gtsummary v2.0 preparation (#110)

* gtsummary v2.0 preparation

* Update R-CMD-check.yaml

* Update DESCRIPTION

* doc update

* Update DESCRIPTION

* Update DESCRIPTION

* Update NEWS.md

* Adding new functions to _pkgdown.yml.

* updates

---------

Co-authored-by: Teng Fei <[email protected]>

.github/workflows/R-CMD-check.yaml

@@ -30,9 +30,6 @@ jobs:
           - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
           - {os: ubuntu-latest,   r: 'release'}
           - {os: ubuntu-latest,   r: 'oldrel-1'}
-          - {os: ubuntu-latest,   r: 'oldrel-2'}
-          - {os: ubuntu-latest,   r: 'oldrel-3'}
-          - {os: ubuntu-latest,   r: 'oldrel-4'}
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: tidycmprsk
 Title: Competing Risks Estimation
-Version: 1.0.0.9000
+Version: 1.0.0.9001
 Authors@R: c(
     person(c("Daniel", "D."), "Sjoberg", , "[email protected]", role = c("aut", "cre", "cph"),
            comment = c(ORCID = "0000-0003-0862-2018")),
@@ -16,22 +16,25 @@ License: AGPL (>= 3)
 URL: https://mskcc-epi-bio.github.io/tidycmprsk/, https://github.com/MSKCC-Epi-Bio/tidycmprsk
 BugReports: https://github.com/MSKCC-Epi-Bio/tidycmprsk/issues
 Depends: 
-    R (>= 3.4)
+    R (>= 4.2)
 Imports: 
     broom (>= 1.0.1),
     cli (>= 3.1.0),
     cmprsk (>= 2.2.10),
     dplyr (>= 1.0.7),
     ggplot2 (>= 3.3.5),
-    gtsummary (>= 1.7.2),
+    gtsummary (>= 2.0.0),
     hardhat (>= 1.3.0),
     purrr (>= 0.3.4),
     rlang (>= 1.0.0),
     stringr (>= 1.4.0),
     survival,
     tibble (>= 3.1.6),
     tidyr (>= 1.1.4)
-Suggests: 
+Suggests:  
+    aod,
+    broom.helpers (>= 1.15.0),
+    cardx (>= 0.2.0),
     covr (>= 3.5.1),
     ggsurvfit,
     knitr (>= 1.36),
@@ -42,4 +45,4 @@ Encoding: UTF-8
 Language: en-US
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.2

NAMESPACE

@@ -12,6 +12,7 @@ S3method(cuminc,default)
 S3method(cuminc,formula)
 S3method(glance,tidycrr)
 S3method(glance,tidycuminc)
+S3method(global_pvalue_fun,tidycrr)
 S3method(inline_text,tbl_cuminc)
 S3method(model.frame,tidycrr)
 S3method(model.frame,tidycuminc)
@@ -21,6 +22,7 @@ S3method(predict,tidycrr)
 S3method(print,tidycrr)
 S3method(print,tidycuminc)
 S3method(tbl_cuminc,tidycuminc)
+S3method(tbl_regression,tidycrr)
 S3method(terms,tidycrr)
 S3method(tidy,tidycrr)
 S3method(tidy,tidycuminc)
@@ -35,8 +37,10 @@ export(autoplot)
 export(crr)
 export(cuminc)
 export(glance)
+export(global_pvalue_fun)
 export(inline_text)
 export(tbl_cuminc)
+export(tbl_regression)
 export(tidy)
 importFrom(broom,augment)
 importFrom(broom,glance)
@@ -58,7 +62,9 @@ importFrom(ggplot2,ggplot)
 importFrom(gtsummary,add_n)
 importFrom(gtsummary,add_nevent)
 importFrom(gtsummary,add_p)
+importFrom(gtsummary,global_pvalue_fun)
 importFrom(gtsummary,inline_text)
+importFrom(gtsummary,tbl_regression)
 importFrom(purrr,"%||%")
 importFrom(rlang,":=")
 importFrom(rlang,.data)

