Merge branch 'master' into gh-pages

Author: jgabry

.github/CONTRIBUTING.md

@@ -0,0 +1,56 @@
+# Contributing to bayesplot
+
+This outlines how to propose a change to bayesplot and is based on similar
+instructions for tidyverse packages, including the contributing guidelines
+generated by `usethis::use_tidy_contributing()`.
+
+## Fixing typos
+
+You can fix typos, spelling mistakes, or grammatical errors in the documentation
+directly using the GitHub web interface, as long as the changes are made in the
+_source_ file. This generally means you'll need to edit 
+[roxygen2 comments](https://roxygen2.r-lib.org/articles/roxygen2.html) in an `.R`, 
+not a `.Rd` file. You can find the `.R` file that generates the `.Rd` by reading
+the comment in the first line.
+
+## Bigger changes
+
+If you want to make a bigger change, it's a good idea to first file an issue and
+make sure someone from the team agrees that it’s needed. If you’ve found a bug,
+please file an issue that illustrates the bug with a minimal reproducible
+example (see e.g. the [tidyverse reprex instructions](https://www.tidyverse.org/help/#reprex)). 
+The tidyverse guide on [how to create a great issue](https://code-review.tidyverse.org/issues/) 
+has more advice.
+
+### Pull request process
+
+If you are new to creating pull requests here are some tips. Using the functions
+from the `usethis` package is not required but can be helpful if this process is
+new to you.
+
+*   Fork the package and clone onto your computer. If you haven't done this before, we recommend using `usethis::create_from_github("stan-dev/bayesplot", fork = TRUE)`.
+
+*   Install all development dependencies with `devtools::install_dev_deps()`, and then make sure the package passes R CMD check by running `devtools::check()`. 
+    If R CMD check doesn't pass cleanly, it's a good idea to ask for help before continuing. 
+*   Create a Git branch for your pull request (PR). We recommend using `usethis::pr_init("brief-description-of-change")`.
+
+*   Make your changes, commit to git, and then create a PR by running `usethis::pr_push()`, and following the prompts in your browser.
+    The title of your PR should briefly describe the change.
+    The body of your PR should contain `Fixes #issue-number`.
+
+*  For user-facing changes, add a bullet to the top of `NEWS.md` (i.e. just below the first header). Follow the style already used in `NEWS.md`.
+
+### Code style
+
+*  New code should attempt to follow the style used in the package. When in doubt follow the tidyverse [style guide](https://style.tidyverse.org). 
+
+*  We use [roxygen2](https://cran.r-project.org/package=roxygen2), with [Markdown syntax](https://cran.r-project.org/web/packages/roxygen2/vignettes/rd-formatting.html), for documentation.  
+
+*  We use [testthat](https://cran.r-project.org/package=testthat) for unit tests. 
+   Contributions with test cases included are easier to accept.  
+
+## Code of Conduct
+
+Please note that the bayesplot project follows the Stan project's 
+[Code of Conduct](https://discourse.mc-stan.org/t/announcing-our-new-stan-code-of-conduct/23764).
+By contributing to this project you agree to abide by its terms.

.gitignore

@@ -11,3 +11,4 @@ tests/testthat/Rplots.pdf
 cran-comments.md
 revdep/*
 CRAN-RELEASE
+CRAN-SUBMISSION

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: bayesplot
 Type: Package
 Title: Plotting for Bayesian Models
-Version: 1.10.0
-Date: 2022-11-16
+Version: 1.11.0
+Date: 2024-01-30
 Authors@R: c(person("Jonah", "Gabry", role = c("aut", "cre"), email = "jsg2201@columbia.edu"),
              person("Tristan", "Mahr", role = "aut"),
              person("Paul-Christian", "Bürkner", role = "ctb"),
@@ -29,8 +29,8 @@ Depends:
     R (>= 3.1.0)
 Imports:
     dplyr (>= 0.8.0),
-    ggplot2 (>= 3.0.0),
-    ggridges,
+    ggplot2 (>= 3.4.0),
+    ggridges (>= 0.5.5),
     glue,
     posterior,
     reshape2,
@@ -55,7 +55,7 @@ Suggests:
     survival,
     testthat (>= 2.0.0),
     vdiffr (>= 1.0.2)
-RoxygenNote: 7.2.2
+RoxygenNote: 7.3.0
 VignetteBuilder: knitr
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)

