Formally addresses implementing the observed hospitalizations module #39

ghost · 2024-03-21T19:21:48Z

This PR contributes to the support of the hospital admissions signal. It includes the following:

Adds process.DeterministicProcess and observation.DeterministicObs to the corresponding modules. This can be used to wrap fixed quantities when needed.
Updates latent.HospitalAdmisions latent class to treat IHR, weekday effect, and p hosp as RandomVariable. Again, with the DeterministicObs these can be passed as fixed quantities (or inferred).
Adds more details to the hospitalization bit of the equations.md file, mostly pointing to the wastewater model.
Re-organizes the getting-started.qmd documentation to clarify.
latent.Infections now receives a RandomVariable for the generation interval. Before it was a fixed array.
Extends testing of model.Hospitalizations assessing that the new bits that can either do inference or reuse some of the new components (e.g., generation weekday effect).

* Create typos.yaml * Does this make it run on the whole repo? * remove trailing whitespace * Delete .github/workflows/typos.yaml trying to use typos in pre-commit instead * Update .pre-commit-config.yaml add typos to pre-commit * fixed typos

* Porting to quarto and adding a makefile entry to render them * Now it should be easier to deal with pre-commit under docs (only skipping cache) * Forgot to remove the pyrenew_demo notebook * Update model/Makefile * Fixing typos * Removes progress bar - adds doc/ figures - sets jupyter as kernel * Update model/docs/getting-started.qmd Co-authored-by: Dylan H. Morris <[email protected]> --------- Co-authored-by: Dylan H. Morris <[email protected]>

* Update description of discrete delay distributions * remove double desciption * minor eq fix * Update equations.md * update equations.md contents * Update equations.md * fix contents

dylanhmorris

Some comments @gvegayon

model/docs/getting-started.qmd

model/Makefile

model/src/pyrenew/process/deterministic.py

model/src/test/test_model_hospitalizations.py

Co-authored-by: Dylan H. Morris <[email protected]>

gvegayon · 2024-03-29T17:52:07Z

OK, @dylanhmorris. I've included the discussed changes. More improvements will be addressed/discussed during the next sprint!

dylanhmorris

High-level comment: we need to standardize language on "Hospital admissions" versus "Hospitalizations". I prefer the former ("Hospital admissions"), because there's less chance of confusion between incidence and prevalence.

model/docs/getting-started.qmd

gvegayon · 2024-03-29T18:15:23Z

High-level comment: we need to standardize language on "Hospital admissions" versus "Hospitalizations". I prefer the former ("Hospital admissions"), because there's less chance of confusion between incidence and prevalence.

Yes, I think it is worthwhile having a single issue to standardize language across the package. And have a document to summarize all.

gvegayon · 2024-04-02T19:07:30Z

Implemented requested changes in 33d9ed0 and 39c54c4. The two existing models do not have any default values now.

model/README.md

model/docs/getting-started.md

AFg6K7h4fhy2

Closely reviewed some files and skimmed those remaining. Generally speaking, the changes look fit for merge. The newest changes (regarding modified titles) look good as well.

dylanhmorris

A few final tweaks needed.

model/src/pyrenew/latent/hospitaladmissions.py

model/src/test/test_model_hospitalizations.py

Co-authored-by: Dylan H. Morris <[email protected]>

model/src/pyrenew/latent/hospitaladmissions.py

model/src/test/test_model_hospitalizations.py

Co-authored-by: Dylan H. Morris <[email protected]>

dylanhmorris

Still needs this: #39 (comment)

Also: the deploy step of the Sphinx build workflow should only run on main, otherwise we'll get failures like the one we have here. Update: will be addressed when #62 is merged.

Missed one thing that still needs changing

gvegayon

All suggestions have been addressed. This is a bit of a bottle neck for other issues, so I'll go ahead and merge it. Thanks for your input, @dylanhmorris!

