[skip vbump] release v0.3.2

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: crane
 Title: Supplements the 'gtsummary' Package for Pharmaceutical Reporting
-Version: 0.3.1.9044
+Version: 0.3.2
 Authors@R: c(
     person("Daniel D.", "Sjoberg", , "danield.sjoberg@gmail.com", role = "aut",
            comment = c(ORCID = "0000-0003-0862-2018", note = "Original creator of the package")),
@@ -28,12 +28,12 @@ URL: https://github.com/insightsengineering/crane,
     https://insightsengineering.github.io/crane/
 BugReports: https://github.com/insightsengineering/crane/issues
 Depends: 
-    gtsummary (>= 2.5.0),
+    gtsummary (>= 2.5.1),
     R (>= 4.2)
 Imports:
     broom (>= 1.0.8),
-    cards (>= 0.7.0),
-    cardx (>= 0.3.0),
+    cards (>= 0.8.0),
+    cardx (>= 0.3.3),
     cli (>= 3.6.4),
     cowplot (>= 1.2.0),
     dplyr (>= 1.2.0),
@@ -62,10 +62,6 @@ Suggests:
     tidyselect,
     withr (>= 3.0.1),
     yaml
-Remotes:
-    ddsjoberg/gtsummary@main,
-    insightsengineering/cards@main,
-    insightsengineering/cardx@main
 Config/Needs/check: hms
 Config/Needs/website: rmarkdown, yaml
 Config/testthat/edition: 3

NEWS.md

@@ -1,4 +1,4 @@
-# crane 0.3.1.9044
+# crane 0.3.2
 
 ## New Functions and Functionality
 

R/add_forest.R

@@ -52,19 +52,23 @@
 #'   add_forest(table_engine = "gt")
 #'
 #' # Realistic example ---------------------------------------------------------
-#' trial |>
-#'   tbl_roche_subgroups(
-#'     rsp = "response",
-#'     by = "trt",
-#'     subgroups = c("grade"),
-#'     ~ glm(response ~ trt, data = .x) |>
-#'       gtsummary::tbl_regression(
-#'         show_single_row = trt,
-#'         exponentiate = TRUE # , tidy_fun = broom.helpers::tidy_parameters
-#'       )
-#'   ) |>
-#'   add_forest(pvalue = starts_with("p.value"), table_engine = "flextable") |>
-#'   flextable::set_header_labels(ggplot = "---------")
+#' \donttest{
+#' if (requireNamespace("broom.helpers", quietly = TRUE)) {
+#'   trial |>
+#'     tbl_roche_subgroups(
+#'       rsp = "response",
+#'       by = "trt",
+#'       subgroups = c("grade"),
+#'       ~ glm(response ~ trt, data = .x) |>
+#'         gtsummary::tbl_regression(
+#'           show_single_row = trt,
+#'           exponentiate = TRUE # , tidy_fun = broom.helpers::tidy_parameters
+#'         )
+#'     ) |>
+#'     add_forest(pvalue = starts_with("p.value"), table_engine = "flextable") |>
+#'     flextable::set_header_labels(ggplot = "---------")
+#' }
+#' }
 #' @export
 add_forest <- function(x,
                        estimate = starts_with("estimate"),

R/adjust_stat_columns_wrap.R

@@ -16,8 +16,14 @@
 #'   Defaults to `"protect"`.
 #'
 #' @return A modified `gtsummary` object.
-#'
 #' @export
+#' @examples
+#' tbl <- gtsummary::tbl_summary(
+#'   trial,
+#'   by = trt,
+#'   include = c(age, grade)
+#' )
+#' adjust_stat_columns_wrap(tbl, "protect")
 adjust_stat_columns_wrap <- function(tbl, mode = c("protect", "unprotect")) {
   # Robustly match the argument (defaults to "protect" if not provided)
   mode <- rlang::arg_match(mode)

R/annotate_gg_pkc.R

@@ -23,7 +23,7 @@
 #'   The font size for the table text. Defaults to `3.5`.
 #' @param rel_height_plot (`numeric`)\cr
 #'   Relative height of the plot vs the table. Defaults to `0.75`.
-#'
+#' @returns A ggplot2 object: a plot with a table at the bottom.
 #' @seealso [gg_pkc_lineplot()] for related functionalities.
 #' @examples
 #' # Prepare PK Data using the built-in Theoph dataset

R/deprecated.R

@@ -5,6 +5,9 @@
 #' supported.
 #'
 #' @name deprecated
+#' @returns Warnings
+#' @examples
+#' NULL
 #' @keywords internal
 NULL
 
@@ -25,7 +28,7 @@ tbl_demographics <- function(..., nonmissing = "always") {
 #' @export
 g_lineplot <- function(...) {
   lifecycle::deprecate_soft(
-    "0.3.1.9017",
+    "0.3.2",
     "crane::g_lineplot()",
     "crane::gg_lineplot"
   )
@@ -35,7 +38,7 @@ g_lineplot <- function(...) {
 #' @export
 g_lineplot_table <- function(...) {
   lifecycle::deprecate_soft(
-    "0.3.1.9017",
+    "0.3.2",
     "crane::g_lineplot_table()",
     "crane::annotate_gg()"
   )
@@ -45,7 +48,7 @@ g_lineplot_table <- function(...) {
 #' @export
 preprocess_lineplot_data <- function(...) {
   lifecycle::deprecate_soft(
-    "0.3.1.9017",
+    "0.3.2",
     "crane::preprocess_lineplot_data()",
     "crane::annotate_gg()"
   )

