{(\code{integer(1)}) optional number of decimal places to use when rounding the p-value.} } \value{ Character with stats. For \code{\link[stats:cor.test]{stats::cor.test()}} correlation coefficient and p-value. diff --git a/man/shared_params.Rd b/man/shared_params.Rd index a31e7e22f..395dbacd5 100644 --- a/man/shared_params.Rd +++ b/man/shared_params.Rd @@ -27,21 +27,21 @@ The argument is merged with options variable \code{teal.basic_table_args} and de For more details see the vignette: \code{vignette("custom-basic-table-arguments", package = "teal.widgets")}} -\item{pre_output}{(\code{shiny.tag}, optional) Text or UI element to be displayed before the module's output, +\item{pre_output}{(\code{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.} -\item{post_output}{(\code{shiny.tag}, optional) Text or UI element to be displayed after the module's output, +\item{post_output}{(\code{shiny.tag}) optional text or UI element to be displayed after the module's output, adding context or further instructions. Elements like \code{shiny::helpText()} are useful.} -\item{alpha}{(\code{integer(1)} or \code{integer(3)}, optional) Specifies point opacity. +\item{alpha}{(\code{integer(1)} or \code{integer(3)}) optional specifies point opacity. \itemize{ \item When the length of \code{alpha} is one: the plot points will have a fixed opacity. \item When the length of \code{alpha} is three: the plot points opacity are dynamically adjusted based on vector of \code{value}, \code{min}, and \code{max}. }} -\item{size}{(\code{integer(1)} or \code{integer(3)}, optional) Specifies point size. +\item{size}{(\code{integer(1)} or \code{integer(3)}) optional specifies point size. \itemize{ \item When the length of \code{size} is one: the plot point sizes will have a fixed size. \item When the length of \code{size} is three: the plot points size are dynamically adjusted based on diff --git a/man/tm_a_pca.Rd b/man/tm_a_pca.Rd index c2d91f5e2..350732603 100644 --- a/man/tm_a_pca.Rd +++ b/man/tm_a_pca.Rd @@ -45,32 +45,32 @@ For more details see the vignette: \code{vignette("custom-ggplot2-arguments", pa \item{rotate_xaxis_labels}{optional, (\code{logical}) Whether to rotate plot X axis labels. Does not rotate by default (\code{FALSE}).} -\item{font_size}{(\code{numeric}, optional) Specifies font size. +\item{font_size}{(\code{numeric}) optional specifies font size. It controls the font size for plot titles, axis labels, and legends. \itemize{ \item If vector of \code{length == 1} then the font sizes will have a fixed size. \item while vector of \code{value}, \code{min}, and \code{max} allows dynamic adjustment. }} -\item{alpha}{(\code{integer(1)} or \code{integer(3)}, optional) Specifies point opacity. +\item{alpha}{(\code{integer(1)} or \code{integer(3)}) optional specifies point opacity. \itemize{ \item When the length of \code{alpha} is one: the plot points will have a fixed opacity. \item When the length of \code{alpha} is three: the plot points opacity are dynamically adjusted based on vector of \code{value}, \code{min}, and \code{max}. }} -\item{size}{(\code{integer(1)} or \code{integer(3)}, optional) Specifies point size. +\item{size}{(\code{integer(1)} or \code{integer(3)}) optional specifies point size. \itemize{ \item When the length of \code{size} is one: the plot point sizes will have a fixed size. \item When the length of \code{size} is three: the plot points size are dynamically adjusted based on vector of \code{value}, \code{min}, and \code{max}. }} -\item{pre_output}{(\code{shiny.tag}, optional) Text or UI element to be displayed before the module's output, +\item{pre_output}{(\code{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.} -\item{post_output}{(\code{shiny.tag}, optional) Text or UI element to be displayed after the module's output, +\item{post_output}{(\code{shiny.tag}) optional text or UI element to be displayed after the module's output, adding context or further instructions. Elements like \code{shiny::helpText()} are useful.} } \value{ diff --git a/man/tm_a_regression.Rd b/man/tm_a_regression.Rd index 0c59a0f66..0ff22c563 100644 --- a/man/tm_a_regression.Rd +++ b/man/tm_a_regression.Rd @@ -37,14 +37,14 @@ Response variables from an incoming dataset with filtering and selecting.} \item{plot_width}{optional, (\code{numeric}) Specifies the plot width as a three-element vector of \code{value}, \code{min}, and \code{max} for a slider encoding the plot width.} -\item{alpha}{(\code{integer(1)} or \code{integer(3)}, optional) Specifies point opacity. +\item{alpha}{(\code{integer(1)} or \code{integer(3)}) optional specifies point opacity. \itemize{ \item When the length of \code{alpha} is one: the plot points will have a fixed opacity. \item When the length of \code{alpha} is three: the plot points opacity are dynamically adjusted based on vector of \code{value}, \code{min}, and \code{max}. }} -\item{size}{(\code{integer(1)} or \code{integer(3)}, optional) Specifies point size. +\item{size}{(\code{integer(1)} or \code{integer(3)}) optional specifies point size. \itemize{ \item When the length of \code{size} is one: the plot point sizes will have a fixed size. \item When the length of \code{size} is three: the plot points size are dynamically adjusted based on @@ -61,14 +61,14 @@ List names should match the following: \verb{c("default", "Response vs Regressor For more details see the vignette: \code{vignette("custom-ggplot2-arguments", package = "teal.widgets")}.} -\item{pre_output}{(\code{shiny.tag}, optional) Text or UI element to be displayed before the module's output, +\item{pre_output}{(\code{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.} -\item{post_output}{(\code{shiny.tag}, optional) Text or UI element to be displayed after the module's output, +\item{post_output}{(\code{shiny.tag}) optional text or UI element to be displayed after the module's output, adding context or further instructions. Elements like \code{shiny::helpText()} are useful.} -\item{default_plot_type}{(\code{numeric}, optional) Defaults to Response vs Regressor. +\item{default_plot_type}{(\code{numeric}) optional defaults to "Response vs Regressor". \enumerate{ \item Response vs Regressor \item Residuals vs Fitted @@ -79,7 +79,7 @@ adding context or further instructions. Elements like \code{shiny::helpText()} a \item Cook's dist vs Leverage }} -\item{default_outlier_label}{(\code{character}, optional) The default column selected to label outliers.} +\item{default_outlier_label}{(\code{character}) optional default column selected to label outliers.} \item{label_segment_threshold}{(\code{numeric(1)} or \code{numeric(3)}) Minimum distance between label and point on the plot that triggers the creation of diff --git a/man/tm_data_table.Rd b/man/tm_data_table.Rd index 06abb22b2..f2f3950df 100644 --- a/man/tm_data_table.Rd +++ b/man/tm_data_table.Rd @@ -40,11 +40,11 @@ Note: Only datasets of the \code{data.frame} class are compatible.} \item{server_rendering}{(\code{logical}) should the data table be rendered server side (see \code{server} argument of \code{\link[DT:dataTableOutput]{DT::renderDataTable()}})} -\item{pre_output}{(\code{shiny.tag}, optional) Text or UI element to be displayed before the module's output, +\item{pre_output}{(\code{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.} -\item{post_output}{(\code{shiny.tag}, optional) Text or UI element to be displayed after the module's output, +\item{post_output}{(\code{shiny.tag}) optional text or UI element to be displayed after the module's output, adding context or further instructions. Elements like \code{shiny::helpText()} are useful.} } \value{ diff --git a/man/tm_g_association.Rd b/man/tm_g_association.Rd index 1222d29d3..202abdeb4 100644 --- a/man/tm_g_association.Rd +++ b/man/tm_g_association.Rd @@ -43,11 +43,11 @@ with reference variable. Defaults to \code{TRUE}.} \item{distribution_theme, association_theme}{(\code{character}) optional \code{ggplot2} themes to be used by default. Default to \code{"gray"}.} -\item{pre_output}{(\code{shiny.tag}, optional) Text or UI element to be displayed before the module's output, +\item{pre_output}{(\code{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.} -\item{post_output}{(\code{shiny.tag}, optional) Text or UI element to be displayed after the module's output, +\item{post_output}{(\code{shiny.tag}) optional text or UI element to be displayed after the module's output, adding context or further instructions. Elements like \code{shiny::helpText()} are useful.} \item{ggplot2_args}{optional, (\code{ggplot2_args}) object created by \code{\link[teal.widgets:ggplot2_args]{teal.widgets::ggplot2_args()}} diff --git a/man/tm_g_bivariate.Rd b/man/tm_g_bivariate.Rd index 62f35aa01..be9558dc8 100644 --- a/man/tm_g_bivariate.Rd +++ b/man/tm_g_bivariate.Rd @@ -41,38 +41,38 @@ No empty selections are allowed.} Variable names selected to plot along the y-axis by default. Can be numeric, factor or character.} -\item{row_facet}{(\code{data_extract_spec} or \code{list} of multiple \code{data_extract_spec}, optional) -Variables for row facetting.} +\item{row_facet}{(\code{data_extract_spec} or \code{list} of multiple \code{data_extract_spec}) optional +specification of the data variable(s) to use for faceting rows.} -\item{col_facet}{(\code{data_extract_spec} or \code{list} of multiple \code{data_extract_spec}, optional) -Variables for column facetting.} +\item{col_facet}{(\code{data_extract_spec} or \code{list} of multiple \code{data_extract_spec}) optional +specification of the data variable(s) to use for faceting columns.} -\item{facet}{(\code{logical}, optional) to specify whether the facet encodings \code{ui} elements are toggled +\item{facet}{(\code{logical}) optional specifies whether the facet encodings \code{ui} elements are toggled on and shown to the user by default. Defaults to \code{TRUE} if either \code{row_facet} or \code{column_facet} are supplied.} -\item{color}{(\code{data_extract_spec} or \code{list} of multiple \code{data_extract_spec}, optional) -Variables selected for the outline color inside the coloring settings. +\item{color}{(\code{data_extract_spec} or \code{list} of multiple \code{data_extract_spec}) optional +specification of the data variable(s) selected for the outline color inside the coloring settings. It will be applied when \code{color_settings} is set to \code{TRUE}.} -\item{fill}{(\code{data_extract_spec} or \code{list} of multiple \code{data_extract_spec}, optional) -Variables selected for the fill color inside the coloring settings. +\item{fill}{(\code{data_extract_spec} or \code{list} of multiple \code{data_extract_spec}) optional +specification of the data variable(s) selected for the fill color inside the coloring settings. It will be applied when \code{color_settings} is set to \code{TRUE}.} -\item{size}{(\code{data_extract_spec} or \code{list} of multiple \code{data_extract_spec}, optional) -Variables selected for the size of \code{geom_point} plots inside the coloring settings. +\item{size}{(\code{data_extract_spec} or \code{list} of multiple \code{data_extract_spec}) optional +specification of the data variable(s) selected for the size of \code{geom_point} plots inside the coloring settings. It will be applied when \code{color_settings} is set to \code{TRUE}.