Merge branch 'master' into prepare-v1.11.0

R/mcmc-diagnostics-nuts.R

@@ -127,15 +127,16 @@ NULL
 
 #' @rdname MCMC-nuts
 #' @export
-#' @param binwidth An optional value passed to [ggplot2::geom_histogram()] to
-#'   override the default binwidth.
+#' @template args-hist
 #'
 mcmc_nuts_acceptance <-
   function(x,
            lp,
            chain = NULL,
            ...,
-           binwidth = NULL) {
+           binwidth = NULL,
+           bins = NULL,
+           breaks = NULL) {
     suggested_package("gridExtra")
     check_ignored_arguments(...)
 
@@ -160,7 +161,9 @@ mcmc_nuts_acceptance <-
         color = get_color("lh"),
         linewidth = 0.25,
         na.rm = TRUE,
-        binwidth = binwidth
+        binwidth = binwidth,
+        bins = bins,
+        breaks = breaks
       ) +
       bayesplot_theme_get()
 
@@ -209,7 +212,9 @@ mcmc_nuts_acceptance <-
           color = NA,
           alpha = 0.5,
           na.rm = TRUE,
-          binwidth = binwidth
+          binwidth = binwidth,
+          bins = bins,
+          breaks = breaks
         )
 
       chain_scatter_data <- data.frame(
@@ -417,6 +422,8 @@ mcmc_nuts_energy <-
   function(x,
            ...,
            binwidth = NULL,
+           bins = NULL,
+           breaks = NULL,
            alpha = 0.5,
            merge_chains = FALSE) {
     check_ignored_arguments(...)
@@ -446,7 +453,9 @@ mcmc_nuts_energy <-
         ),
         linewidth = 0.25,
         na.rm = TRUE,
-        binwidth = binwidth
+        binwidth = binwidth,
+        bins = bins,
+        breaks = breaks
       ) +
       geom_histogram(
         aes(
@@ -457,7 +466,9 @@ mcmc_nuts_energy <-
         linewidth = 0.25,
         na.rm = TRUE,
         alpha = alpha,
-        binwidth = binwidth
+        binwidth = binwidth,
+        bins = bins,
+        breaks = breaks
       ) +
       scale_fill_manual("", values = fills, labels = aes_labs) +
       scale_color_manual("", values = clrs, labels = aes_labs) +

R/mcmc-parcoord.R

@@ -146,7 +146,7 @@ mcmc_parcoord <-
       graph <- graph +
         geom_line(
           data = div_draws,
-          size = np_style$size[["div"]],
+          linewidth = np_style$size[["div"]],
           alpha = np_style$alpha[["div"]],
           color = np_style$color[["div"]]
         )

R/mcmc-scatterplots.R

@@ -13,7 +13,7 @@
 #' @param ... Currently ignored.
 #' @param size,alpha For `mcmc_scatter()`, passed to
 #'   [ggplot2::geom_point()] to control the appearance of the points.
-#' @param binwidth For `mcmc_hex()`, an optional numeric vector of
+#' @param bins,binwidth For `mcmc_hex()`, an optional numeric vector of
 #'   *length two* passed to [ggplot2::geom_hex()] to override the
 #'   default binwidth in both the vertical and horizontal directions.
 #'
@@ -156,6 +156,7 @@ mcmc_hex <- function(x,
                      regex_pars = character(),
                      transformations = list(),
                      ...,
+                     bins = 30,
                      binwidth = NULL) {
   suggested_package("scales")
   suggested_package("hexbin")
@@ -166,6 +167,7 @@ mcmc_hex <- function(x,
     regex_pars = regex_pars,
     transformations = transformations,
     hex = TRUE,
+    bins = bins,
     binwidth = binwidth,
     size = NULL,
     alpha = NULL
@@ -641,6 +643,7 @@ pairs_condition <- function(chains = NULL, draws = NULL, nuts = NULL) {
                           hex = FALSE,
                           size = 2.5,
                           alpha = 0.8,
+                          bins = 30,
                           binwidth = NULL,
                           np = NULL,
                           np_style = scatter_style_np()) {
@@ -702,6 +705,7 @@ pairs_condition <- function(chains = NULL, draws = NULL, nuts = NULL) {
     graph <- graph +
       geom_hex(
         aes(fill = scales::rescale(after_stat(density))),
+        bins = bins,
         binwidth = binwidth
       ) +
       scale_fill_gradientn(

