Research Compendium Template

This is a research compendium template geared towards producing a manuscript output as a Word document reproducibly using the targets package for workflow management. See the targets documentation for more information on how to program analyses in this style. I’ve found that writing paper.Rmd using RStudio’s visual markdown editor and automatic text wrapping (with each sentence as a new line) works best for version control and collaboration with git and GitHub. The visual editor also integrates seamlessly with Zotero for adding in-text citations and bibliographies. The renv package my also be useful for collaboration to keep package version synced across collaborators. Before submitting the manuscript, I like to archive my GitHub repository with Zenodo and add a DOI badge to the README, and a link to the Zenodo archive to the Data Availability Statement. In the review directory, you’ll find my preferred way of structuring response to reviewers complete with the ability to cross-reference responses to avoid repeating yourself.

GithHub Actions This template also uses GitHub actions to automatically render a .html version of the manuscript every time an edit to docs/paper.Rmd is made. If GitHub pages are active, then the rendered draft is viewable at <username>.github.io/<repository name>/paper.html. The workflow for this lives in .github/workflows/build-manuscript.yaml and can be disabled on GitHub in the “Actions” tab.

Readme text for your repository below:

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This repository contains data and code for a manuscript by ______ written for submission to ______ tentatively titled: _____.

The most recent draft of the manuscript is available here.

Reproducibility

This research compendium has been developed using the statistical programming language R. To work with the compendium, you will need installed on your computer the R software itself and RStudio Desktop.

You can download the compendium as a zip file from from this URL: master.zip.

To run the compendium and reproduce all outputs:

• Open the project in RStudio by double-clicking the .Rproj file.
• Install packages listed in packages.R (if this compendium uses renv, this may happen automatically or with renv::restore()).
• Run scripts in /R/ in numerical order.
• Knit /doc/paper.Rmd to produce output

Additional instructions if project uses targets:

• Install the targets package.
• Run targets::tar_make() or targets::tar_make_clustermq() from the R console to run all code and produce all outputs.

NOTE: the GitHub actions in .github/workflows/build-manuscript.yaml will not work with a targets project. Consider targets::tar_github_actions() as an alternative