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‎.Rbuildignore‎

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^renv$
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^renv\.lock$
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^.*\.Rproj$
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^\.Rproj\.user$
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^LICENSE\.md$
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^CONTRIBUTING\.md$
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^docs$
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^images$
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^\.github$
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^\.lintr$
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^outputs$
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^rmarkdown$
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^CITATION\.cff$
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^run_rmarkdown\.sh$
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^inputs$
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^mock_paper\.md$

‎.Rprofile‎

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source("renv/activate.R")

‎.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]
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workflow_dispatch:
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inputs:
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os_choice:
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description: 'Operating system to run on'
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required: true
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default: 'all'
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type: choice
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options:
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- all
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- ubuntu
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- macos
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- windows
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name: R-CMD-check.yaml
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permissions: read-all
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jobs:
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setup-matrix:
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runs-on: ubuntu-latest
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outputs:
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matrix: ${{ steps.setup-matrix.outputs.matrix }}
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steps:
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- id: setup-matrix
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run: |
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if [[ "${{ github.event_name }}" == "push" || "${{ github.event.inputs.os_choice }}" == "all" ]]; then
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echo 'matrix={"config":[{"os":"macos-latest","r":"release"},{"os":"windows-latest","r":"release"},{"os":"ubuntu-latest","r":"release"}]}' >> $GITHUB_OUTPUT
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elif [[ "${{ github.event.inputs.os_choice }}" == "ubuntu" ]]; then
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echo 'matrix={"config":[{"os":"ubuntu-latest","r":"release"}]}' >> $GITHUB_OUTPUT
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elif [[ "${{ github.event.inputs.os_choice }}" == "macos" ]]; then
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echo 'matrix={"config":[{"os":"macos-latest","r":"release"}]}' >> $GITHUB_OUTPUT
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elif [[ "${{ github.event.inputs.os_choice }}" == "windows" ]]; then
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echo 'matrix={"config":[{"os":"windows-latest","r":"release"}]}' >> $GITHUB_OUTPUT
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fi
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R-CMD-check:
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needs: setup-matrix
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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: ${{ fromJson(needs.setup-matrix.outputs.matrix) }}
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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
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build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

‎.github/workflows/lint.yaml‎

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# This file will lint the specified files/directories.
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# Workflow adapted from https://github.com/r-lib/actions/tree/v2/examples
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on:
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push:
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branches: [main]
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workflow_dispatch:
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name: lint
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permissions: read-all
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jobs:
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lint:
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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::lintr, any::cyclocomp, local::.
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needs: lint
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- name: Lint package
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run: lintr::lint_package()
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shell: Rscript {0}
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env:
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LINTR_ERROR_ON_LINT: true
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- name: Lint rmarkdown
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run: lintr::lint_dir("rmarkdown")
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shell: Rscript {0}
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env:
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LINTR_ERROR_ON_LINT: true

‎.gitignore‎

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# History files
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.Rhistory
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.Rapp.history
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# Session Data files
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.RData
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.RDataTmp
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# User-specific files
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.Ruserdata
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# Example code in package build process
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*-Ex.R
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# Output files from R CMD build
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/*.tar.gz
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# Output files from R CMD check
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/*.Rcheck/
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# RStudio files
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.Rproj.user/
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# produced vignettes
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vignettes/*.html
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vignettes/*.pdf
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# OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3
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.httr-oauth
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# knitr and R markdown default cache directories
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*_cache/
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/cache/
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# Temporary files created by R markdown
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*.utf8.md
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*.knit.md
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# R Environment Variables
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.Renviron
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# pkgdown site
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docs/
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# translation temp files
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po/*~
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# RStudio Connect folder
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rsconnect/

‎.lintr‎

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linters: all_linters(packages = "lintr")
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encoding: "UTF-8"
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exclusions: list("renv", "packrat", "tests/testthat.R")

‎CITATION.cff‎

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# This CITATION.cff file was generated with cffinit.
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# Visit https://bit.ly/cffinit to generate yours today!
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cff-version: 1.2.0
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title: >-
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R DES RAP Template
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message: >-
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If you use this software, please cite it using the
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metadata from this file.
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type: software
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authors:
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- given-names: Amy
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family-names: Heather
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email: a.heather2@exeter.ac.uk
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affiliation: University of Exeter
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orcid: 'https://orcid.org/0000-0002-6596-3479'
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repository-code: >-
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https://github.com/pythonhealthdatascience/rdesrap_mms
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abstract: >-
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A template for creating discrete-event simulation (DES) models in R
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within a reproducible analytical pipeline (RAP).
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version: 0.4.0
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date-released: '2025-06-04'

‎CONTRIBUTING.md‎

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# Contributing
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🎉 Thank you for checking out our project! 🎉
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This file contains guidelines on how to get in touch with us and potentially contribute towards this repository.
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## Email
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You can contact the researchers on this project using the provided email addresses in `CITATION.cff`.
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## Suggesting changes
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If you spot an issue, you are welcome to raise this either by:
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* Using **GitHub Issues**.
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* **Forking** the repository, make your changes and submit a pull request for review.

‎DESCRIPTION‎

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Package: simulation
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Type: Package
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Title: Simulation
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Version: 0.1.0
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Authors@R: c(
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person(
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"Amy", "Heather",
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email = "a.heather2@exeter.ac.uk",
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role = c("aut", "cre")
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)
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)
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URL: https://github.com/pythonhealthdatascience/rdesrap_mms
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Description: Template reproducible analytical pipeline (RAP) for simple R
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discrete-event simulation (DES) model.
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License: MIT + file LICENSE
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Encoding: UTF-8
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LazyData: true
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RoxygenNote: 7.3.2
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Imports:
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simmer,
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magrittr,
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dplyr,
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purrr,
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rlang,
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tidyr,
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tidyselect,
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future,
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future.apply,
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ggplot2,
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tibble,
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gridExtra,
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R6
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Suggests:
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testthat (>= 3.0.0),
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patrick,
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lintr,
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devtools,
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xtable,
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data.table,
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mockery,
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fitdistrplus,
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lubridate,
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plotly
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Config/testthat/edition: 3

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