Merge branch 'master' into hexbin-to-suggests

Author: jgabry

.travis.yml

@@ -6,7 +6,8 @@ cache: packages
 
 r_github_packages:
   - r-lib/covr
-  
+  - tidyverse/ggplot2
+
 r_build_args: '--no-build-vignettes'
 r_check_args: '--ignore-vignettes'
 

DESCRIPTION

@@ -24,16 +24,18 @@ Depends:
 Imports:
     dplyr (>= 0.8.0),
     ggplot2 (>= 2.2.1),
+    ggridges,
     reshape2,
-    stats,
-    utils,
     rlang (>= 0.3.0),
-    ggridges
+    stats,
+    tibble,
+    utils
 Suggests: 
     gridExtra (>= 2.2.1),
     hexbin,
     knitr (>= 1.16),
     loo (>= 2.0.0),
+    RColorBrewer,
     rmarkdown (>= 1.0.0),
     rstan (>= 2.17.1),
     rstanarm (>= 2.17.4),
@@ -45,3 +47,4 @@ Suggests:
 RoxygenNote: 6.1.1
 VignetteBuilder: knitr
 Encoding: UTF-8
+Roxygen: list(markdown = TRUE)

NAMESPACE

@@ -70,6 +70,8 @@ export(mcmc_nuts_treedepth)
 export(mcmc_pairs)
 export(mcmc_parcoord)
 export(mcmc_parcoord_data)
+export(mcmc_rank_hist)
+export(mcmc_rank_overlay)
 export(mcmc_recover_hist)
 export(mcmc_recover_intervals)
 export(mcmc_recover_scatter)
@@ -78,6 +80,7 @@ export(mcmc_rhat_data)
 export(mcmc_rhat_hist)
 export(mcmc_scatter)
 export(mcmc_trace)
+export(mcmc_trace_data)
 export(mcmc_trace_highlight)
 export(mcmc_violin)
 export(neff_ratio)

NEWS.md

@@ -6,8 +6,31 @@
 
 <!-- Items for next release go here* -->
 
+* Two new plots have been added for inspecting the distribution of ranks.
+  Rank-normalized histograms were introduced by the Stan team's [new paper on 
+  MCMC diagnostics](https://arxiv.org/abs/1903.08008). (#178, #179)
+
+  `mcmc_rank_hist()`: A traditional traceplot (`mcmc_trace()`) visualizes how
+  sampled values the MCMC chains mix over the course of sampling. A
+  rank-normalized histogram (`mcmc_rank_hist()`) visualizes how the *ranks* of
+  values from the chains mix together. An ideal plot would show the ranks mixing
+  or overlapping in a uniform distribution. 
+  
+  `mcmc_rank_overlay()`: Instead of drawing each chain's histogram in a separate
+  panel, this plot draws the top edge of the chains' histograms in a single
+  panel.
+  
+* Added `mcmc_trace_data()`, which returns the data used for plotting the trace
+  plots and rank histograms. (Advances #97)
+
+* [ColorBrewer](http://colorbrewer2.org) palettes are now available as color
+  schemes via
+  [`color_scheme_set()`](https://mc-stan.org/bayesplot/reference/bayesplot-colors.html).
+  For example, `color_scheme_set("brewer-Spectral")` will use the Spectral 
+  palette. (#177, #190)
+
 * MCMC plots now also accept objects with an `as.array` method as 
-  input. (#175, #184)
+  input (e.g., stanfit objects). (#175, #184)
 
 * [`mcmc_trace()`](https://mc-stan.org/bayesplot/reference/MCMC-traces.html)
   gains an argument `iter1` which can be used to label the traceplot starting
@@ -43,8 +66,15 @@
 * The examples in
   [`?ppc_loo_pit_overlay()`](https://mc-stan.org/bayesplot/reference/PPC-loo.html)
   now work as expected. (#166, #167)
+  
+* Added `"viridisD"` as an alternative name for `"viridis"` to the supported 
+  colors.
+
+* Added `"viridisE"` (the [cividis](https://github.com/marcosci/cividis) 
+  version of viridis) to the supported colors. 
 
