update to pomp 2 syntax #89

	name: Build and Deploy RMarkdown Website
	on:
	workflow_dispatch:
	push:
	branches: main
	pull_request:
	branches: main

	permissions:
	contents: write

	jobs:
	build-and-deploy:
	runs-on: ubuntu-20.04
	steps:
	- uses: actions/checkout@v2

	- uses: r-lib/actions/setup-pandoc@v1

	- uses: r-lib/actions/setup-r@v1
	with:
	install-r: false
	use-public-rspm: true

	- name: Install R system requirements
	run: \|
	sudo apt-get update
	sudo apt-get install libcurl4-openssl-dev libnetcdf-dev

	- name: Install R dependencies
	env:
	GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
	run: \|
	install.packages(c("remotes", "rmarkdown", "rbi", "rbi.helpers", "pomp"))
	remotes::install_github("sbfnk/fitR", dependencies = TRUE)
	shell: Rscript {0}

	- name: Render Site
	run: Rscript -e "rmarkdown::render_site(input = 'Rmd', encoding = 'UTF-8')"

	- name: Deploy 🚀
	id: deployment
	uses: JamesIves/github-pages-deploy-action@v4
	with:
	folder: Rmd/_site
	clean: false

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