Release candidate 0.1.3

.github/workflows/build-package.yaml

@@ -13,15 +13,16 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v7
 
       - name: Setup R
         uses: r-lib/actions/setup-r@v2
 
       - name: Setup Pandoc
         uses: r-lib/actions/setup-pandoc@v2
 
-      - uses: r-lib/actions/setup-r-dependencies@v2
+      - name: Setup R dependencies
+        uses: r-lib/actions/setup-r-dependencies@v2
         with:
           extra-packages: |
             any::rcmdcheck

.github/workflows/check-style-coverage.yaml

@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v7
 
       - name: Setup R
         uses: r-lib/actions/setup-r@v2

.github/workflows/test-package.yaml

@@ -18,26 +18,29 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: ubuntu-22.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
-          - {os: ubuntu-22.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
-          - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {os: ubuntu-26.04, r: 'devel'}
+          - {os: ubuntu-26.04, r: 'release'}
+          - {os: ubuntu-24.04, r: 'release'}
           - {os: macOS-latest, r: 'release'}
           - {os: windows-latest, r: 'release'}
 
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
-      RSPM: ${{ matrix.config.rspm }}
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v7
 
       - name: Setup R
         uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
 
+      - name: Get OS and R version
+        shell: bash
+        run: Rscript -e 'cat(sessionInfo()$running, "\n"); cat(R.version.string, "\n")'
+
       - name: Setup Pandoc
         uses: r-lib/actions/setup-pandoc@v2
 

DESCRIPTION

@@ -4,7 +4,7 @@ Version: 0.1.3
 Authors@R: c(
     person(given = "Simon", family = "Lyddon", role = c("aut"), email = "simon.lyddon@stats.ox.ac.uk"),
     person(given = "Miguel", family = "Morin", role = c("aut"), email = "info@turing.ac.uk"),
-    person(given = "James", family = "Robinson", role = c("aut", "cre"), email = "james.em.robinson@gmail.com"),
+    person(given = "James", family = "Robinson", role = c("aut", "cre"), email = "jrobinson@turing.ac.uk"),
     person(given = "Matt", family = "Craddock", role = c("ctb"), email = "mcraddock@turing.ac.uk"),
     person("The Alan Turing Institute", role=c("cph"), email = "info@turing.ac.uk"))
 Description: An implementation of a non-parametric statistical model using a
@@ -18,7 +18,7 @@ Description: An implementation of a non-parametric statistical model using a
     close to the simplified variational Bayes logistic regression. The method is
     described in full in the paper Lyddon, Walker, and Holmes (2018),
     "Nonparametric learning from Bayesian models with randomized objective
-    functions" <arXiv:1806.11544>.
+    functions" <doi:10.48550/arXiv.1806.11544>.
 Language: en-GB
 License: MIT + file LICENSE
 Encoding: UTF-8
@@ -44,4 +44,4 @@ Suggests:
 VignetteBuilder: knitr, rmarkdown
 URL: https://github.com/alan-turing-institute/PosteriorBootstrap/
 BugReports: https://github.com/alan-turing-institute/PosteriorBootstrap/issues
-RoxygenNote: 7.2.3
+RoxygenNote: 8.1.0

NEWS.md

@@ -1,5 +1,6 @@
 # PosteriorBootstrap 0.1.3
-- Updated package documentation to use correct Roxygen "_PACKAGE" sentinel
+- updated package documentation to use correct Roxygen "_PACKAGE" sentinel
+- updated Stan array syntax
 
 # PosteriorBootstrap 0.1.2
 - moved RStan from Imports to Suggests.

README.md

@@ -98,11 +98,7 @@ large the bootstrap samples, and always below 1. For large samples with
 
 ## Reproducing the results on Azure
 
-To run the results in this section automatically, you'll need a [Microsoft Azure
-subscription](https://azure.microsoft.com/en-gb/) (one of the [free
-subscriptions](https://azure.microsoft.com/en-gb/free/) for example) and the
-[Azure Command-Line
-Interface (CLI)](https://learn.microsoft.com/en-us/cli/azure/install-azure-cli-macos).
+To run the results in this section automatically, you'll need a [Microsoft Azure subscription](https://azure.microsoft.com/en-gb) (one of the [free subscriptions](https://azure.microsoft.com/en-gb/pricing/purchase-options/azure-account?icid=azurefreeaccount) for example) and the [Azure Command-Line Interface (CLI)](https://learn.microsoft.com/en-us/cli/azure/install-azure-cli-macos).
 You will need to login to your Azure account with the Azure CLI:
 
 ```bash

cran-comments.md

@@ -1,10 +1,10 @@
 ## Test environments
-* macOS 13.2.1 (local) R 4.2.2
-* Ubuntu 20.04.5 (on GitHub Actions) R 2023-03-10 r83967
-* Ubuntu 20.04.5 (on GitHub Actions) R 4.2.2
-* Ubuntu 18.04.6 (on GitHub Actions) R 4.2.2
-* macOS 12.6.3 (on GitHub Actions) R 4.2.2
-* Microsoft Windows Server 2022 (on GitHub Actions) R 4.2.2
+* macOS Tahoe 26.6.2 (local) R 4.6.1 (2026-06-24)
+* Ubuntu 26.04.1 LTS (on GitHub Actions) R r90498 (2026-09-06)
+* Ubuntu 26.04.1 LTS (on GitHub Actions) R 4.6.1 (2026-06-24)
+* Ubuntu 24.04.4 LTS (on GitHub Actions) R 4.6.1 (2026-06-24)
+* macOS Tahoe 26.6.2 (on GitHub Actions) R 4.6.1 (2026-06-24)
+* Microsoft Windows Server 2025 (on GitHub Actions) R 4.6.1 (2026-06-24)
 
 ## devtools::check() results
 There were no ERRORs, WARNINGs or NOTEs.

inst/extdata/bayes_logit.stan

@@ -3,7 +3,7 @@ data {
   int<lower=0> n; // number of observations
   int<lower=0> p; // number of covariates
   matrix[n,p] x; // Matrix of covariates
-  int<lower=0,upper=1> y[n]; // Responses
+  array[n] int<lower=0,upper=1> y; // Responses
   real<lower=0> beta_sd; // Stdev of beta
 }
 parameters {