52 standardise optional notation

R/argument_convention.R

@@ -12,7 +12,7 @@
 #' @param label (`character(1)`)\cr
 #'  menu item label of the module in the teal app.
 #'
-#' @param dataname (\code{character(1)})\cr
+#' @param dataname (`character(1)`)\cr
 #'  analysis data used in the teal module, needs to be
 #'  available in the list passed to the `data` argument of [teal::init()].
 #'

R/teal.osprey.R

@@ -1,6 +1,6 @@
 #' teal.osprey: Enabling you to write modules in teal
 #'
-#' The \code{teal.osprey} R package contains interactive \code{\link{teal}} modules for the outputs
+#' The `teal.osprey` R package contains interactive [`teal`] modules for the outputs
 #'
 #' @import dplyr osprey shiny teal formatters teal.transform
 #' @keywords internal

R/tm_g_butterfly.R

@@ -7,27 +7,27 @@
 #'
 #' @inheritParams teal.widgets::standard_layout
 #' @inheritParams argument_convention
-#' @param filter_var (\code{choices_selected}) variable name of data filter, please see details regarding
-#'   expected values, default is \code{NULL}. \code{choices}
-#'   vector with \code{filter_var} choices, default is
-#'   \code{NULL}
-#' @param right_var (\code{choices_selected}) dichotomization variable for right side
-#' @param left_var (\code{choices_selected}) dichotomization variable for left side
-#' @param category_var (\code{choices_selected}) category (y axis) variable
-#' @param color_by_var (\code{choices_selected}) variable defines color blocks within each bar
-#' @param count_by_var (\code{choices_selected}) variable defines how x axis is calculated
-#' @param facet_var (\code{choices_selected}) variable for row facets
-#' @param sort_by_var (\code{choices_selected}) argument for order of class and term elements in table,
+#' @param filter_var (`choices_selected`) variable name of data filter, please see details regarding
+#'   expected values, default is`NULL`.`choices`
+#'   vector with `filter_var` choices, default is
+#'   `NULL`
+#' @param right_var (`choices_selected`) dichotomization variable for right side
+#' @param left_var (`choices_selected`) dichotomization variable for left side
+#' @param category_var (`choices_selected`) category (y axis) variable
+#' @param color_by_var (`choices_selected`) variable defines color blocks within each bar
+#' @param count_by_var (`choices_selected`) variable defines how x axis is calculated
+#' @param facet_var (`choices_selected`) variable for row facets
+#' @param sort_by_var (`choices_selected`) argument for order of class and term elements in table,
 #'   default here is "count"
-#' @param legend_on (\code{boolean}) value for whether legend is displayed
+#' @param legend_on (`boolean`) value for whether legend is displayed
 #'
-#' @details \code{filter_var} option is designed to work in conjunction with
-#'   filtering function provided by \code{teal} (encoding panel on the right
+#' @details `filter_var` option is designed to work in conjunction with
+#'   filtering function provided by `teal` (encoding panel on the right
 #'   hand side of the shiny app). It can be used as quick access to predefined
 #'   subsets of the domain datasets (not subject-level dataset) to be used for
 #'   analysis, denoted by an value of "Y". Each variable within the
-#'   \code{filter_var_choices} is expected to contain values of either "Y" or
-#'   "N". If multiple variables are selected as \code{filter_var}, only
+#'   `filter_var_choices` is expected to contain values of either "Y" or
+#'   "N". If multiple variables are selected as `filter_var`, only
 #'   observations with "Y" value in each and every selected variables will be
 #'   used for subsequent analysis. Flag variables (from `ADaM` datasets) can be
 #'   used directly as filter.

