# Case study on disease transmission models in Stan

**URL:** <https://discourse.mc-stan.org/t/case-study-on-disease-transmission-models-in-stan/14867>\
**Category:** General\
**Created:** [May 5, 2020, 1:27pm UTC](https://discourse.mc-stan.org/t/case-study-on-disease-transmission-models-in-stan/14867 "2020-05-05T13:27:35Z")\
**Posts on this page:** 6\
**Page:** 1

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**Author:** ![charlesm93](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.mc-stan.org/charlesm93/32/4634_2.png) [@charlesm93](https://discourse.mc-stan.org/u/charlesm93)\
**Post date:** [May 5, 2020, 1:27pm UTC](https://discourse.mc-stan.org/t/case-study-on-disease-transmission-models-in-stan/14867/1 "2020-05-05T13:27:35Z")

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Following the instructions on [https://mc-stan.org/users/documentation/case-studies](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](https://mc-stan.org/users/documentation/case-studies/boarding_school_case_study.html)!

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**Author:** ![bbbales2](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.mc-stan.org/bbbales2/32/77_2.png) [@bbbales2](https://discourse.mc-stan.org/u/bbbales2)\
**Post date:** [May 5, 2020, 2:12pm UTC](https://discourse.mc-stan.org/t/case-study-on-disease-transmission-models-in-stan/14867/2 "2020-05-05T14:12:33Z")

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I think the case studies live in folders here: [https://github.com/stan-dev/example-models/tree/master/knitr](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.

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**Author:** ![mitzimorris](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.mc-stan.org/mitzimorris/32/29_2.png) [@mitzimorris](https://discourse.mc-stan.org/u/mitzimorris)\
**Post date:** [May 5, 2020, 4:39pm UTC](https://discourse.mc-stan.org/t/case-study-on-disease-transmission-models-in-stan/14867/3 "2020-05-05T16:39:14Z")

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> I think the case studies live in folders here: [https://github.com/stan-dev/example-models/tree/master/knitr](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](https://github.com/stan-dev/stan-dev.github.io/wiki/Using-the-Jeykll-Based-Website) for instructions on changing and testing the website.

Case studies listings follow this template:

```no-highlight
## 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](https://github.com/stan-dev/stan-dev.github.io/wiki/Adding-a-case-study-to-the-Stan-Case-Studies-listing)

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**Author:** ![saudiwin](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.mc-stan.org/saudiwin/32/1137_2.png) [@saudiwin](https://discourse.mc-stan.org/u/saudiwin)\
**Post date:** [May 6, 2020, 4:04am UTC](https://discourse.mc-stan.org/t/case-study-on-disease-transmission-models-in-stan/14867/4 "2020-05-06T04:04:34Z")

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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?).

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**Author:** ![charlesm93](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.mc-stan.org/charlesm93/32/4634_2.png) [@charlesm93](https://discourse.mc-stan.org/u/charlesm93)\
**Post date:** [May 6, 2020, 7:33pm UTC](https://discourse.mc-stan.org/t/case-study-on-disease-transmission-models-in-stan/14867/5 "2020-05-06T19:33:17Z")

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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](https://mc-stan.org/users/documentation/case-studies.html). We (the authors) hope this will be helpful to modelers, and welcome feedback and questions.

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**Author:** ![charlesm93](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.mc-stan.org/charlesm93/32/4634_2.png) [@charlesm93](https://discourse.mc-stan.org/u/charlesm93)\
**Post date:** [May 6, 2020, 7:40pm UTC](https://discourse.mc-stan.org/t/case-study-on-disease-transmission-models-in-stan/14867/6 "2020-05-06T19:40:56Z")

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Yeah, that appendix is work in progress :P