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Package skeleton
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‎.Rbuildignore

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^scripts$
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^Makefile$
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^README\.Rmd$
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^\.travis\.yml$
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^docs$
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^\.lintr$
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^tests/testthat/.*\.o$
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^tests/testthat/.*\.so$
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^tests/testthat/.*\.dll$
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\.dylib$
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^appveyor\.yml$
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^docker$
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^\.hadolint\.yaml$
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\.valgrind_ignore$
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^scripts$
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\.gcda$
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\.gcno$
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^pkgdown$
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^LICENSE\.md$
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^buildkite$
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^\.covrignore$
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^\.github$
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\.*gcov$

‎.github/.gitignore

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*.html

‎.github/workflows/R-CMD-check.yaml

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# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
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# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
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on:
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push:
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branches: [main, master]
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pull_request:
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branches: [main, 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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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: macos-latest, r: 'release'}
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- {os: windows-latest, r: 'release'}
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- {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'}
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- {os: ubuntu-latest, r: 'release'}
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- {os: ubuntu-latest, r: 'oldrel-1'}
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env:
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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R_KEEP_PKG_SOURCE: yes
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steps:
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- uses: actions/checkout@v4
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- uses: r-lib/actions/setup-pandoc@v2
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- uses: r-lib/actions/setup-r@v2
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with:
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r-version: ${{ matrix.config.r }}
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http-user-agent: ${{ matrix.config.http-user-agent }}
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use-public-rspm: true
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- uses: r-lib/actions/setup-r-dependencies@v2
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with:
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extra-packages: any::rcmdcheck
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needs: check
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- uses: r-lib/actions/check-r-package@v2
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with:
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upload-snapshots: true

‎.github/workflows/pkgdown.yaml

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# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
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# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
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on:
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push:
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branches: [main, master]
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pull_request:
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branches: [main, master]
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release:
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types: [published]
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workflow_dispatch:
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name: pkgdown
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jobs:
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pkgdown:
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runs-on: ubuntu-latest
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# Only restrict concurrency for non-PR jobs
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concurrency:
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group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
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env:
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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permissions:
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contents: write
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steps:
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- uses: actions/checkout@v4
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- uses: r-lib/actions/setup-pandoc@v2
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- uses: r-lib/actions/setup-r@v2
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with:
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use-public-rspm: true
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- uses: r-lib/actions/setup-r-dependencies@v2
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with:
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extra-packages: any::pkgdown, local::.
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needs: website
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- name: Build site
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run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
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shell: Rscript {0}
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- name: Deploy to GitHub pages 🚀
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if: github.event_name != 'pull_request'
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uses: JamesIves/[email protected]
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with:
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clean: false
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branch: gh-pages
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folder: docs

‎.github/workflows/test-coverage.yaml

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# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
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# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
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on:
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push:
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branches: [main, master]
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pull_request:
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branches: [main, master]
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name: test-coverage
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jobs:
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test-coverage:
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runs-on: ubuntu-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@v4
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- uses: r-lib/actions/setup-r@v2
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with:
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use-public-rspm: true
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- uses: r-lib/actions/setup-r-dependencies@v2
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with:
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extra-packages: any::covr
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needs: coverage
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- name: Test coverage
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run: |
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covr::codecov(
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quiet = FALSE,
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clean = FALSE,
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install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
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)
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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: |
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## --------------------------------------------------------------------
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find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true
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shell: bash
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- name: Upload test results
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if: failure()
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uses: actions/upload-artifact@v4
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with:
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name: coverage-test-failures
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path: ${{ runner.temp }}/package

‎.gitignore

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.Rproj.user
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.Rhistory
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.RData
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.Ruserdata
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.DS_Store
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TODO.md
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docs
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*.o
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*.so
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*.dll
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*.dylib
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*.gcda
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*.gcno
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*.gcov
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.valgrind_ignore
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inst/doc
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pkgdown

