Merge pull request #1 from stan-dev/master

Update fork

.Rbuildignore

@@ -1,10 +1,17 @@
+^CRAN-RELEASE$
 ^.*\.Rproj$
 ^\.Rproj\.user$
 LICENSE
 ^\.travis\.yml$
 ^README\.md$
 .gitignore
+.git/*
 ^cran-comments\.md$
 ^revdep$
 man-roxygen/*
 images/*
+book/*
+docs/*
+Rplots.pdf
+tests/figs/*
+^\.github$

.github/.gitignore

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

.github/FUNDING.yml

@@ -0,0 +1,2 @@
+github: stan-dev
+custom: https://mc-stan.org/support/

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

@@ -0,0 +1,103 @@
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+    branches:
+      - master
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    if: "! contains(github.event.head_commit.message, '[ci skip]')"
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: windows-latest, r: 'release'}
+          - {os: macOS-latest, r: 'release'}
+          - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {os: ubuntu-20.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+    env:
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      RSPM: ${{ matrix.config.rspm }}
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-r@master
+        with:
+          r-version: ${{ matrix.config.r }}
+
+      - uses: r-lib/actions/setup-pandoc@master
+
+      - name: Query dependencies
+        run: |
+          install.packages('remotes')
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
+        shell: Rscript {0}
+
+      - name: Cache R packages
+        if: runner.os != 'Windows'
+        uses: actions/cache@v1
+        with:
+          path: ${{ env.R_LIBS_USER }}
+          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
+
+      - name: Install system dependencies for linux
+        if: runner.os == 'Linux'
+        env:
+          RHUB_PLATFORM: linux-x86_64-ubuntu-gcc
+        run: |
+          Rscript -e "remotes::install_github('r-hub/sysreqs')"
+          sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))")
+          sudo -s eval "$sysreqs"
+
+      - name: Install system dependencies for mac
+        if: runner.os == 'MacOS'
+        run: |
+           curl -sL  https://mac.r-project.org/libs-4/ |
+           sed -n 's/.*href=\([^>]*x86_64.tar.gz\).*/\1/p' |
+           xargs -I % sh -c 'curl https://mac.r-project.org/libs-4/% --output %; sudo tar fvxz % -C /usr/local --strip 2'
+           ls -la /usr/local/lib
+           ls -la /usr/local/include
+
+      - name: Install dependencies
+        run: |
+          remotes::install_deps(dependencies = TRUE)
+          remotes::install_cran("rcmdcheck")
+        shell: Rscript {0}
+
+      - name: Session info
+        run: |
+          options(width = 100)
+          pkgs <- installed.packages()[, "Package"]
+          sessioninfo::session_info(pkgs, include_base = TRUE)
+        shell: Rscript {0}
+
+      - name: Check
+        env:
+          _R_CHECK_CRAN_INCOMING_: false
+          _R_CHECK_FORCE_SUGGESTS_: false
+        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
+        shell: Rscript {0}
+
+      - name: Show testthat output
+        if: always()
+        run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload check results
+        if: failure()
+        uses: actions/upload-artifact@master
+        with:
+          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
+          path: check

.github/workflows/codecov.yaml

@@ -0,0 +1,46 @@
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+    branches:
+      - master
+
+name: test-coverage
+
+jobs:
+  test-coverage:
+    if: "! contains(github.event.head_commit.message, '[ci skip]')"
+    runs-on: macOS-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-r@master
+
+      - uses: r-lib/actions/setup-pandoc@master
+
+      - name: Query dependencies
+        run: |
+          install.packages('remotes')
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+        shell: Rscript {0}
+
+      - name: Cache R packages
+        uses: actions/cache@v1
+        with:
+          path: ${{ env.R_LIBS_USER }}
+          key: macOS-r-4.0-1-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: macOS-r-4.0-1-
+
+      - name: Install dependencies
+        run: |
+          install.packages(c("remotes"))
+          remotes::install_deps(dependencies = TRUE)
+          remotes::install_cran("covr")
+        shell: Rscript {0}
+
+      - name: Test coverage
+        run: covr::codecov()
+        shell: Rscript {0}

