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Features - summary_heterogeneity() function to summarize the heterogeneity of the RoBMA models (prediction interval, tau, tau^2, I^2, and H^2) - check_RoBMA_convergence() function to check the convergence of the RoBMA models - adds informed prior distributions for binary and time-to-event outcomes via BayesTools 0.2.17 Fixes - checking and fixing the number of available cores upon loading the package (fixes: Error when parallel = TRUE #25) - update() function re-evaluates convergence checks of individual models (fixes: update() should update convergence checks on individual model level #34) - Updates vignettes (fixes: #31 and fixes #32) - Also add renv to hopefully fix unit tests
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| Original file line number | Diff line number | Diff line change |
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| @@ -1,3 +1,5 @@ | ||
| ^renv$ | ||
| ^renv\.lock$ | ||
| ^RoBMA\.Rproj$ | ||
| ^\.Rproj\.user$ | ||
| ^do-not-share$ | ||
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| Original file line number | Diff line number | Diff line change |
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| # For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag. | ||
| # https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions | ||
| name: R-CMD-tests | ||
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| on: | ||
| push: | ||
| branches: | ||
| - main | ||
| - master | ||
| - pre-release | ||
| branches: [main, master, pre-release] | ||
| pull_request: | ||
| branches: | ||
| - main | ||
| - master | ||
| - pre-release | ||
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| name: R-CMD-tests | ||
| branches: [main, master, pre-release] | ||
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| jobs: | ||
| R-CMD-check: | ||
| build: | ||
| runs-on: ${{ matrix.config.os }} | ||
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| name: ${{ matrix.config.os }} (${{ matrix.config.r }}) | ||
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| strategy: | ||
| fail-fast: false | ||
| matrix: | ||
| config: | ||
| - {os: windows-latest, r: 'release'} | ||
| - {os: ubuntu-20.04, r: 'release'} | ||
| # - {os: macOS-11.6.2, r: 'release'} # the release C++ version does not compile properly | ||
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| env: | ||
| R_REMOTES_NO_ERRORS_FROM_WARNINGS: true | ||
| RSPM: ${{ matrix.config.rspm }} | ||
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | ||
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| - {os: ubuntu-latest, r: 'release'} | ||
| - {os: macOS-latest, r: 'release'} | ||
| steps: | ||
| - uses: actions/checkout@v2 | ||
| - uses: actions/checkout@v4 | ||
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| - uses: r-lib/actions/setup-r@v2 | ||
| - name: Setup R | ||
| uses: r-lib/actions/setup-r@v2 | ||
| with: | ||
| r-version: ${{ matrix.config.r }} | ||
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| - uses: r-lib/actions/setup-pandoc@v2 | ||
| # Install JAGS and system dependencies on Linux | ||
| - name: Install System Dependencies (Linux) | ||
| if: runner.os == 'Linux' | ||
| run: | | ||
| sudo apt-get update | ||
| sudo apt-get install -y \ | ||
| libssl-dev \ | ||
| libcurl4-openssl-dev \ | ||
| libxml2-dev \ | ||
| libfontconfig1-dev \ | ||
| libharfbuzz-dev \ | ||
| libfribidi-dev \ | ||
| libfreetype6-dev \ | ||
| libpng-dev \ | ||
| libtiff5-dev \ | ||
| libjpeg-dev \ | ||
| libcairo2-dev \ | ||
| jags | ||
| - name: Query dependencies | ||
| # Install JAGS on Windows | ||
| - name: Install JAGS (Windows) | ||
| if: runner.os == 'Windows' | ||
| shell: cmd | ||
