Merge pull request #485 from utkarshpawade/fix/use-expansion-helper-in-scale-expand

Replace c(mult, add) with expansion() in scale expand args

Author: jgabry

NEWS.md

@@ -11,6 +11,7 @@
 * New functions `mcmc_dots` and `mcmc_dots_by_chain` for dot plots of MCMC draws by @behramulukir (#402)
 * Default to `quantiles=100` for all dot plots by @behramulukir (#402)
 * Use `"neff_ratio"` consistently in diagnostic color scale helpers to avoid relying on partial matching of `"neff"`.
+* Replace `expand = c(mult, add)` with `ggplot2::expansion()` helper in scale functions for consistency with ggplot2 >= 3.3.0 style.
 * Replace uses of `geom_bar(stat = "identity")` with the more idiomatic ggplot2 form `geom_col()` 
 
 # bayesplot 1.15.0

R/helpers-gg.R

@@ -37,10 +37,10 @@ modify_aes <- function(mapping, ...) {
 facet_wrap_parsed <- function(...) {
   facet_wrap(..., labeller = label_parsed)
 }
-dont_expand_y_axis <- function(expand = c(0,0)) {
+dont_expand_y_axis <- function(expand = expansion(0, 0)) {
   scale_y_continuous(expand = expand)
 }
-dont_expand_x_axis <- function(expand = c(0,0)) {
+dont_expand_x_axis <- function(expand = expansion(0, 0)) {
   scale_x_continuous(expand = expand)
 }
 dont_expand_axes <- function() {

R/mcmc-diagnostics-nuts.R

@@ -183,7 +183,7 @@ mcmc_nuts_acceptance <-
         )
     }
     hists <- hists +
-      dont_expand_y_axis(c(0.005, 0)) +
+      dont_expand_y_axis(expansion(mult = 0.005, add = 0)) +
       facet_wrap(vars(.data$Parameter), scales = "free") +
       yaxis_text(FALSE) +
       yaxis_title(FALSE) +
@@ -483,8 +483,8 @@ mcmc_nuts_energy <-
       ) +
       scale_fill_manual("", values = fills, labels = aes_labs) +
       scale_color_manual("", values = clrs, labels = aes_labs) +
-      dont_expand_y_axis(c(0.005, 0)) +
-      scale_x_continuous(expand = c(0.2, 0)) +
+      dont_expand_y_axis(expansion(mult = 0.005, add = 0)) +
+      scale_x_continuous(expand = expansion(mult = 0.2, add = 0)) +
       labs(y = NULL, x = expression(E - bar(E))) +
       bayesplot_theme_get() +
       space_legend_keys()  +

R/mcmc-diagnostics.R

@@ -170,8 +170,8 @@ mcmc_rhat <- function(rhat, ..., size = NULL) {
     labs(y = NULL, x = expression(hat(R))) +
     scale_fill_diagnostic("rhat") +
     scale_color_diagnostic("rhat") +
-    scale_x_continuous(breaks = brks, expand = c(0, .01)) +
-    scale_y_discrete(expand = c(.025,0)) +
+    scale_x_continuous(breaks = brks, expand = expansion(mult = 0, add = 0.01)) +
+    scale_y_discrete(expand = expansion(mult = 0.025, add = 0)) +
     yaxis_title(FALSE) +
     yaxis_text(FALSE) +
     yaxis_ticks(FALSE)
@@ -199,7 +199,7 @@ mcmc_rhat_hist <- function(rhat, ..., binwidth = NULL, bins = NULL, breaks = NUL
     scale_color_diagnostic("rhat") +
     scale_fill_diagnostic("rhat") +
     labs(x = expression(hat(R)), y = NULL) +
-    dont_expand_y_axis(c(0.005, 0)) +
+    dont_expand_y_axis(expansion(mult = 0.005, add = 0)) +
     bayesplot_theme_get() +
     yaxis_title(FALSE) +
     yaxis_text(FALSE) +
@@ -262,7 +262,7 @@ mcmc_neff <- function(ratio, ..., size = NULL) {
       # as.character truncates trailing zeroes, while ggplot default does not
       labels = as.character(breaks),
       limits = c(0, max(1, max_ratio) + 0.05),
-      expand = c(0, 0)) +
+      expand = expansion(0, 0)) +
     bayesplot_theme_get() +
     yaxis_text(FALSE) +
     yaxis_title(FALSE) +
@@ -290,7 +290,7 @@ mcmc_neff_hist <- function(ratio, ..., binwidth = NULL, bins = NULL, breaks = NU
     scale_color_diagnostic("neff_ratio") +
     scale_fill_diagnostic("neff_ratio") +
     labs(x = expression(N[eff]/N), y = NULL) +
-    dont_expand_y_axis(c(0.005, 0)) +
+    dont_expand_y_axis(expansion(mult = 0.005, add = 0)) +
     yaxis_title(FALSE) +
     yaxis_text(FALSE) +
     yaxis_ticks(FALSE) +
@@ -572,7 +572,7 @@ drop_NAs_and_warn <- function(x) {
       scale_x_continuous(
         limits = c(-0.5, lags + 0.5),
         breaks = function(x) as.integer(pretty(x, n = 3)),
-        expand = c(0, 0)
+        expand = expansion(0, 0)
       ) +
       labs(x = "Lag", y = "Autocorrelation") +
       force_axes_in_facets()

