Merge branch 'master' into test/data-functions-edge-cases

Author: utkarshpawade

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

@@ -41,12 +41,18 @@ jobs:
           r-version: ${{ matrix.config.r }}
           http-user-agent: ${{ matrix.config.http-user-agent }}
           use-public-rspm: true
+          extra-repositories: |
+            https://community.r-multiverse.org
+            https://stan-dev.r-universe.dev
 
       - 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, any::cmdstanr
           needs: check
 
+      - name: Install CmdStan
+        run: Rscript -e "cmdstanr::install_cmdstan()"
+
       - uses: r-lib/actions/check-r-package@v2
         with:
           upload-snapshots: true

.github/workflows/pkgdown.yml

@@ -30,6 +30,9 @@ jobs:
       - uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true
+          extra-repositories: |
+            https://community.r-multiverse.org
+            https://stan-dev.r-universe.dev
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:

.github/workflows/test-coverage.yaml

@@ -23,12 +23,16 @@ jobs:
       - uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true
+          extra-repositories: 'https://stan-dev.r-universe.dev'
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::covr, any::xml2, any::vdiffr
+          extra-packages: any::covr, any::xml2, any::vdiffr, any::cmdstanr
           needs: coverage
 
+      - name: Install CmdStan
+        run: Rscript -e "cmdstanr::install_cmdstan()"
+
       - name: Test coverage
         run: |
           cov <- covr::package_coverage(

DESCRIPTION

@@ -44,6 +44,7 @@ Imports:
     tidyselect,
     utils
 Suggests:
+    cmdstanr,
     ggdist,
     ggfortify,
     gridExtra (>= 2.2.1),
@@ -65,3 +66,4 @@ VignetteBuilder: knitr
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 Config/testthat/edition: 3
+Additional_repositories: https://stan-dev.r-universe.dev/

NEWS.md

@@ -1,6 +1,9 @@
 # bayesplot (development version)
 
 * Added singleton-dimension edge-case tests for exported `_data()` functions.
+* `ppc_ecdf_overlay()`, `ppc_ecdf_overlay_grouped()`, and `ppd_ecdf_overlay()` now always use `geom_step()`. The `discrete` argument is deprecated.
+* Fixed missing `drop = FALSE` in `nuts_params.CmdStanMCMC()`.
+* Replace `apply()` with `storage.mode()` for integer-to-numeric matrix conversion in `validate_predictions()`.
 * Fixed `is_chain_list()` to correctly reject empty lists instead of silently returning `TRUE`.
 * Added unit tests for `mcmc_areas_ridges_data()`, `mcmc_parcoord_data()`, and `mcmc_trace_data()`.
 * Added unit tests for `ppc_error_data()` and `ppc_loo_pit_data()` covering output structure, argument handling, and edge cases.

R/bayesplot-extractors.R

@@ -175,7 +175,7 @@ nuts_params.list <- function(object, pars = NULL, ...) {
 nuts_params.CmdStanMCMC <- function(object, pars = NULL, ...) {
   arr <- object$sampler_diagnostics()
   if (!is.null(pars)) {
-    arr <- arr[,, pars]
+    arr <- arr[,, pars, drop = FALSE]
   }
   out <- reshape2::melt(arr)
   colnames(out)[colnames(out) == "variable"] <- "parameter"

R/helpers-ppc.R

@@ -73,12 +73,7 @@ validate_predictions <- function(predictions, n_obs = NULL) {
   }
 
   if (is.integer(predictions)) {
-    if (nrow(predictions) == 1) {
-      predictions[1, ] <- as.numeric(predictions[1,, drop = FALSE])
-    }
-    else {
-      predictions <- apply(predictions, 2, as.numeric)
-    }
+    storage.mode(predictions) <- "numeric"
   }
 
