Rebase branch, add update workflow

.github/workflows/R-CMD-check.yaml

@@ -4,9 +4,11 @@ on:
   push:
     branches:
       - master
+      - survival-rstantools
   pull_request:
     branches:
       - master
+      - survival-rstantools
 
 name: R-CMD-check
 
@@ -20,26 +22,25 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: macOS-latest, r: 'devel', rstan: 'CRAN'}
-          - {os: macOS-latest, r: 'release', rstan: 'CRAN'}
-          - {os: windows-latest, r: 'devel', rstan: 'CRAN'}
-          - {os: windows-latest, r: 'release', rstan: 'CRAN'}
-          - {os: ubuntu-latest, r: 'devel', rstan: 'CRAN'}
-          - {os: ubuntu-latest, r: 'release', rstan: 'CRAN'}
-          - {os: ubuntu-latest, r: 'oldrel', rstan: 'CRAN'}
-
-          - {os: macOS-latest, r: 'release', rstan: 'Preview'}
-          - {os: windows-latest, r: 'release', rstan: 'Preview'}
+          - { os: macOS-latest, r: 'devel' }
+          - { os: macOS-latest, r: 'release' }
+          - { os: macOS-latest, r: 'oldrel' }
+          - { os: windows-latest, r: 'devel' }
+          - { os: windows-latest, r: 'release' }
+          - { os: windows-latest, r: 'oldrel' }
+          - { os: ubuntu-latest, r: 'devel' }
+          - { os: ubuntu-latest, r: 'release' }
+          - { os: ubuntu-latest, r: 'oldrel' }
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
       RSPM: ${{ matrix.config.rspm }}
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      TESTTHAT_CPUS: 4
 
     steps:
       - uses: n1hility/cancel-previous-runs@v2
         with:
           token: ${{ secrets.GITHUB_TOKEN }}
-          workflow: R-CMD-check.yaml
         if: "!startsWith(github.ref, 'refs/tags/') && github.ref != 'refs/heads/master'"
 
       - uses: actions/checkout@v3
@@ -51,24 +52,5 @@ jobs:
       - uses: r-lib/actions/setup-pandoc@v2
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          cache-version: 2
           extra-packages: any::rcmdcheck any::betareg any::HSAUR3 any::biglm any::gamm4 any::V8
-
-      - name: Install RStan Preview if Needed
-        run: |
-          if ("${{ matrix.config.rstan }}" == "Preview") {
-            install.packages("rstan", repos = c("https://mc-stan.org/r-packages/", getOption("repos")))
-          }
-        shell: Rscript {0}
-
       - uses: r-lib/actions/check-r-package@v2
-        with:
-          args: 'c("--no-manual", "--as-cran", "--ignore-vignettes")'
-          build_args: '"--no-build-vignettes"'
-
-      - name: Upload check results
-        if: failure()
-        uses: actions/upload-artifact@main
-        with:
-          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
-          path: check

.github/workflows/update-branch.yml

@@ -0,0 +1,26 @@
+name: Update Branch
+permissions:
+  contents: write
+
+on:
+  push:
+    branches:
+      - feature/survival
+
+jobs:
+  update-branch:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v2
+
+      - name: Rebase survival-rstantools branch
+        run: |
+          git checkout survival-rstantools
+          git pull origin survival-rstantools
+          git rebase feature/survival
+
+      - name: Push changes
+        run: |
+          git push origin survival-rstantools

.gitignore

@@ -8,11 +8,15 @@ src/stan_files/*.hpp
 src/rstanarm.so
 src/rstanarm.dll
 src/init.o
-man/*.Rd
 !man/rstanarm-internal.Rd
 vignettes/*.R
 !vignettes/*.Rmd
 vignettes/*.html
 vignettes/*_files
 .DS_Store
 revdep/*
+*.o
+*.cc
+*.h
+src/Makevars
+R/stanmodels.R

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: rstanarm
 Type: Package
 Title: Bayesian Applied Regression Modeling via Stan
-Version: 2.32.1
-Date: 2024-01-15
+Version: 2.35.0.9000
+Date: 2024-05-18
 Encoding: UTF-8
 Authors@R: c(person("Jonah", "Gabry", email = "[email protected]", role = "aut"),
              person("Imad", "Ali", role = "ctb"),
@@ -42,7 +42,7 @@ Imports:
     loo (>= 2.1.0),
     Matrix (>= 1.2-13),
     nlme (>= 3.1-124),
-    posterior, 
+    posterior,
     rstan (>= 2.32.0),
     rstantools (>= 2.1.0),
     shinystan (>= 2.3.0),
@@ -79,4 +79,4 @@ UseLTO: true
 NeedsCompilation: yes
 URL: https://mc-stan.org/rstanarm/, https://discourse.mc-stan.org
 BugReports: https://github.com/stan-dev/rstanarm/issues
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1