R/mcmc-distributions.R

@@ -332,7 +332,7 @@ mcmc_dens_chains <- function(
     labs(color = "Chain") +
     scale_y_discrete(
       limits = unique(rev(data$parameter)),
-      expand = c(0.05, .6)
+      expand = expansion(mult = 0.05, add = 0.6)
     ) +
     scale_color +
     bayesplot_theme_get() +
@@ -523,7 +523,7 @@ mcmc_dots_by_chain <- function(
   }
 
   graph +
-    dont_expand_y_axis(c(0.005, 0)) +
+    dont_expand_y_axis(expansion(mult = 0.005, add = 0)) +
     bayesplot_theme_get() +
     yaxis_text(FALSE) +
     yaxis_title(FALSE) +
@@ -642,7 +642,7 @@ mcmc_dots_by_chain <- function(
   }
 
   graph +
-    dont_expand_y_axis(c(0.005, 0)) +
+    dont_expand_y_axis(expansion(mult = 0.005, add = 0)) +
     bayesplot_theme_get() +
     yaxis_text(FALSE) +
     yaxis_ticks(FALSE) +
@@ -703,7 +703,7 @@ mcmc_dots_by_chain <- function(
   }
 
   graph +
-    dont_expand_y_axis(c(0.005, 0)) +
+    dont_expand_y_axis(expansion(mult = 0.005, add = 0)) +
     bayesplot_theme_get() +
     yaxis_text(FALSE) +
     yaxis_title(FALSE) +

R/mcmc-parcoord.R

@@ -159,7 +159,7 @@ mcmc_parcoord <-
     }
 
     graph +
-      scale_x_discrete(expand = c(0,0), labels = levels(draws$Parameter)) +
+      scale_x_discrete(expand = expansion(0, 0), labels = levels(draws$Parameter)) +
       expand_limits(x = nlevels(draws$Parameter) + 0.25) +
       labs(x = NULL, y = NULL)
   }

R/mcmc-traces.R

@@ -446,7 +446,7 @@ mcmc_rank_hist <- function(x,
     geom_blank(data = data_boundaries) +
     facet_call +
     force_x_axis_in_facets() +
-    dont_expand_y_axis(c(0.005, 0)) +
+    dont_expand_y_axis(expansion(mult = 0.005, add = 0)) +
     bayesplot_theme_get() +
     theme(
       axis.line.y = element_blank(),

R/ppc-test-statistics.R

@@ -263,7 +263,7 @@ ppc_stat_freqpoly <-
         values = set_names(get_color(c("m", "dh")), c("yrep", "y")),
         labels = c(yrep = Tyrep_label(), y = Ty_label())
       ) +
-      dont_expand_y_axis(c(0.005, 0)) +
+      dont_expand_y_axis(expansion(mult = 0.005, add = 0)) +
       bayesplot_theme_get() +
       xaxis_title(FALSE) +
       yaxis_text(FALSE) +

R/ppd-test-statistics.R

@@ -143,7 +143,7 @@ ppd_stat_freqpoly <-
         name = stat_legend_title(stat, deparse(substitute(stat))),
         labels = Typred_label()
       ) +
-      dont_expand_y_axis(c(0.005, 0)) +
+      dont_expand_y_axis(expansion(mult = 0.005, add = 0)) +
       bayesplot_theme_get() +
       xaxis_title(FALSE) +
       yaxis_text(FALSE) +

tests/testthat/test-mcmc-diagnostics.R

@@ -79,6 +79,14 @@ test_that("'description' & 'rating' columns are correct (#176)", {
   expect_equal(df$description, expected_descriptions)
 })
 
+test_that("mcmc_rhat uses the expected panel expansion", {
+  rhats <- seq(from = 1, to = 1.20, length.out = 10)
+  built <- ggplot2::ggplot_build(mcmc_rhat(rhats))
+
+  expect_equal(built$layout$panel_params[[1]]$x.range, c(0.99, 1.21))
+  expect_equal(built$layout$panel_params[[1]]$y.range, c(0.775, 10.225))
+})
+
 test_that("mcmc_acf & mcmc_acf_bar return a ggplot object", {
   expect_gg(mcmc_acf(arr, pars = "beta[1]", regex_pars = "x\\:[2,5]"))
   expect_gg(mcmc_acf_bar(arr, pars = "beta[1]", regex_pars = "x\\:[2,5]"))