Merge branch 'master' into gh-pages

Author: jgabry

.Rbuildignore

@@ -1,3 +1,4 @@
+^CRAN-SUBMISSION$
 ^CRAN-RELEASE$
 ^.*\.Rproj$
 ^\.Rproj\.user$

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

@@ -4,9 +4,11 @@ on:
   push:
     branches: [main, master]
   pull_request:
-    branches: [main, master, patch-for-cran]
+    branches: [main, master]
+
+name: R-CMD-check.yaml
 
-name: R-CMD-check
+permissions: read-all
 
 jobs:
   R-CMD-check:
@@ -29,7 +31,7 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -41,13 +43,10 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: |
-            any::rcmdcheck
-            any::BH
-            any::RcppEigen
-            any::vdiffr
+          extra-packages: any::rcmdcheck, any::BH, any::RcppEigen, any::vdiffr
           needs: check
 
       - uses: r-lib/actions/check-r-package@v2
         with:
           upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

.github/workflows/test-coverage.yaml

@@ -4,9 +4,10 @@ on:
   push:
     branches: [main, master]
   pull_request:
-    branches: [main, master, patch-for-cran]
 
-name: test-coverage
+name: test-coverage.yaml
+
+permissions: read-all
 
 jobs:
   test-coverage:
@@ -15,38 +16,46 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: |
-            any::covr
-            any::vdiffr
+          extra-packages: any::covr, any::xml2, any::vdiffr
           needs: coverage
 
       - name: Test coverage
         run: |
-          covr::codecov(
+          cov <- covr::package_coverage(
             quiet = FALSE,
             clean = FALSE,
-            install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package")
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
           )
+          covr::to_cobertura(cov)
         shell: Rscript {0}
 
+      - uses: codecov/codecov-action@v4
+        with:
+          # Fail if error if not on PR, or if on PR and token is given
+          fail_ci_if_error: ${{ github.event_name != 'pull_request' || secrets.CODECOV_TOKEN }}
+          file: ./cobertura.xml
+          plugin: noop
+          disable_search: true
+          token: ${{ secrets.CODECOV_TOKEN }}
+
       - name: Show testthat output
         if: always()
         run: |
           ## --------------------------------------------------------------------
-          find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true
+          find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
         shell: bash
 
       - name: Upload test results
         if: failure()
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: coverage-test-failures
           path: ${{ runner.temp }}/package

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: bayesplot
 Type: Package
 Title: Plotting for Bayesian Models
-Version: 1.11.0
-Date: 2024-01-30
+Version: 1.12.0
+Date: 2025-04-09
 Authors@R: c(person("Jonah", "Gabry", role = c("aut", "cre"), email = "jsg2201@columbia.edu"),
              person("Tristan", "Mahr", role = "aut"),
              person("Paul-Christian", "Bürkner", role = "ctb"),
@@ -37,6 +37,7 @@ Imports:
     rlang (>= 0.3.0),
     stats,
     tibble (>= 2.0.0),
+    tidyr,
     tidyselect,
     utils
 Suggests:
@@ -55,7 +56,7 @@ Suggests:
     survival,
     testthat (>= 2.0.0),
     vdiffr (>= 1.0.2)
-RoxygenNote: 7.3.0
+RoxygenNote: 7.3.2
 VignetteBuilder: knitr
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)

NEWS.md

@@ -1,4 +1,20 @@
-<!-- See http://style.tidyverse.org/news.html for advice on writing news -->
+# bayesplot 1.12.0
+
+* Expand checking workflows to more platforms by @andrjohns (#324)
+* Skip tests depending on Suggested dependency rstantools if not installed by @MichaelChirico (#325)
+* Skip tests depending on Suggested dependency gridExtra if not installed by @MichaelChirico (#326) 
+* Fix missing legends for unobserved levels in rhat and neff plots (#328)
+* Document problems with `ppc_stat` with `stat="mean"` (#329)
+* Ensure rank overlay plot starts at 0 even if not all bins present, thanks @sims1253 (#332)
+* Compatibility with ggplot2 3.6.0 by @teunbrand (#337)
+* Update GitHub actions workflows (#338)
+* Remove deprecated functions from `available_ppc()` (#340)
+* Fix missing counts in `ppc_bars_data()` by @TeemuSailynoja, thanks @famuvie (#342)
+
+
+# bayesplot 1.11.1
+
+* Limit maximum number of evaluation points in `ppc_pit_ecdf` functions by default to 1000. by @TeemuSailynoja in #318
 
 # bayesplot 1.11.0
 

R/available-module-functions.R

@@ -130,6 +130,9 @@ print.bayesplot_function_list <- function(x, ...) {
       )
     }
 
+    # remove deprecated functions
+    return_funs <- setdiff(return_funs, "ppc_loo_pit")
+
     structure(
       return_funs,
       class = c("bayesplot_function_list", "character"),

R/helpers-ppc.R

@@ -319,7 +319,7 @@ adjust_gamma <- function(N,
     abort("Value of 'prob' must be in (0,1).")
   }
   if (is.null(interpolate_adj)) {
-    if (K <= 200) {
+    if (K <= 200 || N < 100) {
       interpolate_adj <- FALSE
     } else {
       interpolate_adj <- TRUE

R/mcmc-diagnostics.R

@@ -142,7 +142,8 @@ mcmc_rhat <- function(rhat, ..., size = NULL) {
       mapping = aes(
         yend = .data$parameter,
         xend = ifelse(min(.data$value) < 1, 1, -Inf)),
-      na.rm = TRUE) +
+      na.rm = TRUE,
+      show.legend = TRUE) +
       bayesplot_theme_get()
 
   if (min(data$value) < 1) {
@@ -238,7 +239,8 @@ mcmc_neff <- function(ratio, ..., size = NULL) {
       fill = .data$rating)) +
     geom_segment(
       aes(yend = .data$parameter, xend = -Inf),
-      na.rm = TRUE) +
+      na.rm = TRUE,
+      show.legend = TRUE) +
     diagnostic_points(size) +
     vline_at(
       c(0.1, 0.5, 1),
@@ -408,7 +410,7 @@ zero_pad_int <- function(xs) {
 }
 
 diagnostic_points <- function(size = NULL) {
-  args <- list(shape = 21, na.rm = TRUE)
+  args <- list(shape = 21, na.rm = TRUE, show.legend = TRUE)
   do.call("geom_point", c(args, size = size))
 }
 
@@ -454,7 +456,6 @@ diagnostic_colors <- function(diagnostic = c("rhat", "neff_ratio"),
   }
 
   color_labels <- diagnostic_color_labels[[diagnostic]]
-
   list(diagnostic = diagnostic,
        aesthetic = aesthetic,
        color_levels = color_levels,

R/mcmc-distributions.R

@@ -394,7 +394,7 @@ mcmc_violin <- function(
       set_hist_aes(freq),
       fill = get_color("mid"),
       color = get_color("mid_highlight"),
-      size = .25,
+      linewidth = .25,
       na.rm = TRUE,
       binwidth = binwidth,
       bins = bins,

R/mcmc-overview.R

@@ -26,7 +26,7 @@
 #' an additional column `"Chain"` that contains the chain number (an integer)
 #' corresponding to each row in the data frame.
 #' * __draws__: Any of the `draws` formats supported by the
-#' \pkg{\link{posterior}} package.
+#' \pkg{posterior} package.
 #'
 #' __Note__: typically the user should *not* include warmup iterations
 #' in the object passed to **bayesplot** plotting functions, although for