   if (anyNA(predictions)) {

R/ppc-distributions.R

@@ -41,11 +41,10 @@
 #'   }
 #'   \item{`ppc_ecdf_overlay()`, `ppc_dens_overlay()`,
 #'          `ppc_ecdf_overlay_grouped()`, `ppc_dens_overlay_grouped()`}{
-#'    Kernel density or empirical CDF estimates of each dataset (row) in
-#'    `yrep` are overlaid, with the distribution of `y` itself on top
-#'    (and in a darker shade). When using `ppc_ecdf_overlay()` with discrete
-#'    data, set the `discrete` argument to `TRUE` for better results.
-#'    For an example of `ppc_dens_overlay()` also see Gabry et al. (2019).
+#'    Kernel density or empirical CDF estimates of each dataset (row) in `yrep`
+#'    are overlaid, with the distribution of `y` itself on top (and in a darker
+#'    shade). For an example of `ppc_dens_overlay()` also see Gabry et al.
+#'    (2019).
 #'   }
 #'   \item{`ppc_violin_grouped()`}{
 #'    The density estimate of `yrep` within each level of a grouping
@@ -85,7 +84,7 @@
 #'
 #' ppc_dens_overlay(y, yrep[1:25, ])
 #' \donttest{
-#' # ppc_ecdf_overlay with continuous data (set discrete=TRUE if discrete data)
+#' # ppc_ecdf_overlay
 #' ppc_ecdf_overlay(y, yrep[sample(nrow(yrep), 25), ])
 #'
 #' # PIT-ECDF and PIT-ECDF difference plot of the PIT values of y compared to
@@ -258,20 +257,28 @@ ppc_dens_overlay_grouped <- function(y,
 
 #' @export
 #' @rdname PPC-distributions
-#' @param discrete For `ppc_ecdf_overlay()`, should the data be treated as
-#'   discrete? The default is `FALSE`, in which case `geom="line"` is
-#'   passed to [ggplot2::stat_ecdf()]. If `discrete` is set to
-#'   `TRUE` then `geom="step"` is used.
+#' @param discrete `r lifecycle::badge("deprecated")` The `discrete` argument is
+#'   deprecated. The ECDF is a step function by definition, so `geom_step()` is
+#'   now always used.
 #' @param pad A logical scalar passed to [ggplot2::stat_ecdf()].
 #'
 ppc_ecdf_overlay <- function(y,
                              yrep,
                              ...,
-                             discrete = FALSE,
+                             discrete = deprecated(),
                              pad = TRUE,
                              size = 0.25,
                              alpha = 0.7) {
   check_ignored_arguments(...)
+
+  if (is_present(discrete)) {
+    deprecate_warn(
+      "1.16.0",
+      "ppc_ecdf_overlay(discrete)",
+      details = "The ECDF is now always plotted as a step function."
+    )
+  }
+
   data <- ppc_data(y, yrep)
 
   ggplot(data) +
@@ -291,15 +298,15 @@ ppc_ecdf_overlay <- function(y,
     stat_ecdf(
       data = function(x) dplyr::filter(x, !.data$is_y),
       mapping = aes(group = .data$rep_id, color = "yrep"),
-      geom = if (discrete) "step" else "line",
+      geom = "step",
       linewidth = size,
       alpha = alpha,
       pad = pad
     ) +
     stat_ecdf(
       data = function(x) dplyr::filter(x, .data$is_y),
       mapping = aes(color = "y"),
-      geom = if (discrete) "step" else "line",
+      geom = "step",
       linewidth = 1,
       pad = pad
     ) +
@@ -316,17 +323,24 @@ ppc_ecdf_overlay_grouped <- function(y,
                                      yrep,
                                      group,
                                      ...,
-                                     discrete = FALSE,
+                                     discrete = deprecated(),
                                      pad = TRUE,
                                      size = 0.25,
                                      alpha = 0.7) {
   check_ignored_arguments(...)
 
+  if (is_present(discrete)) {
+    deprecate_warn(
+      "1.16.0",
+      "ppc_ecdf_overlay_grouped(discrete)",
+      details = "The ECDF is now always plotted as a step function."
+    )
+  }
+
   p_overlay <- ppc_ecdf_overlay(
     y = y,
     yrep = yrep,
     ...,
-    discrete = discrete,
     pad = pad,
     size = size,
     alpha = alpha

R/ppd-distributions.R

@@ -83,12 +83,20 @@ ppd_dens_overlay <-
 ppd_ecdf_overlay <-
   function(ypred,
            ...,
-           discrete = FALSE,
+           discrete = deprecated(),
            pad = TRUE,
            size = 0.25,
            alpha = 0.7) {
     check_ignored_arguments(...)
 
+    if (is_present(discrete)) {
+      deprecate_warn(
+        "1.16.0",
+        "ppd_ecdf_overlay(discrete)",
+        details = "The ECDF is now always plotted as a step function."
+      )
+    }
+
     data <- ppd_data(ypred)
     ggplot(data, mapping = aes(x = .data$value)) +
       hline_at(
@@ -99,7 +107,7 @@ ppd_ecdf_overlay <-
       ) +
       stat_ecdf(
         mapping = aes(group = .data$rep_id, color = "ypred"),
-        geom = if (discrete) "step" else "line",
+        geom = "step",
         linewidth = size,
         alpha = alpha,
         pad = pad