R/mcmc-traces.R

@@ -665,7 +665,11 @@ mcmc_trace_data <- function(x,
   }
 
   geom_args <- list()
-  geom_args$size <- size %||% ifelse(style == "line", 1/3, 1)
+  if (style == "line") {
+    geom_args$linewidth = size %||% 1 / 3
+  } else {
+    geom_args$size = size %||% 1
+  }
   layer_draws <- do.call(paste0("geom_", style), geom_args)
 
   coord_window <- if (!is.null(window)) {

R/ppc-distributions.R

@@ -402,6 +402,7 @@ ppc_freqpoly <-
            yrep,
            ...,
            binwidth = NULL,
+           bins = NULL,
            freq = TRUE,
            size = 0.5,
            alpha = 1) {
@@ -420,6 +421,7 @@ ppc_freqpoly <-
       geom_area(
         stat = "bin",
         binwidth = binwidth,
+        bins = bins,
         linewidth = size,
         alpha = alpha
       ) +
@@ -446,6 +448,7 @@ ppc_freqpoly_grouped <-
            group,
            ...,
            binwidth = NULL,
+           bins = NULL,
            freq = TRUE,
            size = 0.5,
            alpha = 1) {

R/ppc-errors.R

@@ -164,6 +164,7 @@ ppc_error_hist_grouped <-
            ...,
            facet_args = list(),
            binwidth = NULL,
+           bins = NULL,
            breaks = NULL,
            freq = TRUE) {
 

R/ppc-test-statistics.R

@@ -165,6 +165,7 @@ ppc_stat_grouped <-
            ...,
            facet_args = list(),
            binwidth = NULL,
+           bins = NULL,
            breaks = NULL,
            freq = TRUE) {
     check_ignored_arguments(...)
@@ -185,6 +186,7 @@ ppc_stat_freqpoly <-
            ...,
            facet_args = list(),
            binwidth = NULL,
+           bins = NULL,
            freq = TRUE) {
     stopifnot(length(stat) == 1)
     dots <- list(...)
@@ -208,7 +210,8 @@ ppc_stat_freqpoly <-
         aes(color = "yrep"),
         linewidth = 0.5,
         na.rm = TRUE,
-        binwidth = binwidth
+        binwidth = binwidth,
+        bins = bins
       ) +
       geom_vline(
         data = dplyr::filter(data, .data$variable == "y"),
@@ -240,6 +243,7 @@ ppc_stat_freqpoly_grouped <-
            ...,
            facet_args = list(),
            binwidth = NULL,
+           bins = NULL,
            freq = TRUE) {
     check_ignored_arguments(...)
     call <- match.call(expand.dots = FALSE)

R/ppd-distributions.R

@@ -194,6 +194,7 @@ ppd_freqpoly <-
   function(ypred,
            ...,
            binwidth = NULL,
+           bins = NULL,
            freq = TRUE,
            size = 0.5,
            alpha = 1) {
@@ -213,6 +214,7 @@ ppd_freqpoly <-
       geom_area(
         stat = "bin",
         binwidth = binwidth,
+        bins = bins,
         size = size,
         alpha = alpha
       ) +
@@ -238,6 +240,7 @@ ppd_freqpoly_grouped <-
            group,
            ...,
            binwidth = NULL,
+           bins = NULL,
            freq = TRUE,
            size = 0.5,
            alpha = 1) {

R/ppd-test-statistics.R

@@ -85,6 +85,7 @@ ppd_stat_grouped <-
            ...,
            facet_args = list(),
            binwidth = NULL,
+           bins = NULL,
            breaks = NULL,
            freq = TRUE) {
     check_ignored_arguments(...)
@@ -104,6 +105,7 @@ ppd_stat_freqpoly <-
            ...,
            facet_args = list(),
            binwidth = NULL,
+           bins = NULL,
            freq = TRUE) {
     stopifnot(length(stat) == 1)
     dots <- list(...)
@@ -122,7 +124,8 @@ ppd_stat_freqpoly <-
         aes(color = "ypred"),
         linewidth = 0.5,
         na.rm = TRUE,
-        binwidth = binwidth
+        binwidth = binwidth,
+        bins = bins
       ) +
       scale_color_ppd(
         name = stat_legend_title(stat, deparse(substitute(stat))),
@@ -146,6 +149,7 @@ ppd_stat_freqpoly_grouped <-
            ...,
            facet_args = list(),
            binwidth = NULL,
+           bins = NULL,
            freq = TRUE) {
     check_ignored_arguments(...)
     call <- match.call(expand.dots = FALSE)