R/tm_g_decorate.R

@@ -3,12 +3,12 @@
 #' @description
 #' `r lifecycle::badge("stable")`
 #'
-#' This is used in \code{\link{tm_g_ae_oview}} and \code{\link{tm_g_events_term_id}}.
+#' This is used in [tm_g_ae_oview()] and [tm_g_events_term_id()].
 #'
-#' @param id (\code{character}) id of this module. set to `NULL` if you want to make it identical
+#' @param id (`character`) id of this module. set to `NULL` if you want to make it identical
 #' to the module who called it.
-#' @param titles (\code{character}) default titles
-#' @param footnotes (\code{character}) default footnotes
+#' @param titles (`character`) default titles
+#' @param footnotes (`character`) default footnotes
 #' @inheritParams argument_convention
 #' @export
 ui_g_decorate <- function(id,
@@ -33,12 +33,12 @@ ui_g_decorate <- function(id,
 #' @description
 #' `r lifecycle::badge("stable")`
 #'
-#' This is used in \code{\link{tm_g_ae_oview}} and \code{\link{tm_g_events_term_id}}.
+#' This is used in [tm_g_ae_oview()] and [tm_g_events_term_id()].
 #'
 #' @inheritParams shared_params
-#' @param id (\code{character}) id of the module
-#' @param plot_id (\code{character}) id for plot output
-#' @param plt (\code{reactive}) a reactive object of graph object
+#' @param id (`character`) id of the module
+#' @param plot_id (`character`) id for plot output
+#' @param plt (`reactive`) a reactive object of graph object
 #'
 #' @export
 srv_g_decorate <- function(id,
@@ -90,7 +90,7 @@ srv_g_decorate <- function(id,
 #' @description
 #' `r lifecycle::badge("stable")`
 #'
-#' @param id (\code{character}) id of this element
+#' @param id (`character`) id of this element
 #'
 #' @export
 plot_decorate_output <- function(id) {

R/tm_g_events_term_id.R

@@ -7,7 +7,7 @@
 #'
 #' @inheritParams teal.widgets::standard_layout
 #' @inheritParams argument_convention
-#' @param term_var \code{\link[teal.transform]{choices_selected}} object with all available choices
+#' @param term_var [teal.transform::choices_selected] object with all available choices
 #' and pre-selected option names that can be used to specify the term for events
 #'
 #' @inherit argument_convention return

R/tm_g_heat_bygrade.R

@@ -7,27 +7,27 @@
 #'
 #' @inheritParams teal.widgets::standard_layout
 #' @inheritParams argument_convention
-#' @param sl_dataname (\code{character}) subject level dataset name,
-#' needs to be available in the list passed to the \code{data}
-#' argument of \code{\link[teal]{init}}
-#' @param ex_dataname (\code{character}) exposures dataset name,
-#' needs to be available in the list passed to the \code{data}
-#' argument of \code{\link[teal]{init}} \cr
-#' @param ae_dataname (\code{character}) adverse events dataset name,
-#' needs to be available in the list passed to the \code{data}
-#' argument of \code{\link[teal]{init}} \cr
-#' @param cm_dataname (\code{character}) concomitant medications dataset name,
-#' needs to be available in the list passed to the \code{data}
-#' argument of \code{\link[teal]{init}} \cr
-#' specify to \code{NA} if no concomitant medications data is available
-#' @param id_var (\code{choices_seleced}) unique subject ID variable
-#' @param visit_var (\code{choices_seleced}) analysis visit variable
-#' @param ongo_var (\code{choices_seleced}) study ongoing status variable,
-#' This variable is a derived logical variable. Usually it can be derived from \code{EOSSTT}.
-#' @param anno_var (\code{choices_seleced}) annotation variable
-#' @param heat_var (\code{choices_seleced}) heatmap variable
-#' @param conmed_var (\code{choices_seleced}) concomitant medications variable,
-#' specify to \code{NA} if no concomitant medications data is available
+#' @param sl_dataname (`character`) subject level dataset name,
+#' needs to be available in the list passed to the `data`
+#' argument of [teal::init()]
+#' @param ex_dataname (`character`) exposures dataset name,
+#' needs to be available in the list passed to the `data`
+#' argument of [teal::init()] \cr
+#' @param ae_dataname (`character`) adverse events dataset name,
+#' needs to be available in the list passed to the `data`
+#' argument of [teal::init()] \cr
+#' @param cm_dataname (`character`) concomitant medications dataset name,
+#' needs to be available in the list passed to the `data`
+#' argument of [teal::init()] \cr
+#' specify to `NA` if no concomitant medications data is available
+#' @param id_var (`choices_seleced`) unique subject ID variable
+#' @param visit_var (`choices_seleced`) analysis visit variable
+#' @param ongo_var (`choices_seleced`) study ongoing status variable,
+#' This variable is a derived logical variable. Usually it can be derived from `EOSSTT`.
+#' @param anno_var (`choices_seleced`) annotation variable
+#' @param heat_var (`choices_seleced`) heatmap variable
+#' @param conmed_var (`choices_seleced`) concomitant medications variable,
+#' specify to `NA` if no concomitant medications data is available
 #'
 #' @inherit argument_convention return
 #'

