From 37236af3712fe7d03b7ca759e4843042b9f7713c Mon Sep 17 00:00:00 2001 From: unknown Date: Thu, 7 Mar 2024 19:29:41 +0530 Subject: [PATCH 01/14] standardise optional notation and updating Roxygen tags --- R/argument_convention.R | 2 +- R/teal.osprey.R | 2 +- R/tm_g_butterfly.R | 32 ++++++++++---------- R/tm_g_decorate.R | 18 +++++------ R/tm_g_events_term_id.R | 2 +- R/tm_g_heat_bygrade.R | 42 +++++++++++++------------- R/tm_g_patient_profile.R | 60 ++++++++++++++++++------------------- R/tm_g_swimlane.R | 24 +++++++-------- R/tm_g_waterfall.R | 50 +++++++++++++++---------------- R/utils.R | 8 ++--- man/shared_params.Rd | 4 +-- man/srv_g_decorate.Rd | 6 ++-- man/tm_g_butterfly.Rd | 2 +- man/tm_g_events_term_id.Rd | 2 +- man/tm_g_heat_bygrade.Rd | 8 ++--- man/tm_g_patient_profile.Rd | 20 ++++++------- man/tm_g_swimlane.Rd | 14 ++++----- man/tm_g_waterfall.Rd | 24 +++++++-------- man/ui_g_decorate.Rd | 2 +- 19 files changed, 160 insertions(+), 162 deletions(-) diff --git a/R/argument_convention.R b/R/argument_convention.R index d41b0177..277ddbb5 100644 --- a/R/argument_convention.R +++ b/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()]. #' diff --git a/R/teal.osprey.R b/R/teal.osprey.R index 68a862db..6a915628 100644 --- a/R/teal.osprey.R +++ b/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 diff --git a/R/tm_g_butterfly.R b/R/tm_g_butterfly.R index 4b6b4df0..daebe003 100644 --- a/R/tm_g_butterfly.R +++ b/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. diff --git a/R/tm_g_decorate.R b/R/tm_g_decorate.R index 82bba899..bc26c5b0 100644 --- a/R/tm_g_decorate.R +++ b/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) { diff --git a/R/tm_g_events_term_id.R b/R/tm_g_events_term_id.R index e8f7974d..c34a8485 100644 --- a/R/tm_g_events_term_id.R +++ b/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 diff --git a/R/tm_g_heat_bygrade.R b/R/tm_g_heat_bygrade.R index 7ca4592e..d6577b08 100644 --- a/R/tm_g_heat_bygrade.R +++ b/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 #' diff --git a/R/tm_g_patient_profile.R b/R/tm_g_patient_profile.R index 0704564d..fe19d5f4 100644 --- a/R/tm_g_patient_profile.R +++ b/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{houx14@gene.com} #' @author Tina Cho (chot) \email{tina.cho@roche.com} @@ -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 #' diff --git a/R/tm_g_swimlane.R b/R/tm_g_swimlane.R index 8804bf21..3cc44166 100644 --- a/R/tm_g_swimlane.R +++ b/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 diff --git a/R/tm_g_waterfall.R b/R/tm_g_waterfall.R index 5c9f05de..22ac1d37 100644 --- a/R/tm_g_waterfall.R +++ b/R/tm_g_waterfall.R @@ -8,36 +8,36 @@ #' @inheritParams teal.widgets::standard_layout #' @inheritParams argument_convention #' @param dataname_tr tumor burden analysis data used in teal module to plot as bar height, needs to -#' be available in the list passed to the \code{data} argument of \code{\link[teal]{init}} +#' be available in the list passed to the `data` argument of [teal::init()] #' @param dataname_rs response analysis data used in teal module to label response parameters, needs to -#' be available in the list passed to the \code{data} argument of \code{\link[teal]{init}} -#' @param bar_paramcd (\code{choices_selected}) parameter in tumor burden data that will be plotted as +#' be available in the list passed to the `data` argument of [teal::init()] +#' @param bar_paramcd `choices_selected` parameter in tumor burden data that will be plotted as #' bar height -#' @param bar_var (\code{choices_selected}) numeric variable from dataset to plot the bar height, e.g., `PCHG` -#' @param bar_color_var (\code{choices_selected}) color by variable (subject level), \code{None} corresponds -#' to \code{NULL} +#' @param bar_var `choices_selected` numeric variable from dataset to plot the bar height, e.g., `PCHG` +#' @param bar_color_var `choices_selected` color by variable (subject level), `None` corresponds +#' to `NULL` #' @param bar_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{bar_color_var} values, -#' otherwise color will be assigned by \code{ggplot} default, please note that \code{NULL} needs to be specified +#' If not `NULL`, please make sure this contains all possible values for `bar_color_var` values, +#' otherwise color will be assigned by `ggplot` default, please note that `NULL` needs to be specified #' in this case -#' @param sort_var (\code{choices_selected}) sort by variable (subject level), \code{None} corresponds -#' to \code{NULL} -#' @param add_label_var_sl (\code{choices_selected}) add label to bars (subject level), \code{None} -#' corresponds to \code{NULL} -#' @param add_label_paramcd_rs (\code{choices_selected}) add label to bars (response dataset), \code{None} -#' corresponds to \code{NULL}. At least one of \code{add_label_var_sl} and \code{add_label_paramcd_rs} needs -#' to be \code{NULL} -#' @param anno_txt_var_sl (\code{choices_selected}) subject level variables to be displayed in the annotation -#' table, default is \code{NULL} -#' @param anno_txt_paramcd_rs (\code{choices_selected}) analysis dataset variables to be displayed in the -#' annotation table, default is \code{NULL} -#' @param facet_var (\code{choices_selected}) facet by variable (subject level), \code{None} corresponds to -#' \code{NULL} -#' @param ytick_at bar height axis interval, default is \code{20} -#' @param href_line numeric vector to plot horizontal reference lines, default is \code{NULL} +#' @param sort_var `choices_selected` sort by variable (subject level), `None` corresponds +#' to `NULL` +#' @param add_label_var_sl `choices_selected` add label to bars (subject level), `None` +#' corresponds to `NULL` +#' @param add_label_paramcd_rs `choices_selected` add label to bars (response dataset), `None` +#' corresponds to `NULL`. At least one of `add_label_var_sl` and `add_label_paramcd_rs` needs +#' to be `NULL` +#' @param anno_txt_var_sl `choices_selected` subject level variables to be displayed in the annotation +#' table, default is `NULL` +#' @param anno_txt_paramcd_rs `choices_selected` analysis dataset variables to be displayed in the +#' annotation table, default is `NULL` +#' @param facet_var `choices_selected` facet by variable (subject level), `None` corresponds to +#' `NULL` +#' @param ytick_at bar height axis interval, default is 20 +#' @param href_line numeric vector to plot horizontal reference lines, default is `NULL` #' @param gap_point_val singular numeric value for adding bar break when some bars are significantly higher -#' than others, default is \code{NULL} -#' @param show_value boolean of whether value of bar height is shown, default is \code{TRUE} +#' than others, default is `NULL` +#' @param show_value boolean of whether value of bar height is shown, default is `TRUE` #' #' @inherit argument_convention return #' diff --git a/R/utils.R b/R/utils.R index 2d1bdc1a..33345a84 100644 --- a/R/utils.R +++ b/R/utils.R @@ -1,13 +1,13 @@ #' Shared Parameters #' #' @description Contains arguments that are shared between multiple functions -#' in the package to avoid repetition using \code{inheritParams}. +#' in the package to avoid repetition using `inheritParams`. #' -#' @param plot_height optional, (\code{numeric}) a vector of length three with \code{c(value, min, max)}. Specifies +#' @param plot_height (`numeric`) optional, a vector of length three with `c(value, min, max)`. Specifies #' the height of the main plot. -#' @param plot_width optional, (\code{numeric}) a vector of length three with \code{c(value, min, max)}. Specifies +#' @param plot_width (`numeric`) optional, a vector of length three with `c(value, min, max)`. Specifies #' the width of the main plot and renders a slider on the plot to interactively adjust the plot width. -#' @param label (\code{character}) module label in the teal app. Please note that this module is developed based on +#' @param label (`character`) module label in the teal app. Please note that this module is developed based on #' `ADaM` data structure and `ADaM` variables. #' #' @name shared_params diff --git a/man/shared_params.Rd b/man/shared_params.Rd index 8a086e66..30ff4271 100644 --- a/man/shared_params.Rd +++ b/man/shared_params.Rd @@ -4,10 +4,10 @@ \alias{shared_params} \title{Shared Parameters} \arguments{ -\item{plot_height}{optional, (\code{numeric}) a vector of length three with \code{c(value, min, max)}. Specifies +\item{plot_height}{(\code{numeric}) optional, a vector of length three with \code{c(value, min, max)}. Specifies the height of the main plot.} -\item{plot_width}{optional, (\code{numeric}) a vector of length three with \code{c(value, min, max)}. Specifies +\item{plot_width}{(\code{numeric}) optional, a vector of length three with \code{c(value, min, max)}. Specifies the width of the main plot and renders a slider on the plot to interactively adjust the plot width.} \item{label}{(\code{character}) module label in the teal app. Please note that this module is developed based on diff --git a/man/srv_g_decorate.Rd b/man/srv_g_decorate.Rd index aed5d67a..592d4035 100644 --- a/man/srv_g_decorate.Rd +++ b/man/srv_g_decorate.Rd @@ -19,14 +19,14 @@ srv_g_decorate( \item{plt}{(\code{reactive}) a reactive object of graph object} -\item{plot_height}{optional, (\code{numeric}) a vector of length three with \code{c(value, min, max)}. Specifies +\item{plot_height}{(\code{numeric}) optional, a vector of length three with \code{c(value, min, max)}. Specifies the height of the main plot.} -\item{plot_width}{optional, (\code{numeric}) a vector of length three with \code{c(value, min, max)}. Specifies +\item{plot_width}{(\code{numeric}) optional, a vector of length three with \code{c(value, min, max)}. Specifies the width of the main plot and renders a slider on the plot to interactively adjust the plot width.} } \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#stable}{\figure{lifecycle-stable.svg}{options: alt='[Stable]'}}}{\strong{[Stable]}} -This is used in \code{\link{tm_g_ae_oview}} and \code{\link{tm_g_events_term_id}}. +This is used in \link{tm_g_ae_oview} and \link{tm_g_events_term_id}. } diff --git a/man/tm_g_butterfly.Rd b/man/tm_g_butterfly.Rd index 8c32d3c7..b57286ea 100644 --- a/man/tm_g_butterfly.Rd +++ b/man/tm_g_butterfly.Rd @@ -32,7 +32,7 @@ analysis data used in the teal module, needs to be available in the list passed to the \code{data} argument of \code{\link[teal:init]{teal::init()}}.} \item{filter_var}{(\code{choices_selected}) variable name of data filter, please see details regarding -expected values, default is \code{NULL}. \code{choices} +expected values, default is\code{NULL}.\code{choices} vector with \code{filter_var} choices, default is \code{NULL}} diff --git a/man/tm_g_events_term_id.Rd b/man/tm_g_events_term_id.Rd index c4f32148..915dab8a 100644 --- a/man/tm_g_events_term_id.Rd +++ b/man/tm_g_events_term_id.Rd @@ -22,7 +22,7 @@ menu item label of the module in the teal app.} analysis data used in the teal module, needs to be available in the list passed to the \code{data} argument of \code{\link[teal:init]{teal::init()}}.} -\item{term_var}{\code{\link[teal.transform]{choices_selected}} object with all available choices +\item{term_var}{\link[teal.transform:choices_selected]{teal.transform::choices_selected} object with all available choices and pre-selected option names that can be used to specify the term for events} \item{arm_var}{(\code{choices_selected})\cr diff --git a/man/tm_g_heat_bygrade.Rd b/man/tm_g_heat_bygrade.Rd index 3350496c..d5043a3b 100644 --- a/man/tm_g_heat_bygrade.Rd +++ b/man/tm_g_heat_bygrade.Rd @@ -27,19 +27,19 @@ menu item label of the module in the teal app.