} -\item{use_density}{(\code{logical}, optional) Indicates whether to plot density (\code{TRUE}) or frequency (\code{FALSE}). +\item{use_density}{(\code{logical}) optional indicates whether to plot density (\code{TRUE}) or frequency (\code{FALSE}). Defaults to frequency (\code{FALSE}).} \item{color_settings}{(\code{logical}) Whether coloring, filling and size should be applied and \code{UI} tool offered to the user.} -\item{free_x_scales}{(\code{logical}, optional) Whether X scaling shall be changeable. +\item{free_x_scales}{(\code{logical}) optional whether X scaling shall be changeable. Does not allow scaling to be changed by default (\code{FALSE}).} -\item{free_y_scales}{(\code{logical}, optional) Whether Y scaling shall be changeable. +\item{free_y_scales}{(\code{logical}) optional whether Y scaling shall be changeable. Does not allow scaling to be changed by default (\code{FALSE}).} \item{plot_height}{optional, (\code{numeric}) Specifies the plot height as a three-element vector of @@ -84,7 +84,7 @@ Does not allow scaling to be changed by default (\code{FALSE}).} \item{rotate_xaxis_labels}{optional, (\code{logical}) Whether to rotate plot X axis labels. Does not rotate by default (\code{FALSE}).} -\item{swap_axes}{(\code{logical}, optional) Whether to swap X and Y axes. Defaults to \code{FALSE}.} +\item{swap_axes}{(\code{logical}) optional whether to swap X and Y axes. Defaults to \code{FALSE}.} \item{ggtheme}{optional, (\code{character}) \code{ggplot2} theme to be used by default. Defaults to \code{"gray"}.} @@ -94,11 +94,11 @@ The argument is merged with options variable \code{teal.ggplot2_args} and defaul For more details see the vignette: \code{vignette("custom-ggplot2-arguments", package = "teal.widgets")}} -\item{pre_output}{(\code{shiny.tag}, optional) Text or UI element to be displayed before the module's output, +\item{pre_output}{(\code{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.} -\item{post_output}{(\code{shiny.tag}, optional) Text or UI element to be displayed after the module's output, +\item{post_output}{(\code{shiny.tag}) optional text or UI element to be displayed after the module's output, adding context or further instructions. Elements like \code{shiny::helpText()} are useful.} } \value{ diff --git a/man/tm_g_distribution.Rd b/man/tm_g_distribution.Rd index 53a229e97..4d751a18f 100644 --- a/man/tm_g_distribution.Rd +++ b/man/tm_g_distribution.Rd @@ -32,7 +32,7 @@ Categorical variable used to split the distribution analysis.} \item{group_var}{(\code{data_extract_spec} or \code{list} of multiple \code{data_extract_spec}) Variable used for faceting plot into multiple panels.} -\item{freq}{(\code{logical}, optional) Whether to display frequency (\code{TRUE}) or density (\code{FALSE}). +\item{freq}{(\code{logical}) optional whether to display frequency (\code{TRUE}) or density (\code{FALSE}). Defaults to density (\code{FALSE}).} \item{ggtheme}{optional, (\code{character}) \code{ggplot2} theme to be used by default. Defaults to \code{"gray"}.} @@ -45,7 +45,7 @@ List names should match the following: \code{c("default", "Histogram", "QQplot") For more details see the vignette: \code{vignette("custom-ggplot2-arguments", package = "teal.widgets")}.} -\item{bins}{(\code{integer(1)} or \code{integer(3)}, optional) Determines the number of bins for the histogram. +\item{bins}{(\code{integer(1)} or \code{integer(3)}) optional specifies the number of bins for the histogram. \itemize{ \item When the length of \code{bins} is one: The histogram bins will have a fixed size based on the \code{bins} provided. \item When the length of \code{bins} is three: The histogram bins are dynamically adjusted based on vector of \code{value}, \code{min}, diff --git a/man/tm_g_response.Rd b/man/tm_g_response.Rd index 772736fad..5d95838cf 100644 --- a/man/tm_g_response.Rd +++ b/man/tm_g_response.Rd @@ -74,11 +74,11 @@ The argument is merged with options variable \code{teal.ggplot2_args} and defaul For more details see the vignette: \code{vignette("custom-ggplot2-arguments", package = "teal.widgets")}} -\item{pre_output}{(\code{shiny.tag}, optional) Text or UI element to be displayed before the module's output, +\item{pre_output}{(\code{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.} -\item{post_output}{(\code{shiny.tag}, optional) Text or UI element to be displayed after the module's output, +\item{post_output}{(\code{shiny.tag}) optional text or UI element to be displayed after the module's output, adding context or further instructions. Elements like \code{shiny::helpText()} are useful.} } \value{ diff --git a/man/tm_g_scatterplot.Rd b/man/tm_g_scatterplot.Rd index 815fc0931..f67f5cc85 100644 --- a/man/tm_g_scatterplot.Rd +++ b/man/tm_g_scatterplot.Rd @@ -36,17 +36,17 @@ variable names selected to plot along the x-axis by default.} \item{y}{(\code{data_extract_spec} or \code{list} of multiple \code{data_extract_spec}) Specifies variable names selected to plot along the y-axis by default.} -\item{color_by}{(\code{data_extract_spec} or \code{list} of multiple \code{data_extract_spec}, optional) -Defines the color encoding. If \code{NULL} then no color encoding option will be displayed.} +\item{color_by}{(\code{data_extract_spec} or \code{list} of multiple \code{data_extract_spec}) optional +defines the color encoding. If \code{NULL} then no color encoding option will be displayed.} -\item{size_by}{(\code{data_extract_spec} or \code{list} of multiple \code{data_extract_spec}, optional) -Defines the point size encoding. If \code{NULL} then no size encoding option will be displayed.} +\item{size_by}{(\code{data_extract_spec} or \code{list} of multiple \code{data_extract_spec}) optional +defines the point size encoding. If \code{NULL} then no size encoding option will be displayed.} -\item{row_facet}{(\code{data_extract_spec} or \code{list} of multiple \code{data_extract_spec}, optional) -Specifies the variable(s) for faceting rows.} +\item{row_facet}{(\code{data_extract_spec} or \code{list} of multiple \code{data_extract_spec}) optional +specifies the variable(s) for faceting rows.} -\item{col_facet}{(\code{data_extract_spec} or \code{list} of multiple \code{data_extract_spec}, optional) -Specifies the variable(s) for faceting columns.} +\item{col_facet}{(\code{data_extract_spec} or \code{list} of multiple \code{data_extract_spec}) optional +specifies the variable(s) for faceting columns.} \item{plot_height}{optional, (\code{numeric}) Specifies the plot height as a three-element vector of \code{value}, \code{min}, and \code{max} intended for use with a slider UI element.} @@ -54,39 +54,39 @@ Specifies the variable(s) for faceting columns.} \item{plot_width}{optional, (\code{numeric}) Specifies the plot width as a three-element vector of \code{value}, \code{min}, and \code{max} for a slider encoding the plot width.} -\item{alpha}{(\code{integer(1)} or \code{integer(3)}, optional) Specifies point opacity. +\item{alpha}{(\code{integer(1)} or \code{integer(3)}) optional specifies point opacity. \itemize{ \item When the length of \code{alpha} is one: the plot points will have a fixed opacity. \item When the length of \code{alpha} is three: the plot points opacity are dynamically adjusted based on vector of \code{value}, \code{min}, and \code{max}. }} -\item{shape}{(\code{character}, optional) A character vector with the names of the +\item{shape}{(\code{character}) optional character vector with the names of the shape, e.g. \code{c("triangle", "square", "circle")}. It defaults to \code{shape_names}. This is a complete list from \code{vignette("ggplot2-specs", package="ggplot2")}.} -\item{size}{(\code{integer(1)} or \code{integer(3)}, optional) Specifies point size. +\item{size}{(\code{integer(1)} or \code{integer(3)}) optional specifies point size. \itemize{ \item When the length of \code{size} is one: the plot point sizes will have a fixed size. \item When the length of \code{size} is three: the plot points size are dynamically adjusted based on vector of \code{value}, \code{min}, and \code{max}. }} -\item{max_deg}{(\code{integer}, optional) The maximum degree for the polynomial trend line. Must not be less than 1.} +\item{max_deg}{(\code{integer}) optional maximum degree for the polynomial trend line. Must not be less than 1.} \item{rotate_xaxis_labels}{optional, (\code{logical}) Whether to rotate plot X axis labels. Does not rotate by default (\code{FALSE}).} \item{ggtheme}{optional, (\code{character}) \code{ggplot2} theme to be used by default. Defaults to \code{"gray"}.} -\item{pre_output}{(\code{shiny.tag}, optional) Text or UI element to be displayed before the module's output, +\item{pre_output}{(\code{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.} -\item{post_output}{(\code{shiny.tag}, optional) Text or UI element to be displayed after the module's output, +\item{post_output}{(\code{shiny.tag}) optional text or UI element to be displayed after the module's output, adding context or further instructions. Elements like \code{shiny::helpText()} are useful.} -\item{table_dec}{(\code{integer}, optional) Number of decimal places used to round numeric values in the table.} +\item{table_dec}{(\code{integer}) optional number of decimal places used to round numeric values in the table.} \item{ggplot2_args}{(\code{ggplot2_args}) object created by \code{\link[teal.widgets:ggplot2_args]{teal.widgets::ggplot2_args()}} with settings for the module plot. diff --git a/man/tm_g_scatterplotmatrix.Rd b/man/tm_g_scatterplotmatrix.Rd index 46db4256d..75dfdd22f 100644 --- a/man/tm_g_scatterplotmatrix.Rd +++ b/man/tm_g_scatterplotmatrix.Rd @@ -28,11 +28,11 @@ rendered according to selection order.} \item{plot_width}{optional, (\code{numeric}) Specifies the plot width as a three-element vector of \code{value}, \code{min}, and \code{max} for a slider encoding the plot width.} -\item{pre_output}{(\code{shiny.tag}, optional) Text or UI element to be displayed before the module's output, +\item{pre_output}{(\code{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.} -\item{post_output}{(\code{shiny.tag}, optional) Text or UI element to be displayed after the module's output, +\item{post_output}{(\code{shiny.tag}) optional text or UI element to be displayed after the module's output, adding context or further instructions. Elements like \code{shiny::helpText()} are useful.} } \value{ diff --git a/man/tm_missing_data.Rd b/man/tm_missing_data.Rd index 39900e40d..b1d517326 100644 --- a/man/tm_missing_data.Rd +++ b/man/tm_missing_data.Rd @@ -31,7 +31,7 @@ For \code{modules()} defaults to \code{"root"}. See \code{Details}.} If provided and exists, enables additional analysis "by subject". For non-\code{CDISC} data, this parameter can be ignored.} -\item{ggtheme}{(\code{character}, optional) Specifies the default \code{ggplot2} theme for plots. Defaults to \code{classic}.} +\item{ggtheme}{(\code{character}) optional specifies the default \code{ggplot2} theme for plots. Defaults to \code{classic}.} \item{ggplot2_args}{optional, (\code{ggplot2_args}) object created by \code{\link[teal.widgets:ggplot2_args]{teal.widgets::ggplot2_args()}} with settings for all the plots or named list of \code{ggplot2_args} objects for plot-specific settings. @@ -41,11 +41,11 @@ List names should match the following: \code{c("default", "Summary Obs", "Summar For more details see the vignette: \code{vignette("custom-ggplot2-arguments", package = "teal.widgets")}.