Add Getting Started section on plotting with {epicontacts}

[jamesmbaazam]

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]

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(Note that results may be inaccurate if you branched from an outdated version of the target branch.)

[jamesmbaazam]

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(Note that results may be inaccurate if you branched from an outdated version of the target branch.)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

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(Note that results may be inaccurate if you branched from an outdated version of the target branch.)

[github-actions]

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(Note that results may be inaccurate if you branched from an outdated version of the target branch.)

[jamesmbaazam]

@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.

[jamesmbaazam]

@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?

[joshwlambert]

I don't think the issue is with the code block highlighted here, but rather with the vignette yaml header.

I experienced similar issues getting the interactive {epicontacts} plotting to work in {simulist}. In the end, the solution that I chose was to use rmarkdown::html_vignette as the output rendering. https://github.com/epiverse-trace/simulist/pull/22/files#diff-6c0ddf0e8bb8afdcb174c0f67c09aabd60c69f62f0fa169d889119fe5600bef0

This however has some downsides. See this bullet point in the Design principles vignette in {simulist} where I explain what the limitations are and why I chose the options I did in order to get the interactive plotting to work correctly.

It's a tradeoff, I preferred the interactive plotting over the other vignette features for {simulist}, but you may decide differently depending on the importance of this code chunk.

If this info does not solve your issue let me know and I'd be happy to take another look.

[jamesmbaazam]

Thanks, Josh. It was indeed the output format. This worked for me. I'll assess the drawbacks and see if it's worth it.

[github-actions]

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.)

[github-actions]

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.)

[codecov-commenter]

Codecov Report

All modified and coverable lines are covered by tests ✅

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

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #256   +/-   ##
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  Coverage   99.03%   99.03%           
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  Files           8        8           
  Lines         729      729           
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  Hits          722      722           
  Misses          7        7           

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