} \item{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}}} +argument of \code{\link[teal:init]{teal::init()}}} \item{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} +argument of \code{\link[teal:init]{teal::init()}} \cr} \item{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} +argument of \code{\link[teal:init]{teal::init()}} \cr} \item{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 +argument of \code{\link[teal:init]{teal::init()}} \cr specify to \code{NA} if no concomitant medications data is available} \item{id_var}{(\code{choices_seleced}) unique subject ID variable} diff --git a/man/tm_g_patient_profile.Rd b/man/tm_g_patient_profile.Rd index 29158bf4..77d3fe6c 100644 --- a/man/tm_g_patient_profile.Rd +++ b/man/tm_g_patient_profile.Rd @@ -36,24 +36,24 @@ menu item label of the module in the teal app.} \item{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}}} +argument of \code{\link[teal:init]{teal::init()}}} \item{ex_dataname, ae_dataname, rs_dataname, cm_dataname, lb_dataname}{(\code{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 +argument of \code{\link[teal:init]{teal::init()}}\cr set to NA (default) to omit from analysis} -\item{sl_start_date}{(\code{choices_selected}) study start date variable, usually set to +\item{sl_start_date}{\code{choices_selected} study start date variable, usually set to treatment start date or randomization date} -\item{ex_var}{(\code{choices_selected}) exposure variable to plot as each line \cr +\item{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} -\item{ae_var}{(\code{choices_selected}) adverse event variable to plot as each line \cr +\item{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} -\item{ae_line_col_var}{(\code{choices_selected}) variable for coloring \code{AE} lines \cr +\item{ae_line_col_var}{\code{choices_selected} variable for coloring \code{AE} lines \cr leave unspecified or set to \code{NULL} if adverse events data is not available} \item{ae_line_col_opt}{aesthetic values to map color values @@ -62,19 +62,19 @@ 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} -\item{rs_var}{(\code{choices_selected}) response variable to plot as each line \cr +\item{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} -\item{cm_var}{(\code{choices_selected}) concomitant medication variable +\item{cm_var}{\code{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} -\item{lb_var}{(\code{choices_selected}) lab variable to plot as each line \cr +\item{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} \item{x_limit}{a single \code{character} string with two numbers separated by a comma indicating the x-axis limit, -default is \code{"-28, 365"}} +default is "-28, 365"} \item{plot_height}{(\code{numeric(3)})\cr vector to indicate default value, minimum and maximum values.} diff --git a/man/tm_g_swimlane.Rd b/man/tm_g_swimlane.Rd index 81442e31..bd010285 100644 --- a/man/tm_g_swimlane.Rd +++ b/man/tm_g_swimlane.Rd @@ -29,20 +29,20 @@ tm_g_swimlane( menu item label of the module in the teal app.} \item{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, \code{"ADSL"} should be +argument of \code{\link[teal:init]{teal::init()}}. If no markers are to be plotted in the module, \code{"ADSL"} should be the input. If markers are to be plotted, data name for the marker data should be the input} -\item{bar_var}{(\code{\link[teal.transform]{choices_selected}}) subject-level numeric variable from dataset +\item{bar_var}{\link[teal.transform:choices_selected]{teal.transform::choices_selected} subject-level numeric variable from dataset to plot as the bar length} -\item{bar_color_var}{(\code{\link[teal.transform]{choices_selected}}) color by variable (subject-level)} +\item{bar_color_var}{\link[teal.transform:choices_selected]{teal.transform::choices_selected} color by variable (subject-level)} -\item{sort_var}{(\code{choices_selected}) sort by variable (subject-level)} +\item{sort_var}{\code{choices_selected} sort by variable (subject-level)} -\item{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})} +\item{marker_pos_var}{\link[teal.transform:choices_selected]{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}} -\item{marker_shape_var}{(\code{\link[teal.transform]{choices_selected}}) marker shape variable from marker data} +\item{marker_shape_var}{\link[teal.transform:choices_selected]{teal.transform::choices_selected} marker shape variable from marker data} \item{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, diff --git a/man/tm_g_waterfall.Rd b/man/tm_g_waterfall.Rd index b4fbc4a1..91c236a4 100644 --- a/man/tm_g_waterfall.Rd +++ b/man/tm_g_waterfall.Rd @@ -33,17 +33,17 @@ tm_g_waterfall( menu item label of the module in the teal app.} \item{dataname_tr}{tumor burden analysis data used in teal module to plot as bar height, needs to -be available in the list passed to the \code{data} argument of \code{\link[teal]{init}}} +be available in the list passed to the \code{data} argument of \code{\link[teal:init]{teal::init()}}} \item{dataname_rs}{response analysis data used in teal module to label response parameters, needs to -be available in the list passed to the \code{data} argument of \code{\link[teal]{init}}} +be available in the list passed to the \code{data} argument of \code{\link[teal:init]{teal::init()}}} -\item{bar_paramcd}{(\code{choices_selected}) parameter in tumor burden data that will be plotted as +\item{bar_paramcd}{\code{choices_selected} parameter in tumor burden data that will be plotted as bar height} -\item{bar_var}{(\code{choices_selected}) numeric variable from dataset to plot the bar height, e.g., \code{PCHG}} +\item{bar_var}{\code{choices_selected} numeric variable from dataset to plot the bar height, e.g., \code{PCHG}} -\item{bar_color_var}{(\code{choices_selected}) color by variable (subject level), \code{None} corresponds +\item{bar_color_var}{\code{choices_selected} color by variable (subject level), \code{None} corresponds to \code{NULL}} \item{bar_color_opt}{aesthetic values to map color values (named vector to map color values to each name). @@ -51,26 +51,26 @@ If not \code{NULL}, please make sure this contains