NAMESPACE

@@ -2,16 +2,31 @@
 
 S3method("[",neff_ratio)
 S3method("[",rhat)
+S3method(apply_transformations,array)
+S3method(apply_transformations,matrix)
+S3method(diagnostic_factor,neff_ratio)
+S3method(diagnostic_factor,rhat)
 S3method(log_posterior,CmdStanMCMC)
 S3method(log_posterior,stanfit)
 S3method(log_posterior,stanreg)
+S3method(melt_mcmc,matrix)
+S3method(melt_mcmc,mcmc_array)
 S3method(neff_ratio,CmdStanMCMC)
 S3method(neff_ratio,stanfit)
 S3method(neff_ratio,stanreg)
+S3method(num_chains,data.frame)
+S3method(num_chains,mcmc_array)
+S3method(num_iters,data.frame)
+S3method(num_iters,mcmc_array)
+S3method(num_params,data.frame)
+S3method(num_params,mcmc_array)
 S3method(nuts_params,CmdStanMCMC)
 S3method(nuts_params,list)
 S3method(nuts_params,stanfit)
 S3method(nuts_params,stanreg)
+S3method(parameter_names,array)
+S3method(parameter_names,default)
+S3method(parameter_names,matrix)
 S3method(plot,bayesplot_grid)
 S3method(plot,bayesplot_scheme)
 S3method(pp_check,default)

NEWS.md

@@ -1,5 +1,17 @@
 <!-- See http://style.tidyverse.org/news.html for advice on writing news -->
 
+# bayesplot 1.11.0
+
+* Update for new ggplot2 release by @teunbrand in #309
+* Add `bins` argument to many histogram plots by @paul-buerkner in #300
+* Follow ggplot2 updates on `facet_grid()` and `facet_wrap()` by @heavywatal in #305
+* Better `ppc_loo_pit_qq` plots by @avehtari in #307
+* Check `prob` is numeric for intervals plots by @tony-stone in #299
+* Add `bins` and `breaks` arguments to more histogram and hex plots by @heavywatal in #313
+* Replace `size` argument with `linewidth` for `geom_line` and `geom_ridgeline` by @heavywatal in #314
+* All LOO plots now accept `psis_object` argument by @jgabry in #311
+* `ppc_pit_ecdf()` and `ppc_pit_ecdf_grouped()` now support discrete variables, and their default method for selecting the number of ECDF evaluation points has been updated. by @TeemuSailynoja in #316
+
 # bayesplot 1.10.0
 
 * New function `mcmc_rank_ecdf()` for rank ecdf plots with confidence bands for
@@ -44,14 +56,14 @@ previous releases, but the new ones in this release are:
    - `ppc_error_hist_grouped()`
    - `ppc_error_scatter()`
    - `ppc_error_binned()`
-   
+
 * New plotting function `ppc_km_overlay_grouped()`, the grouped variant of
   `ppc_km_overlay()`. (#260, @fweber144)
 
 * `ppc_scatter()`, `ppc_scatter_avg()`, and `ppc_scatter_avg_grouped()` gain an
   argument `ref_line`, which can be set to `FALSE` to turn off the `x=y` line
   drawn behind the scatterplot.
-  
+
 * `ppc_ribbon()` and `ppc_ribbon_grouped()` gain argument `y_draw` that specifies whether the observed y should be plotted using a point, line, or both. (#257, @charlesm93)
 
 * `mcmc_*()` functions now support all draws formats from the **posterior** package. (#277, @Ozan147)

R/bayesplot-ggplot-themes.R

@@ -54,8 +54,7 @@ theme_default <-
         panel.spacing = unit(1.5, "lines"),
         legend.position = "right",
         legend.background = element_blank(),
-        legend.text = element_text(size = 13),
-        legend.text.align = 0,
+        legend.text = element_text(size = 13, hjust = 0),
         legend.key = element_blank()
       )
   }

R/bayesplot-helpers.R

@@ -333,7 +333,11 @@ calc_intervals <- function(x, p, med = TRUE, ...) {
 #'   equivalent to using `legend_none()`.
 #'
 legend_move <- function(position = "right") {
-  theme(legend.position = position)
+  if (is.numeric(position) && "legend.position.inside" %in% fn_fmls_names(theme)) {
+    theme(legend.position = "inside", legend.position.inside = position)
+  } else {
+    theme(legend.position = position)
+  }
 }
 #' @rdname bayesplot-helpers
 #' @export

R/helpers-mcmc.R

@@ -51,13 +51,13 @@ prepare_mcmc_array <- function(x,
   if (is.matrix(x)) {
     x <- x[, pars, drop=FALSE]
     if (length(transformations)) {
-      x <- apply_transformations(x, transformations)
+      x <- apply_transformations(x, transformations = transformations)
     }
     x <- array(x, dim = c(nrow(x), 1, ncol(x)))
   } else {
     x <- x[, , pars, drop = FALSE]
     if (length(transformations)) {
-      x <- apply_transformations(x, transformations)
+      x <- apply_transformations(x, transformations = transformations)
     }
   }
 
@@ -124,6 +124,8 @@ select_parameters <-
 #' @return A molten data frame.
 #'
 melt_mcmc <- function(x, ...) UseMethod("melt_mcmc")
+
+#' @export
 melt_mcmc.mcmc_array <- function(x,
                                  varnames =
                                    c("Iteration", "Chain", "Parameter"),
@@ -144,6 +146,7 @@ melt_mcmc.mcmc_array <- function(x,
 }
 
