Merge branch 'master' into ppc-rootogram-grouped

Author: jgabry

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

@@ -29,6 +29,7 @@ jobs:
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       R_KEEP_PKG_SOURCE: yes
+      R_VERSION_TYPE: ${{ matrix.config.r }}
 
     steps:
       - uses: actions/checkout@v6

.github/workflows/test-coverage.yaml

@@ -7,7 +7,9 @@ on:
 
 name: test-coverage.yaml
 
-permissions: read-all
+permissions:
+  contents: read
+  id-token: write
 
 jobs:
   test-coverage:
@@ -45,7 +47,7 @@ jobs:
           files: ./cobertura.xml
           plugins: noop
           disable_search: true
-          token: ${{ secrets.CODECOV_TOKEN }}
+          use_oidc: true
 
       - name: Show testthat output
         if: always()
@@ -56,7 +58,7 @@ jobs:
 
       - name: Upload test results
         if: failure()
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v7
         with:
           name: coverage-test-failures
           path: ${{ runner.temp }}/package

DESCRIPTION

@@ -30,13 +30,14 @@ SystemRequirements: pandoc (>= 1.12.3), pandoc-citeproc
 Depends:
     R (>= 4.1.0)
 Imports:
-    dplyr (>= 0.8.0),
+    dplyr (>= 1.0.0),
     ggplot2 (>= 3.4.0),
     ggridges (>= 0.5.5),
     glue,
+    lifecycle,
     posterior,
     reshape2,
-    rlang (>= 0.3.0),
+    rlang (>= 1.0.0),
     stats,
     tibble (>= 2.0.0),
     tidyr,

NAMESPACE

@@ -74,6 +74,8 @@ export(mcmc_dens)
 export(mcmc_dens_chains)
 export(mcmc_dens_chains_data)
 export(mcmc_dens_overlay)
+export(mcmc_dots)
+export(mcmc_dots_by_chain)
 export(mcmc_hex)
 export(mcmc_hist)
 export(mcmc_hist_by_chain)
@@ -225,3 +227,6 @@ importFrom(dplyr,top_n)
 importFrom(dplyr,ungroup)
 importFrom(dplyr,vars)
 importFrom(ggplot2,"%+replace%")
+importFrom(lifecycle,deprecate_warn)
+importFrom(lifecycle,deprecated)
+importFrom(lifecycle,is_present)

NEWS.md

@@ -1,5 +1,14 @@
 # bayesplot (development version)
 
+* Fix assignment-in-call bug in `mcmc_rank_ecdf()` (#).
+* Replaced deprecated `dplyr` and `tidyselect` functions (`top_n`, `one_of`, `group_indices`) with their modern equivalents to ensure future compatibility. (#431)
+* Documentation added for all exported `*_data()` functions (#209)
+* Improved documentation for `binwidth`, `bins`, and `breaks` arguments to clarify they are passed to `ggplot2::geom_area()` and `ggdist::stat_dots()` in addition to `ggplot2::geom_histogram()`
+* Improved documentation for `freq` argument to clarify it applies to frequency polygons in addition to histograms
+* Fixed test in `test-ppc-distributions.R` that incorrectly used `ppc_dens()` instead of `ppd_dens()` when testing PPD functions
+* New functions `mcmc_dots` and `mcmc_dots_by_chain` for dot plots of MCMC draws by @behramulukir (#402)
+* Default to `quantiles=100` for all dot plots by @behramulukir (#402)
+
 # bayesplot 1.15.0
 
 * Add `shape` argument to `mcmc_scatter` by @behramulukir (#375)

R/bayesplot-helpers.R

@@ -446,19 +446,28 @@ plot_bg <- function(on = TRUE, ...) {
 
 #' @rdname bayesplot-helpers
 #' @export
-#' @param color,size Passed to [ggplot2::element_line()].
-#'
-grid_lines <- function(color = "gray50", size = 0.2) {
+#' @param color,linewidth Passed to [ggplot2::element_line()].
+#' @param size `r lifecycle::badge("deprecated")` Use `linewidth` instead.
+#'
+grid_lines <- function(color = "gray50", linewidth = 0.2, size = deprecated()) {
+  if (lifecycle::is_present(size)) {
+    lifecycle::deprecate_warn(
+      "1.16.0",
+      "grid_lines(size)",
+      "grid_lines(linewidth)"
+    )
+    linewidth <- size
+  }
   theme(
-    panel.grid.major = element_line(color = color, linewidth = size),
-    panel.grid.minor = element_line(color = color, linewidth = size * 0.5)
+    panel.grid.major = element_line(color = color, linewidth = linewidth),
+    panel.grid.minor = element_line(color = color, linewidth = linewidth * 0.5)
   )
 }
 
-grid_lines_y <- function(color = "gray50", size = 0.2) {
+grid_lines_y <- function(color = "gray50", linewidth = 0.2) {
   theme(
-    panel.grid.major.y = element_line(color = color, linewidth = size),
-    panel.grid.minor.y = element_line(color = color, linewidth = size * 0.5)
+    panel.grid.major.y = element_line(color = color, linewidth = linewidth),
+    panel.grid.minor.y = element_line(color = color, linewidth = linewidth * 0.5)
   )
 }
 

R/bayesplot-package.R

@@ -5,6 +5,7 @@
 #'
 #' @import ggplot2 stats rlang
 #' @importFrom dplyr %>% summarise group_by select
+#' @importFrom lifecycle deprecated deprecate_warn is_present
 #'
 #' @description
 #' \if{html}{

R/helpers-gg.R

@@ -24,17 +24,10 @@ geom_ignore <- function(...) {
 
 #' Add new aesthetic mappings to a list of aesthetic mappings
 #'
-#' @param mapping a list of `uneval` aesthetic mappings (created by `aes_()`)
-#' @param ... additional mappings to add, e.g., `color = ~ parameter`
+#' @param mapping a list of `uneval` aesthetic mappings (created by `aes()`)
+#' @param ... additional mappings to add using `.data$` syntax
 #' @return the updated list
 #' @noRd
-modify_aes_ <- function(mapping, ...) {
-  utils::modifyList(mapping, aes_(...))
-}
-
-#' Same as `modify_aes_` but using `aes()` instead of `aes_()` (now deprecated).
-#' Often `...` will need to contain expression of the form `.data$x` to avoid R cmd check warnings
-#' @noRd
 modify_aes <- function(mapping, ...) {
   utils::modifyList(mapping, aes(...))
 }

R/mcmc-diagnostics.R

@@ -18,6 +18,13 @@
 #'
 #' @section Plot Descriptions:
 #' \describe{
+#' \item{`mcmc_rhat_data()`, `mcmc_neff_data()`}{
+#'   Data-preparation back ends for the R-hat and effective sample size plots.
+#'   Users can call these functions directly to obtain the data frame of
+#'   diagnostic values with rating labels and create custom diagnostic
+#'   visualizations with **ggplot2**.
+#' }
+#'
 #' \item{`mcmc_rhat()`, `mcmc_rhat_hist()`}{
 #'   Rhat values as either points or a histogram. Values are colored using
 #'   different shades (lighter is better). The chosen thresholds are somewhat
@@ -70,7 +77,7 @@
 #' (p <- mcmc_acf_bar(x, pars = c("alpha", "beta[1]")))
 #'
 #' # add horiztonal dashed line at 0.5
-#' p + hline_at(0.5, linetype = 2, size = 0.15, color = "gray")
+#' p + hline_at(0.5, linetype = 2, linewidth = 0.15, color = "gray")
 #' }
 #'
 #' # fake rhat values to use for demonstration