all possible values for \code otherwise color will be assigned by \code{ggplot} default, please note that \code{NULL} needs to be specified in this case} -\item{sort_var}{(\code{choices_selected}) sort by variable (subject level), \code{None} corresponds +\item{sort_var}{\code{choices_selected} sort by variable (subject level), \code{None} corresponds to \code{NULL}} -\item{add_label_var_sl}{(\code{choices_selected}) add label to bars (subject level), \code{None} +\item{add_label_var_sl}{\code{choices_selected} add label to bars (subject level), \code{None} corresponds to \code{NULL}} -\item{add_label_paramcd_rs}{(\code{choices_selected}) add label to bars (response dataset), \code{None} +\item{add_label_paramcd_rs}{\code{choices_selected} add label to bars (response dataset), \code{None} corresponds to \code{NULL}. At least one of \code{add_label_var_sl} and \code{add_label_paramcd_rs} needs to be \code{NULL}} -\item{anno_txt_var_sl}{(\code{choices_selected}) subject level variables to be displayed in the annotation +\item{anno_txt_var_sl}{\code{choices_selected} subject level variables to be displayed in the annotation table, default is \code{NULL}} -\item{anno_txt_paramcd_rs}{(\code{choices_selected}) analysis dataset variables to be displayed in the +\item{anno_txt_paramcd_rs}{\code{choices_selected} analysis dataset variables to be displayed in the annotation table, default is \code{NULL}} -\item{facet_var}{(\code{choices_selected}) facet by variable (subject level), \code{None} corresponds to +\item{facet_var}{\code{choices_selected} facet by variable (subject level), \code{None} corresponds to \code{NULL}} -\item{ytick_at}{bar height axis interval, default is \code{20}} +\item{ytick_at}{bar height axis interval, default is 20} \item{href_line}{numeric vector to plot horizontal reference lines, default is \code{NULL}} diff --git a/man/ui_g_decorate.Rd b/man/ui_g_decorate.Rd index d8a408e9..9bb817f6 100644 --- a/man/ui_g_decorate.Rd +++ b/man/ui_g_decorate.Rd @@ -27,5 +27,5 @@ plot.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#stable}{\figure{lifecycle-stable.svg}{options: alt='[Stable]'}}}{\strong{[Stable]}} -This is used in \code{\link{tm_g_ae_oview}} and \code{\link{tm_g_events_term_id}}. +This is used in \link{tm_g_ae_oview} and \link{tm_g_events_term_id}. } From e7b09a39f20e42e4cd9520a8aaf74e036c89c49f Mon Sep 17 00:00:00 2001 From: unknown Date: Fri, 8 Mar 2024 00:57:27 +0530 Subject: [PATCH 02/14] fixing spellcheck --- R/tm_g_decorate.R | 4 ++-- man/srv_g_decorate.Rd | 2 +- man/ui_g_decorate.Rd | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/R/tm_g_decorate.R b/R/tm_g_decorate.R index bc26c5b0..604513e1 100644 --- a/R/tm_g_decorate.R +++ b/R/tm_g_decorate.R @@ -3,7 +3,7 @@ #' @description #' `r lifecycle::badge("stable")` #' -#' This is used in [tm_g_ae_oview] and [tm_g_events_term_id]. +#' This is used in [tm_g_ae_oview()] and [tm_g_events_term_id()]. #' #' @param id (`character`) id of this module. set to `NULL` if you want to make it identical #' to the module who called it. @@ -33,7 +33,7 @@ ui_g_decorate <- function(id, #' @description #' `r lifecycle::badge("stable")` #' -#' This is used in [tm_g_ae_oview] and [tm_g_events_term_id]. +#' This is used in [tm_g_ae_oview()] and [tm_g_events_term_id()]. #' #' @inheritParams shared_params #' @param id (`character`) id of the module diff --git a/man/srv_g_decorate.Rd b/man/srv_g_decorate.Rd index 592d4035..c55cbd38 100644 --- a/man/srv_g_decorate.Rd +++ b/man/srv_g_decorate.Rd @@ -28,5 +28,5 @@ the width of the main plot and renders a slider on the plot to interactively adj \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#stable}{\figure{lifecycle-stable.svg}{options: alt='[Stable]'}}}{\strong{[Stable]}} -This is used in \link{tm_g_ae_oview} and \link{tm_g_events_term_id}. +This is used in \code{\link[=tm_g_ae_oview]{tm_g_ae_oview()}} and \code{\link[=tm_g_events_term_id]{tm_g_events_term_id()}}. } diff --git a/man/ui_g_decorate.Rd b/man/ui_g_decorate.Rd index 9bb817f6..e6877795 100644 --- a/man/ui_g_decorate.Rd +++ b/man/ui_g_decorate.Rd @@ -27,5 +27,5 @@ plot.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#stable}{\figure{lifecycle-stable.svg}{options: alt='[Stable]'}}}{\strong{[Stable]}} -This is used in \link{tm_g_ae_oview} and \link{tm_g_events_term_id}. +This is used in \code{\link[=tm_g_ae_oview]{tm_g_ae_oview()}} and \code{\link[=tm_g_events_term_id]{tm_g_events_term_id()}}. } From 9b12e7d3474d5e9be97871286549f1995fce1fea Mon Sep 17 00:00:00 2001 From: "27856297+dependabot-preview[bot]@users.noreply.github.com" <27856297+dependabot-preview[bot]@users.noreply.github.com> Date: Thu, 7 Mar 2024 19:31:53 +0000 Subject: [PATCH 03/14] [skip roxygen] [skip vbump] Roxygen Man Pages Auto Update --- man/tm_g_butterfly.Rd | 4 ++-- man/tm_g_patient_profile.Rd | 4 ++-- man/tm_g_spiderplot.Rd | 4 ++-- man/tm_g_swimlane.Rd | 4 ++-- man/tm_g_waterfall.Rd | 4 ++-- 5 files changed, 10 insertions(+), 10 deletions(-) diff --git a/man/tm_g_butterfly.Rd b/man/tm_g_butterfly.Rd index b57286ea..edef8704 100644 --- a/man/tm_g_butterfly.Rd +++ b/man/tm_g_butterfly.Rd @@ -59,10 +59,10 @@ vector to indicate default value, minimum and maximum values.} \item{plot_width}{(\code{numeric(3)})\cr vector to indicate default value, minimum and maximum values.} -\item{pre_output}{(\code{shiny.tag}, optional)\cr +\item{pre_output}{(\code{shiny.tag}) optional,\cr with text placed before the output to put the output into context. For example a title.} -\item{post_output}{(\code{shiny.tag}, optional) with text placed after the output to put the output +\item{post_output}{(\code{shiny.tag}) optional, with text placed after the output to put the output into context. For example the \code{\link[shiny:helpText]{shiny::helpText()}} elements are useful.