Update model function names

[amanda-minter]

Function names in {epidemics} are now model_X() following this PR

[github-actions]

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Thank you for your pull request 😃

🤖 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:

• 🎯 correct output
• 🖼️ correct figures
• ❓ new warnings
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Rendered Changes

🔍 Inspect the changes: https://github.com/epiverse-trace/tutorials/compare/md-outputs..md-outputs-PR-55

The following changes were observed in the rendered markdown documents:

 compare-interventions.md                        |   5 +--
 fig/simulating-transmission-rendered-plot-1.png | Bin 14897 -> 14781 bytes
 md5sum.txt                                      |   8 ++--
 model-choices.md                                |  16 ++++----
 modelling-interventions.md                      |  41 ++++---------------
 simulating-transmission.md                      |  50 +++++++-----------------
 6 files changed, 35 insertions(+), 85 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.

⏱️ Updated at 2023-11-09 13:33:19 +0000

[avallecam]

I will need more time to look into this. Possibly on Friday or next Monday. Does it work for you?

[amanda-minter]

Please take a look as soon as you can, this is high priority as it affects the live site examples and is a blocker for @CarmenTamayo to review the materials.

[avallecam]

Is the replacement of model_ebola_r instead of the model_ebola_cpp is coherent?

From the vignette, in the "Run epidemic model" subtitle:

We run the model using the function model_ebola_r(). While there is a C++ equivalent of this model, it was not found to be much faster than the R-only version, and is not made available to users.

[avallecam]

I did the step of "Update with rebase" here on GitHub. So if you need to make new changes locally, probably you need to pull content first? Let me know if this generates any issues.

[avallecam]

I see a "branch cannot be rebased due to conflicts". I'm afraid that if it is not possible to resolve conflicts, then we should "squash and merge" for this one, again.

I think I will avoid the "Update with rebase" option in GitHub, and we as developers can do the rebasing in the local repos only by running git pull origin main to rebase the feature branch. I'll update on this in a separate issue/PR.

[amanda-minter]

I see a "branch cannot be rebased due to conflicts". I'm afraid that if it is not possible to resolve conflicts, then we should "squash and merge" for this one, again.

I think I will avoid the "Update with rebase" option in GitHub, and we as developers can do the rebasing in the local repos only by running git pull origin main to rebase the feature branch. I'll update on this in a separate issue/PR.

Thanks Andree, I will have to squash and merge this PR