NEWS.md

@@ -1,5 +1,10 @@
 # tidycmprsk (development version)
 
+* Updating package to account for changes in {gtsummary} v2.0. To use `gtsummary::tbl_regression()` with `tidycmprsk::crr()` models, the {tidycmprsk} package must be loaded (to access the S3 methods below). In the next release of gtsummary, tidycmprsk will no longer be a dependency.
+  - Added {broom.helpers}, {cardx}, and {aod} to Suggests field.
+  - Added `tbl_regression.tidycrr()` method.
+  - Added `global_pvalue_fun.tidycrr()` method, which changes the default calculation in `gtsummary::add_global_p(anova_fun)` to use the Wald test.
+
 # tidycmprsk 1.0.0
 
 * Corrected a previous regression bug and `cuminc()` can again handle models with no observed censoring. (#89)

R/gtsummary_s3_methods.R

@@ -0,0 +1,41 @@
+#' gtsummary methods
+#'
+#' @description
+#' These functions are S3 methods for working with [`tidycmprsk::crr()`] model
+#' results.
+#'
+#' - `tbl_regression.tidycrr()`: This function sets the tidycmprsk tidier for `crr()` models.
+#' - `global_pvalue_fun.tidycrr()`: This function ensures that `gtsummary::add_global_p(anova_fun)` uses
+#'     the Wald test by default (instead of `car::Anova()`, which does not support this model type).
+#'     The Wald test is executed with `cardx::ard_aod_wald_test()`, which wraps `aod::wald.test()`.
+#'
+#' @param x (`tidycrr`)\cr
+#'   `tidycmprsk::crr()` regression object
+#' @param tidy_fun (`function`)\cr
+#'    Tidier function for the model. Default is `tidycmprsk::tidy()`.
+#' @param type not used
+#' @inheritParams gtsummary::tbl_regression
+#'
+#' @name gtsummary_s3_methods
+#' @return gtsummary table or data frame of results
+#'
+#' @examples
+#' crr(Surv(ttdeath, death_cr) ~ age + grade, trial) |>
+#'   gtsummary::tbl_regression() |>
+#'   gtsummary::add_global_p() |>
+#'   gtsummary::as_gt()
+NULL
+
+#' @rdname gtsummary_s3_methods
+#' @export
+tbl_regression.tidycrr <- function(x, tidy_fun = tidycmprsk::tidy, ...) {
+  asNamespace("gtsummary")[["tbl_regression.default"]](x = x, tidy_fun = tidy_fun, ...)
+}
+
+#' @rdname gtsummary_s3_methods
+#' @export
+global_pvalue_fun.tidycrr <- function(x, type, ...) {
+  check_pkg_installed("cardx", reference_pkg = "tidycmprisk")
+
+  cardx::ard_aod_wald_test(x, ...)
+}