} } \value{ diff --git a/man/tm_g_patient_profile.Rd b/man/tm_g_patient_profile.Rd index 77d3fe6c..a53152f0 100644 --- a/man/tm_g_patient_profile.Rd +++ b/man/tm_g_patient_profile.Rd @@ -82,10 +82,10 @@ vector to indicate default value, minimum and maximum values.} \item{plot_width}{(\code{numeric(3)})\cr vector to indicate default value, minimum and maximum values.} -\item{pre_output}{(\code{shiny.tag}, optional)\cr +\item{pre_output}{(\code{shiny.tag}) optional,\cr with text placed before the output to put the output into context. For example a title.} -\item{post_output}{(\code{shiny.tag}, optional) with text placed after the output to put the output +\item{post_output}{(\code{shiny.tag}) optional, with text placed after the output to put the output into context. For example the \code{\link[shiny:helpText]{shiny::helpText()}} elements are useful.} } \value{ diff --git a/man/tm_g_spiderplot.Rd b/man/tm_g_spiderplot.Rd index 7d1e44d5..b4fe33d9 100644 --- a/man/tm_g_spiderplot.Rd +++ b/man/tm_g_spiderplot.Rd @@ -62,10 +62,10 @@ vector to indicate default value, minimum and maximum values.} \item{plot_width}{(\code{numeric(3)})\cr vector to indicate default value, minimum and maximum values.} -\item{pre_output}{(\code{shiny.tag}, optional)\cr +\item{pre_output}{(\code{shiny.tag}) optional,\cr with text placed before the output to put the output into context. For example a title.} -\item{post_output}{(\code{shiny.tag}, optional) with text placed after the output to put the output +\item{post_output}{(\code{shiny.tag}) optional, with text placed after the output to put the output into context. For example the \code{\link[shiny:helpText]{shiny::helpText()}} elements are useful.} } \value{ diff --git a/man/tm_g_swimlane.Rd b/man/tm_g_swimlane.Rd index bd010285..8429e65a 100644 --- a/man/tm_g_swimlane.Rd +++ b/man/tm_g_swimlane.Rd @@ -64,10 +64,10 @@ vector to indicate default value, minimum and maximum values.} \item{plot_width}{(\code{numeric(3)})\cr vector to indicate default value, minimum and maximum values.} -\item{pre_output}{(\code{shiny.tag}, optional)\cr +\item{pre_output}{(\code{shiny.tag}) optional,\cr with text placed before the output to put the output into context. For example a title.} -\item{post_output}{(\code{shiny.tag}, optional) with text placed after the output to put the output +\item{post_output}{(\code{shiny.tag}) optional, with text placed after the output to put the output into context. For example the \code{\link[shiny:helpText]{shiny::helpText()}} elements are useful.} \item{x_label}{the label of the x axis} diff --git a/man/tm_g_waterfall.Rd b/man/tm_g_waterfall.Rd index 91c236a4..36815938 100644 --- a/man/tm_g_waterfall.Rd +++ b/man/tm_g_waterfall.Rd @@ -85,10 +85,10 @@ vector to indicate default value, minimum and maximum values.} \item{plot_width}{(\code{numeric(3)})\cr vector to indicate default value, minimum and maximum values.} -\item{pre_output}{(\code{shiny.tag}, optional)\cr +\item{pre_output}{(\code{shiny.tag}) optional,\cr with text placed before the output to put the output into context. For example a title.} -\item{post_output}{(\code{shiny.tag}, optional) with text placed after the output to put the output +\item{post_output}{(\code{shiny.tag}) optional, with text placed after the output to put the output into context. For example the \code{\link[shiny:helpText]{shiny::helpText()}} elements are useful.} } \value{ From 8709a826417c691992f23cfdc192290c3759694e Mon Sep 17 00:00:00 2001 From: m7pr Date: Thu, 14 Mar 2024 11:41:55 +0100 Subject: [PATCH 04/14] clean DESCRIPTION --- .Rbuildignore | 1 + DESCRIPTION | 10 +++++----- 2 files changed, 6 insertions(+), 5 deletions(-) diff --git a/.Rbuildignore b/.Rbuildignore index 5c04b7d7..703ad2f6 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -1,6 +1,7 @@ ^renv$ ^renv\.lock$ CODE_OF_CONDUCT.md +LICENSE SECURITY.md ^_dev$ ^.*\.Rproj$ diff --git a/DESCRIPTION b/DESCRIPTION index c421d257..3f46fc3e 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: teal.osprey -Title: R Package of Teal Module for TLG Functions in Osprey +Title: 'teal' Modules for TLG Functions in Osprey Version: 0.1.16.9012 Date: 2024-03-06 Authors@R: c( @@ -13,10 +13,10 @@ Authors@R: c( person("Tina", "Cho", role = "ctb"), person("F. Hoffmann-La Roche AG", role = c("cph", "fnd")) ) -Description: Community efforts to collect teal modules for TLGs defined in - the osprey package. The teal modules add an encoding panel to - interactively change the encoding within teal. -License: Apache License 2.0 | file LICENSE +Description: Community efforts to collect 'teal' modules for TLGs defined in + the osprey package. 'teal' modules add an encoding panel to + interactively change the encoding within 'teal' apps. +License: Apache License 2.0 URL: https://insightsengineering.github.io/teal.osprey/, https://github.com/insightsengineering/teal.osprey/ BugReports: https://github.com/insightsengineering/teal.osprey/issues From 589902cbb6dd248dbbf63883587f0b7a0c8ac727 Mon Sep 17 00:00:00 2001 From: kartikeya kirar Date: Thu, 14 Mar 2024 16:21:37 +0530 Subject: [PATCH 05/14] Update R/tm_g_heat_bygrade.R Co-authored-by: Marcin <133694481+m7pr@users.noreply.github.com> Signed-off-by: kartikeya kirar --- R/tm_g_heat_bygrade.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/tm_g_heat_bygrade.R b/R/tm_g_heat_bygrade.R index d6577b08..c676b769 100644 --- a/R/tm_g_heat_bygrade.R +++ b/R/tm_g_heat_bygrade.R @@ -22,7 +22,7 @@ #' 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, +#' @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 From ab7779f31335ae92b978fd0b18502f955afbf3b0 Mon Sep 17 00:00:00 2001 From: m7pr Date: Thu, 14 Mar 2024 11:54:59 +0100 Subject: [PATCH 06/14] update description --- DESCRIPTION | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 3f46fc3e..04ad7f65 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -13,9 +13,8 @@ Authors@R: c( person("Tina", "Cho", role = "ctb"), person("F. Hoffmann-La Roche AG", role = c("cph", "fnd")) ) -Description: Community efforts to collect 'teal' modules for TLGs defined in - the osprey package. 