use epicontacts::get_degree() to replace wrangling steps from epicontacts to fitdistrplus

[avallecam]

This aims to simply the epicontacts to fitdistrplus connection, as discussed in epiverse-trace/superspreading#121 (comment)

Also, fix #170 to use only_linelist = TRUE to count the secondary cases from observed infections without onward transmission (infectees).

This also edits some text to define graph concepts and facilitate readability in unrelated sections.

---

Update:

Fix #184

[github-actions]

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🤖 This automated message can help you check the rendered files in your submission for clarity. If you have any questions, please feel free to open an issue in {sandpaper}.

If you have files that automatically render output (e.g. R Markdown), then you should check for the following:

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Rendered Changes

🔍 Inspect the changes: https://github.com/epiverse-trace/tutorials-middle/compare/md-outputs..md-outputs-PR-169

The following changes were observed in the rendered markdown documents:

 ...eading-estimate-rendered-unnamed-chunk-10-1.png | Bin 17026 -> 9096 bytes
 ...-estimate-rendered-unnamed-chunk-13-1.png (new) | Bin 0 -> 19283 bytes
 ...reading-estimate-rendered-unnamed-chunk-4-1.png | Bin 6053403 -> 5983697 bytes
 ...g-estimate-rendered-unnamed-chunk-8-1.png (new) | Bin 0 -> 9426 bytes
 ...reading-estimate-rendered-unnamed-chunk-9-1.png | Bin 9426 -> 17026 bytes
 md5sum.txt                                         |   2 +-
 network.html                                       |   6 +-
 superspreading-estimate.md                         | 183 ++++++++++++++-------
 webshot.png                                        | Bin 6053403 -> 5983697 bytes
 9 files changed, 125 insertions(+), 66 deletions(-)

What does this mean?

If you have source files that require output and figures to be generated (e.g. R Markdown), then it is important to make sure the generated figures and output are reproducible.

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⏱️ Updated at 2025-05-01 21:04:42 +0000

[avallecam]

minor edits

[joshwlambert]

Nice work @avallecam! I read through the .Rmd file changes and everything looks good. I've left a few comments on the file. I haven't rendered the tutorial to see how it looks as a web page but happy to take a look once this is merged and live and I'll open an issue if I spot anything that needs changing/fixing.

[avallecam]

thanks @joshwlambert. Could you take a look at the edits in response to your questions?

[joshwlambert]

@avallecam I've read through the responses and all of your proposed updates look good to me. I don't have any further comments so please feel free to merge when you're ready.

Nice work on putting this together; I think this comprehensively covers the discussions we had around epiverse-trace/superspreading#121.