Case study on disease transmission models in Stan

General
1

Following the instructions on https://mc-stan.org/users/documentation/case-studies, I’m posting on the Stan forum about a new case study on ODE based models for disease transmissions.

Should we share the code and html file on this thread or submit a PR to the case studies page?

EDIT: here’s the link to the posted case study!

6 Likes
2

I think the case studies live in folders here: https://github.com/stan-dev/example-models/tree/master/knitr, so make a pull request to put it there.

I’m not sure how they appear on the website. That would be something else. @mitzimorris knows this process.

3

I think the case studies live in folders here: https://github.com/stan-dev/example-models/tree/master/knitr, so make a pull request to put it there.

correct - example-models repo, folder knitr.

the website lives in repo stan-dev.github.io

the listing page for all case studies is page: users/documentation/case-studies.md
the folder containing the case studies html is users/documentation/case-studies

see Using the Jeykll Based Website · stan-dev/stan-dev.github.io Wiki · GitHub for instructions on changing and testing the website.

Case studies listings follow this template:

## title

<small> abstract
</small>

[View](case-studies/<your_case_study>l.html) <span class="note">(HTML)</span>

Author
: you

Keywords
: choice, keywords

Source Repository
: [example-models/knitr/your-study](https://github.com/stan-dev/example-models/tree/master/knitr/your-study)
<span class="note">(GitHub)</span>

Dependencies
: <tt style="font-size: 90%">etc</tt>

License
:  BSD (3 clause), CC-BY

OK, added the website info to the website wiki: Adding a case study to the Stan Case Studies listing · stan-dev/stan-dev.github.io Wiki · GitHub

1 Like
4

Excited to read it! If you can save the world/tell us how to stop the coronavirus as well, that would be great (maybe an appendix?).

5

Thank you for the detailed pointers @mitzimorris.

The case study is up on Stan’s case study webpage. See Bayesian Workflow for disease transmission modeling in Stan. We (the authors) hope this will be helpful to modelers, and welcome feedback and questions.

4 Likes
6

Yeah, that appendix is work in progress :P

1 Like