R/tm_g_patient_profile.R

@@ -7,39 +7,39 @@
 #'
 #' @inheritParams teal.widgets::standard_layout
 #' @inheritParams argument_convention
-#' @param patient_id (\code{choices_seleced}) unique subject ID variable
-#' @param sl_dataname (\code{character}) subject level dataset name,
-#' needs to be available in the list passed to the \code{data}
-#' argument of \code{\link[teal]{init}}
+#' @param patient_id (`choices_seleced`) unique subject ID variable
+#' @param sl_dataname (`character`) subject level dataset name,
+#' needs to be available in the list passed to the `data`
+#' argument of [teal::init()]
 #' @param ex_dataname,ae_dataname,rs_dataname,cm_dataname,lb_dataname
-#'        (\code{character(1)}) names of exposure, adverse events, response,
+#'        (`character(1)`) names of exposure, adverse events, response,
 #'        concomitant medications, and labs datasets, respectively;
-#'        must be available in the list passed to the \code{data}
-#'        argument of \code{\link[teal]{init}}\cr
+#'        must be available in the list passed to the `data`
+#'        argument of [teal::init()]\cr
 #'        set to NA (default) to omit from analysis
-#' @param sl_start_date (\code{choices_selected}) study start date variable, usually set to
+#' @param sl_start_date `choices_selected` study start date variable, usually set to
 #'                      treatment start date or randomization date
-#' @param ex_var (\code{choices_selected}) exposure variable to plot as each line \cr
-#'               leave unspecified or set to \code{NULL} if exposure data is not available
-#' @param ae_var (\code{choices_selected}) adverse event variable to plot as each line \cr
-#'               leave unspecified or set to \code{NULL} if adverse events data is not available
-#' @param ae_line_col_var (\code{choices_selected}) variable for coloring `AE` lines \cr
-#'                        leave unspecified or set to \code{NULL} if adverse events data is not available
+#' @param ex_var `choices_selected` exposure variable to plot as each line \cr
+#'               leave unspecified or set to `NULL` if exposure data is not available
+#' @param ae_var `choices_selected` adverse event variable to plot as each line \cr
+#'               leave unspecified or set to `NULL` if adverse events data is not available
+#' @param ae_line_col_var `choices_selected` variable for coloring `AE` lines \cr
+#'                        leave unspecified or set to `NULL` if adverse events data is not available
 #' @param ae_line_col_opt aesthetic values to map color values
 #'                        (named vector to map color values to each name).
-#'                        If not \code{NULL}, please make sure this contains all possible
-#'                        values for \code{ae_line_col_var} values. \cr
-#'                        leave unspecified or set to \code{NULL} if adverse events data is not available
-#' @param rs_var (\code{choices_selected}) response variable to plot as each line \cr
-#'               leave unspecified or set to \code{NULL} if response data is not available
-#' @param cm_var (\code{choices_selected}) concomitant medication variable
+#'                        If not `NULL`, please make sure this contains all possible
+#'                        values for `ae_line_col_var` values. \cr
+#'                        leave unspecified or set to `NULL` if adverse events data is not available
+#' @param rs_var `choices_selected` response variable to plot as each line \cr
+#'               leave unspecified or set to `NULL` if response data is not available
+#' @param cm_var `choices_selected` concomitant medication variable
 #'               to plot as each line \cr
-#'               leave unspecified or set to \code{NULL} if concomitant medications data is not available
-#' @param lb_var (\code{choices_selected}) lab variable to plot as each line \cr
-#'               leave unspecified or set to \code{NULL} if labs data is not available
-#' @param x_limit a single \code{character} string with two numbers
+#'               leave unspecified or set to `NULL` if concomitant medications data is not available
+#' @param lb_var `choices_selected` lab variable to plot as each line \cr
+#'               leave unspecified or set to `NULL` if labs data is not available
+#' @param x_limit a single `character` string with two numbers
 #'                separated by a comma indicating the x-axis limit,
-#'                default is \code{"-28, 365"}
+#'                default is "-28, 365"
 #'
 #' @author Xuefeng Hou (houx14) \email{[email protected]}
 #' @author Tina Cho (chot) \email{[email protected]}
@@ -51,13 +51,11 @@
 #' @details
 #' As the patient profile module plots different domains in one plot, the study day (x-axis)
 #' is derived for consistency based the start date of user's choice in the app (for example,
-#' \code{ADSL.RANDDT} or \code{ADSL.TRTSDT}):
-#' \itemize{
-#' \item In \code{ADAE}, \code{ADEX}, and \code{ADCM}, it would be study day based on \code{ASTDT} and/or
-#'     \code{AENDT} in reference to the start date
-#' \item In \code{ADRS} and \code{ADLB}, it would be study day based on \code{ADT} in reference to
+#' `ADSL.RANDDT` or `ADSL.TRTSDT`):
+#' - In `ADAE`, `ADEX`, and `ADCM`, it would be study day based on `ASTDT` and/or
+#'     `AENDT` in reference to the start date
+#' - In `ADRS` and `ADLB`, it would be study day based on `ADT` in reference to
 #'     the start date
-#' }
 #'
 #' @export
 #'