'teal' modules add an encoding panel to - interactively change the encoding within 'teal' apps. +Description: Community efforts to collect 'teal' modules for TLGs defined in 'osprey' package. + Enables 'teal' app developers to create 'shiny' applications with a use of 'osprey' analysis functions. License: Apache License 2.0 URL: https://insightsengineering.github.io/teal.osprey/, https://github.com/insightsengineering/teal.osprey/ From 889902083e5dd2c27328f5b312f2b3cbdaa08284 Mon Sep 17 00:00:00 2001 From: m7pr Date: Thu, 14 Mar 2024 11:55:08 +0100 Subject: [PATCH 07/14] cleanup teal.osprey --- R/teal.osprey.R | 6 ++++-- man/teal.osprey-package.Rd | 6 ++++-- 2 files changed, 8 insertions(+), 4 deletions(-) diff --git a/R/teal.osprey.R b/R/teal.osprey.R index 6a915628..de5cef82 100644 --- a/R/teal.osprey.R +++ b/R/teal.osprey.R @@ -1,6 +1,8 @@ -#' teal.osprey: Enabling you to write modules in teal +#' `teal.osprey`: `teal` modules for 'osprey' #' -#' The `teal.osprey` R package contains interactive [`teal`] modules for the outputs +#' `teal.osprey` provides community contributed [`teal`] modules of the analysis functions from +#' [`osprey`] package. See package [website](https://insightsengineering.github.io/osprey/). +#' This enables `teal` app developers to easily create applications making use of the `osprey` analysis functions. #' #' @import dplyr osprey shiny teal formatters teal.transform #' @keywords internal diff --git a/man/teal.osprey-package.Rd b/man/teal.osprey-package.Rd index 655c4cad..3bd8d21e 100644 --- a/man/teal.osprey-package.Rd +++ b/man/teal.osprey-package.Rd @@ -4,9 +4,11 @@ \name{teal.osprey-package} \alias{teal.osprey} \alias{teal.osprey-package} -\title{teal.osprey: Enabling you to write modules in teal} +\title{\code{teal.osprey}: \code{teal} modules for 'osprey'} \description{ -The \code{teal.osprey} R package contains interactive \code{\link{teal}} modules for the outputs +\code{teal.osprey} provides community contributed \code{\link{teal}} modules of the analysis functions from +\code{\link{osprey}} package. See package \href{https://insightsengineering.github.io/osprey/}{website}. +This enables \code{teal} app developers to easily create applications making use of the \code{osprey} analysis functions. } \seealso{ Useful links: From 0442d1eaae3c7a0d44e6f98c12666533353ad837 Mon Sep 17 00:00:00 2001 From: "27856297+dependabot-preview[bot]@users.noreply.github.com" <27856297+dependabot-preview[bot]@users.noreply.github.com> Date: Thu, 14 Mar 2024 10:56:16 +0000 Subject: [PATCH 08/14] [skip roxygen] [skip vbump] Roxygen Man Pages Auto Update --- man/tm_g_heat_bygrade.Rd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/man/tm_g_heat_bygrade.Rd b/man/tm_g_heat_bygrade.Rd index d5043a3b..d93e77d0 100644 --- a/man/tm_g_heat_bygrade.Rd +++ b/man/tm_g_heat_bygrade.Rd @@ -46,7 +46,7 @@ specify to \code{NA} if no concomitant medications data is available} \item{visit_var}{(\code{choices_seleced}) analysis visit variable} -\item{ongo_var}{(\code{choices_seleced}) study ongoing status variable, +\item{ongo_var}{(\code{choices_seleced}) study ongoing status variable. This variable is a derived logical variable. Usually it can be derived from \code{EOSSTT}.} \item{anno_var}{(\code{choices_seleced}) annotation variable} From 875d9523d9ed8257fd1c4410e7e70ed8e51e027d Mon Sep 17 00:00:00 2001 From: m7pr Date: Thu, 14 Mar 2024 11:56:44 +0100 Subject: [PATCH 09/14] small cleanup of readme --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index d3df22c1..91324cda 100644 --- a/README.md +++ b/README.md @@ -21,8 +21,8 @@ [![Open Issues](https://img.shields.io/github/issues-raw/insightsengineering/teal.osprey?color=red\&label=open%20issues)](https://github.com/insightsengineering/teal.osprey/issues?q=is%3Aissue+is%3Aopen+sort%3Aupdated-desc) -The teal.osprey package provides community contributed `teal` modules of the analysis functions from the [osprey](https://insightsengineering.github.io/osprey/) R package. -This enables `teal` app developers to easily create applications making use of the `osprey` analysis functions. +`teal.osprey` provides community contributed `teal` modules of analysis functions from [`osprey`](https://insightsengineering.github.io/osprey/) package. +This enables `teal` app developers to easily create applications making use of `osprey`. ## Installation From 57a3c8bbcf66c3926ee0aef5c3dc91440c71176a Mon Sep 17 00:00:00 2001 From: kartikeya kirar Date: Thu, 14 Mar 2024 16:54:21 +0530 Subject: [PATCH 10/14] Update R/utils.R Co-authored-by: Marcin <133694481+m7pr@users.noreply.github.com> Signed-off-by: kartikeya kirar --- R/utils.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/utils.R b/R/utils.R index 33345a84..f35deccd 100644 --- a/R/utils.R +++ b/R/utils.R @@ -5,7 +5,7 @@ #' #' @param plot_height (`numeric`) optional, a vector of length three with `c(value, min, max)`. Specifies #' the height of the main plot. -#' @param plot_width (`numeric`) optional, a vector of length three with `c(value, min, max)`. Specifies +#' @param plot_width (`numeric`) optional vector of length three with `c(value, min, max)`. Specifies #' the width of the main plot and renders a slider on the plot to interactively adjust the plot width. #' @param label (`character`) module label in the teal app. Please note that this module is developed based on #' `ADaM` data structure and `ADaM` variables. From be6bcdfb85b8b5996c1f5d66b261ad65027484a4 Mon Sep 17 00:00:00 2001 From: kartikeya kirar Date: Thu, 14 Mar 2024 16:54:34 +0530 Subject: [PATCH 11/14] Update R/utils.R Co-authored-by: Marcin <133694481+m7pr@users.noreply.github.com> Signed-off-by: kartikeya kirar --- R/utils.