‎DESCRIPTION

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Package: dust2
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Title: Next Generation dust
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Version: 0.1.0
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Authors@R: c(person("Rich", "FitzJohn", role = c("aut", "cre"),
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email = "[email protected]"),
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person("Imperial College of Science, Technology and Medicine",
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role = "cph"))
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Description: Experimental sources for the next generation of dust,
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which will properly adopt the particle filter, have support for
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partial parameter updates, support for multiple parameter sets and
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hopefully better GPU/MPI support.
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License: MIT + file LICENSE
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Encoding: UTF-8
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Roxygen: list(markdown = TRUE)
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RoxygenNote: 7.3.1
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Language: en-GB
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Config/testthat/edition: 3
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URL: https://github.com/mrc-ide/dust2
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BugReports: https://github.com/mrc-ide/dust2/issues
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Suggests:
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testthat (>= 3.0.0)

‎LICENSE

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YEAR: 2024
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COPYRIGHT HOLDER: Imperial College of Science, Technology and Medicine

‎Makefile

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PACKAGE := $(shell grep '^Package:' DESCRIPTION | sed -E 's/^Package:[[:space:]]+//')
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RSCRIPT = Rscript --no-init-file
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all:
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${RSCRIPT} -e 'pkgbuild::compile_dll()'
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test:
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${RSCRIPT} -e 'devtools::test()'
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roxygen:
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@mkdir -p man
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${RSCRIPT} -e "devtools::document()"
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install:
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R CMD INSTALL .
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build:
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R CMD build .
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README.md: README.Rmd
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Rscript -e 'devtools::load_all(); knitr::knit("README.Rmd")'
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sed -i.bak 's/[[:space:]]*$$//' README.md
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rm -f $@.bak
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check:
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_R_CHECK_CRAN_INCOMING_=FALSE make check_all
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check_all:
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${RSCRIPT} -e "rcmdcheck::rcmdcheck(args = c('--as-cran', '--no-manual'))"
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clean:
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rm -f src/*.o src/*.so src/*.gcda src/*.gcno src/*.gcov
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.PHONY: clean all test document install

‎NAMESPACE

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# Generated by roxygen2: do not edit by hand

‎R/util.R

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`%||%` <- function(x, y) { # nolint
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if (is.null(x)) y else x
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}

‎README.md

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# dust2
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<!-- badges: start -->
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[![Project Status: Concept – Minimal or no implementation has been done yet, or the repository is only intended to be a limited example, demo, or proof-of-concept.](https://www.repostatus.org/badges/latest/concept.svg)](https://www.repostatus.org/#concept)
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[![R-CMD-check](https://github.com/mrc-ide/dust2/actions/workflows/R-CMD-check.yaml/badge.svg?branch=main)](https://github.com/mrc-ide/dust2/actions/workflows/R-CMD-check.yaml)
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[![codecov.io](https://codecov.io/github/mrc-ide/dust2/coverage.svg?branch=main)](https://codecov.io/github/mrc-ide/dust2?branch=main)
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<!-- badges: end -->
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## Installation
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To install `dust2`:
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```r
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remotes::install_github("mrc-ide/dust2", upgrade = FALSE)
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```
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## License
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MIT © Imperial College of Science, Technology and Medicine

‎tests/testthat.R

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# This file is part of the standard setup for testthat.
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# It is recommended that you do not modify it.
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#
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# Where should you do additional test configuration?
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# Learn more about the roles of various files in:
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# * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
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# * https://testthat.r-lib.org/articles/special-files.html
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library(testthat)
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library(dust2)
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test_check("dust2")

‎tests/testthat/test-util.R

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test_that("null-or-value works", {
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expect_equal(1 %||% NULL, 1)
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expect_equal(1 %||% 2, 1)
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expect_equal(NULL %||% NULL, NULL)
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expect_equal(NULL %||% 2, 2)
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})

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