.gitignore

@@ -10,3 +10,4 @@ tests/testthat/Rplots.pdf
 
 cran-comments.md
 revdep/*
+CRAN-RELEASE

DESCRIPTION

@@ -1,39 +1,60 @@
 Package: bayesplot
 Type: Package
 Title: Plotting for Bayesian Models
-Version: 1.2.0
-Date: 2017-04-11
+Version: 1.8.0.9000
+Date: 2021-01-07
 Authors@R: c(person("Jonah", "Gabry", role = c("aut", "cre"), email = "[email protected]"),
-             person("Paul-Christian", "Buerkner", role = "ctb"))
+             person("Tristan", "Mahr", role = "aut"),
+             person("Paul-Christian", "Bürkner", role = "ctb"),
+             person("Martin", "Modrák", role = "ctb"),
+             person("Malcolm", "Barrett", role = "ctb"), 
+             person("Frank", "Weber", role = "ctb"),
+             person("Eduardo", "Coronado Sroka", role = "ctb"),
+             person("Aki", "Vehtari", role = "ctb"))
 Maintainer: Jonah Gabry <[email protected]>
-Description: Plotting functions for posterior analysis, model checking,
-    and MCMC diagnostics. The package is designed not only to provide convenient
-    functionality for users, but also a common set of functions that can be
-    easily used by developers working on a variety of R packages for Bayesian
-    modeling, particularly (but not exclusively) packages interfacing with Stan.
+Description: Plotting functions for posterior analysis, MCMC diagnostics,
+    prior and posterior predictive checks, and other visualizations 
+    to support the applied Bayesian workflow advocated in
+    Gabry, Simpson, Vehtari, Betancourt, and Gelman (2019) <doi:10.1111/rssa.12378>.
+    The package is designed not only to provide convenient functionality 
+    for users, but also a common set of functions that can be easily used by 
+    developers working on a variety of R packages for Bayesian modeling, 
+    particularly (but not exclusively) packages interfacing with 'Stan'.
 License: GPL (>= 3)
 LazyData: TRUE
-URL: http://mc-stan.org/, https://groups.google.com/forum/#!forum/stan-users
+URL: https://mc-stan.org/bayesplot/
 BugReports: https://github.com/stan-dev/bayesplot/issues/
+SystemRequirements: pandoc (>= 1.12.3), pandoc-citeproc
 Depends:
     R (>= 3.1.0)
 Imports:
-    dplyr (>= 0.4.3),
-    ggplot2 (>= 2.2.1),
+    dplyr (>= 0.8.0),
+    ggplot2 (>= 3.0.0),
+    ggridges,
+    glue,
     reshape2,
+    rlang (>= 0.3.0),
     stats,
+    tibble,
+    tidyselect,
     utils
-Suggests:
-    arm,
+Suggests: 
+    ggfortify,
     gridExtra (>= 2.2.1),
-    knitr (>= 1.14),
-    loo (>= 1.1.0),
+    hexbin,
+    knitr (>= 1.16),
+    loo (>= 2.0.0),
+    RColorBrewer,
     rmarkdown (>= 1.0.0),
-    rstan (>= 2.14.1),
-    rstanarm (>= 2.14.1),
-    rstantools (>= 1.2.0),
+    rstan (>= 2.17.1),
+    rstanarm (>= 2.17.4),
+    rstantools (>= 1.5.0),
     scales,
     shinystan (>= 2.3.0),
-    testthat
-RoxygenNote: 6.0.1
+    survival,
+    testthat (>= 2.0.0),
+    vdiffr
+RoxygenNote: 7.1.1
 VignetteBuilder: knitr
+Encoding: UTF-8
+Roxygen: list(markdown = TRUE)