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Andreas Gammelgaard Damsbo
2a580965e3
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110 lines
3 KiB
R
110 lines
3 KiB
R
#' Print a flexible baseline characteristics table
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#'
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#' @param data data set
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#' @param fun.args list of arguments passed to
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#' @param fun function to
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#' @param vars character vector of variables to include
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#'
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#' @return object of standard class for fun
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#' @export
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#'
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#' @examples
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#' mtcars |> baseline_table()
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#' mtcars |> baseline_table(fun.args = list(by = "gear"))
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baseline_table <- function(data, fun.args = NULL, fun = gtsummary::tbl_summary, vars = NULL) {
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out <- do.call(fun, c(list(data = data), fun.args))
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return(out)
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}
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#' Create a baseline table
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#'
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#' @param data data
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#' @param ... passed as fun.arg to baseline_table()
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#' @param add.p add comparison/p-value
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#' @param add.overall add overall column
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#' @param by.var specify stratification variable
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#' @param theme set table theme
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#' @param detail_level specify detail level. Either "minimal" or "extended".
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#'
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#' @returns gtsummary table list object
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#' @export
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#'
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#' @examples
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#' mtcars |> create_baseline(by.var = "gear", add.p = "yes" == "yes")
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#' mtcars |> create_baseline(by.var = "gear", detail_level = "extended")
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#' mtcars |> create_baseline(by.var = "gear", detail_level = "extended",type = list(gtsummary::all_dichotomous() ~ "categorical"),theme="nejm")
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#'
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#' create_baseline(default_parsing(mtcars), by.var = "am", add.p = FALSE, add.overall = FALSE, theme = "lancet")
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create_baseline <- function(data, ..., by.var, add.p = FALSE, add.diff=FALSE, add.overall = FALSE, theme = c("jama", "lancet", "nejm", "qjecon"), detail_level = c("minimal", "extended")) {
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theme <- match.arg(theme)
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detail_level <- match.arg(detail_level)
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if (by.var == "none" | !by.var %in% names(data)) {
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by.var <- NULL
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}
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## These steps are to handle logicals/booleans, that messes up the order of columns
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## Has been reported and should be fixed soon (02042025)
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if (!is.null(by.var)) {
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if (identical("logical", class(data[[by.var]]))) {
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data[by.var] <- as.character(data[[by.var]])
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}
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}
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suppressMessages(gtsummary::theme_gtsummary_journal(journal = theme))
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args <- list(...)
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# browser()
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if (!any(hasName(args, c("type", "statistic")))) {
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if (detail_level == "extended") {
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args <-
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modifyList(
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args,
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list(
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type = list(gtsummary::all_continuous() ~ "continuous2",
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gtsummary::all_dichotomous() ~ "categorical"),
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statistic = list(gtsummary::all_continuous() ~ c(
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"{median} ({p25}, {p75})",
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"{mean} ({sd})",
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"{min}, {max}"))
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)
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)
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}
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}
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parameters <- list(
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data = data,
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fun.args = purrr::list_flatten(list(by = by.var, args))
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)
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# browser()
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out <- do.call(
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baseline_table,
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parameters
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)
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if (!is.null(by.var)) {
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if (isTRUE(add.overall)) {
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out <- out |> gtsummary::add_overall()
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}
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if (isTRUE(add.p)) {
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out <- out |>
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gtsummary::add_p() |>
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gtsummary::bold_p()
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}
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if (isTRUE(add.diff)) {
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out <- out |>
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gtsummary::add_difference()
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}
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}
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out
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}
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