update tutorial with epidemics 0.2.0

[avallecam]

Fix #10 Fix #3

This PR updates the code API after the latest epidemics release.

• This edits the code and text mentioning functions and arguments.
• This also updates the renv. lock file
• We also removed the intro episode. We expect that the automatic update next month fix the dependencies of this episode.
• We kept one vaccination hint hidden to later evaluate whether to #12

how to review?

• To quickly diagnose the content, you can read online the knitted content of this PR in branch md-output-PR-11
  • simulating-transmission
  • model-choices
  • modeling-interventions
  • compare-interventions
• To render this locally, follow the steps in the reviewer role section of the contributing.md file. If local rendering doesn't work, please, report them in Issues.

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:robot: 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

:mag: Inspect the changes: https://github.com/epiverse-trace/tutorials-late/compare/md-outputs..md-outputs-PR-11

The following changes were observed in the rendered markdown documents:

 compare-interventions.md                           |   35 +-
 config.yaml (gone)                                 |   84 -
 ...e-interventions-rendered-unnamed-chunk-5-1.png} |  Bin
 ...roduction-rendered-unnamed-chunk-5-1.png (gone) |  Bin 51096 -> 0 bytes
 fig/model-choices-rendered-unnamed-chunk-3-1.png   |  Bin 13491 -> 13005 bytes
 fig/model-choices-rendered-unnamed-chunk-4-1.png   |  Bin 9002 -> 9146 bytes
 ...ing-interventions-rendered-plot_vaccinate-1.png |  Bin 39125 -> 38911 bytes
 fig/simulating-transmission-rendered-diagram-1.png |  Bin 18643 -> 18615 bytes
 fig/simulating-transmission-rendered-plot-1.png    |  Bin 17491 -> 16768 bytes
 introduction.md (gone)                             |  211 --
 md5sum.txt                                         |   29 +-
 model-choices.md                                   |   30 +-
 modelling-interventions.md                         |   48 +-
 renv.lock (gone)                                   | 2201 --------------------
 simulating-transmission.md                         |   37 +-
 15 files changed, 90 insertions(+), 2585 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. This output provides a way for you to inspect the output in a diff-friendly manner so that it's easy to see the changes that occur due to new software versions or randomisation.

:stopwatch: Updated at 2024-03-22 17:35:26 +0000

[avallecam]

@pratikunterwegs can we have your review for these specific changes?

[avallecam]

all edits are now finished - just fixed an overlooked error in https://github.com/epiverse-trace/tutorials-late/pull/11/commits/a005aa69119d621c73d040beb6aff37dc198a38a

[avallecam]

Thanks for the review and comments @pratikunterwegs Appropriate edits suggestions, commits were added to each. Replies to your questions:

The whole file has been deleted - where does the introduction live now?

I mixed issues loosing the specific scope of this! This is also fixing #3 more in https://github.com/epiverse-trace/tutorials-late/pull/11#discussion_r1535770100

A few lines above this is called an SEIR model, would be good to change that.

This is used in the context of non-pharma interventions or to refer to the SEIR definition in first episode. Full reply in https://github.com/epiverse-trace/tutorials-late/pull/11#discussion_r1535900891

I'll merge this after passing checks.