-* `ppc_bars()` and `ppc_bars_grouped()` now allow negative integers as input. (#172)
+* `ppc_bars()` and `ppc_bars_grouped()` now allow negative integers as input.
+  (#172, @jeffpollock9)
 
 
 # bayesplot 1.6.0

R/available-module-functions.R

@@ -1,12 +1,12 @@
 #' Get or view the names of available plotting functions
 #'
 #' @export
-#' @param pattern,fixed,invert Passed to \code{\link[base]{grep}}.
+#' @param pattern,fixed,invert Passed to [base::grep()].
 #' @return A possibly empty character vector of function names with several
-#'   additional attributes (for use by a custom print method). If \code{pattern}
+#'   additional attributes (for use by a custom print method). If `pattern`
 #'   is missing then the returned object contains the names of all available
-#'   plotting functions in the \link{MCMC} or \link{PPC} module, depending on
-#'   which function is called. If \code{pattern} is specified then a subset of
+#'   plotting functions in the [MCMC] or [PPC] module, depending on
+#'   which function is called. If `pattern` is specified then a subset of
 #'   function names is returned.
 #'
 #' @examples
@@ -17,30 +17,30 @@
 #' available_ppc("grouped", invert = TRUE)
 #'
 available_ppc <- function(pattern, fixed = FALSE, invert = FALSE) {
-  .list_module_functions("ppc", .pattern = pattern,
-                         fixed = fixed, invert = invert)
+  .list_module_functions("ppc",
+                         .pattern = pattern,
+                         fixed = fixed,
+                         invert = invert)
 }
 
 #' @rdname available_ppc
 #' @export
 available_mcmc <- function(pattern, fixed = FALSE, invert = FALSE) {
-  .list_module_functions("mcmc", .pattern = pattern,
-                         fixed = fixed, invert = invert)
+  .list_module_functions("mcmc",
+                         .pattern = pattern,
+                         fixed = fixed,
+                         invert = invert)
 }
 
 #' @export
 print.bayesplot_function_list <- function(x, ...) {
   atts <- attributes(x)
   cat("bayesplot", toupper(atts[["module"]]), "module:\n")
-  if (!is.null(atts[["pattern"]]))
-    cat(paste0(
-      "(",
-      ifelse(atts[["inverted"]], "excluding", "matching"),
-      " pattern '",
-      atts[["pattern"]],
-      "')"
-    ), "\n")
-
+  if (!is.null(atts[["pattern"]])) {
+    msg <- paste0("(", ifelse(atts[["inverted"]], "excluding", "matching"),
+                  " pattern '", atts[["pattern"]], "')")
+    cat(msg, "\n")
+  }
   cat(paste0("  ", x), sep = "\n")
   invisible(x)
 }
@@ -54,26 +54,28 @@ print.bayesplot_function_list <- function(x, ...) {
            invert = FALSE) {
 
     .module <- match.arg(.module)
-    if (missing(.pattern))
+    if (missing(.pattern)) {
       .pattern <- NULL
+    }
 
-    funs <- sort(grep(
-      paste0("^", .module, "_"),
-      getNamespaceExports("bayesplot"),
+    all_funs <- grep(
+      pattern = paste0("^", .module, "_"),
+      x = getNamespaceExports("bayesplot"),
       value = TRUE
-    ))
+    )
+    return_funs <- sort(all_funs)
+
+    if (!is.null(.pattern)) {
+      return_funs <- grep(
+        pattern = .pattern,
+        x = return_funs,
+        value = TRUE,
+        fixed = fixed,
+        invert = invert
+      )
+    }
     structure(
-      .Data =
-        if (is.null(.pattern))
-          funs
-        else
-          grep(
-            pattern = .pattern,
-            x = funs,
-            value = TRUE,
-            fixed = fixed,
-            invert = invert
-          ),
+      return_funs,
       class = c("bayesplot_function_list", "character"),
       module = .module,
       pattern = .pattern,