NAMESPACE

@@ -14,7 +14,13 @@ S3method(as_draws_rvars,stanreg)
 S3method(bayes_R2,stanreg)
 S3method(coef,stanmvreg)
 S3method(coef,stanreg)
+S3method(collapse_within_groups,default)
+S3method(collapse_within_groups,matrix)
 S3method(confint,stanreg)
+S3method(evaluate_log_survival,default)
+S3method(evaluate_log_survival,matrix)
+S3method(extract_pars,stanmvreg)
+S3method(extract_pars,stansurv)
 S3method(family,stanmvreg)
 S3method(family,stanreg)
 S3method(fitted,stanmvreg)
@@ -23,6 +29,8 @@ S3method(fixef,stanmvreg)
 S3method(fixef,stanreg)
 S3method(formula,stanmvreg)
 S3method(formula,stanreg)
+S3method(get_model_data,stanmvreg)
+S3method(get_model_data,stansurv)
 S3method(get_surv,stanjm)
 S3method(get_surv,stansurv)
 S3method(get_x,default)
@@ -35,6 +43,15 @@ S3method(get_z,lmerMod)
 S3method(get_z,stanmvreg)
 S3method(kfold,stanreg)
 S3method(launch_shinystan,stanreg)
+S3method(linear_predictor,default)
+S3method(linear_predictor,matrix)
+S3method(linkinv,character)
+S3method(linkinv,family)
+S3method(linkinv,stanmvreg)
+S3method(linkinv,stanreg)
+S3method(ll_args,stanjm)
+S3method(ll_args,stanreg)
+S3method(ll_args,stansurv)
 S3method(log_lik,stanjm)
 S3method(log_lik,stanmvreg)
 S3method(log_lik,stanreg)
@@ -73,6 +90,7 @@ S3method(pp_check,stanreg)
 S3method(predict,stanreg)
 S3method(predictive_error,matrix)
 S3method(predictive_error,ppd)
+S3method(predictive_error,stanmvreg)
 S3method(predictive_error,stanreg)
 S3method(predictive_interval,matrix)
 S3method(predictive_interval,ppd)
@@ -87,18 +105,28 @@ S3method(print,summary.stanreg)
 S3method(print,survfit.stanjm)
 S3method(print,survfit.stansurv)
 S3method(prior_summary,stanreg)
+S3method(psis,stanreg)
+S3method(quadrature_sum,default)
+S3method(quadrature_sum,matrix)
 S3method(ranef,stanmvreg)
 S3method(ranef,stanreg)
+S3method(rename_loos,stanreg)
+S3method(rename_loos,stanreg_list)
 S3method(residuals,stanmvreg)
 S3method(residuals,stanreg)
 S3method(se,stanmvreg)
 S3method(se,stanreg)
 S3method(sigma,stanmvreg)
 S3method(sigma,stanreg)
+S3method(split2,matrix)
+S3method(split2,vector)
 S3method(summary,stanmvreg)
 S3method(summary,stanreg)
 S3method(terms,stanmvreg)
 S3method(terms,stanreg)
+S3method(truncate,numeric)
+S3method(unpad_reTrms,array)
+S3method(unpad_reTrms,default)
 S3method(update,stanjm)
 S3method(update,stanmvreg)
 S3method(update,stanreg)
@@ -115,13 +143,17 @@ export(as_draws_matrix)
 export(as_draws_rvars)
 export(bayes_R2)
 export(cauchy)
+export(collapse_within_groups)
 export(compare_models)
 export(decov)
 export(default_prior_coef)
 export(default_prior_intercept)
 export(dirichlet)
+export(evaluate_log_survival)
 export(exponential)
+export(extract_pars)
 export(fixef)
+export(get_model_data)
 export(get_surv)
 export(get_x)
 export(get_y)
@@ -133,7 +165,10 @@ export(kfold)
 export(laplace)
 export(lasso)
 export(launch_shinystan)
+export(linear_predictor)
+export(linkinv)
 export(lkj)
+export(ll_args)
 export(log_lik)
 export(logit)
 export(loo)
@@ -166,7 +201,9 @@ export(prior_options)
 export(prior_summary)
 export(product_normal)
 export(ps_check)
+export(quadrature_sum)
 export(ranef)
+export(rename_loos)
 export(se)
 export(sigma)
 export(stan_aov)
@@ -196,6 +233,7 @@ export(stanmvreg_list)
 export(stanreg_list)
 export(student_t)
 export(tve)
+export(unpad_reTrms)
 export(waic)
 if(getRversion()>='3.3.0') importFrom(stats, sigma) else
   importFrom(lme4,sigma)