Merge pull request #217 from stan-dev/issue-216

Issue 216

Author: jgabry

DESCRIPTION

@@ -26,7 +26,7 @@ Depends:
     R (>= 3.1.0)
 Imports:
     dplyr (>= 0.8.0),
-    ggplot2 (>= 2.2.1),
+    ggplot2 (>= 3.0.0),
     ggridges,
     glue,
     reshape2,
@@ -49,7 +49,7 @@ Suggests:
     shinystan (>= 2.3.0),
     testthat (>= 2.0.0),
     vdiffr
-RoxygenNote: 7.0.1
+RoxygenNote: 7.0.2
 VignetteBuilder: knitr
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)

R/helpers-gg.R

@@ -97,8 +97,9 @@ space_legend_keys <- function(relative_size = 2, color = "white") {
 
 # set aesthetic mapping for histograms depending on freq argument
 set_hist_aes <- function(freq = TRUE, ...) {
-  if (freq)
+  if (freq) {
     aes_(x = ~ value, ...)
-  else
-    aes_(x = ~ value, y = ~ ..density.., ...)
+  } else {
+    aes_(x = ~ value, y = ~ stat(density), ...)
+  }
 }

R/mcmc-distributions.R

@@ -301,26 +301,30 @@ mcmc_violin <- function(x,
 
 
 
+
 # internal -----------------------------------------------------------------
 .mcmc_hist <- function(x,
-                      pars = character(),
-                      regex_pars = character(),
-                      transformations = list(),
-                      facet_args = list(),
-                      binwidth = NULL,
-                      breaks = NULL,
-                      by_chain = FALSE,
-                      freq = TRUE,
-                      ...) {
+                       pars = character(),
+                       regex_pars = character(),
+                       transformations = list(),
+                       facet_args = list(),
+                       binwidth = NULL,
+                       breaks = NULL,
+                       by_chain = FALSE,
+                       freq = TRUE,
+                       ...) {
   x <- prepare_mcmc_array(x, pars, regex_pars, transformations)
-  if (by_chain && !has_multiple_chains(x))
+
+  if (by_chain && !has_multiple_chains(x)) {
     STOP_need_multiple_chains()
+  }
 
   data <- melt_mcmc(x, value.name = "value")
   n_param <- num_params(data)
 
-  graph <- ggplot(data, set_hist_aes(freq)) +
+  graph <- ggplot(data, aes(x = ~ value)) +
     geom_histogram(
+      set_hist_aes(freq),
       fill = get_color("mid"),
       color = get_color("mid_highlight"),
       size = .25,
@@ -336,15 +340,19 @@ mcmc_violin <- function(x,
       graph <- graph + do.call("facet_wrap", facet_args)
     }
   } else {
-    facet_args[["facets"]] <- if (n_param > 1)
-      "Chain ~ Parameter" else "Chain ~ ."
+    facet_args[["facets"]] <- if (n_param > 1) {
+      "Chain ~ Parameter"
+    } else {
+      "Chain ~ ."
+    }
     graph <- graph +
       do.call("facet_grid", facet_args) +
       force_axes_in_facets()
   }
 
-  if (n_param == 1)
+  if (n_param == 1) {
     graph <- graph + xlab(levels(data$Parameter))
+  }
 
   graph +
     dont_expand_y_axis(c(0.005, 0)) +
@@ -405,8 +413,8 @@ mcmc_violin <- function(x,
     geom_args[["color"]] <- get_color("mid_highlight")
   }
 
-  graph <- ggplot(data, mapping = do.call("aes_", aes_mapping))  +
-      do.call(geom_fun, geom_args)
+  graph <- ggplot(data, mapping = do.call("aes_", aes_mapping)) +
+    do.call(geom_fun, geom_args)
 
   if (!violin) {
     graph <- graph + dont_expand_x_axis()

R/mcmc-intervals.R

@@ -60,7 +60,7 @@
 #' color_scheme_set("brightblue")
 #' mcmc_intervals(x)
 #' mcmc_intervals(x, pars = c("beta[1]", "beta[2]"))
-#' mcmc_areas(x, regex_pars = "beta\\\[[1-3]\\\]",  prob = 0.8) +
+#' mcmc_areas(x, regex_pars = "beta\\[[1-3]\\]",  prob = 0.8) +
 #'  ggplot2::labs(
 #'    title = "Posterior distributions",
 #'    subtitle = "with medians and 80% intervals"

R/mcmc-scatterplots.R

@@ -220,17 +220,17 @@ mcmc_hex <- function(x,
 #'
 #' # pairs plots
 #' # default of condition=NULL implies splitting chains between upper and lower panels
-#' mcmc_pairs(x, pars = "alpha", regex_pars = "beta\\\[[1,4]\\\]",
+#' mcmc_pairs(x, pars = "alpha", regex_pars = "beta\\[[1,4]\\]",
 #'            off_diag_args = list(size = 1, alpha = 0.5))
 #'
 #' # change to density plots instead of histograms and hex plots instead of
 #' # scatterplots
-#' mcmc_pairs(x, pars = "alpha", regex_pars = "beta\\\[[1,4]\\\]",
+#' mcmc_pairs(x, pars = "alpha", regex_pars = "beta\\[[1,4]\\]",
 #'            diag_fun = "dens", off_diag_fun = "hex")
 #'
 #' # plot chain 1 above diagonal and chains 2, 3, and 4 below
 #' color_scheme_set("brightblue")
-#' mcmc_pairs(x, pars = "alpha", regex_pars = "beta\\\[[1,4]\\\]",
+#' mcmc_pairs(x, pars = "alpha", regex_pars = "beta\\[[1,4]\\]",
 #'            diag_fun = "dens", off_diag_fun = "hex",
 #'            condition = pairs_condition(chains = list(1, 2:4)))
 #' }