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/utils.R b/R/utils.R index f35deccd..e2e1f426 100644 --- a/R/utils.R +++ b/R/utils.R @@ -3,7 +3,7 @@ #' @description Contains arguments that are shared between multiple functions #' in the package to avoid repetition using `inheritParams`. #' -#' @param plot_height (`numeric`) optional, a vector of length three with `c(value, min, max)`. Specifies +#' @param plot_height (`numeric`) optional vector of length three with `c(value, min, max)`. Specifies #' the height of the main plot. #' @param plot_width (`numeric`) optional vector of length three with `c(value, min, max)`. Specifies #' the width of the main plot and renders a slider on the plot to interactively adjust the plot width. From b59b15e5d2dcab000bdb8cd398441b2356f9cd46 Mon Sep 17 00:00:00 2001 From: unknown Date: Thu, 14 Mar 2024 16:56:23 +0530 Subject: [PATCH 12/14] updating rd --- man/shared_params.Rd | 4 ++-- man/srv_g_decorate.Rd | 4 ++-- man/tm_g_butterfly.Rd | 4 ++-- man/tm_g_patient_profile.Rd | 4 ++-- man/tm_g_spiderplot.Rd | 4 ++-- man/tm_g_swimlane.Rd | 4 ++-- man/tm_g_waterfall.Rd | 4 ++-- 7 files changed, 14 insertions(+), 14 deletions(-) diff --git a/man/shared_params.Rd b/man/shared_params.Rd index 30ff4271..811c6d9b 100644 --- a/man/shared_params.Rd +++ b/man/shared_params.Rd @@ -4,10 +4,10 @@ \alias{shared_params} \title{Shared Parameters} \arguments{ -\item{plot_height}{(\code{numeric}) optional, a vector of length three with \code{c(value, min, max)}. Specifies +\item{plot_height}{(\code{numeric}) optional vector of length three with \code{c(value, min, max)}. Specifies the height of the main plot.} -\item{plot_width}{(\code{numeric}) optional, a vector of length three with \code{c(value, min, max)}. Specifies +\item{plot_width}{(\code{numeric}) optional vector of length three with \code{c(value, min, max)}. Specifies the width of the main plot and renders a slider on the plot to interactively adjust the plot width.} \item{label}{(\code{character}) module label in the teal app. Please note that this module is developed based on diff --git a/man/srv_g_decorate.Rd b/man/srv_g_decorate.Rd index c55cbd38..92f6a123 100644 --- a/man/srv_g_decorate.Rd +++ b/man/srv_g_decorate.Rd @@ -19,10 +19,10 @@ srv_g_decorate( \item{plt}{(\code{reactive}) a reactive object of graph object} -\item{plot_height}{(\code{numeric}) optional, a vector of length three with \code{c(value, min, max)}. Specifies +\item{plot_height}{(\code{numeric}) optional vector of length three with \code{c(value, min, max)}. Specifies the height of the main plot.} -\item{plot_width}{(\code{numeric}) optional, a vector of length three with \code{c(value, min, max)}. Specifies +\item{plot_width}{(\code{numeric}) optional vector of length three with \code{c(value, min, max)}. Specifies the width of the main plot and renders a slider on the plot to interactively adjust the plot width.} } \description{ diff --git a/man/tm_g_butterfly.Rd b/man/tm_g_butterfly.Rd index edef8704..b57286ea 100644 --- a/man/tm_g_butterfly.Rd +++ b/man/tm_g_butterfly.Rd @@ -59,10 +59,10 @@ vector to indicate default value, minimum and maximum values.} \item{plot_width}{(\code{numeric(3)})\cr vector to indicate default value, minimum and maximum values.} -\item{pre_output}{(\code{shiny.tag}) optional,\cr +\item{pre_output}{(\code{shiny.tag}, optional)\cr with text placed before the output to put the output into context. For example a title.} -\item{post_output}{(\code{shiny.tag}) optional, with text placed after the output to put the output +\item{post_output}{(\code{shiny.tag}, optional) with text placed after the output to put the output into context. For example the \code{\link[shiny:helpText]{shiny::helpText()}} elements are useful.} } \value{ diff --git a/man/tm_g_patient_profile.Rd b/man/tm_g_patient_profile.Rd index a53152f0..77d3fe6c 100644 --- a/man/tm_g_patient_profile.Rd +++ b/man/tm_g_patient_profile.Rd @@ -82,10 +82,10 @@ vector to indicate default value, minimum and maximum values.} \item{plot_width}{(\code{numeric(3)})\cr vector to indicate default value, minimum and maximum values.} -\item{pre_output}{(\code{shiny.tag}) optional,\cr +\item{pre_output}{(\code{shiny.tag}, optional)\cr with text placed before the output to put the output into context. For example a title.} -\item{post_output}{(\code{shiny.tag}) optional, with text placed after the output to put the output +\item{post_output}{(\code{shiny.tag}, optional) with text placed after the output to put the output into context. For example the \code{\link[shiny:helpText]{shiny::helpText()}} elements are useful.} } \value{ diff --git a/man/tm_g_spiderplot.Rd b/man/tm_g_spiderplot.Rd index b4fe33d9..7d1e44d5 100644 --- a/man/tm_g_spiderplot.Rd +++ b/man/tm_g_spiderplot.Rd @@ -62,10 +62,10 @@ vector to indicate default value, minimum and maximum values.} \item{plot_width}{(\code{numeric(3)})\cr vector to indicate default value, minimum and maximum values.} -\item{pre_output}{(\code{shiny.tag}) optional,\cr +\item{pre_output}{(\code{shiny.tag}, optional)\cr with text placed before the output to put the output into context. For example a title.} -\item{post_output}{(\code{shiny.tag}) optional, with text placed after the output to put the output +\item{post_output}{(\code{shiny.tag}, optional) with text placed after the output to put the output into context. For example the \code{\link[shiny:helpText]{shiny::helpText()}} elements are useful.} } \value{ diff --git a/man/tm_g_swimlane.Rd b/man/tm_g_swimlane.Rd index 8429e65a..bd010285 100644 --- a/man/tm_g_swimlane.Rd +++ b/man/tm_g_swimlane.Rd @@ -64,10 +64,10 @@ vector to indicate default value, minimum and maximum values.} \item{plot_width}{(\code{numeric(3)})\cr vector to indicate default value, minimum and maximum values.} -\item{pre_output}{(\code{shiny.tag}) optional,\cr +\item{pre_output}{(\code{shiny.tag}, optional)\cr with text placed before the output to put the output into context. For example a title.} -\item{post_output}{(\code{shiny.tag}) optional, with text placed after the output to put the output +\item{post_output}{(\code{shiny.tag}, optional) with text placed after the output to put the output into context. For example the \code{\link[shiny:helpText]{shiny::helpText()}} elements are useful.