} -\item{pre_output}{(\code{shiny.tag}, optional) Text or UI element to be displayed before the module's output, +\item{pre_output}{(\code{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.} -\item{post_output}{(\code{shiny.tag}, optional) Text or UI element to be displayed after the module's output, +\item{post_output}{(\code{shiny.tag}) optional text or UI element to be displayed after the module's output, adding context or further instructions. Elements like \code{shiny::helpText()} are useful.} } \value{ diff --git a/man/tm_outliers.Rd b/man/tm_outliers.Rd index d36ff08ae..ab367f614 100644 --- a/man/tm_outliers.Rd +++ b/man/tm_outliers.Rd @@ -23,8 +23,8 @@ For \code{modules()} defaults to \code{"root"}. See \code{Details}.} \item{outlier_var}{(\code{data_extract_spec} or \code{list} of multiple \code{data_extract_spec}) Specifies variable(s) to be analyzed for outliers.} -\item{categorical_var}{(\code{data_extract_spec} or \code{list} of multiple \code{data_extract_spec}, optional) -Specifies the categorical variable(s) to split the selected outlier variables on.} +\item{categorical_var}{(\code{data_extract_spec} or \code{list} of multiple \code{data_extract_spec}) optional +specifies the categorical variable(s) to split the selected outlier variables on.} \item{ggtheme}{optional, (\code{character}) \code{ggplot2} theme to be used by default. Defaults to \code{"gray"}.} @@ -42,11 +42,11 @@ For more details see the vignette: \code{vignette("custom-ggplot2-arguments", pa \item{plot_width}{optional, (\code{numeric}) Specifies the plot width as a three-element vector of \code{value}, \code{min}, and \code{max} for a slider encoding the plot width.} -\item{pre_output}{(\code{shiny.tag}, optional) Text or UI element to be displayed before the module's output, +\item{pre_output}{(\code{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.} -\item{post_output}{(\code{shiny.tag}, optional) Text or UI element to be displayed after the module's output, +\item{post_output}{(\code{shiny.tag}) optional text or UI element to be displayed after the module's output, adding context or further instructions. Elements like \code{shiny::helpText()} are useful.} } \value{ diff --git a/man/tm_t_crosstable.Rd b/man/tm_t_crosstable.Rd index 4bc8a68a9..b5fbabb78 100644 --- a/man/tm_t_crosstable.Rd +++ b/man/tm_t_crosstable.Rd @@ -37,11 +37,11 @@ Defaults to \code{TRUE}.} Indicates whether to show total column. Defaults to \code{TRUE}.} -\item{pre_output}{(\code{shiny.tag}, optional) Text or UI element to be displayed before the module's output, +\item{pre_output}{(\code{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.} -\item{post_output}{(\code{shiny.tag}, optional) Text or UI element to be displayed after the module's output, +\item{post_output}{(\code{shiny.tag}) optional text or UI element to be displayed after the module's output, adding context or further instructions. Elements like \code{shiny::helpText()} are useful.} \item{basic_table_args}{(\code{basic_table_args}) object created by \code{\link[teal.widgets:basic_table_args]{teal.widgets::basic_table_args()}} diff --git a/man/tm_variable_browser.Rd b/man/tm_variable_browser.Rd index efe5cbb06..1b8c97c09 100644 --- a/man/tm_variable_browser.Rd +++ b/man/tm_variable_browser.Rd @@ -28,11 +28,11 @@ allow users to not show variables in other datasets which exist in this \code{da This is typically used to remove \code{ADSL} columns in \code{CDISC} data. In non \code{CDISC} data this can be ignored. Defaults to \code{"ADSL"}.} -\item{pre_output}{(\code{shiny.tag}, optional) Text or UI element to be displayed before the module's output, +\item{pre_output}{(\code{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.} -\item{post_output}{(\code{shiny.tag}, optional) Text or UI element to be displayed after the module's output, +\item{post_output}{(\code{shiny.tag}) optional text or UI element to be displayed after the module's output, adding context or further instructions. Elements like \code{shiny::helpText()} are useful.} \item{ggplot2_args}{(\code{ggplot2_args}) object created by \code{\link[teal.widgets:ggplot2_args]{teal.widgets::ggplot2_args()}} From c7c916ed6c8bb4cf2903dfdd53894a0c78b8f971 Mon Sep 17 00:00:00 2001 From: unknown Date: Wed, 28 Feb 2024 16:48:43 +0530 Subject: [PATCH 2/3] updating rd --- man/shared_params.Rd | 8 ++++---- man/tm_a_pca.Rd | 10 +++++----- man/tm_a_regression.Rd | 8 ++++---- man/tm_g_association.Rd | 6 +++--- man/tm_g_bivariate.Rd | 8 ++++---- man/tm_g_distribution.Rd | 8 ++++---- man/tm_g_response.Rd | 8 ++++---- man/tm_g_scatterplot.Rd | 8 ++++---- man/tm_g_scatterplotmatrix.Rd | 4 ++-- man/tm_missing_data.Rd | 6 +++--- man/tm_outliers.Rd | 8 ++++---- 11 files changed, 41 insertions(+), 41 deletions(-) diff --git a/man/shared_params.Rd b/man/shared_params.Rd index 395dbacd5..bef0a1d5e 100644 --- a/man/shared_params.Rd +++ b/man/shared_params.Rd @@ -4,16 +4,16 @@ \alias{shared_params} \title{Shared parameters documentation} \arguments{ -\item{plot_height}{optional, (\code{numeric}) Specifies the plot height as a three-element vector of +\item{plot_height}{(\code{numeric}) optional specifies the plot height as a three-element vector of \code{value}, \code{min}, and \code{max} intended for use with a slider UI element.} -\item{plot_width}{optional, (\code{numeric}) Specifies the plot width as a three-element vector of +\item{plot_width}{(\code{numeric}) optional specifies the plot width as a three-element vector of \code{value}, \code{min}, and \code{max} for a slider encoding the plot width.} -\item{rotate_xaxis_labels}{optional, (\code{logical}) Whether to rotate plot X axis labels. Does not +\item{rotate_xaxis_labels}{(\code{logical}) optional whether to rotate plot X axis labels. Does not rotate by default (\code{FALSE}).} -\item{ggtheme}{optional, (\code{character}) \code{ggplot2} theme to be used by default. Defaults to \code{"gray"}.} +\item{ggtheme}{(\code{character}) optional \code{ggplot2} theme to be used by default. Defaults to \code{"gray"}.} \item{ggplot2_args}{(\code{ggplot2_args}) object created by \code{\link[teal.widgets:ggplot2_args]{teal.widgets::ggplot2_args()}} with settings for the module plot. diff --git a/man/tm_a_pca.Rd b/man/tm_a_pca.Rd index 350732603..cc64ea780 100644 --- a/man/tm_a_pca.Rd +++ b/man/tm_a_pca.Rd @@ -26,15 +26,15 @@ For \code{modules()} defaults to \code{"root"}. See \code{Details}.} \item{dat}{(\code{data_extract_spec} or \code{list} of multiple \code{data_extract_spec}) specifying columns used to compute PCA.} -\item{plot_height}{optional, (\code{numeric}) Specifies the plot height as a three-element vector of +\item{plot_height}{(\code{numeric}) optional specifies the plot height as a three-element vector of \code{value}, \code{min}, and \code{max} intended for use with a slider UI element.} -\item{plot_width}{optional, (\code{numeric}) Specifies the plot width as a three-element vector of +\item{plot_width}{(\code{numeric}) optional specifies the plot width as a three-element vector of \code{value}, \code{min}, and \code{max} for a slider encoding the plot width.} -\item{ggtheme}{optional, (\code{character}) \code{ggplot2} theme to be used by default. Defaults to \code{"gray"}.} +\item{ggtheme}{(\code{character}) optional \code{ggplot2} theme to be used by default. Defaults to \code{"gray"}.} -\item{ggplot2_args}{optional, (\code{ggplot2_args}) object created by \code{\link[teal.widgets:ggplot2_args]{teal.widgets::ggplot2_args()}} +\item{ggplot2_args}{(\code{ggplot2_args}) optional object created by \code{\link[teal.widgets:ggplot2_args]{teal.widgets::ggplot2_args()}} with settings for all the plots or named list of \code{ggplot2_args} objects for plot-specific settings. The argument is merged with options variable \code{teal.ggplot2_args} and default module setup. @@ -42,7 +42,7 @@ List names should match the following: \code{c("default", "Elbow plot", "Circle For more details see the vignette: \code{vignette("custom-ggplot2-arguments", package = "teal.widgets")}.} -\item{rotate_xaxis_labels}{optional, (\code{logical}) Whether to rotate plot X axis labels. Does not +\item{rotate_xaxis_labels}{(\code{logical}) optional whether to rotate plot X axis labels. Does not rotate by default (\code{FALSE}).} \item{font_size}{(\code{numeric}) optional specifies font size. diff --git a/man/tm_a_regression.Rd b/man/tm_a_regression.Rd index 0ff22c563..51c7c9e49 100644 --- a/man/tm_a_regression.Rd +++ b/man/tm_a_regression.Rd @@ -31,10 +31,10 @@ Regressor variables from an incoming dataset with filtering and selecting.} \item{response}{(\code{data_extract_spec} or \code{list} of multiple \code{data_extract_spec}) Response variables from an incoming dataset with filtering and selecting.} -\item{plot_height}{optional, (\code{numeric}) Specifies the plot height as a three-element vector of +\item{plot_height}{(\code{numeric}) optional specifies the plot height as a three-element vector of \code{value}, \code{min}, and \code{max} intended for use with a slider UI element.} -\item{plot_width}{optional, (\code{numeric}) Specifies the plot width as a three-element vector of +\item{plot_width}{(\code{numeric}) optional specifies the plot width as a three-element vector of \code{value}, \code{min}, and \code{max} for a slider encoding the plot width.} \item{alpha}{(\code{integer(1)} or \code{integer(3)}) optional specifies point opacity. @@ -51,9 +51,9 @@ vector of \code{value}, \code{min}, and \code{max}. vector of \code{value}, \code{min}, and \code{max}. }} -\item{ggtheme}{optional, (\code{character}) \code{ggplot2} theme to be used by default. Defaults to \code{"gray"}.} +\item{ggtheme}{(\code{character}) optional \code{ggplot2} theme to be used by default. Defaults to \code{"gray"}.} -\item{ggplot2_args}{optional, (\code{ggplot2_args}) object created by \code{\link[teal.widgets:ggplot2_args]{teal.widgets::ggplot2_args()}} +\item{ggplot2_args}{(\code{ggplot2_args}) optional object created by \code{\link[teal.widgets:ggplot2_args]{teal.widgets::ggplot2_args()}} with settings for all the plots or named list of \code{ggplot2_args} objects for plot-specific settings. The argument is merged with options variable \code{teal.ggplot2_args} and default module setup. diff --git a/man/tm_g_association.Rd b/man/tm_g_association.Rd index 202abdeb4..5f7e0c6ee 100644 --- a/man/tm_g_association.Rd +++ b/man/tm_g_association.Rd @@ -34,10 +34,10 @@ Variables to be associated with the reference variable.} \item{show_association}{(\code{logical}) optional whether show association of \code{vars} with reference variable. Defaults to \code{TRUE}.} -\item{plot_height}{optional, (\code{numeric}) Specifies the plot height as a three-element vector of +\item{plot_height}{(\code{numeric}) optional specifies the plot height as a three-element vector of \code{value}, \code{min}, and \code{max} intended for use with a slider UI element.} -\item{plot_width}{optional, (\code{numeric}) Specifies the plot width as a three-element vector of +\item{plot_width}{(\code{numeric}) optional specifies the plot width as a three-element vector of \code{value}, \code{min}, and \code{max} for a slider encoding the plot width.