Merge branch 'master' into add-cmdstanr-to-gha

Author: VisruthSK

.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:
@@ -16,7 +18,7 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
 
       - uses: r-lib/actions/setup-r@v2
         with:
@@ -49,7 +51,7 @@ jobs:
           files: ./cobertura.xml
           plugins: noop
           disable_search: true
-          token: ${{ secrets.CODECOV_TOKEN }}
+          use_oidc: true
 
       - name: Show testthat output
         if: always()
@@ -60,7 +62,7 @@ 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

@@ -26,17 +26,18 @@ Description: Plotting functions for posterior analysis, MCMC diagnostics,
 License: GPL (>= 3)
 URL: https://mc-stan.org/bayesplot/
 BugReports: https://github.com/stan-dev/bayesplot/issues/
-SystemRequirements: pandoc (>= 1.12.3), pandoc-citeproc
+SystemRequirements: pandoc (>= 1.12.3)
 Depends:
     R (>= 4.1.0)
 Imports:
-    dplyr (>= 0.8.0),
-    ggplot2 (>= 3.4.0),
+    dplyr (>= 1.0.0),
+    ggplot2 (>= 3.5.0),
     ggridges (>= 0.5.5),
     glue,
+    lifecycle,
     posterior,
     reshape2,
-    rlang (>= 0.3.0),
+    rlang (>= 1.0.0),
     stats,
     tibble (>= 2.0.0),
     tidyr,
@@ -54,7 +55,7 @@ Suggests:
     rmarkdown (>= 1.0.0),
     rstan (>= 2.17.1),
     rstanarm (>= 2.17.4),
-    rstantools (>= 1.5.0),
+    rstantools (>= 2.0.0),
     scales,
     shinystan (>= 2.3.0),
     survival,

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)
@@ -155,6 +157,7 @@ export(ppc_ribbon)
 export(ppc_ribbon_data)
 export(ppc_ribbon_grouped)
 export(ppc_rootogram)
+export(ppc_rootogram_grouped)
 export(ppc_scatter)
 export(ppc_scatter_avg)
 export(ppc_scatter_avg_data)
@@ -215,12 +218,14 @@ importFrom(dplyr,inner_join)
 importFrom(dplyr,left_join)
 importFrom(dplyr,mutate)
 importFrom(dplyr,n)
-importFrom(dplyr,one_of)
 importFrom(dplyr,pull)
 importFrom(dplyr,rename)
 importFrom(dplyr,select)
+importFrom(dplyr,slice_min)
 importFrom(dplyr,summarise)
-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 +1,26 @@
 # bayesplot (development version)
 
+* Eliminate redundant data processing in `mcmc_areas_data()` by reusing the prepared MCMC array for both interval and density computation.
+* Validate equal chain lengths in `validate_df_with_chain()`, reject missing
+  chain labels, and renumber data-frame chain labels internally when converting
+  to arrays.
+* Added unit tests for previously untested edge cases in `param_range()`, `param_glue()`, and `tidyselect_parameters()` (no-match, partial-match, and negation behavior).
+* Bumped minimum version for `rstantools` from `>= 1.5.0` to `>= 2.0.0` .
+* Use `rlang::warn()` and `rlang::inform()` for selected PPC user messages instead of base `warning()` and `message()`.
+* Standardize input validation errors in `ppc_km_overlay()` and interpolation helpers to use `rlang::abort()` for consistent error handling.
+* 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)
+* Use `"neff_ratio"` consistently in diagnostic color scale helpers to avoid relying on partial matching of `"neff"`.
+* Replace `expand = c(mult, add)` with `ggplot2::expansion()` helper in scale functions for consistency with ggplot2 >= 3.3.0 style.
+* Replace uses of `geom_bar(stat = "identity")` with the more idiomatic ggplot2 form `geom_col()` 
+* New function `ppc_rootogram_grouped` for grouped rootogram plots by @behramulukir and @jgabry (#419)
+
 # bayesplot 1.15.0
 
 * Add `shape` argument to `mcmc_scatter` by @behramulukir (#375)

R/bayesplot-colors.R

@@ -189,7 +189,7 @@ color_scheme_view <- function(scheme = NULL) {
 
 #' @export
 print.bayesplot_scheme <- function(x, ...) {
-  tab <- data.frame(unlist(x, use.names = FALSE), stringsAsFactors = FALSE)
+  tab <- data.frame(unlist(x, use.names = FALSE))
   colnames(tab) <- attr(x, "scheme_name") %||% "hex_color"
   print(tab, ...)
 }
@@ -222,9 +222,8 @@ plot_scheme <- function(scheme = NULL) {
   )
 
   ggplot(color_data, aes(x = .data$name, y = .data$value, fill = .data$group)) +
-    geom_bar(
+    geom_col(
       width = .5,
-      stat = "identity",
       color = "white",
       linewidth = 0.1
     ) +

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(...))
 }
@@ -44,10 +37,10 @@ modify_aes <- function(mapping, ...) {
 facet_wrap_parsed <- function(...) {
   facet_wrap(..., labeller = label_parsed)
 }
-dont_expand_y_axis <- function(expand = c(0,0)) {
+dont_expand_y_axis <- function(expand = expansion(0, 0)) {
   scale_y_continuous(expand = expand)
 }
-dont_expand_x_axis <- function(expand = c(0,0)) {
+dont_expand_x_axis <- function(expand = expansion(0, 0)) {
   scale_x_continuous(expand = expand)
 }
 dont_expand_axes <- function() {

R/helpers-mcmc.R

@@ -210,6 +210,13 @@ validate_df_with_chain <- function(x) {
     x$chain <- NULL
   }
   x$Chain <- as.integer(x$Chain)
+  if (anyNA(x$Chain)) {
+    abort("Chain values must not be NA.")
+  }
+  rows_per_chain <- table(x$Chain)
+  if (length(unique(rows_per_chain)) != 1) {
+    abort("All chains must have the same number of iterations.")
+  }
   x
 }
 
@@ -218,11 +225,14 @@ validate_df_with_chain <- function(x) {
 df_with_chain2array <- function(x) {
   x <- validate_df_with_chain(x)
   chain <- x$Chain
+  # Renumber arbitrary chain labels to the contiguous 1:N indices used internally.
+  chain <- match(chain, sort(unique(chain)))
   n_chain <- length(unique(chain))
   a <- x[, !colnames(x) %in% "Chain", drop = FALSE]
   parnames <- colnames(a)
   a <- as.matrix(a)
-  x <- array(NA, dim = c(ceiling(nrow(a) / n_chain), n_chain, ncol(a)))
+  n_iter <- nrow(a) %/% n_chain
+  x <- array(NA, dim = c(n_iter, n_chain, ncol(a)))
   for (j in seq_len(n_chain)) {
     x[, j, ] <- a[chain == j,, drop=FALSE]
   }