add read delays episode

[avallecam]

REMINDER: this is a Partial review. Before merging, redirect this to main

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This PR covers the pending review step in epiverse-trace/tutorials#104 (comment)

I'll appreciate your specific feedback providing a clear next step to remove, change or add content.

General questions to guide this are:

• Is the code used and terms explained as intended in the packages?
• What concepts can be left out if needed?

Specific questions:

• Should we adapt this concept map for each episode? #13
• Should we use partial words like "serial" instead of "serial interval" for epidist_db()?
• Should we add assessments on how to input {epiparameter} outputs to {i2extras} or {R0}? #14
• What other data sources can we use to increase the variability of countries or diseases shown?

How to review?

• follow the steps in the reviewer role section of the contributing.md file
• if local rendering doesn't work, please, report them in Issues.
• you can read online the knitted content of this PR in branch md-output-5 (drawback, figure captions not visible)
  • delays-reuse.md
  • delays-functions.md
  • delays-challenges.md

If we manage to render this locally, these two issues can be closed: epiverse-trace/tutorials#39 and epiverse-trace/tutorials#115

[avallecam]

Thank you for your review @joshwlambert! I managed to go through all your specific edit suggestions. I'll re-request your review for your assessment.

Here are replies to your questions.

have you checked that all the images you are using from papers are allowed to be used with only attribution?

added in epiverse-trace/tutorials#12 to solve after this PR

it would be good if you cited the papers mentioned using a bibliography and then provided a references section at the bottom of each page

sadly this is not possibly in the workbench (using bib files and @tags). I still do not know why, but I'll look forward to it. I'm already subscribed to some issues on it.

Getting an {EpiNow2} developer to also check code chunks that use that package would be good

I'll do that! I'll homogenize the code with quantify-transmission episode first.

[joshwlambert]

@avallecam thanks for the changes. Everything looks good. I've unresolved one comment that I believe needs to be double checked. I haven't re-read through all the material, I just looked at the commits that resolve the comments. Feel free to request another review on a future PR if you'd like me to take another thorough look through all the material.

If we manage to render this locally, these two issues can be closed: epiverse-trace/tutorials#39 and epiverse-trace/tutorials#115

I'm having no issues rendering this branch (add-read-delays) locally on macOS, if this helps to close these issues.