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epiverse-trace / epichains

[Under active development] Methods for simulating and analysing the sizes and lengths of infectious disease transmission chains from branching process models
https://epiverse-trace.github.io/epichains/
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Add Getting Started section on plotting with `{epicontacts}` #256

Closed jamesmbaazam closed 3 months ago

jamesmbaazam commented 3 months ago

This PR removes the plotting of aggregated cases section in the README and signposts to a new section in the Getting Started vignette on plotting individual chains with {epicontacts} and aggregated data with base R's plot function.

This PR is inspired by #255 but does not resolve it.

This PR contains unrelated .Rd files that were generated as a result of the renamed scripts in #253.

github-actions[bot] commented 3 months ago

This pull request:

Reach out on slack (#code-review or #help channels) to double check if there are base R alternatives to the new dependencies.

(Note that results may be inaccurate if you branched from an outdated version of the target branch.)

jamesmbaazam commented 3 months ago

This pull request:

  • Adds 7 new dependencies (direct and indirect)
  • Adds 2 new system dependencies
  • Removes 0 existing dependencies (direct and indirect)
  • Removes 0 existing system dependencies

Reach out on slack (#code-review or #help channels) to double check if there are base R alternatives to the new dependencies.

(Note that results may be inaccurate if you branched from an outdated version of the target branch.)

{epicontacts} is a well-maintained and widely used package for plotting transmission chains, so it was a necessary dependency to be taken on.

github-actions[bot] commented 3 months ago

This pull request:

Reach out on slack (#code-review or #help channels) to double check if there are base R alternatives to the new dependencies.

(Note that results may be inaccurate if you branched from an outdated version of the target branch.)

github-actions[bot] commented 3 months ago

This pull request:

Reach out on slack (#code-review or #help channels) to double check if there are base R alternatives to the new dependencies.

(Note that results may be inaccurate if you branched from an outdated version of the target branch.)

jamesmbaazam commented 3 months ago

~@joshwlambert The {epicontacts} plot is not rendering here using pkgdown::build_site() even though it works in my RStudio viewer when the vignette is rendered locally. Could you help me diagnose what might be wrong?~

Moved this comment to the appropriate code block.

github-actions[bot] commented 3 months ago

This pull request:

Reach out on slack (#code-review or #help channels) to double check if there are base R alternatives to the new dependencies.

(Note that results may be inaccurate if you branched from an outdated version of the target branch.)

github-actions[bot] commented 3 months ago

This pull request:

Reach out on slack (#code-review or #help channels) to double check if there are base R alternatives to the new dependencies.

(Note that results may be inaccurate if you branched from an outdated version of the target branch.)

codecov-commenter commented 3 months ago

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 99.03%. Comparing base (514feab) to head (448d4a1). Report is 128 commits behind head on main.

Additional details and impacted files ```diff @@ Coverage Diff @@ ## main #256 +/- ## ======================================= Coverage 99.03% 99.03% ======================================= Files 8 8 Lines 729 729 ======================================= Hits 722 722 Misses 7 7 ```

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