epiverse-trace / epiverse-trace/tutorials-late

Episode suggestion: advanced content on editing models

Open
#55 0 comments 0 reactions 0 assignees View on GitHub
Dominant language
R
Stars
2
Forks
5
Avg merge
4m
Merged PRs (30d)
2

Description

As we build up [options for easier-to-edit {odin} versions](https://github.com/epiverse-trace/epidemics/issues/254) of the scenarios in {epidemics}, it would eventually be useful to have an advanced episode for learners who'd like to tweak the models (as this is a request we get from many who interact with {epidemics}. Note this {odin} option wouldn't change any of the other tutorials, as `model_default` would keep the same inputs and outputs. The only difference would be the model code it points to, and a nicer interface to make tweaks and recompile the mnodel.

In particular, we've narrowed down the conceptual list of potential model edits in this [walkthrough for {epidemics}](https://epiverse-trace.github.io/epidemics/articles/developer-walkthrough.html#adding-or-removing-model-parameters). This could be a useful breakdown for learners, to show many changes are actually just the same thing from a conceptual point of view.

Here's the list of what we thought would cover most things people would need out of a tweaked model:
- Adding or removing model parameters. E.g. adding a uniform, age-independent, background mortality rate that is unrelated to the epidemic itself, or reparameterising $R_0$ and $beta$ inside model equations.
- Modifying compartmental flows without changing the actual compartments. E.g. adding births/deaths, immigration, zoonosis, waning immunity
- Modifying which parameters can be time dependent. E.g. change in infectious period with better isolation or treatment.
- Group-specific infection parameters. E.g. vaccination targeted at certain ages.
- Adding epidemiological compartments. E.g. more complex vaccination or natural history.
- Changing vaccination rates over time. E.g. catch up or pulse vaccination - this was a special category because need to make sure numbers add up sensibly, and vaccines available can be tracked (i.e. when they're used up, can't vaccinate more).

Contributor guide

Open the contributing guide

Assessment

This issue has not been assessed yet.

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.