} \item{distribution_theme, association_theme}{(\code{character}) optional \code{ggplot2} themes to be used by default. @@ -50,7 +50,7 @@ with text placed before the output to put the output into context. For example a \item{post_output}{(\code{shiny.tag}) optional text or UI element to be displayed after the module's output, adding context or further instructions. Elements like \code{shiny::helpText()} are useful.} -\item{ggplot2_args}{optional, (\code{ggplot2_args}) object created by \code{\link[teal.widgets:ggplot2_args]{teal.widgets::ggplot2_args()}} +\item{ggplot2_args}{(\code{ggplot2_args}) optional object created by \code{\link[teal.widgets:ggplot2_args]{teal.widgets::ggplot2_args()}} with settings for all the plots or named list of \code{ggplot2_args} objects for plot-specific settings. The argument is merged with options variable \code{teal.ggplot2_args} and default module setup. diff --git a/man/tm_g_bivariate.Rd b/man/tm_g_bivariate.Rd index be9558dc8..ab8c2a13d 100644 --- a/man/tm_g_bivariate.Rd +++ b/man/tm_g_bivariate.Rd @@ -75,18 +75,18 @@ Does not allow scaling to be changed by default (\code{FALSE}).} \item{free_y_scales}{(\code{logical}) optional whether Y scaling shall be changeable. Does not allow scaling to be changed by default (\code{FALSE}).} -\item{plot_height}{optional, (\code{numeric}) Specifies the plot height as a three-element vector of +\item{plot_height}{(\code{numeric}) optional specifies the plot height as a three-element vector of \code{value}, \code{min}, and \code{max} intended for use with a slider UI element.} -\item{plot_width}{optional, (\code{numeric}) Specifies the plot width as a three-element vector of +\item{plot_width}{(\code{numeric}) optional specifies the plot width as a three-element vector of \code{value}, \code{min}, and \code{max} for a slider encoding the plot width.} -\item{rotate_xaxis_labels}{optional, (\code{logical}) Whether to rotate plot X axis labels. Does not +\item{rotate_xaxis_labels}{(\code{logical}) optional whether to rotate plot X axis labels. Does not rotate by default (\code{FALSE}).} \item{swap_axes}{(\code{logical}) optional whether to swap X and Y axes. Defaults to \code{FALSE}.} -\item{ggtheme}{optional, (\code{character}) \code{ggplot2} theme to be used by default. Defaults to \code{"gray"}.} +\item{ggtheme}{(\code{character}) optional \code{ggplot2} theme to be used by default. Defaults to \code{"gray"}.} \item{ggplot2_args}{(\code{ggplot2_args}) object created by \code{\link[teal.widgets:ggplot2_args]{teal.widgets::ggplot2_args()}} with settings for the module plot. diff --git a/man/tm_g_distribution.Rd b/man/tm_g_distribution.Rd index 4d751a18f..ccfe743e6 100644 --- a/man/tm_g_distribution.Rd +++ b/man/tm_g_distribution.Rd @@ -35,9 +35,9 @@ Variable used for faceting plot into multiple panels.} \item{freq}{(\code{logical}) optional whether to display frequency (\code{TRUE}) or density (\code{FALSE}). Defaults to density (\code{FALSE}).} -\item{ggtheme}{optional, (\code{character}) \code{ggplot2} theme to be used by default. Defaults to \code{"gray"}.} +\item{ggtheme}{(\code{character}) optional \code{ggplot2} theme to be used by default. Defaults to \code{"gray"}.} -\item{ggplot2_args}{optional, (\code{ggplot2_args}) object created by \code{\link[teal.widgets:ggplot2_args]{teal.widgets::ggplot2_args()}} +\item{ggplot2_args}{(\code{ggplot2_args}) optional object created by \code{\link[teal.widgets:ggplot2_args]{teal.widgets::ggplot2_args()}} with settings for all the plots or named list of \code{ggplot2_args} objects for plot-specific settings. The argument is merged with options variable \code{teal.ggplot2_args} and default module setup. @@ -53,10 +53,10 @@ and \code{max}. Defaults to \code{c(30L, 1L, 100L)}. }} -\item{plot_height}{optional, (\code{numeric}) Specifies the plot height as a three-element vector of +\item{plot_height}{(\code{numeric}) optional specifies the plot height as a three-element vector of \code{value}, \code{min}, and \code{max} intended for use with a slider UI element.} -\item{plot_width}{optional, (\code{numeric}) Specifies the plot width as a three-element vector of +\item{plot_width}{(\code{numeric}) optional specifies the plot width as a three-element vector of \code{value}, \code{min}, and \code{max} for a slider encoding the plot width.} \item{pre_output}{(\code{shiny.tag}, optional)\cr diff --git a/man/tm_g_response.Rd b/man/tm_g_response.Rd index 5d95838cf..8da393737 100644 --- a/man/tm_g_response.Rd +++ b/man/tm_g_response.Rd @@ -53,20 +53,20 @@ and the \code{response} variable on the y-axis.} Indicates whether to show count labels. Defaults to \code{TRUE}.} -\item{rotate_xaxis_labels}{optional, (\code{logical}) Whether to rotate plot X axis labels. Does not +\item{rotate_xaxis_labels}{(\code{logical}) optional whether to rotate plot X axis labels. Does not rotate by default (\code{FALSE}).} \item{freq}{(\code{logical(1)}) Indicates whether to display frequency (\code{TRUE}) or density (\code{FALSE}). Defaults to density (\code{FALSE}).} -\item{plot_height}{optional, (\code{numeric}) Specifies the plot height as a three-element vector of +\item{plot_height}{(\code{numeric}) optional specifies the plot height as a three-element vector of \code{value}, \code{min}, and \code{max} intended for use with a slider UI element.} -\item{plot_width}{optional, (\code{numeric}) Specifies the plot width as a three-element vector of +\item{plot_width}{(\code{numeric}) optional specifies the plot width as a three-element vector of \code{value}, \code{min}, and \code{max} for a slider encoding the plot width.} -\item{ggtheme}{optional, (\code{character}) \code{ggplot2} theme to be used by default. Defaults to \code{"gray"}.} +\item{ggtheme}{(\code{character}) optional \code{ggplot2} theme to be used by default. Defaults to \code{"gray"}.} \item{ggplot2_args}{(\code{ggplot2_args}) object created by \code{\link[teal.widgets:ggplot2_args]{teal.widgets::ggplot2_args()}} with settings for the module plot. diff --git a/man/tm_g_scatterplot.Rd b/man/tm_g_scatterplot.Rd index f67f5cc85..5c5022773 100644 --- a/man/tm_g_scatterplot.Rd +++ b/man/tm_g_scatterplot.Rd @@ -48,10 +48,10 @@ specifies the variable(s) for faceting rows.} \item{col_facet}{(\code{data_extract_spec} or \code{list} of multiple \code{data_extract_spec}) optional specifies the variable(s) for faceting columns.} -\item{plot_height}{optional, (\code{numeric}) Specifies the plot height as a three-element vector of +\item{plot_height}{(\code{numeric}) optional specifies the plot height as a three-element vector of \code{value}, \code{min}, and \code{max} intended for use with a slider UI element.} -\item{plot_width}{optional, (\code{numeric}) Specifies the plot width as a three-element vector of +\item{plot_width}{(\code{numeric}) optional specifies the plot width as a three-element vector of \code{value}, \code{min}, and \code{max} for a slider encoding the plot width.} \item{alpha}{(\code{integer(1)} or \code{integer(3)}) optional specifies point opacity. @@ -74,10 +74,10 @@ vector of \code{value}, \code{min}, and \code{max}. \item{max_deg}{(\code{integer}) optional maximum degree for the polynomial trend line. Must not be less than 1.} -\item{rotate_xaxis_labels}{optional, (\code{logical}) Whether to rotate plot X axis labels. Does not +\item{rotate_xaxis_labels}{(\code{logical}) optional whether to rotate plot X axis labels. Does not rotate by default (\code{FALSE}).} -\item{ggtheme}{optional, (\code{character}) \code{ggplot2} theme to be used by default. Defaults to \code{"gray"}.} +\item{ggtheme}{(\code{character}) optional \code{ggplot2} theme to be used by default. Defaults to \code{"gray"}.} \item{pre_output}{(\code{shiny.tag}) optional text or UI element to be displayed before the module's output, providing context or a title. diff --git a/man/tm_g_scatterplotmatrix.Rd b/man/tm_g_scatterplotmatrix.Rd index 75dfdd22f..e30cfd394 100644 --- a/man/tm_g_scatterplotmatrix.Rd +++ b/man/tm_g_scatterplotmatrix.Rd @@ -22,10 +22,10 @@ Specifies plotting variables from an incoming dataset with filtering and selecti \code{data_extract_spec} use \code{select_spec(..., ordered = TRUE)} if plot elements should be rendered according to selection order.} -\item{plot_height}{optional, (\code{numeric}) Specifies the plot height as a three-element vector of +\item{plot_height}{(\code{numeric}) optional specifies the plot height as a three-element vector of \code{value}, \code{min}, and \code{max} intended for use with a slider UI element.} -\item{plot_width}{optional, (\code{numeric}) Specifies the plot width as a three-element vector of +\item{plot_width}{(\code{numeric}) optional specifies the plot width as a three-element vector of \code{value}, \code{min}, and \code{max} for a slider encoding the plot width.} \item{pre_output}{(\code{shiny.tag}) optional text or UI element to be displayed before the module's output, diff --git a/man/tm_missing_data.Rd b/man/tm_missing_data.Rd index b1d517326..b02ad01d8 100644 --- a/man/tm_missing_data.Rd +++ b/man/tm_missing_data.Rd @@ -21,10 +21,10 @@ tm_missing_data( \item{label}{(\code{character(1)}) Label shown in the navigation item for the module or module group. For \code{modules()} defaults to \code{"root"}. See \code{Details}.} -\item{plot_height}{optional, (\code{numeric}) Specifies the plot height as a three-element vector of +\item{plot_height}{(\code{numeric}) optional specifies the plot height as a three-element vector of \code{value}, \code{min}, and \code{max} intended for use with a slider UI element.} -\item{plot_width}{optional, (\code{numeric}) Specifies the plot width as a three-element vector of +\item{plot_width}{(\code{numeric}) optional specifies the plot width as a three-element vector of \code{value}, \code{min}, and \code{max} for a slider encoding the plot width.} \item{parent_dataname}{(\code{character(1)}) Specifies the parent dataset name. Default is \code{ADSL} for \code{CDISC} data. @@ -33,7 +33,7 @@ ignored.} \item{ggtheme}{(\code{character}) optional specifies the default \code{ggplot2} theme for plots. Defaults to \code{classic}.} -\item{ggplot2_args}{optional, (\code{ggplot2_args}) object created by \code{\link[teal.widgets:ggplot2_args]{teal.widgets::ggplot2_args()}} +\item{ggplot2_args}{(\code{ggplot2_args}) optional object created by \code{\link[teal.widgets:ggplot2_args]{teal.widgets::ggplot2_args()}} with settings for all the plots or named list of \code{ggplot2_args} objects for plot-specific settings. The argument is merged with options variable \code{teal.ggplot2_args} and default module setup. diff --git a/man/tm_outliers.Rd b/man/tm_outliers.Rd index ab367f614..27bb8ac5c 100644 --- a/man/tm_outliers.Rd +++ b/man/tm_outliers.Rd @@ -26,9 +26,9 @@ Specifies variable(s) to be analyzed for outliers.} \item{categorical_var}{(\code{data_extract_spec} or \code{list} of multiple \code{data_extract_spec}) optional specifies the categorical variable(s) to split the selected outlier variables on.} -\item{ggtheme}{optional, (\code{character}) \code{ggplot2} theme to be used by default. Defaults to \code{"gray"}.} +\item{ggtheme}{(\code{character}) optional \code{ggplot2} theme to be used by default. Defaults to \code{"gray"}.