Merge pull request #187 from stan-dev/hexbin-to-suggests

Move hexbin package to Suggests

Author: jgabry

DESCRIPTION

@@ -24,15 +24,15 @@ Depends:
 Imports:
     dplyr (>= 0.8.0),
     ggplot2 (>= 2.2.1),
+    ggridges,
     reshape2,
-    stats,
-    utils,
     rlang (>= 0.3.0),
-    ggridges,
+    stats,
     tibble,
-    hexbin
+    utils
 Suggests: 
     gridExtra (>= 2.2.1),
+    hexbin,
     knitr (>= 1.16),
     loo (>= 2.0.0),
     RColorBrewer,

R/mcmc-scatterplots.R

@@ -114,11 +114,13 @@
 #'                  size = .75, linetype = 2)
 #'
 #' \donttest{
-#' # hexagonal heatmap
-#' color_scheme_set("brightblue")
-#' (p <- mcmc_hex(x, pars = c("sigma", "alpha"), transform = list(sigma = "log")))
-#' p + plot_bg(fill = "gray95")
-#' p + plot_bg(fill = "gray95") + panel_bg(fill = "gray70")
+#' if (requireNamespace("hexbin", quietly = TRUE)) {
+#'  # hexagonal heatmap
+#'  color_scheme_set("brightblue")
+#'  (p <- mcmc_hex(x, pars = c("sigma", "alpha"), transform = list(sigma = "log")))
+#'  p + plot_bg(fill = "gray95")
+#'  p + plot_bg(fill = "gray95") + panel_bg(fill = "gray70")
+#' }
 #' }
 NULL
 
@@ -157,6 +159,8 @@ mcmc_hex <- function(x,
                      transformations = list(),
                      ...,
                      binwidth = NULL) {
+  suggested_package("scales")
+  suggested_package("hexbin")
   check_ignored_arguments(...)
   .mcmc_scatter(
     x,
@@ -697,7 +701,6 @@ pairs_condition <- function(chains = NULL, draws = NULL, nuts = NULL) {
         )
     }
   } else { # hex binning
-    suggested_package("scales")
     graph <- graph +
       geom_hex(
         aes_(fill = ~ scales::rescale(..density..)),

tests/testthat/test-mcmc-scatter-and-parcoord.R

@@ -1,6 +1,6 @@
 library(bayesplot)
 suppressPackageStartupMessages(library(rstanarm))
-context("MCMC: scatter and parallel coordinates plots")
+context("MCMC: scatter, hex, and parallel coordinates plots")
 
 source(test_path("data-for-mcmc-tests.R"))
 
@@ -10,6 +10,8 @@ post <- as.array(fit)
 lp <- log_posterior(fit)
 np <- ensure_divergences(nuts_params(fit))
 
+
+# mcmc_scatter/hex --------------------------------------------------------
 test_that("mcmc_scatter returns a ggplot object", {
   expect_gg(mcmc_scatter(arr, pars = c("beta[1]", "beta[2]")))
   expect_gg(mcmc_scatter(arr1chain, regex_pars = "beta", size = 3, alpha = 0.5))
@@ -19,17 +21,11 @@ test_that("mcmc_scatter returns a ggplot object", {
                          pars = c("sigma", "(Intercept)")))
 })
 
-test_that("mcmc_hex returns a ggplot object", {
-  expect_gg(mcmc_hex(arr, pars = c("beta[1]", "beta[2]")))
-  expect_gg(mcmc_hex(arr1chain, regex_pars = "beta", binwidth = c(.5,.5)))
-})
-
-test_that("mcmc_scatter & mcmc_hex throw error if only 1 parameter", {
+test_that("mcmc_scatter throws error if number of parameters is not 2", {
+  expect_error(mcmc_scatter(arr, pars = c("sigma", "beta[1]", "beta[2]")), "exactly 2 parameters")
   expect_error(mcmc_scatter(arr, pars = "sigma"), "exactly 2 parameters")
   expect_error(mcmc_scatter(arr1), "exactly 2 parameters")
   expect_error(mcmc_scatter(mat1), "exactly 2 parameters")
-  expect_error(mcmc_hex(dframe1), "exactly 2 parameters")
-  expect_error(mcmc_hex(chainlist1), "exactly 2 parameters")
 })
 
 test_that("mcmc_scatter accepts NUTS info", {
@@ -42,6 +38,21 @@ test_that("mcmc_scatter accepts NUTS info", {
   expect_named(g$data, c("x", "y", "Divergent"))
 })
 
+test_that("mcmc_hex returns a ggplot object", {
+  skip_if_not_installed("hexbin")
+  expect_gg(mcmc_hex(arr, pars = c("beta[1]", "beta[2]")))
+  expect_gg(mcmc_hex(arr1chain, regex_pars = "beta", binwidth = c(.5,.5)))
+})
+
+test_that("mcmc_hex throws error if number of parameters is not 2", {
+  skip_if_not_installed("hexbin")
+  expect_error(mcmc_hex(arr, pars = c("sigma", "beta[1]", "beta[2]")), "exactly 2 parameters")
+  expect_error(mcmc_hex(arr, pars = "sigma"), "exactly 2 parameters")
+  expect_error(mcmc_hex(arr1), "exactly 2 parameters")
+  expect_error(mcmc_hex(mat1), "exactly 2 parameters")
+})
+
+
 
 # mcmc_pairs  -------------------------------------------------------------
 test_that("mcmc_pairs returns a bayesplot_grid object", {

vignettes/plotting-mcmc-draws.Rmd

@@ -250,7 +250,10 @@ The `mcmc_hex` function creates a similar plot but using hexagonal binning,
 which can be useful to avoid overplotting.
 
 ```{r, mcmc_hex}
-mcmc_hex(posterior, pars = c("(Intercept)", "wt"))
+# requires hexbin package
+if (requireNamespace("hexbin", quietly = TRUE)) {
+  mcmc_hex(posterior, pars = c("(Intercept)", "wt"))
+}
 ```
 
 #### mcmc_pairs