add measles outbreak example

[Degoot-AM]

This PR

1. Adds an introduction to mathematical epidemiology using measles outbreak in Burkina Faso using {epidemics}.
2. use r_eff from {finalsize} as a quick first pass to estimate transmission potential from vaccine coverage.
3. This document goes under more tab as an additional information for learners.

[github-actions]

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Rendered Changes

🔍 Inspect the changes: https://github.com/epiverse-trace/tutorials-late/compare/md-outputs..md-outputs-PR-51

The following changes were observed in the rendered markdown documents:

 BF_measles.md (new)                                | 940 +++++++++++++++++++++
 compare-interventions.md                           |   4 +-
 ...F_measles-rendered-unnamed-chunk-10-1.png (new) | Bin 0 -> 67684 bytes
 ...F_measles-rendered-unnamed-chunk-11-1.png (new) | Bin 0 -> 50927 bytes
 ...BF_measles-rendered-unnamed-chunk-2-1.png (new) | Bin 0 -> 28872 bytes
 ...BF_measles-rendered-unnamed-chunk-6-1.png (new) | Bin 0 -> 64815 bytes
 ...BF_measles-rendered-unnamed-chunk-9-1.png (new) | Bin 0 -> 56781 bytes
 fig/model-choices-rendered-unnamed-chunk-3-1.png   | Bin 19296 -> 14612 bytes
 fig/model-choices-rendered-unnamed-chunk-4-1.png   | Bin 9209 -> 9209 bytes
 fig/t0.drawio.png (new)                            | Bin 0 -> 27089 bytes
 fig/t1.drawio.png (new)                            | Bin 0 -> 25467 bytes
 fig/t2.drawio.png (new)                            | Bin 0 -> 29583 bytes
 fig/t3.drawio.png (new)                            | Bin 0 -> 29649 bytes
 md5sum.txt                                         |  29 +-
 14 files changed, 957 insertions(+), 16 deletions(-)

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⏱️ Updated at 2024-11-20 20:38:34 +0000

[avallecam]

thanks for contributing! I am doing some local edits to make this contribution a Rmd rendered file

[avallecam]

I finished with the edits required to clean this PR. Now we have an Rmd file with four figures. Next week I'll provide my feedback matching this case study and the way we can use it in the training.

[avallecam]

thanks @Degoot-AM for adding this content! I liked the approach of dosifying the content by doing first a well-mixed population model to introduce the rates, population, and initial conditions, and leave to a second stage the addition of the contact matrix.

There are two major request to change that I added as line edit suggestions are:

• change "rate" to "contact" for the usage of a <contacts_intervention> class, and add a reduction rate per age strata
• fix the "nu" parameter to vaccination rate, instead of vaccine efficacy, which is not how this argument is defined in the function.

[avallecam]

one additional minor edit to keep homogeneity across materials. we are using alpha instead of omega