} \item{x_label}{the label of the x axis} diff --git a/man/tm_g_waterfall.Rd b/man/tm_g_waterfall.Rd index 36815938..91c236a4 100644 --- a/man/tm_g_waterfall.Rd +++ b/man/tm_g_waterfall.Rd @@ -85,10 +85,10 @@ vector to indicate default value, minimum and maximum values.} \item{plot_width}{(\code{numeric(3)})\cr vector to indicate default value, minimum and maximum values.} -\item{pre_output}{(\code{shiny.tag}) optional,\cr +\item{pre_output}{(\code{shiny.tag}, optional)\cr with text placed before the output to put the output into context. For example a title.} -\item{post_output}{(\code{shiny.tag}) optional, with text placed after the output to put the output +\item{post_output}{(\code{shiny.tag}, optional) with text placed after the output to put the output into context. For example the \code{\link[shiny:helpText]{shiny::helpText()}} elements are useful.} } \value{ From 56564e0961540bf24e98052cd0034de899c3e9a9 Mon Sep 17 00:00:00 2001 From: "27856297+dependabot-preview[bot]@users.noreply.github.com" <27856297+dependabot-preview[bot]@users.noreply.github.com> Date: Thu, 14 Mar 2024 11:31:04 +0000 Subject: [PATCH 13/14] [skip roxygen] [skip vbump] Roxygen Man Pages Auto Update --- man/tm_g_butterfly.Rd | 4 ++-- man/tm_g_patient_profile.Rd | 4 ++-- man/tm_g_spiderplot.Rd | 4 ++-- man/tm_g_swimlane.Rd | 4 ++-- man/tm_g_waterfall.Rd | 4 ++-- 5 files changed, 10 insertions(+), 10 deletions(-) diff --git a/man/tm_g_butterfly.Rd b/man/tm_g_butterfly.Rd index b57286ea..edef8704 100644 --- a/man/tm_g_butterfly.Rd +++ b/man/tm_g_butterfly.Rd @@ -59,10 +59,10 @@ vector to indicate default value, minimum and maximum values.} \item{plot_width}{(\code{numeric(3)})\cr vector to indicate default value, minimum and maximum values.} -\item{pre_output}{(\code{shiny.tag}, optional)\cr +\item{pre_output}{(\code{shiny.tag}) optional,\cr with text placed before the output to put the output into context. For example a title.} -\item{post_output}{(\code{shiny.tag}, optional) with text placed after the output to put the output +\item{post_output}{(\code{shiny.tag}) optional, with text placed after the output to put the output into context. For example the \code{\link[shiny:helpText]{shiny::helpText()}} elements are useful.} } \value{ diff --git a/man/tm_g_patient_profile.Rd b/man/tm_g_patient_profile.Rd index 77d3fe6c..a53152f0 100644 --- a/man/tm_g_patient_profile.Rd +++ b/man/tm_g_patient_profile.Rd @@ -82,10 +82,10 @@ vector to indicate default value, minimum and maximum values.} \item{plot_width}{(\code{numeric(3)})\cr vector to indicate default value, minimum and maximum values.} -\item{pre_output}{(\code{shiny.tag}, optional)\cr +\item{pre_output}{(\code{shiny.tag}) optional,\cr with text placed before the output to put the output into context. For example a title.} -\item{post_output}{(\code{shiny.tag}, optional) with text placed after the output to put the output +\item{post_output}{(\code{shiny.tag}) optional, with text placed after the output to put the output into context. For example the \code{\link[shiny:helpText]{shiny::helpText()}} elements are useful.} } \value{ diff --git a/man/tm_g_spiderplot.Rd b/man/tm_g_spiderplot.Rd index 7d1e44d5..b4fe33d9 100644 --- a/man/tm_g_spiderplot.Rd +++ b/man/tm_g_spiderplot.Rd @@ -62,10 +62,10 @@ vector to indicate default value, minimum and maximum values.} \item{plot_width}{(\code{numeric(3)})\cr vector to indicate default value, minimum and maximum values.} -\item{pre_output}{(\code{shiny.tag}, optional)\cr +\item{pre_output}{(\code{shiny.tag}) optional,\cr with text placed before the output to put the output into context. For example a title.} -\item{post_output}{(\code{shiny.tag}, optional) with text placed after the output to put the output +\item{post_output}{(\code{shiny.tag}) optional, with text placed after the output to put the output into context. For example the \code{\link[shiny:helpText]{shiny::helpText()}} elements are useful.} } \value{ diff --git a/man/tm_g_swimlane.Rd b/man/tm_g_swimlane.Rd index bd010285..8429e65a 100644 --- a/man/tm_g_swimlane.Rd +++ b/man/tm_g_swimlane.Rd @@ -64,10 +64,10 @@ vector to indicate default value, minimum and maximum values.} \item{plot_width}{(\code{numeric(3)})\cr vector to indicate default value, minimum and maximum values.} -\item{pre_output}{(\code{shiny.tag}, optional)\cr +\item{pre_output}{(\code{shiny.tag}) optional,\cr with text placed before the output to put the output into context. For example a title.} -\item{post_output}{(\code{shiny.tag}, optional) with text placed after the output to put the output +\item{post_output}{(\code{shiny.tag}) optional, with text placed after the output to put the output into context. For example the \code{\link[shiny:helpText]{shiny::helpText()}} elements are useful.} \item{x_label}{the label of the x axis} diff --git a/man/tm_g_waterfall.Rd b/man/tm_g_waterfall.Rd index 91c236a4..36815938 100644 --- a/man/tm_g_waterfall.Rd +++ b/man/tm_g_waterfall.Rd @@ -85,10 +85,10 @@ vector to indicate default value, minimum and maximum values.} \item{plot_width}{(\code{numeric(3)})\cr vector to indicate default value, minimum and maximum values.} -\item{pre_output}{(\code{shiny.tag}, optional)\cr +\item{pre_output}{(\code{shiny.tag}) optional,\cr with text placed before the output to put the output into context. For example a title.} -\item{post_output}{(\code{shiny.tag}, optional) with text placed after the output to put the output +\item{post_output}{(\code{shiny.tag}) optional, with text placed after the output to put the output into context. For example the \code{\link[shiny:helpText]{shiny::helpText()}} elements are useful.} } \value{ From 12ffdfa65b66edfd5de6407a0c5e205e88b9f40b Mon Sep 17 00:00:00 2001 From: kartikeyakirar Date: Thu, 14 Mar 2024 19:07:02 +0530 Subject: [PATCH 14/14] 'trigger'