vingette

[resteorts]

Is there a vignette regarding an example of how to use the simulator?

[aflaxman]

Hi Beka! Thanks for your interest in this project. You can find a "getting started" example here and a more authentic use of vivarium to model a disease moving through a human population here.

If you have questions as you go through these, please don't hesitate to ask.

I'm going close this issue for now, but please feel free to reopen!

[resteorts]

Hi, Abie:

You bet, and thanks for your fast response! I think maybe my question wasn’t well phrased and I’d be happy to take this to email if that would be more helpful. Please just let me know where you prefer to have questions go to.

I was wondering if there is a more traditional vignette (or rather python file that I can run that will generate all the synthetic data files). It’s possible that I’m just missing this and it would be helpful to understand where the main file is to run this as I’m not easily able to find it. Please let me know if anything is unclear or perhaps if this isn’t available yet?

Thanks and have a great day!

Beka

On Mar 16, 2023, at 12:30 PM, Abraham Flaxman @.**@.>> wrote:

Hi Beka! Thanks for your interest in this project. You can find a "getting started" example herehttps://urldefense.com/v3/__https://vivarium.readthedocs.io/en/latest/tutorials/boids.html__;!!OToaGQ!s0YnfMopIDnVVws9PINzYQJL1_IDjMJB_SU6gU5aYaw4rzMq9txVX5Y2mX4r_iR5Y0KACt_WBOP9ZKTJ37LDvNsa-g$ and a more authentic use of vivarium to model a disease moving through a human population herehttps://urldefense.com/v3/__https://vivarium.readthedocs.io/en/latest/tutorials/disease_model.html__;!!OToaGQ!s0YnfMopIDnVVws9PINzYQJL1_IDjMJB_SU6gU5aYaw4rzMq9txVX5Y2mX4r_iR5Y0KACt_WBOP9ZKTJ37LCBuqvrA$.

If you have questions as you go through these, please don't hesitate to ask.

I'm going close this issue for now, but please feel free to reopen!

— Reply to this email directly, view it on GitHubhttps://urldefense.com/v3/__https://github.com/ihmeuw/vivarium/issues/288*issuecomment-1472307783__;Iw!!OToaGQ!s0YnfMopIDnVVws9PINzYQJL1_IDjMJB_SU6gU5aYaw4rzMq9txVX5Y2mX4r_iR5Y0KACt_WBOP9ZKTJ37K_Fgz5vQ$, or unsubscribehttps://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/ABE6NGXFYANFOZBPCWWK5FLW4M54DANCNFSM6AAAAAAV4HSN2I__;!!OToaGQ!s0YnfMopIDnVVws9PINzYQJL1_IDjMJB_SU6gU5aYaw4rzMq9txVX5Y2mX4r_iR5Y0KACt_WBOP9ZKTJ37IkCe2ssQ$. You are receiving this because you authored the thread.Message ID: @.***>

[aflaxman]

We can continue here, in case it is helpful to someone else in the future, but let's move to email or even more real-time communication if things get complicated.

I bet you are interested in a particular use of the vivarium simulation framework that we have been making to simulate data for testing PRL algorithms! I might have sent you a link to the documentation before, but the python code that implements the model is in a different GitHub repo: https://github.com/ihmeuw/vivarium_census_prl_synth_pop/

Unfortunately, I don't think it is in a state that is runnable outside of the IHME cluster currently... our practice has been to develop the code in the open but not move the "artifact" of input data to an openly accessible location until we have finished a project.

This might be TMI, since I'm not even totally sure that this is the vivarium application you are after, but in case it is relevant, we are also developing a python package that will take the output of this sim and use it as input for generating appropriately noisy data for testing PRL algorithms. It is also not-yet-usable, but you can see what we are working on here: https://github.com/ihmeuw/pseudopeople