} -\item{ggplot2_args}{optional, (\code{ggplot2_args}) object created by \code{\link[teal.widgets:ggplot2_args]{teal.widgets::ggplot2_args()}} +\item{ggplot2_args}{(\code{ggplot2_args}) optional object created by \code{\link[teal.widgets:ggplot2_args]{teal.widgets::ggplot2_args()}} with settings for all the plots or named list of \code{ggplot2_args} objects for plot-specific settings. The argument is merged with options variable \code{teal.ggplot2_args} and default module setup. @@ -36,10 +36,10 @@ List names should match the following: \code{c("default", "Boxplot","Density Plo For more details see the vignette: \code{vignette("custom-ggplot2-arguments", package = "teal.widgets")}.} -\item{plot_height}{optional, (\code{numeric}) Specifies the plot height as a three-element vector of +\item{plot_height}{(\code{numeric}) optional specifies the plot height as a three-element vector of \code{value}, \code{min}, and \code{max} intended for use with a slider UI element.} -\item{plot_width}{optional, (\code{numeric}) Specifies the plot width as a three-element vector of +\item{plot_width}{(\code{numeric}) optional specifies the plot width as a three-element vector of \code{value}, \code{min}, and \code{max} for a slider encoding the plot width.} \item{pre_output}{(\code{shiny.tag}) optional text or UI element to be displayed before the module's output, From c9ccb2ce4224ac33291abbcedc7611152257fc30 Mon Sep 17 00:00:00 2001 From: unknown Date: Wed, 28 Feb 2024 18:41:26 +0530 Subject: [PATCH 3/3] @m7pr suggestion --- R/tm_a_pca.R | 2 +- R/tm_a_regression.R | 4 ++-- R/tm_g_association.R | 4 ++-- R/tm_g_bivariate.R | 20 +++++++++---------- R/tm_g_distribution.R | 4 ++-- R/tm_g_scatterplot.R | 14 ++++++------- R/tm_g_scatterplotmatrix.R | 4 ++-- R/tm_missing_data.R | 2 +- R/tm_outliers.R | 2 +- R/utils.R | 18 ++++++++--------- man-roxygen/ggplot2_args_multi.R | 2 +- man/get_scatterplotmatrix_stats.Rd | 4 ++-- man/include_css_files.Rd | 2 +- man/shared_params.Rd | 16 +++++++-------- man/tm_a_pca.Rd | 20 +++++++++---------- man/tm_a_regression.Rd | 20 +++++++++---------- man/tm_data_table.Rd | 4 ++-- man/tm_g_association.Rd | 14 ++++++------- man/tm_g_bivariate.Rd | 32 +++++++++++++++--------------- man/tm_g_distribution.Rd | 12 +++++------ man/tm_g_response.Rd | 12 +++++------ man/tm_g_scatterplot.Rd | 30 ++++++++++++++-------------- man/tm_g_scatterplotmatrix.Rd | 8 ++++---- man/tm_missing_data.Rd | 12 +++++------ man/tm_outliers.Rd | 14 ++++++------- man/tm_t_crosstable.Rd | 4 ++-- man/tm_variable_browser.Rd | 4 ++-- 27 files changed, 142 insertions(+), 142 deletions(-) diff --git a/R/tm_a_pca.R b/R/tm_a_pca.R index d8f7e1872..8d7ef14e2 100644 --- a/R/tm_a_pca.R +++ b/R/tm_a_pca.R @@ -9,7 +9,7 @@ #' @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. +#' @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. diff --git a/R/tm_a_regression.R b/R/tm_a_regression.R index ecd2b16c6..9093d3919 100644 --- a/R/tm_a_regression.R +++ b/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 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 diff --git a/R/tm_g_association.R b/R/tm_g_association.R index a8aa35e5d..9aa928606 100644 --- a/R/tm_g_association.R +++ b/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" diff --git a/R/tm_g_bivariate.R b/R/tm_g_bivariate.R index 08bc83101..36a6c900e 100644 --- a/R/tm_g_bivariate.R +++ b/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 +#' @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 +#' @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 +#' @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 +#' @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 +#' @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 +#' @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 #' diff --git a/R/tm_g_distribution.R b/R/tm_g_distribution.R index 88afa18f1..edac703e8 100644 --- a/R/tm_g_distribution.R +++ b/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 specifies 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`. diff --git a/R/tm_g_scatterplot.R b/R/tm_g_scatterplot.R index 82f1edf8c..00efed7cf 100644 --- a/R/tm_g_scatterplot.R +++ b/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 +#' @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 +#' @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 +#' @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 +#' @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 +#' @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 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 #' diff --git a/R/tm_g_scatterplotmatrix.R b/R/tm_g_scatterplotmatrix.R index 586bd8d83..68115ddff 100644 --- a/R/tm_g_scatterplotmatrix.R +++ b/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. #' diff --git a/R/tm_missing_data.R b/R/tm_missing_data.R index 9c995865b..9af5189f5 100644 --- a/R/tm_missing_data.R +++ b/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 diff --git a/R/tm_outliers.R b/R/tm_outliers.R index 7f5903165..616f81840 100644 --- a/R/tm_outliers.R +++ b/R/tm_outliers.R @@ -9,7 +9,7 @@ #' #' @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 +#' @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" diff --git a/R/utils.R b/R/utils.R index dab35e748..71f822ff4 100644 --- a/R/utils.R +++ b/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 (`numeric`) optional 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 (`numeric`) optional 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 (`logical`) optional 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 (`character`) optional `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 diff --git a/man-roxygen/ggplot2_args_multi.R b/man-roxygen/ggplot2_args_multi.R index f8f2b39c3..dc0497942 100644 --- a/man-roxygen/ggplot2_args_multi.R +++ b/man-roxygen/ggplot2_args_multi.R @@ -1,4 +1,4 @@ -#' @param ggplot2_args (`ggplot2_args`) optional object created by [`teal.widgets::ggplot2_args()`] +#' @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. #' diff --git a/man/get_scatterplotmatrix_stats.Rd b/man/get_scatterplotmatrix_stats.Rd index 7cfe9dd2b..176b24cb1 100644 --- a/man/get_scatterplotmatrix_stats.Rd +++ b/man/get_scatterplotmatrix_stats.Rd @@ -21,9 +21,9 @@ Default \code{stats::cor.test}.} \item{.f_args}{(\code{list}) of arguments to be passed to \code{.f}.} -\item{round_stat}{(\code{integer(1)}) optional number of decimal places to use when rounding the estimate.} +\item{round_stat}{(\code{integer(1)}) optional, number of decimal places to use when rounding the estimate.} -\item{round_pval}{(\code{integer(1)}) optional number of decimal places to use when rounding the p-value.} +\item{round_pval}{(\code{integer(1)}) optional, number of decimal places to use when rounding the p-value.} } \value{ Character with stats. For \code{\link[stats:cor.test]{stats::cor.test()}} correlation coefficient and p-value. diff --git a/man/include_css_files.Rd b/man/include_css_files.Rd index 44c46e76d..5065250b3 100644 --- a/man/include_css_files.Rd +++ b/man/include_css_files.Rd @@ -7,7 +7,7 @@ include_css_files(pattern = "*") } \arguments{ -\item{pattern}{(\code{character}) optional regular expression to match the file names to be included.} +\item{pattern}{(\code{character}) optional, regular expression to match the file names to be included.} } \value{ HTML code that includes \code{CSS} files. diff --git a/man/shared_params.Rd b/man/shared_params.Rd index bef0a1d5e..1ea6b7094 100644 --- a/man/shared_params.Rd +++ b/man/shared_params.Rd @@ -4,16 +4,16 @@ \alias{shared_params} \title{Shared parameters documentation} \arguments{ -\item{plot_height}{(\code{numeric}) optional specifies the plot height as a three-element vector of +\item{plot_height}{(\code{numeric}) optional, specifies the plot height as a three-element vector of \code{value}, \code{min}, and \code{max} intended for use with a slider UI element.} -\item{plot_width}{(\code{numeric}) optional specifies the plot width as a three-element vector of +\item{plot_width}{(\code{numeric}) optional, specifies the plot width as a three-element vector of \code{value}, \code{min}, and \code{max} for a slider encoding the plot width.} -\item{rotate_xaxis_labels}{(\code{logical}) optional whether to rotate plot X axis labels. Does not +\item{rotate_xaxis_labels}{(\code{logical}) optional, whether to rotate plot X axis labels. Does not rotate by default (\code{FALSE}).} -\item{ggtheme}{(\code{character}) optional \code{ggplot2} theme to be used by default. Defaults to \code{"gray"}.} +\item{ggtheme}{(\code{character}) optional, \code{ggplot2} theme to be used by default. Defaults to \code{"gray"}.} \item{ggplot2_args}{(\code{ggplot2_args}) object created by \code{\link[teal.widgets:ggplot2_args]{teal.widgets::ggplot2_args()}} with settings for the module plot. @@ -27,21 +27,21 @@ The argument is merged with options variable \code{teal.basic_table_args} and de For more details see the vignette: \code{vignette("custom-basic-table-arguments", package = "teal.widgets")}} -\item{pre_output}{(\code{shiny.tag}) optional text or UI element to be displayed before the module's output, +\item{pre_output}{(\code{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.} -\item{post_output}{(\code{shiny.tag}) optional text or UI element to be displayed after the module's output, +\item{post_output}{(\code{shiny.tag}) optional, text or UI element to be displayed after the module's output, adding context or further instructions. Elements like \code{shiny::helpText()} are useful.} -\item{alpha}{(\code{integer(1)} or \code{integer(3)}) optional specifies point opacity. +\item{alpha}{(\code{integer(1)} or \code{integer(3)}) optional, specifies point opacity. \itemize{ \item When the length of \code{alpha} is one: the plot points will have a fixed opacity. \item When the length of \code{alpha} is three: the plot points opacity are dynamically adjusted based on vector of \code{value}, \code{min}, and \code{max}. }} -\item{size}{(\code{integer(1)} or \code{integer(3)}) optional specifies point size. +\item{size}{(\code{integer(1)} or \code{integer(3)}) optional, specifies point size. \itemize{ \item When the length of \code{size} is one: the plot point sizes will have a fixed size. \item When the length of \code{size} is three: the plot points size are dynamically adjusted based on diff --git a/man/tm_a_pca.Rd b/man/tm_a_pca.Rd index cc64ea780..a4fa1e679 100644 --- a/man/tm_a_pca.Rd +++ b/man/tm_a_pca.Rd @@ -26,15 +26,15 @@ For \code{modules()} defaults to \code{"root"}. See \code{Details}.} \item{dat}{(\code{data_extract_spec} or \code{list} of multiple \code{data_extract_spec}) specifying columns used to compute PCA.} -\item{plot_height}{(\code{numeric}) optional specifies the plot height as a three-element vector of +\item{plot_height}{(\code{numeric}) optional, specifies the plot height as a three-element vector of \code{value}, \code{min}, and \code{max} intended for use with a slider UI element.} -\item{plot_width}{(\code{numeric}) optional specifies the plot width as a three-element vector of +\item{plot_width}{(\code{numeric}) optional, specifies the plot width as a three-element vector of \code{value}, \code{min}, and \code{max} for a slider encoding the plot width.} -\item{ggtheme}{(\code{character}) optional \code{ggplot2} theme to be used by default. Defaults to \code{"gray"}.} +\item{ggtheme}{(\code{character}) optional, \code{ggplot2} theme to be used by default. Defaults to \code{"gray"}.