Create Hosp Only Model from cdcgov/wastewater-informed-covid-forecasting

[damonbayer]

This PR recreates "Model 2" from the wastewater-informed-covid-forecasting project. The model is described here. Stan code for the model is here.

The tutorial demonstrates how to use the model with stan_data generated in the wastewater-informed-covid-forecasting project. As such, recreating any analysis from that project should be relatively straightforward.

Closes #174.
Closes #13.

[codecov]

Codecov Report

Attention: Patch coverage is 21.73913% with 54 lines in your changes missing coverage. Please review.

Project coverage is 88.12%. Comparing base (bf09a37) to head (22bc13e).

Files	Patch %	Lines
model/src/pyrenew/model/hosp_only_ww_model.py	19.40%	54 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #313      +/-   ##
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- Coverage   93.17%   88.12%   -5.06%     
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  Files          39       40       +1     
  Lines         909      977      +68     
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+ Hits          847      861      +14     
- Misses         62      116      +54     

Flag	Coverage Δ
unittests	88.12% <21.73%> (-5.06%)	⬇️

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[damonbayer]

I think this is ready to be handed off until I am able to work on it again. Things are a bit rough, but I am hoping what I have provided is sufficient for @sbidari to begin validating the model (which I have not done at all). I would accept PR's against this branch, should someone want to make changes here. It is certainly not ready for merging to main.

[damonbayer]

Some notes

• If we want to include the stan_data files. They should go in the same place as the rest of the data and have convenience functions for loading them.
• RtWeeklyDiffProcess should probably not be used (@dylanhmorris can say more)
• There is some strange behavior where simulating from the prior predictive causes the posterior inference to fail.
• I copied variable names from the wastewater-informed-covid-forecasting model, which could probably be improved.

[damonbayer]

Migrated to https://github.com/CDCgov/pyrenew-covid-wastewater/. See CDCgov/pyrenew-covid-wastewater#3 & CDCgov/pyrenew-covid-wastewater#4