dm13450 · dm13450 · Aug 12, 2026 · Jul 29, 2026
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -1,39 +1,60 @@
-# For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag.
-# https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches:
-      - main
-      - master
+    branches: [main, master]
   pull_request:
-    branches:
-      - main
-      - master
 
-name: R-CMD-check
+name: R-CMD-check.yaml
+
+permissions: read-all
 
 jobs:
   R-CMD-check:
-    runs-on: macOS-latest
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macos-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
+
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
     steps:
-      - uses: actions/checkout@v2
-      - uses: r-lib/actions/setup-tinytex@v2
+      - uses: actions/checkout@v6
+      - uses: r-lib/actions/setup-pandoc@v2
+
       - uses: r-lib/actions/setup-r@v2
-      - name: Install dependencies
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+
+      - uses: r-lib/actions/setup-tinytex@v2
+
+      - name: Install additional LaTeX packages
         run: |
-          install.packages(c("remotes", "rcmdcheck", "tinytex",
-                             "ggplot2", "gtools", "mvtnorm",
-                             "testthat", "knitr", "rmarkdown",
-                             "tidyr", "dplyr"))
-          tinytex::tlmgr_install(pkgs = c("ae", "thumbpdf",
-                                          "multirow", "listings",
-                                          "caption", "subcaption",
-                                          "tcolorbox", "pgf",
-                                          "environ", "babel-english",
-                                          "grfext", "hyperref"))
-        shell: Rscript {0}
-      - name: Check
-        run: rcmdcheck::rcmdcheck(args = "--no-manual", error_on = "error")
+          install.packages("tinytex")
+          tinytex::tlmgr_install(c(
+            "thumbpdf", "multirow", "listings", "caption", "subcaption",
+            "tcolorbox", "pgf", "environ", "babel-english", "grfext", "hyperref"
+          ))
         shell: Rscript {0}
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'
diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
@@ -0,0 +1,60 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+
+name: test-coverage.yaml
+
+permissions: read-all
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v6
+
+      - uses: r-lib/actions/setup-r@v2
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::covr, any::xml2
+          needs: coverage
+
+      - name: Test coverage
+        run: |
+          cov <- covr::package_coverage(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
+          )
+          print(cov)
+          covr::to_cobertura(cov)
+        shell: Rscript {0}
+
+      - uses: codecov/codecov-action@fb8b3582c8e4def4969c97caa2f19720cb33a72f # v7
+        with:
+          # Fail if error if not on PR, or if on PR and token is given
+          fail_ci_if_error: ${{ github.event_name != 'pull_request' || secrets.CODECOV_TOKEN }}
+          files: ./cobertura.xml
+          plugins: noop
+          disable_search: true
+          token: ${{ secrets.CODECOV_TOKEN }}
+
+      - name: Show testthat output
+        if: always()
+        run: |
+          ## --------------------------------------------------------------------
+          find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v7
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package
diff --git a/.gitignore b/.gitignore
@@ -5,4 +5,5 @@ inst/doc
 .Rhistory
 clean_bib.sh
 tests/testthat/Rplots.pdf
+.DS_Store
 
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: dirichletprocess
 Type: Package
 Title: Build Dirichlet Process Objects for Bayesian Modelling
-Version: 0.4.2
+Version: 0.4.2.9000
 Authors@R: c(
             person("Gordon", "J. Ross", email="gordon@gordonjross.co.uk", role=c("aut")),
             person("Dean", "Markwick", email="dean.markwick@talk21.com", role=c("aut", "cre")),
@@ -36,4 +36,4 @@ Imports: gtools,
          mvtnorm
 URL: https://github.com/dm13450/dirichletprocess, https://dm13450.github.io/dirichletprocess/
 BugReports: https://github.com/dm13450/dirichletprocess/issues
-RoxygenNote: 7.2.3
+Config/roxygen2/version: 8.0.0
diff --git a/NAMESPACE b/NAMESPACE
@@ -123,6 +123,7 @@ export(plot_dirichletprocess_multivariate)
 export(plot_dirichletprocess_univariate)
 export(true_cluster_labels)
 export(weighted_function_generator)
+importFrom(ggplot2,.data)
 importFrom(stats,dbeta)
 importFrom(stats,dbinom)
 importFrom(stats,dexp)

diff --git a/NEWS.md b/NEWS.md
@@ -1,4 +1,10 @@
-# dirichletprocess 0.4.0.9000
+# dirichletprocess 0.4.2.9000
+
+* Updated GitHub Actions
+* Fixed ggplot deprecation
+* Added some missing tests
+
+# dirichletprocess 0.4.2
 
 * Added PriorFunction and PriorClusters to draw from the base measure. 
 * Fixed a bug in the likelihood calculation (#21) by Filippo Fiocchi.

diff --git a/R/diagnostic_plots.R b/R/diagnostic_plots.R
@@ -36,16 +36,15 @@ DiagnosticPlots <- function(dpobj, gg = FALSE) {
 