} -\item{ggplot2_args}{(\code{ggplot2_args}) optional object created by \code{\link[teal.widgets:ggplot2_args]{teal.widgets::ggplot2_args()}} +\item{ggplot2_args}{(\code{ggplot2_args}) optional, object created by \code{\link[teal.widgets:ggplot2_args]{teal.widgets::ggplot2_args()}} with settings for all the plots or named list of \code{ggplot2_args} objects for plot-specific settings. The argument is merged with options variable \code{teal.ggplot2_args} and default module setup. @@ -42,35 +42,35 @@ List names should match the following: \code{c("default", "Elbow plot", "Circle For more details see the vignette: \code{vignette("custom-ggplot2-arguments", package = "teal.widgets")}.} -\item{rotate_xaxis_labels}{(\code{logical}) optional whether to rotate plot X axis labels. Does not +\item{rotate_xaxis_labels}{(\code{logical}) optional, whether to rotate plot X axis labels. Does not rotate by default (\code{FALSE}).} -\item{font_size}{(\code{numeric}) optional specifies font size. +\item{font_size}{(\code{numeric}) optional, specifies font size. It controls the font size for plot titles, axis labels, and legends. \itemize{ \item If vector of \code{length == 1} then the font sizes will have a fixed size. \item while vector of \code{value}, \code{min}, and \code{max} allows dynamic adjustment. }} -\item{alpha}{(\code{integer(1)} or \code{integer(3)}) optional specifies point opacity. +\item{alpha}{(\code{integer(1)} or \code{integer(3)}) optional, specifies point opacity. \itemize{ \item When the length of \code{alpha} is one: the plot points will have a fixed opacity. \item When the length of \code{alpha} is three: the plot points opacity are dynamically adjusted based on vector of \code{value}, \code{min}, and \code{max}. }} -\item{size}{(\code{integer(1)} or \code{integer(3)}) optional specifies point size. +\item{size}{(\code{integer(1)} or \code{integer(3)}) optional, specifies point size. \itemize{ \item When the length of \code{size} is one: the plot point sizes will have a fixed size. \item When the length of \code{size} is three: the plot points size are dynamically adjusted based on vector of \code{value}, \code{min}, and \code{max}. }} -\item{pre_output}{(\code{shiny.tag}) optional text or UI element to be displayed before the module's output, +\item{pre_output}{(\code{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.} -\item{post_output}{(\code{shiny.tag}) optional text or UI element to be displayed after the module's output, +\item{post_output}{(\code{shiny.tag}) optional, text or UI element to be displayed after the module's output, adding context or further instructions. Elements like \code{shiny::helpText()} are useful.} } \value{ diff --git a/man/tm_a_regression.Rd b/man/tm_a_regression.Rd index 51c7c9e49..dc4f458f3 100644 --- a/man/tm_a_regression.Rd +++ b/man/tm_a_regression.Rd @@ -31,29 +31,29 @@ Regressor variables from an incoming dataset with filtering and selecting.} \item{response}{(\code{data_extract_spec} or \code{list} of multiple \code{data_extract_spec}) Response variables from an incoming dataset with filtering and selecting.} -\item{plot_height}{(\code{numeric}) optional specifies the plot height as a three-element vector of +\item{plot_height}{(\code{numeric}) optional, specifies the plot height as a three-element vector of \code{value}, \code{min}, and \code{max} intended for use with a slider UI element.} -\item{plot_width}{(\code{numeric}) optional specifies the plot width as a three-element vector of +\item{plot_width}{(\code{numeric}) optional, specifies the plot width as a three-element vector of \code{value}, \code{min}, and \code{max} for a slider encoding the plot width.} -\item{alpha}{(\code{integer(1)} or \code{integer(3)}) optional specifies point opacity. +\item{alpha}{(\code{integer(1)} or \code{integer(3)}) optional, specifies point opacity. \itemize{ \item When the length of \code{alpha} is one: the plot points will have a fixed opacity. \item When the length of \code{alpha} is three: the plot points opacity are dynamically adjusted based on vector of \code{value}, \code{min}, and \code{max}. }} -\item{size}{(\code{integer(1)} or \code{integer(3)}) optional specifies point size. +\item{size}{(\code{integer(1)} or \code{integer(3)}) optional, specifies point size. \itemize{ \item When the length of \code{size} is one: the plot point sizes will have a fixed size. \item When the length of \code{size} is three: the plot points size are dynamically adjusted based on vector of \code{value}, \code{min}, and \code{max}. }} -\item{ggtheme}{(\code{character}) optional \code{ggplot2} theme to be used by default. Defaults to \code{"gray"}.} +\item{ggtheme}{(\code{character}) optional, \code{ggplot2} theme to be used by default. Defaults to \code{"gray"}.} -\item{ggplot2_args}{(\code{ggplot2_args}) optional object created by \code{\link[teal.widgets:ggplot2_args]{teal.widgets::ggplot2_args()}} +\item{ggplot2_args}{(\code{ggplot2_args}) optional, object created by \code{\link[teal.widgets:ggplot2_args]{teal.widgets::ggplot2_args()}} with settings for all the plots or named list of \code{ggplot2_args} objects for plot-specific settings. The argument is merged with options variable \code{teal.ggplot2_args} and default module setup. @@ -61,14 +61,14 @@ List names should match the following: \verb{c("default", "Response vs Regressor For more details see the vignette: \code{vignette("custom-ggplot2-arguments", package = "teal.widgets")}.} -\item{pre_output}{(\code{shiny.tag}) optional text or UI element to be displayed before the module's output, +\item{pre_output}{(\code{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.} -\item{post_output}{(\code{shiny.tag}) optional text or UI element to be displayed after the module's output, +\item{post_output}{(\code{shiny.tag}) optional, text or UI element to be displayed after the module's output, adding context or further instructions. Elements like \code{shiny::helpText()} are useful.} -\item{default_plot_type}{(\code{numeric}) optional defaults to "Response vs Regressor". +\item{default_plot_type}{(\code{numeric}) optional, defaults to "Response vs Regressor". \enumerate{ \item Response vs Regressor \item Residuals vs Fitted @@ -79,7 +79,7 @@ adding context or further instructions. Elements like \code{shiny::helpText()} a \item Cook's dist vs Leverage }} -\item{default_outlier_label}{(\code{character}) optional default column selected to label outliers.} +\item{default_outlier_label}{(\code{character}) optional, default column selected to label outliers.} \item{label_segment_threshold}{(\code{numeric(1)} or \code{numeric(3)}) Minimum distance between label and point on the plot that triggers the creation of diff --git a/man/tm_data_table.Rd b/man/tm_data_table.Rd index f2f3950df..f9e799750 100644 --- a/man/tm_data_table.Rd +++ b/man/tm_data_table.Rd @@ -40,11 +40,11 @@ Note: Only datasets of the \code{data.frame} class are compatible.} \item{server_rendering}{(\code{logical}) should the data table be rendered server side (see \code{server} argument of \code{\link[DT:dataTableOutput]{DT::renderDataTable()}})} -\item{pre_output}{(\code{shiny.tag}) optional text or UI element to be displayed before the module's output, +\item{pre_output}{(\code{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.} -\item{post_output}{(\code{shiny.tag}) optional text or UI element to be displayed after the module's output, +\item{post_output}{(\code{shiny.tag}) optional, text or UI element to be displayed after the module's output, adding context or further instructions. Elements like \code{shiny::helpText()} are useful.} } \value{ diff --git a/man/tm_g_association.Rd b/man/tm_g_association.Rd index 5f7e0c6ee..ef47169a7 100644 --- a/man/tm_g_association.Rd +++ b/man/tm_g_association.Rd @@ -31,26 +31,26 @@ to ensure single selection option.} \item{vars}{(\code{data_extract_spec} or \code{list} of multiple \code{data_extract_spec}) Variables to be associated with the reference variable.} -\item{show_association}{(\code{logical}) optional whether show association of \code{vars} +\item{show_association}{(\code{logical}) optional, whether show association of \code{vars} with reference variable. Defaults to \code{TRUE}.} -\item{plot_height}{(\code{numeric}) optional specifies the plot height as a three-element vector of +\item{plot_height}{(\code{numeric}) optional, specifies the plot height as a three-element vector of \code{value}, \code{min}, and \code{max} intended for use with a slider UI element.} -\item{plot_width}{(\code{numeric}) optional specifies the plot width as a three-element vector of +\item{plot_width}{(\code{numeric}) optional, specifies the plot width as a three-element vector of \code{value}, \code{min}, and \code{max} for a slider encoding the plot width.} -\item{distribution_theme, association_theme}{(\code{character}) optional \code{ggplot2} themes to be used by default. +\item{distribution_theme, association_theme}{(\code{character}) optional, \code{ggplot2} themes to be used by default. Default to \code{"gray"}.} -\item{pre_output}{(\code{shiny.tag}) optional text or UI element to be displayed before the module's output, +\item{pre_output}{(\code{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.} -\item{post_output}{(\code{shiny.tag}) optional text or UI element to be displayed after the module's output, +\item{post_output}{(\code{shiny.tag}) optional, text or UI element to be displayed after the module's output, adding context or further instructions. Elements like \code{shiny::helpText()} are useful.} -\item{ggplot2_args}{(\code{ggplot2_args}) optional object created by \code{\link[teal.widgets:ggplot2_args]{teal.widgets::ggplot2_args()}} +\item{ggplot2_args}{(\code{ggplot2_args}) optional, object created by \code{\link[teal.widgets:ggplot2_args]{teal.widgets::ggplot2_args()}} with settings for all the plots or named list of \code{ggplot2_args} objects for plot-specific settings. The argument is merged with options variable \code{teal.ggplot2_args} and default module setup. diff --git a/man/tm_g_bivariate.Rd b/man/tm_g_bivariate.Rd index ab8c2a13d..a88344f08 100644 --- a/man/tm_g_bivariate.Rd +++ b/man/tm_g_bivariate.Rd @@ -41,52 +41,52 @@ No empty selections are allowed.} Variable names selected to plot along the y-axis by default. Can be numeric, factor or character.} -\item{row_facet}{(\code{data_extract_spec} or \code{list} of multiple \code{data_extract_spec}) optional +\item{row_facet}{(\code{data_extract_spec} or \code{list} of multiple \code{data_extract_spec}) optional, specification of the data variable(s) to use for faceting rows.} -\item{col_facet}{(\code{data_extract_spec} or \code{list} of multiple \code{data_extract_spec}) optional +\item{col_facet}{(\code{data_extract_spec} or \code{list} of multiple \code{data_extract_spec}) optional, specification of the data variable(s) to use for faceting columns.} -\item{facet}{(\code{logical}) optional specifies whether the facet encodings \code{ui} elements are toggled +\item{facet}{(\code{logical}) optional, specifies whether the facet encodings \code{ui} elements are toggled on and shown to the user by default. Defaults to \code{TRUE} if either \code{row_facet} or \code{column_facet} are supplied.} -\item{color}{(\code{data_extract_spec} or \code{list} of multiple \code{data_extract_spec}) optional +\item{color}{(\code{data_extract_spec} or \code{list} of multiple \code{data_extract_spec}) optional, specification of the data variable(s) selected for the outline color inside the coloring settings. It will be applied when \code{color_settings} is set to \code{TRUE}.