mirror of
https://github.com/agdamsbo/FreesearchR.git
synced 2025-09-12 09:59:39 +02:00
79 lines
2 KiB
R
79 lines
2 KiB
R
#' Print a flexible baseline characteristics table
|
|
#'
|
|
#' @param data data set
|
|
#' @param fun.args list of arguments passed to
|
|
#' @param fun function to
|
|
#' @param vars character vector of variables to include
|
|
#'
|
|
#' @return object of standard class for fun
|
|
#' @export
|
|
#'
|
|
#' @examples
|
|
#' mtcars |> baseline_table()
|
|
#' mtcars |> baseline_table(fun.args = list(by = "gear"))
|
|
baseline_table <- function(data, fun.args = NULL, fun = gtsummary::tbl_summary, vars = NULL) {
|
|
|
|
out <- do.call(fun, c(list(data = data), fun.args))
|
|
return(out)
|
|
}
|
|
|
|
|
|
|
|
#' Create a baseline table
|
|
#'
|
|
#' @param data data
|
|
#' @param ... passed as fun.arg to baseline_table()
|
|
#' @param strat.var grouping/strat variable
|
|
#' @param add.p add comparison/p-value
|
|
#' @param add.overall add overall column
|
|
#'
|
|
#' @returns gtsummary table list object
|
|
#' @export
|
|
#'
|
|
#' @examples
|
|
#' mtcars |> create_baseline(by.var = "gear", add.p = "yes" == "yes")
|
|
#' create_baseline(default_parsing(mtcars), by.var = "am", add.p = FALSE, add.overall = FALSE, theme = "lancet")
|
|
create_baseline <- function(data, ..., by.var, add.p = FALSE, add.overall = FALSE, theme = c("jama", "lancet", "nejm", "qjecon")) {
|
|
theme <- match.arg(theme)
|
|
|
|
if (by.var == "none" | !by.var %in% names(data)) {
|
|
by.var <- NULL
|
|
}
|
|
|
|
## These steps are to handle logicals/booleans, that messes up the order of columns
|
|
## Has been reported and should be fixed soon (02042025)
|
|
|
|
if (!is.null(by.var)) {
|
|
if (identical("logical", class(data[[by.var]]))) {
|
|
data[by.var] <- as.character(data[[by.var]])
|
|
}
|
|
}
|
|
|
|
suppressMessages(gtsummary::theme_gtsummary_journal(journal = theme))
|
|
|
|
args <- list(...)
|
|
|
|
parameters <- list(
|
|
data = data,
|
|
fun.args = list(by = by.var, ...)
|
|
)
|
|
|
|
out <- do.call(
|
|
baseline_table,
|
|
parameters
|
|
)
|
|
|
|
|
|
if (!is.null(by.var)) {
|
|
if (isTRUE(add.overall)) {
|
|
out <- out |> gtsummary::add_overall()
|
|
}
|
|
if (isTRUE(add.p)) {
|
|
out <- out |>
|
|
gtsummary::add_p() |>
|
|
gtsummary::bold_p()
|
|
}
|
|
}
|
|
|
|
out
|
|
}
|