Add missing packages to renv

[joshwlambert]

This PR closes #90.

I have added the packages used in the transmissibility rmd documents as well as {episoap} to the renv::use() call in the skeleton document.

[Bisaloo]

Thanks for the report & PR!

I would like to avoid to include packages that are not directly used in the report in the citation. The underlying cause of this issue is that renv::dependencies() is used to identify dependencies and it will by default look at all files recursively in the current working directory. The best fix would be to find a way to just look at the main files and actually used child documents.

[Bisaloo]

The proper fix seems to be using grateful::cite_packages(output = "paragraph", out.dir = ".", pkgs = "Session") to only cite packages actually loaded in the session.

[joshwlambert]

@Bisaloo thanks for the fix. I've tested it and it seems to work well. I've made the update in the last commit.

[codecov-commenter]

Codecov Report

Merging #92 (f8b894a) into main (a913d79) will not change coverage.
The diff coverage is n/a.

❗ Current head f8b894a differs from pull request most recent head a676ae1. Consider uploading reports for the commit a676ae1 to get more accurate results

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  Lines          23       23           
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  Hits           17       17           
  Misses          6        6           

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[Bisaloo]

Thanks!