R/import-standalone-check_pkg_installed.R

@@ -0,0 +1,191 @@
+# Standalone file: do not edit by hand
+# Source: <https://github.com/ddsjoberg/standalone/blob/main/R/standalone-check_pkg_installed.R>
+# ----------------------------------------------------------------------
+#
+# ---
+# repo: ddsjoberg/standalone
+# file: standalone-check_pkg_installed.R
+# last-updated: 2024-04-19
+# license: https://unlicense.org
+# dependencies: standalone-cli_call_env.R
+# imports: [rlang, dplyr, tidyr]
+# ---
+#
+# This file provides functions to check package installation.
+#
+# ## Changelog
+# nocov start
+# styler: off
+
+#' Check Package Installation
+#'
+#' @description
+#' - `check_pkg_installed()`: checks whether a package is installed and
+#'   returns an error if not available, or interactively asks user to install
+#'   missing dependency. If a package search is provided,
+#'   the function will check whether a minimum version of a package is required and installed.
+#'
+#' - `is_pkg_installed()`: checks whether a package is installed and
+#'   returns `TRUE` or `FALSE` depending on availability. If a package search is provided,
+#'   the function will check whether a minimum version of a package is required and installed.
+#'
+#' - `get_pkg_dependencies()` returns a tibble with all
+#'   dependencies of a specific package.
+#'
+#' - `get_min_version_required()` will return, if any, the minimum version
+#'   of `pkg` required by `reference_pkg`.
+#'
+#' @param pkg (`character`)\cr
+#'   vector of package names to check.
+#' @param call (`environment`)\cr
+#'   frame for error messaging. Default is [get_cli_abort_call()].
+#' @param reference_pkg (`string`)\cr
+#'   name of the package the function will search for a minimum required version from.
+#' @param lib.loc (`path`)\cr
+#'   location of `R` library trees to search through, see [utils::packageDescription()].
+#'
+#' @return `is_pkg_installed()` and `check_pkg_installed()` returns a logical or error,
+#' `get_min_version_required()` returns a data frame with the minimum version required,
+#' `get_pkg_dependencies()` returns a tibble.
+#'
+#' @examples
+#' check_pkg_installed("dplyr")
+#'
+#' is_pkg_installed("dplyr")
+#'
+#' get_pkg_dependencies()
+#'
+#' get_min_version_required("dplyr")
+#'
+#' @name check_pkg_installed
+#' @noRd
+NULL
+
+#' @inheritParams check_pkg_installed
+#' @keywords internal
+#' @noRd
+check_pkg_installed <- function(pkg,
+                                reference_pkg = "cards",
+                                call = get_cli_abort_call()) {
+  # get min version data -------------------------------------------------------
+  df_pkg_min_version <-
+    get_min_version_required(pkg = pkg, reference_pkg = reference_pkg, call = call)
+
+  # prompt user to install package ---------------------------------------------
+  rlang::check_installed(
+    pkg = df_pkg_min_version$pkg,
+    version = df_pkg_min_version$version,
+    compare = df_pkg_min_version$compare
+  ) |>
+    # this can be removed after this issue is resolved https://github.com/r-lib/rlang/issues/1694
+    suppressWarnings()
+}
+
+#' @inheritParams check_pkg_installed
+#' @keywords internal
+#' @noRd
+is_pkg_installed <- function(pkg,
+                             reference_pkg = "cards",
+                             call = get_cli_abort_call()) {
+  # get min version data -------------------------------------------------------
+  df_pkg_min_version <-
+    get_min_version_required(pkg = pkg, reference_pkg = reference_pkg, call = call)
+
+  # check installation TRUE/FALSE ----------------------------------------------
+  rlang::is_installed(
+    pkg = df_pkg_min_version$pkg,
+    version = df_pkg_min_version$version,
+    compare = df_pkg_min_version$compare
+  ) |>
+    # this can be removed after this issue is resolved https://github.com/r-lib/rlang/issues/1694
+    suppressWarnings()
+}
+
+#' @inheritParams check_pkg_installed
+#' @keywords internal
+#' @noRd
+get_pkg_dependencies <- function(reference_pkg = "cards", lib.loc = NULL, call = get_cli_abort_call()) {
+  if (rlang::is_empty(reference_pkg)) {
+    return(.empty_pkg_deps_df())
+  }
+
+  description <- utils::packageDescription(reference_pkg, lib.loc = lib.loc) |> suppressWarnings()
+  if (identical(description, NA)) {
+    return(.empty_pkg_deps_df())
+  }
+  description |>
+    unclass() |>
+    dplyr::as_tibble() |>
+    dplyr::select(
+      dplyr::any_of(c(
+        "Package", "Version", "Imports", "Depends",
+        "Suggests", "Enhances", "LinkingTo"
+      ))
+    ) |>
+    dplyr::rename(
+      reference_pkg = "Package",
+      reference_pkg_version = "Version"
+    ) |>
+    tidyr::pivot_longer(
+      -dplyr::all_of(c("reference_pkg", "reference_pkg_version")),
+      values_to = "pkg",
+      names_to = "dependency_type",
+    ) |>
+    tidyr::separate_rows("pkg", sep = ",") |>
+    dplyr::mutate(
+      pkg = trimws(
+        x = gsub(x = .data$pkg, pattern = "\\s+", replacement = " "),
+        which = "both", whitespace = "[ \t\r\n]"
+      )
+    ) |>
+    dplyr::filter(!is.na(.data$pkg)) |>
+    tidyr::separate(
+      .data$pkg,
+      into = c("pkg", "version"),
+      sep = " ", extra = "merge", fill = "right"
+    ) |>
+    dplyr::mutate(
+      compare = .data$version |> stringr::str_extract(pattern = "[>=<]+"),
+      version = .data$version |> stringr::str_remove_all(pattern = "[\\(\\) >=<]")
+    )
+}
+
+.empty_pkg_deps_df <- function() {
+  dplyr::tibble(
+    reference_pkg = character(0L), reference_pkg_version = character(0L),
+    dependency_type = character(0L), pkg = character(0L),
+    version = character(0L), compare = character(0L)
+  )
+}
+
+#' @inheritParams check_pkg_installed
+#' @keywords internal
+#' @noRd
+get_min_version_required <- function(pkg, reference_pkg = "cards",
+                                     lib.loc = NULL, call = get_cli_abort_call()) {
+  # if no package reference, return a df with just the pkg names
+  if (rlang::is_empty(reference_pkg)) {
+    return(
+      .empty_pkg_deps_df() |>
+        dplyr::full_join(
+          dplyr::tibble(pkg = pkg),
+          by = "pkg"
+        )
+    )
+  }
+
+  # get the package_ref deps and subset on requested pkgs, also supplement df with pkgs
+  # that may not be proper deps of the reference package (these pkgs don't have min versions)
+  res <-
+    get_pkg_dependencies(reference_pkg, lib.loc = lib.loc) |>
+    dplyr::filter(.data$pkg %in% .env$pkg) |>
+    dplyr::full_join(
+      dplyr::tibble(pkg = pkg),
+      by = "pkg"
+    )
+
+  res
+}
+
+# nocov end
+# styler: on