 # If all chains are already merged
+#' @export
 melt_mcmc.matrix <- function(x,
                              varnames = c("Draw", "Parameter"),
                              value.name = "Value",
@@ -305,13 +308,17 @@ chain_list2array <- function(x) {
 
 # Get parameter names from a 3-D array
 parameter_names <- function(x) UseMethod("parameter_names")
+
+#' @export
 parameter_names.array <- function(x) {
   stopifnot(is_3d_array(x))
   dimnames(x)[[3]] %||% abort("No parameter names found.")
 }
+#' @export
 parameter_names.default <- function(x) {
   colnames(x) %||% abort("No parameter names found.")
 }
+#' @export
 parameter_names.matrix <- function(x) {
   colnames(x) %||% abort("No parameter names found.")
 }
@@ -388,10 +395,12 @@ validate_transformations <-
 #'   functions.
 #' @return x, with tranformations having been applied to some parameters.
 #'
-apply_transformations <- function(x, transformations = list(), ...) {
+apply_transformations <- function(x, ...) {
   UseMethod("apply_transformations")
 }
-apply_transformations.matrix <- function(x, transformations = list()) {
+
+#' @export
+apply_transformations.matrix <- function(x, ..., transformations = list()) {
   pars <- colnames(x)
   x_transforms <- validate_transformations(transformations, pars)
   for (p in names(x_transforms)) {
@@ -400,7 +409,9 @@ apply_transformations.matrix <- function(x, transformations = list()) {
 
   x
 }
-apply_transformations.array <- function(x, transformations = list()) {
+
+#' @export
+apply_transformations.array <- function(x, ..., transformations = list()) {
   stopifnot(length(dim(x)) == 3)
   pars <- dimnames(x)[[3]]
   x_transforms <- validate_transformations(transformations, pars)
@@ -437,17 +448,23 @@ num_chains <- function(x, ...) UseMethod("num_chains")
 num_iters <- function(x, ...) UseMethod("num_iters")
 num_params <- function(x, ...) UseMethod("num_params")
 
+#' @export
 num_params.mcmc_array <- function(x, ...) dim(x)[3]
+#' @export
 num_chains.mcmc_array <- function(x, ...) dim(x)[2]
+#' @export
 num_iters.mcmc_array <- function(x, ...) dim(x)[1]
+#' @export
 num_params.data.frame <- function(x, ...) {
   stopifnot("Parameter" %in% colnames(x))
   length(unique(x$Parameter))
 }
+#' @export
 num_chains.data.frame <- function(x, ...) {
   stopifnot("Chain" %in% colnames(x))
   length(unique(x$Chain))
 }
+#' @export
 num_iters.data.frame <- function(x, ...) {
   cols <- colnames(x)
   stopifnot("Iteration" %in% cols || "Draws" %in% cols)

R/helpers-ppc.R

@@ -416,12 +416,12 @@ adjust_gamma_simulate <- function(N, L, K, prob, M) {
 #' simultaneous coverage of the ECDF traces.
 #' @noRd
 interpolate_gamma <- function(N, K, prob, L) {
-  # Find the precomputed values ueful for the interpolation task.
+  # Find the precomputed values useful for the interpolation task.
   vals <- get_interpolation_values(N, K, L, prob)
   # Largest lower bound and smalles upper bound for N among precomputed values.
   N_lb <- max(vals[vals$N <= N, ]$N)
   N_ub <- min(vals[vals$N >= N, ]$N)
-  # Approximate largest lower bound and smalles upper bound for gamma.
+  # Approximate largest lower bound and smallest upper bound for gamma.
   log_gamma_lb <- approx(
     x = log(vals[vals$N == N_lb, ]$K),
     y = log(vals[vals$N == N_lb, ]$val),

R/mcmc-diagnostics-nuts.R

@@ -117,7 +117,7 @@
 #' mcmc_nuts_energy(np)
 #' mcmc_nuts_energy(np, merge_chains = TRUE, binwidth = .15)
 #' mcmc_nuts_energy(np) +
-#'  facet_wrap(~ Chain, nrow = 1) +
+#'  facet_wrap(vars(Chain), nrow = 1) +
 #'  coord_fixed(ratio = 150) +
 #'  ggtitle("NUTS Energy Diagnostic")
 #' }
@@ -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()
 
@@ -180,7 +183,7 @@ mcmc_nuts_acceptance <-
     }
     hists <- hists +
       dont_expand_y_axis(c(0.005, 0)) +
-      facet_wrap(~ Parameter, scales = "free") +
+      facet_wrap(vars(.data$Parameter), scales = "free") +
       yaxis_text(FALSE) +
       yaxis_title(FALSE) +
       yaxis_ticks(FALSE) +
@@ -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) +
@@ -476,7 +487,7 @@ mcmc_nuts_energy <-
     }
 
     graph +
-      facet_wrap(~ Chain) +
+      facet_wrap(vars(.data$Chain)) +
       force_axes_in_facets()
   }