Copy doc from wastewater model on Hosp Admin to class

d8cca42

ghost linked an issue Mar 21, 2024 that may be closed by this pull request

Observation model for hospital signals #16

Closed

4 tasks

George G Vega Yon and others added 12 commits March 26, 2024 15:00

Rename metaclasses to metaclass (#36)

80ed623

Create typos.yaml (#42)

b00687c

* Create typos.yaml * Does this make it run on the whole repo? * remove trailing whitespace * Delete .github/workflows/typos.yaml trying to use typos in pre-commit instead * Update .pre-commit-config.yaml add typos to pre-commit * fixed typos

Extra mathematical description of discrete delay distributions (#44)

db7e6dc

* Update description of discrete delay distributions * remove double desciption * minor eq fix * Update equations.md * update equations.md contents * Update equations.md * fix contents

Escaping tau

dee97dd

Adding deterministic obs and process to the equation

2bd532c

Correcting conflicts

3109000

Cleaning the quarto documents and working on the getting started diagram

a0e2d4d

Flexible IHR (now RandomVariable)

fe16c18

Adding weekday and phosp effect to latent hosp

ec4fc35

Adding back figures

cb6bf98

Adding a test for deterministic/stochastic weekday effect

a568921

ghost marked this pull request as ready for review March 27, 2024 22:45

ghost requested review from dylanhmorris, SamuelBrand1 and AFg6K7h4fhy2 March 27, 2024 22:46

dylanhmorris reviewed Mar 28, 2024

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gvegayon and others added 5 commits March 28, 2024 12:18

Typo

e6a63b4

Co-authored-by: Dylan H. Morris <[email protected]>

Correcting tests (class name) and improving readme a bit

2a7151e

Adding deterministic module (midway, expected to fail) [skip ci]

a8865fd

Refactoring I0 and gen_int (expected to fail) [skip ci]

d8bc5c1

gen_int and I0 now are directly passed to the models

24a515e

gvegayon requested a review from dylanhmorris March 29, 2024 17:51

dylanhmorris reviewed Mar 29, 2024

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gvegayon mentioned this pull request Mar 29, 2024

Standardize language #50

Closed

In latent hosp, change inf_hosp_int to inform_hosp (clearer name)

517fce1

AFg6K7h4fhy2 reviewed Apr 3, 2024

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Commas and title

25fa66a

AFg6K7h4fhy2 previously approved these changes Apr 3, 2024

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Update model/src/pyrenew/latent/hospitaladmissions.py

4bc34e7

Co-authored-by: Dylan H. Morris <[email protected]>

gvegayon dismissed AFg6K7h4fhy2’s stale review via 4bc34e7 April 3, 2024 16:26

gvegayon added 3 commits April 3, 2024 10:35

Renaming hosp reporting variable in latent var

134f786

Renaming hosp report

b8a6374

Resolving conflicts

dd37e00

gvegayon had a problem deploying to github-pages April 3, 2024 17:39 — with GitHub Actions Failure

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Update model/src/pyrenew/latent/hospitaladmissions.py

af7de70

Co-authored-by: Dylan H. Morris <[email protected]>

gvegayon had a problem deploying to github-pages April 3, 2024 17:56 — with GitHub Actions Failure

Final renaming of vars in tests

580a09c

gvegayon had a problem deploying to github-pages April 3, 2024 18:01 — with GitHub Actions Failure

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dylanhmorris mentioned this pull request Apr 3, 2024

Only try to deploy docs from pushes to main, not PRs #61

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gvegayon had a problem deploying to github-pages April 3, 2024 19:21 — with GitHub Actions Failure

gvegayon had a problem deploying to github-pages April 3, 2024 19:25 — with GitHub Actions Failure

dylanhmorris and others added 2 commits April 3, 2024 15:27

Merge branch 'main' into 16-observation-model-for-hospital-signals

1c2ba0a

Different vector for hosp_report_prob_dist in tests

90627e6

gvegayon requested review from gvegayon and removed request for SamuelBrand1 April 3, 2024 19:32

gvegayon approved these changes Apr 3, 2024

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gvegayon merged commit 5a06ab2 into main Apr 3, 2024
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gvegayon deleted the 16-observation-model-for-hospital-signals branch April 3, 2024 19:34

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Formally addresses implementing the observed hospitalizations module #39

Formally addresses implementing the observed hospitalizations module #39

ghost commented Mar 21, 2024 •

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Formally addresses implementing the observed hospitalizations module #39

Formally addresses implementing the observed hospitalizations module #39

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