 }
 
-
-
 #' @export
-#' @describeIn  DiagnosticPlots Trace plot of alpha.
+#' @describeIn DiagnosticPlots Trace plot of alpha.
+#' @importFrom ggplot2 .data
 AlphaTraceplot <- function(dpobj, gg = TRUE) {
 
   if (gg) {
     p <- ggplot2::ggplot(data.frame(Alpha = dpobj$alphaChain,
                                Index = seq_along(dpobj$alphaChain)),
-                    ggplot2::aes_string("Index", "Alpha")) +
+                    ggplot2::aes(x=.data$Index, y=.data$Alpha)) +
       ggplot2::geom_line() +
       ggplot2::ggtitle("Traceplot of alpha")
     return(p)
@@ -58,6 +57,7 @@ AlphaTraceplot <- function(dpobj, gg = TRUE) {
 
 #' @export
 #' @describeIn  DiagnosticPlots Plot of the prior and posterior of alpha.
+#' @importFrom ggplot2 .data
 AlphaPriorPosteriorPlot <- function(dpobj, prior_color = "#2c7fb8", post_color = "#d95f02", gg = TRUE) {
 
   dap <- dpobj$alphaPriorParameters
@@ -69,14 +69,17 @@ AlphaPriorPosteriorPlot <- function(dpobj, prior_color = "#2c7fb8", post_color =
 
     p <- ggplot2::ggplot() +
       ggplot2::geom_histogram(data = data.frame(Alpha = dpobj$alphaChain),
-                              mapping = ggplot2::aes_string("Alpha",
-                                                            "..density..",
-                                                            colour = "'Posterior'", fill = "'Posterior'"),
+                              mapping = ggplot2::aes(x=.data$Alpha,
+                                                     ggplot2::after_stat(.data$density),
+                                                     colour = "'Posterior'",
+                                                     fill = "'Posterior'"),
                               bins = min(its / 10, 100)) +
       ggplot2::stat_function(fun = prior_fun,
-                             mapping = ggplot2::aes_string(colour = "'Prior'")) +
+                             mapping = ggplot2::aes(colour = "'Prior'")) +
       ggplot2::ggtitle("Prior and posterior of alpha") +
-      ggplot2::scale_colour_manual(labels = c("Posterior", "Prior"), values = c(prior_color, post_color), aesthetics = c("colour", "fill"), name = " ")
+      ggplot2::scale_colour_manual(labels = c("Posterior", "Prior"),
+                                   values = c(prior_color, post_color),
+                                   aesthetics = c("colour", "fill"), name = " ")
     return(p)
   } else {
     graphics::hist(dpobj$alphaChain, freq = FALSE, breaks = min(its / 10, 100),
@@ -90,14 +93,15 @@ AlphaPriorPosteriorPlot <- function(dpobj, prior_color = "#2c7fb8", post_color =
 
 #' @export
 #' @describeIn  DiagnosticPlots Trace plot of the number of clusters.
+#' @importFrom ggplot2 .data
 ClusterTraceplot <- function(dpobj, gg = TRUE) {
 
   n_clust <- vapply(dpobj$labelsChain, function(x) length(unique(x)), numeric(1))
 
   if (gg) {
     p <- ggplot2::ggplot(data.frame(nclust = n_clust,
                                Index = seq_along(n_clust)),
-                    ggplot2::aes_string("Index", "nclust")) +
+                    ggplot2::aes(x=.data$Index, y=.data$nclust)) +
       ggplot2::geom_line() +
       ggplot2::ylab("Number of clusters") +
       ggplot2::ggtitle("Traceplot of the number of clusters")
@@ -117,7 +121,7 @@ LikelihoodTraceplot <- function(dpobj, gg = TRUE) {
   if (gg) {
     p <- ggplot2::ggplot(data.frame(Lik = dpobj$likelihoodChain,
                                Index = seq_along(dpobj$likelihoodChain)),
-                    ggplot2::aes_string("Index", "Lik")) +
+                    ggplot2::aes(x=.data$Index, y=.data$Lik)) +
       ggplot2::geom_line() +
       ggplot2::ylab("Log-likelihood") +
       ggplot2::ggtitle("Traceplot of the log-likelihood")

diff --git a/R/dirichletprocess-package.R b/R/dirichletprocess-package.R
@@ -0,0 +1,6 @@
+#' @keywords internal
+"_PACKAGE"
+
+## usethis namespace: start
+## usethis namespace: end
+NULL
diff --git a/R/plot_dirichletprocess.R b/R/plot_dirichletprocess.R
@@ -32,6 +32,7 @@ plot_dirichletprocess.mvnormal <- function(x, ...) {
 
 #' @export
 #' @rdname plot.dirichletprocess
+#' @importFrom ggplot2 .data
 plot_dirichletprocess_univariate <- function(x,
                                              likelihood  = FALSE,
                                              single      = TRUE,
@@ -43,15 +44,17 @@ plot_dirichletprocess_univariate <- function(x,
                                              quant_pts   = 100,
                                              xlim        = NA) {
 
