Merge branch 'master' into issue-258

Author: jgabry

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: bayesplot
 Type: Package
 Title: Plotting for Bayesian Models
-Version: 1.8.0.9000
-Date: 2021-01-07
+Version: 1.8.1
+Date: 2021-06-13
 Authors@R: c(person("Jonah", "Gabry", role = c("aut", "cre"), email = "[email protected]"),
              person("Tristan", "Mahr", role = "aut"),
              person("Paul-Christian", "Bürkner", role = "ctb"),
@@ -21,7 +21,6 @@ Description: Plotting functions for posterior analysis, MCMC diagnostics,
     developers working on a variety of R packages for Bayesian modeling, 
     particularly (but not exclusively) packages interfacing with 'Stan'.
 License: GPL (>= 3)
-LazyData: TRUE
 URL: https://mc-stan.org/bayesplot/
 BugReports: https://github.com/stan-dev/bayesplot/issues/
 SystemRequirements: pandoc (>= 1.12.3), pandoc-citeproc

NEWS.md

@@ -1,8 +1,8 @@
 <!-- See http://style.tidyverse.org/news.html for advice on writing news -->
 
-# bayesplot 1.8.0.9000
+# bayesplot 1.8.1
 
-Items for next release go here
+* Fix R cmd check error on linux for CRAN 
 
 * `mcmc_dens()` and `mcmc_dens_overlay()` gain arguments for controlling the 
   the density calculation. (#258)

R/mcmc-recover.R

@@ -315,6 +315,7 @@ mcmc_recover_hist <-
 
     vline_data <- data.frame(Parameter = colnames(x), True = true)
     hist_data <- melt_mcmc(x)[, -1]
+    vline_data$Parameter <- factor(vline_data$Parameter, levels = levels(hist_data$Parameter))
 
     facet_args[["facets"]] <- "Parameter"
     facet_args[["scales"]] <- facet_args[["scales"]] %||% "free"

R/ppc-intervals.R

@@ -173,14 +173,17 @@ ppc_intervals_grouped <- function(y,
 
 #' @rdname PPC-intervals
 #' @export
+#' @param y_draw For ribbon plots only, a string specifying how to draw `y`. Can
+#'   be `"line"` (the default), `"points"`, or `"both"`.
 ppc_ribbon <- function(y,
                        yrep,
                        x = NULL,
                        ...,
                        prob = 0.5,
                        prob_outer = 0.9,
                        alpha = 0.33,
-                       size = 0.25) {
+                       size = 0.25,
+                       y_draw = c("line", "points", "both")) {
   check_ignored_arguments(...)
 
   data <- ppc_intervals_data(
@@ -197,7 +200,8 @@ ppc_ribbon <- function(y,
     size = size,
     grouped = FALSE,
     style = "ribbon",
-    x_lab = label_x(x)
+    x_lab = label_x(x),
+    y_draw = y_draw
   )
 }
 
@@ -213,7 +217,8 @@ ppc_ribbon_grouped <- function(y,
                                prob = 0.5,
                                prob_outer = 0.9,
                                alpha = 0.33,
-                               size = 0.25) {
+                               size = 0.25,
+                               y_draw = c("line", "points", "both")) {
   check_ignored_arguments(...)
 
   data <- ppc_intervals_data(
@@ -234,7 +239,8 @@ ppc_ribbon_grouped <- function(y,
     size = size,
     grouped = TRUE,
     style = "ribbon",
-    x_lab = label_x(x)
+    x_lab = label_x(x),
+    y_draw = y_draw
   )
 }
 
@@ -319,9 +325,11 @@ label_x <- function(x) {
            size = 1,
            grouped = FALSE,
            style = c("intervals", "ribbon"),
-           x_lab = NULL) {
+           x_lab = NULL,
+           y_draw = c("line", "points", "both")) {
 
   style <- match.arg(style)
+  y_draw <- match.arg(y_draw)
 
   graph <- ggplot(
     data = data,
@@ -349,11 +357,22 @@ label_x <- function(x) {
         aes_(color = "yrep"),
         size = size/2
       ) +
-      geom_blank(aes_(fill = "y")) +
-      geom_line(
+      geom_blank(aes_(fill = "y"))
+
+    if (y_draw == "line" || y_draw == "both") {
+      graph <- graph + geom_line(
         aes_(y = ~ y_obs, color = "y"),
         size = 0.5
       )
+    }
+
+    if (y_draw == "points" || y_draw == "both") {
+      graph <- graph + geom_point(
+        mapping = aes_(y = ~ y_obs, color = "y", fill = "y"),
+        shape = 21,
+        size = 1.5
+      )
+    }
   } else {
     graph <- graph +
       geom_pointrange(

man/PPC-intervals.Rd

@@ -1,3 +1,3 @@
 - vdiffr-svg-engine: 1.0
-- vdiffr: 0.3.2.2
-- freetypeharfbuzz: 0.2.5
+- vdiffr: 0.3.3
+- freetypeharfbuzz: 0.2.6