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Merge pull request #1 from stan-dev/master
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‎.Rbuildignore

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

‎.github/.gitignore

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*.html

‎.github/FUNDING.yml

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github: stan-dev
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custom: https://mc-stan.org/support/

‎.github/workflows/R-CMD-check.yaml

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

‎.github/workflows/codecov.yaml

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

‎.gitignore

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cran-comments.md
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revdep/*
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CRAN-RELEASE

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‎DESCRIPTION

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

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