} -\item{fill}{(\code{data_extract_spec} or \code{list} of multiple \code{data_extract_spec}) optional +\item{fill}{(\code{data_extract_spec} or \code{list} of multiple \code{data_extract_spec}) optional, specification of the data variable(s) selected for the fill color inside the coloring settings. It will be applied when \code{color_settings} is set to \code{TRUE}.} -\item{size}{(\code{data_extract_spec} or \code{list} of multiple \code{data_extract_spec}) optional +\item{size}{(\code{data_extract_spec} or \code{list} of multiple \code{data_extract_spec}) optional, specification of the data variable(s) selected for the size of \code{geom_point} plots inside the coloring settings. It will be applied when \code{color_settings} is set to \code{TRUE}.} -\item{use_density}{(\code{logical}) optional indicates whether to plot density (\code{TRUE}) or frequency (\code{FALSE}). +\item{use_density}{(\code{logical}) optional, indicates whether to plot density (\code{TRUE}) or frequency (\code{FALSE}). Defaults to frequency (\code{FALSE}).} \item{color_settings}{(\code{logical}) Whether coloring, filling and size should be applied and \code{UI} tool offered to the user.} -\item{free_x_scales}{(\code{logical}) optional whether X scaling shall be changeable. +\item{free_x_scales}{(\code{logical}) optional, whether X scaling shall be changeable. Does not allow scaling to be changed by default (\code{FALSE}).} -\item{free_y_scales}{(\code{logical}) optional whether Y scaling shall be changeable. +\item{free_y_scales}{(\code{logical}) optional, whether Y scaling shall be changeable. Does not allow scaling to be changed by default (\code{FALSE}).} -\item{plot_height}{(\code{numeric}) optional specifies the plot height as a three-element vector of +\item{plot_height}{(\code{numeric}) optional, specifies the plot height as a three-element vector of \code{value}, \code{min}, and \code{max} intended for use with a slider UI element.} -\item{plot_width}{(\code{numeric}) optional specifies the plot width as a three-element vector of +\item{plot_width}{(\code{numeric}) optional, specifies the plot width as a three-element vector of \code{value}, \code{min}, and \code{max} for a slider encoding the plot width.} -\item{rotate_xaxis_labels}{(\code{logical}) optional whether to rotate plot X axis labels. Does not +\item{rotate_xaxis_labels}{(\code{logical}) optional, whether to rotate plot X axis labels. Does not rotate by default (\code{FALSE}).} -\item{swap_axes}{(\code{logical}) optional whether to swap X and Y axes. Defaults to \code{FALSE}.} +\item{swap_axes}{(\code{logical}) optional, whether to swap X and Y axes. Defaults to \code{FALSE}.} -\item{ggtheme}{(\code{character}) optional \code{ggplot2} theme to be used by default. Defaults to \code{"gray"}.} +\item{ggtheme}{(\code{character}) optional, \code{ggplot2} theme to be used by default. Defaults to \code{"gray"}.} \item{ggplot2_args}{(\code{ggplot2_args}) object created by \code{\link[teal.widgets:ggplot2_args]{teal.widgets::ggplot2_args()}} with settings for the module plot. @@ -94,11 +94,11 @@ The argument is merged with options variable \code{teal.ggplot2_args} and defaul For more details see the vignette: \code{vignette("custom-ggplot2-arguments", package = "teal.widgets")}} -\item{pre_output}{(\code{shiny.tag}) optional text or UI element to be displayed before the module's output, +\item{pre_output}{(\code{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.} -\item{post_output}{(\code{shiny.tag}) optional text or UI element to be displayed after the module's output, +\item{post_output}{(\code{shiny.tag}) optional, text or UI element to be displayed after the module's output, adding context or further instructions. Elements like \code{shiny::helpText()} are useful.} } \value{ diff --git a/man/tm_g_distribution.Rd b/man/tm_g_distribution.Rd index ccfe743e6..df5c8775d 100644 --- a/man/tm_g_distribution.Rd +++ b/man/tm_g_distribution.Rd @@ -32,12 +32,12 @@ Categorical variable used to split the distribution analysis.} \item{group_var}{(\code{data_extract_spec} or \code{list} of multiple \code{data_extract_spec}) Variable used for faceting plot into multiple panels.} -\item{freq}{(\code{logical}) optional whether to display frequency (\code{TRUE}) or density (\code{FALSE}). +\item{freq}{(\code{logical}) optional, whether to display frequency (\code{TRUE}) or density (\code{FALSE}). Defaults to density (\code{FALSE}).} -\item{ggtheme}{(\code{character}) optional \code{ggplot2} theme to be used by default. Defaults to \code{"gray"}.} +\item{ggtheme}{(\code{character}) optional, \code{ggplot2} theme to be used by default. Defaults to \code{"gray"}.} -\item{ggplot2_args}{(\code{ggplot2_args}) optional object created by \code{\link[teal.widgets:ggplot2_args]{teal.widgets::ggplot2_args()}} +\item{ggplot2_args}{(\code{ggplot2_args}) optional, object created by \code{\link[teal.widgets:ggplot2_args]{teal.widgets::ggplot2_args()}} with settings for all the plots or named list of \code{ggplot2_args} objects for plot-specific settings. The argument is merged with options variable \code{teal.ggplot2_args} and default module setup. @@ -45,7 +45,7 @@ List names should match the following: \code{c("default", "Histogram", "QQplot") For more details see the vignette: \code{vignette("custom-ggplot2-arguments", package = "teal.widgets")}.} -\item{bins}{(\code{integer(1)} or \code{integer(3)}) optional specifies the number of bins for the histogram. +\item{bins}{(\code{integer(1)} or \code{integer(3)}) optional, specifies the number of bins for the histogram. \itemize{ \item When the length of \code{bins} is one: The histogram bins will have a fixed size based on the \code{bins} provided. \item When the length of \code{bins} is three: The histogram bins are dynamically adjusted based on vector of \code{value}, \code{min}, @@ -53,10 +53,10 @@ and \code{max}. Defaults to \code{c(30L, 1L, 100L)}. }} -\item{plot_height}{(\code{numeric}) optional specifies the plot height as a three-element vector of +\item{plot_height}{(\code{numeric}) optional, specifies the plot height as a three-element vector of \code{value}, \code{min}, and \code{max} intended for use with a slider UI element.} -\item{plot_width}{(\code{numeric}) optional specifies the plot width as a three-element vector of +\item{plot_width}{(\code{numeric}) optional, specifies the plot width as a three-element vector of \code{value}, \code{min}, and \code{max} for a slider encoding the plot width.} \item{pre_output}{(\code{shiny.tag}, optional)\cr diff --git a/man/tm_g_response.Rd b/man/tm_g_response.Rd index 8da393737..6e9e1e93c 100644 --- a/man/tm_g_response.Rd +++ b/man/tm_g_response.Rd @@ -53,20 +53,20 @@ and the \code{response} variable on the y-axis.} Indicates whether to show count labels. Defaults to \code{TRUE}.} -\item{rotate_xaxis_labels}{(\code{logical}) optional whether to rotate plot X axis labels. Does not +\item{rotate_xaxis_labels}{(\code{logical}) optional, whether to rotate plot X axis labels. Does not rotate by default (\code{FALSE}).} \item{freq}{(\code{logical(1)}) Indicates whether to display frequency (\code{TRUE}) or density (\code{FALSE}). Defaults to density (\code{FALSE}).} -\item{plot_height}{(\code{numeric}) optional specifies the plot height as a three-element vector of +\item{plot_height}{(\code{numeric}) optional, specifies the plot height as a three-element vector of \code{value}, \code{min}, and \code{max} intended for use with a slider UI element.} -\item{plot_width}{(\code{numeric}) optional specifies the plot width as a three-element vector of +\item{plot_width}{(\code{numeric}) optional, specifies the plot width as a three-element vector of \code{value}, \code{min}, and \code{max} for a slider encoding the plot width.} -\item{ggtheme}{(\code{character}) optional \code{ggplot2} theme to be used by default. Defaults to \code{"gray"}.} +\item{ggtheme}{(\code{character}) optional, \code{ggplot2} theme to be used by default. Defaults to \code{"gray"}.} \item{ggplot2_args}{(\code{ggplot2_args}) object created by \code{\link[teal.widgets:ggplot2_args]{teal.widgets::ggplot2_args()}} with settings for the module plot. @@ -74,11 +74,11 @@ The argument is merged with options variable \code{teal.ggplot2_args} and defaul For more details see the vignette: \code{vignette("custom-ggplot2-arguments", package = "teal.widgets")}} -\item{pre_output}{(\code{shiny.tag}) optional text or UI element to be displayed before the module's output, +\item{pre_output}{(\code{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.} -\item{post_output}{(\code{shiny.tag}) optional text or UI element to be displayed after the module's output, +\item{post_output}{(\code{shiny.tag}) optional, text or UI element to be displayed after the module's output, adding context or further instructions. Elements like \code{shiny::helpText()} are useful.} } \value{ diff --git a/man/tm_g_scatterplot.Rd b/man/tm_g_scatterplot.Rd index 5c5022773..466294031 100644 --- a/man/tm_g_scatterplot.Rd +++ b/man/tm_g_scatterplot.Rd @@ -36,57 +36,57 @@ variable names selected to plot along the x-axis by default.} \item{y}{(\code{data_extract_spec} or \code{list} of multiple \code{data_extract_spec}) Specifies variable names selected to plot along the y-axis by default.} -\item{color_by}{(\code{data_extract_spec} or \code{list} of multiple \code{data_extract_spec}) optional +\item{color_by}{(\code{data_extract_spec} or \code{list} of multiple \code{data_extract_spec}) optional, defines the color encoding. If \code{NULL} then no color encoding option will be displayed.} -\item{size_by}{(\code{data_extract_spec} or \code{list} of multiple \code{data_extract_spec}) optional +\item{size_by}{(\code{data_extract_spec} or \code{list} of multiple \code{data_extract_spec}) optional, defines the point size encoding. If \code{NULL} then no size encoding option will be displayed.} -\item{row_facet}{(\code{data_extract_spec} or \code{list} of multiple \code{data_extract_spec}) optional +\item{row_facet}{(\code{data_extract_spec} or \code{list} of multiple \code{data_extract_spec}) optional, specifies the variable(s) for faceting rows.} -\item{col_facet}{(\code{data_extract_spec} or \code{list} of multiple \code{data_extract_spec}) optional +\item{col_facet}{(\code{data_extract_spec} or \code{list} of multiple \code{data_extract_spec}) optional, specifies the variable(s) for faceting columns.} -\item{plot_height}{(\code{numeric}) optional specifies the plot height as a three-element vector of +\item{plot_height}{(\code{numeric}) optional, specifies the plot height as a three-element vector of \code{value}, \code{min}, and \code{max} intended for use with a slider UI element.} -\item{plot_width}{(\code{numeric}) optional specifies the plot width as a three-element vector of +\item{plot_width}{(\code{numeric}) optional, specifies the plot width as a three-element vector of \code{value}, \code{min}, and \code{max} for a slider encoding the plot width.