Fix violin plot deprecation warnings from ggplot2 4.0

Author: jgabry

R/mcmc-distributions.R

@@ -460,13 +460,13 @@ mcmc_violin <- function(
     ...
   ) {
 
-    bw <- bw %||% "nrd0"
-    adjust <- adjust %||% 1
-    kernel <- kernel %||% "gaussian"
-    n_dens <- n_dens %||% 1024
-    bounds <- validate_density_bounds(bounds)
+  bw <- bw %||% "nrd0"
+  adjust <- adjust %||% 1
+  kernel <- kernel %||% "gaussian"
+  n_dens <- n_dens %||% 1024
+  bounds <- validate_density_bounds(bounds)
 
-    x <- prepare_mcmc_array(x, pars, regex_pars, transformations)
+  x <- prepare_mcmc_array(x, pars, regex_pars, transformations)
   data <- melt_mcmc.mcmc_array(x)
   data$Chain <- factor(data$Chain)
   n_param <- num_params(data)
@@ -486,16 +486,21 @@ mcmc_violin <- function(
   geom_args <- list(linewidth = 0.5, na.rm = TRUE, alpha = alpha)
   if (violin) {
     geom_args[["draw_quantiles"]] <- probs
-    } else {
-      geom_args[["trim"]] <- trim
-      geom_args[["bw"]] <- bw
-      geom_args[["adjust"]] <- adjust
-      geom_args[["kernel"]] <- kernel
-      geom_args[["n"]] <- n_dens
-      if (!is.null(bounds)) {
-        geom_args[["bounds"]] <- bounds
-      }
+    if (utils::packageVersion("ggplot2") >= "4.0.0") {
+      geom_args[["draw_quantiles"]] <- NULL
+      geom_args[["quantiles"]] <- probs
+      geom_args[["quantile.linetype"]] <- 1
     }
+  } else {
+    geom_args[["trim"]] <- trim
+    geom_args[["bw"]] <- bw
+    geom_args[["adjust"]] <- adjust
+    geom_args[["kernel"]] <- kernel
+    geom_args[["n"]] <- n_dens
+    if (!is.null(bounds)) {
+      geom_args[["bounds"]] <- bounds
+    }
+  }
   if (by_chain) {
     # aes_mapping[["color"]] <- ~ Chain
     # aes_mapping[["group"]] <- ~ Chain

R/ppc-distributions.R

@@ -566,9 +566,8 @@ ppc_dots <-
 
 #' @rdname PPC-distributions
 #' @export
-#' @param probs A numeric vector passed to [ggplot2::geom_violin()]'s
-#'   `draw_quantiles` argument to specify at which quantiles to draw
-#'   horizontal lines. Set to `NULL` to remove the lines.
+#' @param probs A numeric vector of probabilities controlling where quantile
+#'   lines are drawn. Set to `NULL` to remove the lines.
 #' @param y_draw For `ppc_violin_grouped()`, a string specifying how to draw
 #'   `y`: `"violin"` (default), `"points"` (jittered points), or `"both"`.
 #' @param y_jitter,y_size,y_alpha For `ppc_violin_grouped()`, if `y_draw` is
@@ -602,6 +601,11 @@ ppc_violin_grouped <-
       alpha = alpha,
       linewidth = size
     )
+    if (utils::packageVersion("ggplot2") >= "4.0.0") {
+      args_violin_yrep$draw_quantiles <- NULL
+      args_violin_yrep$quantiles <- probs
+      args_violin_yrep$quantile.linetype <- 1
+    }
 
     args_violin_y <- list(
       data = function(x) dplyr::filter(x, .data$is_y),

man/MCMC-distributions.Rd

@@ -21,19 +21,19 @@ test_that("density PPC/PPD plots reject invalid bounds", {
   # non-numeric bounds
   expect_error(ppc_dens_overlay(y, yrep, bounds = c("a", "b")),
                "`bounds` must be a numeric vector of length 2")
-  
+
   # bounds with length != 2
   expect_error(ppc_dens_overlay(y, yrep, bounds = c(0, 1, 2)),
                "`bounds` must be a numeric vector of length 2")
   expect_error(ppc_dens_overlay(y, yrep, bounds = 1),
                "`bounds` must be a numeric vector of length 2")
-  
+
   # bounds with NA values
   expect_error(ppc_dens_overlay(y, yrep, bounds = c(0, NA)),
                "`bounds` must be a numeric vector of length 2")
   expect_error(ppc_dens_overlay(y, yrep, bounds = c(NA, 1)),
                "`bounds` must be a numeric vector of length 2")
-  
+
   # bounds where bounds[1] >= bounds[2]
   expect_error(ppc_dens_overlay(y, yrep, bounds = c(1, 0)),
                "`bounds` must satisfy bounds\\[1\\] < bounds\\[2\\]")
@@ -393,6 +393,17 @@ test_that("ppc_violin_grouped renders correctly", {
     "ppc_violin_grouped (points, low jitter)",
     p_dots_jitter)
 
+  p_probs <- ppc_violin_grouped(
+    y = vdiff_y,
+    yrep = vdiff_yrep,
+    group = vdiff_group,
+    y_draw = "points",
+    probs = c(0.1, 0.9)
+  )
+  vdiffr::expect_doppelganger(
+    "ppc_violin_grouped (points, probs)",
+    p_probs)
+
   set.seed(seed = NULL)
 })