R/gg_km_utils.R

@@ -10,6 +10,8 @@
 #' @return A numeric vector of x-axis tick positions.
 #'
 #' @keywords internal
+#' @examples
+#' NULL
 h_xticks <- function(data, xticks = NULL, max_time = NULL) {
   if (is.null(xticks)) {
     if (is.null(max_time)) {
@@ -46,6 +48,8 @@ h_xticks <- function(data, xticks = NULL, max_time = NULL) {
 #' @return A data frame with columns "N", "Median", and the confidence interval label.
 #'
 #' @keywords internal
+#' @examples
+#' NULL
 h_tbl_median_surv <- function(fit_km, strata_levels = "All") {
   y <- if (is.null(fit_km$strata)) {
     as.data.frame(t(summary(fit_km)$table), row.names = strata_levels)

R/tbl_coxph.R

@@ -143,6 +143,14 @@ tbl_coxph <- function(pairwise_df) {
 #' @return A `gtsummary` object containing the stacked summary statistics.
 #'
 #' @keywords internal
+#' @examples
+#' tbl <- tibble::tibble(
+#'   comparison_label = "A-B",
+#'   hr_formatted = "5.21",
+#'   ci_formatted = "0.25-0.35",
+#'   pval_formatted = 0.005
+#' )
+#' crane:::.get_single_comp_table(tbl, pval_label = "p-val")
 .get_single_comp_table <- function(data_subset, pval_label = NULL) {
   # Check which pre-formatted columns made it into the subset
   has_pval <- "pval_formatted" %in% names(data_subset)
@@ -214,6 +222,8 @@ tbl_coxph <- function(pairwise_df) {
 #'
 #' @returns A character vector of formatted p-values.
 #' @keywords internal
+#' @examples
+#' crane:::.format_pvalue(0.000156)
 .format_pvalue <- function(x) {
   if (is.character(x)) {
     return(x)

R/tbl_listing.R

@@ -34,7 +34,7 @@
 #'    parameters used in [gtsummary::tbl_split_by_rows()]. See example 4.
 #'  * Split by columns - you can split the data frame by columns by using `split_by_columns` parameter. Use the same
 #'    parameters from [gtsummary::tbl_split_by_rows()]. See example 5.
-#'
+#' @returns A table listing of class "tbl_listing".
 #' @examplesIf crane:::is_pkg_installed("labelled")
 #' # Load the trial dataset
 #' trial_data <- trial |>

R/tbl_null_report.R

@@ -4,7 +4,7 @@
 #'
 #' @param label (`string`)\cr label to display in the header of the null report. It defaults to
 #'   "No observations met the reporting criteria for this output."
-#'
+#' @returns A gtsummary object of class tbl_null_report.
 #' @examples
 #' tbl_null_report(label = "No data available for the selected criteria.")
 #'

R/tbl_rmpt.R

@@ -84,6 +84,7 @@
 #'
 #' # Example 2 --------------------------------
 #' # Add overall column at the end
+#' \donttest{
 #' tbl_rmpt(
 #'   data = df_adex,
 #'   variable = AVAL_CAT,
@@ -103,6 +104,7 @@
 #'   denominator = df_adsl,
 #'   label = "Treatment Exposure Duration"
 #' )
+#' }
 #'
 NULL
 #' @rdname tbl_rmpt

R/tbl_roche_subgroups.R

@@ -17,7 +17,7 @@
 #'
 #' @returns a 'gtsummary' table
 #'
-#' @examples
+#' @examplesIf identical(Sys.getenv("NOT_CRAN"), "true")
 #' set.seed(1)
 #'
 #' # prepare sample data
@@ -49,6 +49,7 @@
 #' # coxph regression ----------------------------------------------------------
 #' # please use browser() inside .tbl_fun to check if the coxph model throws an error
 #' # and use tryCatch to modify the input/output accordingly
+#' \donttest{
 #' df_adtte |>
 #'   tbl_roche_subgroups(
 #'     rsp = status,
@@ -66,7 +67,7 @@
 #'       )
 #'   ) |>
 #'   modify_header(starts_with("estimate") ~ "**Hazard Ratio**")
-#'
+#' }
 #' @export
 tbl_roche_subgroups <- function(data, rsp, by, subgroups, .tbl_fun, time_to_event = NULL) {
   set_cli_abort_call()

README.md

@@ -52,7 +52,7 @@ tbl <- trial |>
   tbl_roche_summary(by = trt, include = c(age, grade), nonmissing = "always")
 ```
 
-<img src="man/figures/README-tbl_print_simple-1.png" width="40%" />
+<img src="man/figures/README-tbl_print_simple-1.png" alt="" width="40%" />
 
 The package also exports functions for Roche adverse event reporting,
 functions for shift tables, and others.