add reference paper for the reproduction number calculation #68

	# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
	# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
	on:
	workflow_dispatch:
	pull_request:
	branches: [main, master]
	paths:
	- '**.R'
	- '**.Rmd'
	- '**/.lintr'
	- '**/.lintr.R'

	name: lint-changed-files

	concurrency:
	group: ${{ github.workflow }}-${{ github.ref }}
	cancel-in-progress: true

	jobs:
	lint-changed-files:
	runs-on: ubuntu-latest
	env:
	GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
	steps:
	- uses: actions/checkout@v4

	- uses: r-lib/actions/setup-r@v2
	with:
	use-public-rspm: true

	- uses: r-lib/actions/setup-r-dependencies@v2
	with:
	extra-packages: \|
	any::gh
	any::lintr
	any::purrr
	epiverse-trace/etdev
	needs: check

	- name: Install package
	run: R CMD INSTALL .

	- name: Extract and lint files changed by this PR
	run: \|
	files <- gh::gh("/repos/${{ github.repository }}/pulls/${{ github.event.pull_request.number }}/files")
	changed_files <- purrr::map_chr(files, "filename")
	all_files <- list.files(recursive = TRUE)
	exclusions_list <- as.list(setdiff(all_files, changed_files))
	lintr::lint_package(exclusions = exclusions_list)
	shell: Rscript {0}
	env:
	LINTR_ERROR_ON_LINT: true

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