R/import-standalone-cli_call_env.R

@@ -0,0 +1,53 @@
+# Standalone file: do not edit by hand
+# Source: <https://github.com/ddsjoberg/standalone/blob/main/R/standalone-cli_call_env.R>
+# ----------------------------------------------------------------------
+#
+# ---
+# repo: ddsjoberg/standalone
+# file: standalone-cli_call_env.R
+# last-updated: 2024-04-10
+# license: https://unlicense.org
+# imports: [rlang, cli]
+# ---
+#
+# This file provides functions to set and access the call environment to use in cli::cli_abort() in check functions.
+#
+# ## Changelog
+# nocov start
+# styler: off
+
+#' Set Call Environment for [cli::cli_abort()]
+#'
+#' Set a call environment to be used as the `call` parameter in [cli::cli_abort()] for package checks. This function
+#' is used to ensure that the correct user-facing function is reported for errors generated by internal checks that
+#' use [cli::cli_abort()].
+#'
+#' @param env (`enviroment`)\cr
+#'   call environment used as the `call` parameter in [cli::cli_abort()] for package checks
+#'
+#' @seealso [get_cli_abort_call()]
+#'
+#' @keywords internal
+#' @noRd
+set_cli_abort_call <- function(env = rlang::caller_env()) {
+  if (getOption("cli_abort_call") |> is.null()) {
+    options(cli_abort_call = env)
+    set_call <- as.call(list(function() options(cli_abort_call = NULL)))
+    do.call(on.exit, list(expr = set_call, add = TRUE, after = FALSE), envir = env)
+  }
+  invisible()
+}
+
+#' Get Call Environment for [cli::cli_abort()]
+#'
+#' @inheritParams set_cli_abort_call
+#' @seealso [set_cli_abort_call()]
+#'
+#' @keywords internal
+#' @noRd
+get_cli_abort_call <- function() {
+  getOption("cli_abort_call", default = parent.frame())
+}
+
+# nocov end
+# styler: on