-  graph <- ggplot2::ggplot(data.frame(dt = x$data), ggplot2::aes_(x = ~dt)) +
+  graph <- ggplot2::ggplot(data.frame(dt = x$data), ggplot2::aes(x = .data$dt)) +
     ggplot2::theme(axis.title = ggplot2::element_blank())
 
   if (data_method == "density") {
     graph <- graph + ggplot2::geom_density(fill = data_fill,
-                                           bw = ifelse(is.null(data_bw), "nrd0", data_bw))
+                                           bw = ifelse(is.null(data_bw),
+                                                       "nrd0",
+                                                       data_bw))
   } else if (data_method == "hist" | data_method == "histogram") {
-    graph <- graph + ggplot2::geom_histogram(ggplot2::aes_(x = ~dt,
-                                                           y = ~..density..),
+    graph <- graph + ggplot2::geom_histogram(ggplot2::aes(x = .data$dt,
+                                                          ggplot2::after_stat(.data$density)),
                                              fill = data_fill,
                                              binwidth = data_bw)
   } else if (data_method != "none") {
@@ -76,9 +79,9 @@ plot_dirichletprocess_univariate <- function(x,
                        quantile, probs = c(ci_size/2, 0.5, 1 - ci_size/2),
                        na.rm = TRUE)
 
-  graph <- graph + ggplot2::geom_line(data=data.frame(x=x_grid, y=posteriorCI[1,]), ggplot2::aes_(x=~x,y=~y, colour="Posterior"), linetype=2)
-  graph <- graph + ggplot2::geom_line(data=data.frame(x=x_grid, y=posteriorCI[2,]), ggplot2::aes_(x=~x,y=~y, colour="Posterior"))
-  graph <- graph + ggplot2::geom_line(data=data.frame(x=x_grid, y=posteriorCI[3,]), ggplot2::aes_(x=~x,y=~y, colour="Posterior"), linetype=2)
+  graph <- graph + ggplot2::geom_line(data=data.frame(x=x_grid, y=posteriorCI[1,]), ggplot2::aes(x=.data$x,y=.data$y, colour="Posterior"), linetype=2)
+  graph <- graph + ggplot2::geom_line(data=data.frame(x=x_grid, y=posteriorCI[2,]), ggplot2::aes(x=.data$x,y=.data$y, colour="Posterior"))
+  graph <- graph + ggplot2::geom_line(data=data.frame(x=x_grid, y=posteriorCI[3,]), ggplot2::aes(x=.data$x,y=.data$y, colour="Posterior"), linetype=2)
 
   if (likelihood) {
     graph <- graph + ggplot2::stat_function(fun = function(z) LikelihoodFunction(x)(z),
@@ -93,11 +96,17 @@ plot_dirichletprocess_univariate <- function(x,
 
 #' @export
 #' @rdname plot.dirichletprocess
+#' @importFrom ggplot2 .data
 plot_dirichletprocess_multivariate <- function(x) {
 
-  plotFrame <- data.frame(x1=x$data[,1], x2=x$data[,2], Cluster=as.factor(x$clusterLabel))
+  plotFrame <- data.frame(x1=x$data[,1],
+                          x2=x$data[,2],
+                          Cluster=as.factor(x$clusterLabel))
 
-  graph <- ggplot2::ggplot(plotFrame, ggplot2::aes_(x=~x1, y=~x2, colour=~Cluster)) +
+  graph <- ggplot2::ggplot(plotFrame,
+                           ggplot2::aes(x=.data$x1,
+                                        y=.data$x2,
+                                        colour=.data$Cluster)) +
     ggplot2::geom_point()
   return(graph)
 }
diff --git a/README.Rmd b/README.Rmd
@@ -17,10 +17,12 @@ knitr::opts_chunk$set(
 
 # dirichletprocess
 
-[![R build status](https://github.com/dm13450/dirichletprocess/workflows/R-CMD-check/badge.svg)](https://github.com/dm13450/dirichletprocess/actions)
+<!-- badges: start -->
+[![R-CMD-check](https://github.com/dm13450/dirichletprocess/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/dm13450/dirichletprocess/actions/workflows/R-CMD-check.yaml)
 [![AppVeyor Build Status](https://ci.appveyor.com/api/projects/status/github/dm13450/dirichletprocess?branch=master&svg=true)](https://ci.appveyor.com/project/dm13450/dirichletprocess)
 [![Coverage Status](https://codecov.io/gh/dm13450/dirichletprocess/branch/master/graph/badge.svg)](https://app.codecov.io/gh/dm13450/dirichletprocess)
-
+[![Codecov test coverage](https://codecov.io/gh/dm13450/dirichletprocess/graph/badge.svg)](https://app.codecov.io/gh/dm13450/dirichletprocess)
+<!-- badges: end -->
 
 The dirichletprocess package provides tools for you to build custom Dirichlet process mixture models. You can use the pre-built Normal/Weibull/Beta distributions or create your own following the instructions in the vignette. In as little as four lines of code you can be modelling your data nonparametrically.