| run: | | ||
| install.packages('remotes') | ||
| saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) | ||
| writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version") | ||
| shell: Rscript {0} | ||
| curl -o jags-installer.exe -L https://sourceforge.net/projects/mcmc-jags/files/JAGS/4.x/Windows/JAGS-4.3.1.exe/download | ||
| jags-installer.exe /S | ||
| del jags-installer.exe | ||
| - name: Restore R package cache | ||
| uses: actions/cache@v2 | ||
| 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- | ||
| # Set JAGS environment variables on Windows | ||
| - name: Set JAGS environment variables (Windows) | ||
| if: runner.os == 'Windows' | ||
| shell: cmd | ||
| run: | | ||
| echo JAGS_ROOT=C:\Program Files\JAGS\JAGS-4.3.1>> %GITHUB_ENV% | ||
| echo JAGS_MAJOR_VERSION=4>> %GITHUB_ENV% | ||
| echo PATH=C:\Program Files\JAGS\JAGS-4.3.1\bin;%PATH%>> %GITHUB_ENV% | ||
| - name: Install system dependencies | ||
| if: runner.os == 'Linux' | ||
| # Install JAGS on macOS | ||
| - name: Install JAGS (macOS) | ||
| if: runner.os == 'macOS' | ||
| run: | | ||
| while read -r cmd | ||
| do | ||
| eval sudo $cmd | ||
| done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))') | ||
| brew update | ||
| brew install jags | ||
| - name: Install JAGS (windows-latest) | ||
| if: runner.os == 'Windows' | ||
| # Find and Set JAGS Paths | ||
| - name: Set Environment Variables (macOS) | ||
| if: runner.os == 'macOS' | ||
| run: | | ||
| curl.exe -o wjags.exe --url https://deac-fra.dl.sourceforge.net/project/mcmc-jags/JAGS/4.x/Windows/JAGS-4.3.1.exe | ||
| wjags.exe /S | ||
| del wjags.exe | ||
| shell: cmd | ||
| JAGS_BIN=$(brew --prefix jags)/bin | ||
| echo "JAGS_ROOT=$(brew --prefix jags)" >> $GITHUB_ENV | ||
| echo "PATH=$JAGS_BIN:$PATH" >> $GITHUB_ENV | ||
| echo "PKG_CONFIG_PATH=$(brew --prefix jags)/lib/pkgconfig" >> $GITHUB_ENV | ||
| - name: Install JAGS (macOS-latest) | ||
| # Create Symlink for jags-terminal (if necessary) | ||
| - name: Create Symlink for jags-terminal (macOS) | ||
| if: runner.os == 'macOS' | ||
| run : | | ||
| rm '/usr/local/bin/gfortran' | ||
| brew install automake jags | ||
| run: | | ||
| sudo mkdir -p $(brew --prefix)/libexec | ||
| sudo ln -s $(brew --prefix jags)/bin/jags $(brew --prefix)/libexec/jags-terminal | ||
| - name: Install and test RoBMA (non-Windows) | ||
| if: runner.os != 'Windows' | ||
| env: | ||
| _R_CHECK_CRAN_INCOMING_REMOTE_: false | ||
| # Set up renv | ||
| - name: Setup renv | ||
| uses: r-lib/actions/setup-renv@v2 | ||
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| # Install the package | ||
| - name: Install devtools and the RoBMA Package | ||
| run: | | ||
| remotes::install_deps(dependencies = TRUE) | ||
| install.packages(c("rcmdcheck", "devtools", "testthat", "vdiffr")) | ||
| install.packages(c('devtools', 'metaBMA', 'metafor', 'weightr', 'lme4', 'fixest', 'emmeans', 'metadat', 'vdiffr', 'testthat', 'covr', 'pandoc')) | ||
| devtools::install() | ||
| library(vdiffr) | ||
| library(testthat) | ||
| devtools::test() | ||
| shell: Rscript {0}" | ||
| shell: Rscript {0} | ||
|
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| - name: Install and test RoBMA (Windows) | ||
| if: runner.os == 'Windows' | ||
| env: | ||
| _R_CHECK_CRAN_INCOMING_REMOTE_: false | ||
| JAGS_ROOT: "/c/progra~1/JAGS/JAGS-4.3.1" | ||
| JAGS_MAJOR_VERSION: 4 | ||
| # Run tests | ||
| - name: Run Tests | ||
| run: | | ||
| remotes::install_deps(dependencies = TRUE) | ||
| install.packages(c("rcmdcheck", "devtools", "testthat", "vdiffr")) | ||
| devtools::install() | ||
| library(vdiffr) | ||
| library(testthat) | ||
| devtools::test() | ||
| shell: Rscript {0} |
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