} -\item{alpha}{(\code{integer(1)} or \code{integer(3)}) optional specifies point opacity. +\item{alpha}{(\code{integer(1)} or \code{integer(3)}) optional, specifies point opacity. \itemize{ \item When the length of \code{alpha} is one: the plot points will have a fixed opacity. \item When the length of \code{alpha} is three: the plot points opacity are dynamically adjusted based on vector of \code{value}, \code{min}, and \code{max}. }} -\item{shape}{(\code{character}) optional character vector with the names of the +\item{shape}{(\code{character}) optional, character vector with the names of the shape, e.g. \code{c("triangle", "square", "circle")}. It defaults to \code{shape_names}. This is a complete list from \code{vignette("ggplot2-specs", package="ggplot2")}.} -\item{size}{(\code{integer(1)} or \code{integer(3)}) optional specifies point size. +\item{size}{(\code{integer(1)} or \code{integer(3)}) optional, specifies point size. \itemize{ \item When the length of \code{size} is one: the plot point sizes will have a fixed size. \item When the length of \code{size} is three: the plot points size are dynamically adjusted based on vector of \code{value}, \code{min}, and \code{max}. }} -\item{max_deg}{(\code{integer}) optional maximum degree for the polynomial trend line. Must not be less than 1.} +\item{max_deg}{(\code{integer}) optional, maximum degree for the polynomial trend line. Must not be less than 1.} -\item{rotate_xaxis_labels}{(\code{logical}) optional whether to rotate plot X axis labels. Does not +\item{rotate_xaxis_labels}{(\code{logical}) optional, whether to rotate plot X axis labels. Does not rotate by default (\code{FALSE}).} -\item{ggtheme}{(\code{character}) optional \code{ggplot2} theme to be used by default. Defaults to \code{"gray"}.} +\item{ggtheme}{(\code{character}) optional, \code{ggplot2} theme to be used by default. Defaults to \code{"gray"}.} -\item{pre_output}{(\code{shiny.tag}) optional text or UI element to be displayed before the module's output, +\item{pre_output}{(\code{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.} -\item{post_output}{(\code{shiny.tag}) optional text or UI element to be displayed after the module's output, +\item{post_output}{(\code{shiny.tag}) optional, text or UI element to be displayed after the module's output, adding context or further instructions. Elements like \code{shiny::helpText()} are useful.} -\item{table_dec}{(\code{integer}) optional number of decimal places used to round numeric values in the table.} +\item{table_dec}{(\code{integer}) optional, number of decimal places used to round numeric values in the table.} \item{ggplot2_args}{(\code{ggplot2_args}) object created by \code{\link[teal.widgets:ggplot2_args]{teal.widgets::ggplot2_args()}} with settings for the module plot. diff --git a/man/tm_g_scatterplotmatrix.Rd b/man/tm_g_scatterplotmatrix.Rd index e30cfd394..65672cb11 100644 --- a/man/tm_g_scatterplotmatrix.Rd +++ b/man/tm_g_scatterplotmatrix.Rd @@ -22,17 +22,17 @@ Specifies plotting variables from an incoming dataset with filtering and selecti \code{data_extract_spec} use \code{select_spec(..., ordered = TRUE)} if plot elements should be rendered according to selection order.} -\item{plot_height}{(\code{numeric}) optional specifies the plot height as a three-element vector of +\item{plot_height}{(\code{numeric}) optional, specifies the plot height as a three-element vector of \code{value}, \code{min}, and \code{max} intended for use with a slider UI element.} -\item{plot_width}{(\code{numeric}) optional specifies the plot width as a three-element vector of +\item{plot_width}{(\code{numeric}) optional, specifies the plot width as a three-element vector of \code{value}, \code{min}, and \code{max} for a slider encoding the plot width.} -\item{pre_output}{(\code{shiny.tag}) optional text or UI element to be displayed before the module's output, +\item{pre_output}{(\code{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.} -\item{post_output}{(\code{shiny.tag}) optional text or UI element to be displayed after the module's output, +\item{post_output}{(\code{shiny.tag}) optional, text or UI element to be displayed after the module's output, adding context or further instructions. Elements like \code{shiny::helpText()} are useful.} } \value{ diff --git a/man/tm_missing_data.Rd b/man/tm_missing_data.Rd index b02ad01d8..878adeb14 100644 --- a/man/tm_missing_data.Rd +++ b/man/tm_missing_data.Rd @@ -21,19 +21,19 @@ tm_missing_data( \item{label}{(\code{character(1)}) Label shown in the navigation item for the module or module group. For \code{modules()} defaults to \code{"root"}. See \code{Details}.} -\item{plot_height}{(\code{numeric}) optional specifies the plot height as a three-element vector of +\item{plot_height}{(\code{numeric}) optional, specifies the plot height as a three-element vector of \code{value}, \code{min}, and \code{max} intended for use with a slider UI element.} -\item{plot_width}{(\code{numeric}) optional specifies the plot width as a three-element vector of +\item{plot_width}{(\code{numeric}) optional, specifies the plot width as a three-element vector of \code{value}, \code{min}, and \code{max} for a slider encoding the plot width.} \item{parent_dataname}{(\code{character(1)}) Specifies the parent dataset name. Default is \code{ADSL} for \code{CDISC} data. If provided and exists, enables additional analysis "by subject". For non-\code{CDISC} data, this parameter can be ignored.} -\item{ggtheme}{(\code{character}) optional specifies the default \code{ggplot2} theme for plots. Defaults to \code{classic}.} +\item{ggtheme}{(\code{character}) optional, specifies the default \code{ggplot2} theme for plots. Defaults to \code{classic}.} -\item{ggplot2_args}{(\code{ggplot2_args}) optional object created by \code{\link[teal.widgets:ggplot2_args]{teal.widgets::ggplot2_args()}} +\item{ggplot2_args}{(\code{ggplot2_args}) optional, object created by \code{\link[teal.widgets:ggplot2_args]{teal.widgets::ggplot2_args()}} with settings for all the plots or named list of \code{ggplot2_args} objects for plot-specific settings. The argument is merged with options variable \code{teal.ggplot2_args} and default module setup. @@ -41,11 +41,11 @@ List names should match the following: \code{c("default", "Summary Obs", "Summar For more details see the vignette: \code{vignette("custom-ggplot2-arguments", package = "teal.widgets")}.} -\item{pre_output}{(\code{shiny.tag}) optional text or UI element to be displayed before the module's output, +\item{pre_output}{(\code{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.} -\item{post_output}{(\code{shiny.tag}) optional text or UI element to be displayed after the module's output, +\item{post_output}{(\code{shiny.tag}) optional, text or UI element to be displayed after the module's output, adding context or further instructions. Elements like \code{shiny::helpText()} are useful.} } \value{ diff --git a/man/tm_outliers.Rd b/man/tm_outliers.Rd index 27bb8ac5c..4ca23deeb 100644 --- a/man/tm_outliers.Rd +++ b/man/tm_outliers.Rd @@ -23,12 +23,12 @@ For \code{modules()} defaults to \code{"root"}. See \code{Details}.} \item{outlier_var}{(\code{data_extract_spec} or \code{list} of multiple \code{data_extract_spec}) Specifies variable(s) to be analyzed for outliers.} -\item{categorical_var}{(\code{data_extract_spec} or \code{list} of multiple \code{data_extract_spec}) optional +\item{categorical_var}{(\code{data_extract_spec} or \code{list} of multiple \code{data_extract_spec}) optional, specifies the categorical variable(s) to split the selected outlier variables on.} -\item{ggtheme}{(\code{character}) optional \code{ggplot2} theme to be used by default. Defaults to \code{"gray"}.} +\item{ggtheme}{(\code{character}) optional, \code{ggplot2} theme to be used by default. Defaults to \code{"gray"}.} -\item{ggplot2_args}{(\code{ggplot2_args}) optional object created by \code{\link[teal.widgets:ggplot2_args]{teal.widgets::ggplot2_args()}} +\item{ggplot2_args}{(\code{ggplot2_args}) optional, object created by \code{\link[teal.widgets:ggplot2_args]{teal.widgets::ggplot2_args()}} with settings for all the plots or named list of \code{ggplot2_args} objects for plot-specific settings. The argument is merged with options variable \code{teal.ggplot2_args} and default module setup. @@ -36,17 +36,17 @@ List names should match the following: \code{c("default", "Boxplot","Density Plo For more details see the vignette: \code{vignette("custom-ggplot2-arguments", package = "teal.widgets")}.} -\item{plot_height}{(\code{numeric}) optional specifies the plot height as a three-element vector of +\item{plot_height}{(\code{numeric}) optional, specifies the plot height as a three-element vector of \code{value}, \code{min}, and \code{max} intended for use with a slider UI element.} -\item{plot_width}{(\code{numeric}) optional specifies the plot width as a three-element vector of +\item{plot_width}{(\code{numeric}) optional, specifies the plot width as a three-element vector of \code{value}, \code{min}, and \code{max} for a slider encoding the plot width.} -\item{pre_output}{(\code{shiny.tag}) optional text or UI element to be displayed before the module's output, +\item{pre_output}{(\code{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.} -\item{post_output}{(\code{shiny.tag}) optional text or UI element to be displayed after the module's output, +\item{post_output}{(\code{shiny.tag}) optional, text or UI element to be displayed after the module's output, adding context or further instructions. Elements like \code{shiny::helpText()} are useful.} } \value{ diff --git a/man/tm_t_crosstable.Rd b/man/tm_t_crosstable.Rd index b5fbabb78..54b96b06e 100644 --- a/man/tm_t_crosstable.Rd +++ b/man/tm_t_crosstable.Rd @@ -37,11 +37,11 @@ Defaults to \code{TRUE}.} Indicates whether to show total column. Defaults to \code{TRUE}.} -\item{pre_output}{(\code{shiny.tag}) optional text or UI element to be displayed before the module's output, +\item{pre_output}{(\code{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.} -\item{post_output}{(\code{shiny.tag}) optional text or UI element to be displayed after the module's output, +\item{post_output}{(\code{shiny.tag}) optional, text or UI element to be displayed after the module's output, adding context or further instructions. Elements like \code{shiny::helpText()} are useful.} \item{basic_table_args}{(\code{basic_table_args}) object created by \code{\link[teal.widgets:basic_table_args]{teal.widgets::basic_table_args()}} diff --git a/man/tm_variable_browser.Rd b/man/tm_variable_browser.Rd index 1b8c97c09..00d3548b7 100644 --- a/man/tm_variable_browser.Rd +++ b/man/tm_variable_browser.Rd @@ -28,11 +28,11 @@ allow users to not show variables in other datasets which exist in this \code{da This is typically used to remove \code{ADSL} columns in \code{CDISC} data. In non \code{CDISC} data this can be ignored. Defaults to \code{"ADSL"}.} -\item{pre_output}{(\code{shiny.tag}) optional text or UI element to be displayed before the module's output, +\item{pre_output}{(\code{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.} -\item{post_output}{(\code{shiny.tag}) optional text or UI element to be displayed after the module's output, +\item{post_output}{(\code{shiny.tag}) optional, text or UI element to be displayed after the module's output, adding context or further instructions. Elements like \code{shiny::helpText()} are useful.} \item{ggplot2_args}{(\code{ggplot2_args}) object created by \code{\link[teal.widgets:ggplot2_args]{teal.widgets::ggplot2_args()}}