diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index db50e234..3e54db1c 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -40,12 +40,16 @@ jobs: r-version: ${{ matrix.config.r }} http-user-agent: ${{ matrix.config.http-user-agent }} use-public-rspm: true + extra-repositories: 'https://stan-dev.r-universe.dev' - uses: r-lib/actions/setup-r-dependencies@v2 with: - extra-packages: any::rcmdcheck, any::BH, any::RcppEigen, any::vdiffr + extra-packages: any::rcmdcheck, any::BH, any::RcppEigen, any::vdiffr, any::cmdstanr needs: check + - name: Install CmdStan + run: Rscript -e "cmdstanr::install_cmdstan()" + - uses: r-lib/actions/check-r-package@v2 with: upload-snapshots: true diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml index 447fb9de..46c1a68f 100644 --- a/.github/workflows/test-coverage.yaml +++ b/.github/workflows/test-coverage.yaml @@ -21,12 +21,16 @@ jobs: - uses: r-lib/actions/setup-r@v2 with: use-public-rspm: true + extra-repositories: 'https://stan-dev.r-universe.dev' - uses: r-lib/actions/setup-r-dependencies@v2 with: - extra-packages: any::covr, any::xml2, any::vdiffr + extra-packages: any::covr, any::xml2, any::vdiffr, any::cmdstanr needs: coverage + - name: Install CmdStan + run: Rscript -e "cmdstanr::install_cmdstan()" + - name: Test coverage run: | cov <- covr::package_coverage( diff --git a/DESCRIPTION b/DESCRIPTION index df6b5f7d..6aa9a87b 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -42,6 +42,7 @@ Imports: tidyselect, utils Suggests: + cmdstanr, ggdist, ggfortify, gridExtra (>= 2.2.1), @@ -63,3 +64,4 @@ VignetteBuilder: knitr Encoding: UTF-8 Roxygen: list(markdown = TRUE) Config/testthat/edition: 3 +Additional_repositories: https://stan-dev.r-universe.dev/ diff --git a/vignettes/visual-mcmc-diagnostics.Rmd b/vignettes/visual-mcmc-diagnostics.Rmd index 9e24ec57..1b6ee6a6 100644 --- a/vignettes/visual-mcmc-diagnostics.Rmd +++ b/vignettes/visual-mcmc-diagnostics.Rmd @@ -154,7 +154,7 @@ schools_mod_ncp <- stan_model("schools_mod_ncp.stan") We then fit the model by calling Stan's MCMC algorithm using the `sampling` function (the increased `adapt_delta` param is to make the sampler a bit more "careful" and avoid false positive divergences), ```{r fit-models-hidden, results='hide', message=FALSE} -fit_cp <- sampling(schools_mod_cp, data = schools_dat, seed = 803214055, control = list(adapt_delta = 0.9)) +fit_cp <- sampling(schools_mod_cp, data = schools_dat, seed = 20251208, control = list(adapt_delta = 0.9)) fit_ncp <- sampling(schools_mod_ncp, data = schools_dat, seed = 457721433, control = list(adapt_delta = 0.9)) ``` and extract a `iterations x chains x parameters` array of posterior draws with