Merge branch 'master' into gh-pages

.Rbuildignore

@@ -22,3 +22,4 @@
 ^docs$
 ^_pkgdown\.yml$
 ^CRAN-RELEASE$
+^CRAN-SUBMISSION$

.github/.gitignore

@@ -0,0 +1 @@
+*.html

.github/ISSUE_TEMPLATE.md

@@ -0,0 +1,2 @@
+#### Please note:
+The brms issue tracker is reserved for bug reports and feature requests. brms-related questions should rather be asked on https://discourse.mc-stan.org/ in order to reach a wider community.

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

@@ -0,0 +1,85 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/master/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:
+    branches: [main, master]
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          # - {os: macOS-latest,   r: 'release', rtools: ''}
+          - {os: windows-latest, r: 'release', rtools: '42'}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release', rtools: ''}
+          - {os: ubuntu-latest,   r: 'release', rtools: ''}
+          - {os: ubuntu-latest,   r: 'oldrel-1', rtools: ''}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v2
+      - uses: n1hility/cancel-previous-runs@v2
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+
+      - uses: r-lib/actions/setup-pandoc@v2
+      - uses: r-lib/actions/[email protected]
+        with:
+          r-version: ${{ matrix.config.r }}
+          rtools-version: ${{ matrix.config.rtools }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      # As cmdstanr is not yet on CRAN, configure the action to only install the
+      # 'Depends' packages by default and then manually specify the 'Suggests'
+      # packages that are needed for R CMD CHECK
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          dependencies: NA
+          extra-packages: |
+            R.rsp
+            knitr
+            rcmdcheck
+            rmarkdown
+            lme4
+            mice
+            BH
+            MCMCglmm
+            ape
+            stan-dev/cmdstanr
+            RcppEigen
+            testthat
+            emmeans
+            projpred
+            RWiener
+            rtdists
+            extraDistr
+            spdep
+            mnormt
+            splines2
+            arm
+            statmod
+            diffobj
+
+      - name: Build Cmdstan
+        run: |
+          cmdstanr::check_cmdstan_toolchain(fix = TRUE)
+          cmdstanr::install_cmdstan(cores = parallel::detectCores())
+        shell: Rscript {0}
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          build_args: 'c("--no-manual", "--no-build-vignettes")'
+          args: 'c("--no-manual", "--as-cran", "--ignore-vignettes")'

.github/workflows/test-coverage.yaml

@@ -0,0 +1,68 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/master/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:
+    branches: [main, master]
+
+name: test-coverage
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v2
+      - uses: n1hility/cancel-previous-runs@v2
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      # As cmdstanr is not yet on CRAN, configure the action to only install the
+      # 'Depends' packages by default and then manually specify the 'Suggests'
+      # packages that are needed for R CMD CHECK
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          dependencies: NA
+          extra-packages: |
+            R.rsp
+            knitr
+            rcmdcheck
+            rmarkdown
+            lme4
+            mice
+            BH
+            MCMCglmm
+            ape
+            stan-dev/cmdstanr
+            RcppEigen
+            emmeans
+            projpred
+            RWiener
+            rtdists
+            extraDistr
+            spdep
+            mnormt
+            splines2
+            arm
+            statmod
+            diffobj
+            usethis
+            testthat
+            covr
+
+      - name: Build Cmdstan
+        run: |
+          cmdstanr::check_cmdstan_toolchain(fix = TRUE)
+          cmdstanr::install_cmdstan(cores = parallel::detectCores())
+        shell: Rscript {0}
+
+      - name: Test coverage
+        run: covr::codecov()
+        shell: Rscript {0}

.gitignore

@@ -9,3 +9,4 @@ tests/local/models_0.8.0.Rda
 tests/local/models_0.10.0.Rda
 tests/local/models_1.2.0.Rda
 tests/local/Rplots.pdf
+/Meta/

CRAN-SUBMISSION

@@ -0,0 +1,3 @@
+Version: 2.20.4
+Date: 2023-09-25 11:44:24 UTC
+SHA: ca12a94a39318c10cdebe96425dc578f9ad926ab