R/tm_g_swimlane.R

@@ -7,23 +7,23 @@
 #'
 #' @inheritParams teal.widgets::standard_layout
 #' @inheritParams argument_convention
-#' @param dataname analysis data used for plotting, needs to be available in the list passed to the \code{data}
-#' argument of \code{\link[teal]{init}}. If no markers are to be plotted in the module, `"ADSL"` should be
+#' @param dataname analysis data used for plotting, needs to be available in the list passed to the `data`
+#' argument of [teal::init()]. If no markers are to be plotted in the module, `"ADSL"` should be
 #' the input. If markers are to be plotted, data name for the marker data should be the input
-#' @param bar_var (\code{\link[teal.transform]{choices_selected}}) subject-level numeric variable from dataset
+#' @param bar_var [teal.transform::choices_selected] subject-level numeric variable from dataset
 #' to plot as the bar length
-#' @param bar_color_var (\code{\link[teal.transform]{choices_selected}}) color by variable (subject-level)
-#' @param sort_var (\code{choices_selected}) sort by variable (subject-level)
-#' @param marker_pos_var (\code{\link[teal.transform]{choices_selected}}) variable for marker position from marker data
-#' (Note: make sure that marker position has the same relative start day as bar length variable \code{bar_var})
-#' @param marker_shape_var (\code{\link[teal.transform]{choices_selected}}) marker shape variable from marker data
+#' @param bar_color_var [teal.transform::choices_selected] color by variable (subject-level)
+#' @param sort_var `choices_selected` sort by variable (subject-level)
+#' @param marker_pos_var [teal.transform::choices_selected] variable for marker position from marker data
+#' (Note: make sure that marker position has the same relative start day as bar length variable `bar_var`
+#' @param marker_shape_var [teal.transform::choices_selected] marker shape variable from marker data
 #' @param marker_shape_opt aesthetic values to map shape values (named vector to map shape values to each name).
-#' If not \code{NULL}, please make sure this contains all possible values for \code{marker_shape_var} values,
-#' otherwise shape will be assigned by \code{ggplot} default
+#' If not `NULL`, please make sure this contains all possible values for `marker_shape_var` values,
+#' otherwise shape will be assigned by `ggplot` default
 #' @param marker_color_var marker color variable from marker data
 #' @param marker_color_opt aesthetic values to map color values (named vector to map color values to each name).
-#' If not \code{NULL}, please make sure this contains all possible values for \code{marker_color_var} values,
-#' otherwise color will be assigned by \code{ggplot} default
+#' If not `NULL`, please make sure this contains all possible values for `marker_color_var` values,
+#' otherwise color will be assigned by `ggplot` default
 #' @param vref_line vertical reference lines
 #' @param anno_txt_var character vector with subject-level variable names that are selected as annotation
 #' @param x_label the label of the x axis