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adding
prior_mixture() and spike-and-slab style model-averaging upg…
…rades (#30) ### Features - adding `prior_mixture()` function for creating a mixture of prior distributions - adding `as_mixed_posteriors()` and `as_marginal_inference()` functions for a single JAGS models (with spike and slab or mixture priors) to enabling tables and figures based on the corresponding output - adding `interpret2()` function for another way of creating textual summaries without the need of inference and samples objects - speedup and improvements to the `runjags_estimates_table()` function ### Fixes - small fixes for expansion of the RoBMA functionality
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| ^renv$ | ||
| ^renv\.lock$ | ||
| ^.*\.Rproj$ | ||
| ^\.Rproj\.user$ | ||
| ^do-not-share$ | ||
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| if(interactive()){ | ||
| library(devtools) | ||
| library(testthat) | ||
| library(vdiffr) | ||
| } |
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| name: pkgdown | ||
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| on: | ||
| push: | ||
| branches: | ||
| - main | ||
| - master | ||
| tags: | ||
| -'*' | ||
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| name: pkgdown | ||
| - '*' | ||
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| jobs: | ||
| pkgdown: | ||
| 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: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} | ||
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| env: | ||
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | ||
| - {os: windows-latest, r: 'release'} | ||
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| 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: ${{ matrix.config.r }} | ||
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| - uses: r-lib/actions/setup-pandoc@v2 | ||
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| - name: Install harfbuzz freetype2 fribidi Headers | ||
| if: runner.os == 'Linux' | ||
| run: sudo apt-get install libharfbuzz-dev libfribidi-dev | ||
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| - name: Query dependencies | ||
| # Install JAGS on Windows | ||
| - name: Install JAGS (Windows) | ||
| if: runner.os == 'Windows' | ||
| shell: cmd | ||
| run: | | ||
| install.packages('remotes') | ||
| saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) | ||
| writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version") | ||
| shell: Rscript {0} | ||
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| - 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- | ||
| 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: Install system dependencies | ||
| if: runner.os == 'Linux' | ||
| run: | | ||
| while read -r cmd | ||
| do | ||
| eval sudo $cmd | ||
| done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))') | ||
| - name: Install JAGS (windows-latest) | ||
| # Set JAGS environment variables on Windows | ||
| - name: Set JAGS environment variables (Windows) | ||
| if: runner.os == 'Windows' | ||
| 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 | ||
| 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 JAGS (macOS-latest) | ||
| if: runner.os == 'macOS' | ||
| run : | | ||
| rm '/usr/local/bin/gfortran' | ||
| brew install automake jags | ||
| - name: Install dependencies | ||
| # Install Pandoc | ||
| - name: Setup Pandoc | ||
| uses: r-lib/actions/setup-pandoc@v2 | ||
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| # Install the package and its dependencies | ||
| - name: Install required packages | ||
| run: | | ||
| remotes::install_deps(dependencies = TRUE) | ||
| install.packages("pkgdown") | ||
| options(repos = c(CRAN = "https://cloud.r-project.org")) | ||
| install.packages('devtools') | ||
| install.packages('pkgdown') | ||
| install.packages(c('BayesFactor', 'RoBMA', 'runjags', 'rjags', 'rstan', 'scales', 'vdiffr', 'testthat', 'covr', 'pandoc')) | ||
| devtools::install() | ||
| shell: Rscript {0} | ||
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| - name: Install package | ||
| run: R CMD INSTALL . | ||
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| - name: Deploy package | ||
| run: | | ||
| git config --local user.email "[email protected]" | ||
| git config --local user.name "GitHub Actions" | ||
| Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE)' | ||
| Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE)' |
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