DESCRIPTION

@@ -2,9 +2,9 @@ Package: brms
 Encoding: UTF-8
 Type: Package
 Title: Bayesian Regression Models using 'Stan'
-Version: 2.16.2
-Date: 2021-08-26
-Authors@R: 
+Version: 2.20.6
+Date: 2023-11-13
+Authors@R:
     c(person("Paul-Christian", "Bürkner", email = "[email protected]",
              role = c("aut", "cre")),
       person("Jonah", "Gabry", role = c("ctb")),
@@ -13,13 +13,16 @@ Authors@R:
       person("Martin", "Modrak", role = c("ctb")),
       person("Hamada S.", "Badr", role = c("ctb")),
       person("Frank", "Weber", role = c("ctb")),
-      person("Mattan S.", "Ben-Shachar", role = c("ctb")))
-Depends: 
-    R (>= 3.5.0),
+      person("Mattan S.", "Ben-Shachar", role = c("ctb")),
+      person("Hayden", "Rabel", role = c("ctb")),
+      person("Simon C.", "Mills", role = c("ctb")),
+      person("Stephen", "Wild", role = c("ctb")))
+Depends:
+    R (>= 3.6.0),
     Rcpp (>= 0.12.0),
     methods
-Imports: 
-    rstan (>= 2.19.2),
+Imports:
+    rstan (>= 2.26.0),
     ggplot2 (>= 2.0.0),
     loo (>= 2.3.1),
     posterior (>= 1.0.0),
@@ -28,9 +31,9 @@ Imports:
     rstantools (>= 2.1.1),
     bayesplot (>= 1.5.0),
     shinystan (>= 2.4.0),
-    projpred (>= 2.0.0),
     bridgesampling (>= 0.3-0),
     glue (>= 1.3.0),
+    rlang (>= 1.0.0),
     future (>= 1.19.0),
     matrixStats,
     nleqslv,
@@ -42,12 +45,15 @@ Imports:
     parallel,
     grDevices,
     backports
-Suggests: 
+Suggests:
     testthat (>= 0.9.1),
     emmeans (>= 1.4.2),
-    cmdstanr (>= 0.4.0),
+    cmdstanr (>= 0.5.0),
+    projpred (>= 2.0.0),
     RWiener,
     rtdists,
+    extraDistr,
+    processx,
     mice,
     spdep,
     mnormt,
@@ -65,28 +71,30 @@ Suggests:
     knitr,
     rmarkdown
 Description: Fit Bayesian generalized (non-)linear multivariate multilevel models
-    using 'Stan' for full Bayesian inference. A wide range of distributions 
-    and link functions are supported, allowing users to fit -- among others -- 
-    linear, robust linear, count data, survival, response times, ordinal, 
-    zero-inflated, hurdle, and even self-defined mixture models all in a 
-    multilevel context. Further modeling options include non-linear and 
-    smooth terms, auto-correlation structures, censored data, meta-analytic 
-    standard errors, and quite a few more. In addition, all parameters of the 
-    response distribution can be predicted in order to perform distributional 
-    regression. Prior specifications are flexible and explicitly encourage 
-    users to apply prior distributions that actually reflect their beliefs.
-    Model fit can easily be assessed and compared with posterior predictive 
-    checks and leave-one-out cross-validation. References: Bürkner (2017)
-    <doi:10.18637/jss.v080.i01>; Bürkner (2018) <doi:10.32614/RJ-2018-017>;
-    Carpenter et al. (2017) <doi:10.18637/jss.v076.i01>.
+    using 'Stan' for full Bayesian inference. A wide range of distributions
+    and link functions are supported, allowing users to fit -- among others --
+    linear, robust linear, count data, survival, response times, ordinal,
+    zero-inflated, hurdle, and even self-defined mixture models all in a
+    multilevel context. Further modeling options include both theory-driven and
+    data-driven non-linear terms, auto-correlation structures, censoring and 
+    truncation, meta-analytic standard errors, and quite a few more. 
+    In addition, all parameters of the response distribution can be predicted 
+    in order to perform distributional regression. Prior specifications are 
+    flexible and explicitly encourage users to apply prior distributions that
+    actually reflect their prior knowledge. Models can easily be evaluated and
+    compared using several methods assessing posterior or prior predictions. 
+    References: Bürkner (2017) <doi:10.18637/jss.v080.i01>; 
+    Bürkner (2018) <doi:10.32614/RJ-2018-017>;
+    Bürkner (2021) <doi:10.18637/jss.v100.i05>; Carpenter et al. (2017)
+    <doi:10.18637/jss.v076.i01>.
 LazyData: true
 NeedsCompilation: no
 License: GPL-2
-URL: https://github.com/paul-buerkner/brms, https://discourse.mc-stan.org/
+URL: https://github.com/paul-buerkner/brms, https://discourse.mc-stan.org/, https://paul-buerkner.github.io/brms/
 BugReports: https://github.com/paul-buerkner/brms/issues
 Additional_repositories:
     https://mc-stan.org/r-packages/
-VignetteBuilder: 
+VignetteBuilder:
     knitr,
     R.rsp
-RoxygenNote: 7.1.1
+RoxygenNote: 7.2.3