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Modularize model in preparation for fitting real NHSN data #277

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merged 10 commits into from
Jan 7, 2025

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dylanhmorris
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@dylanhmorris dylanhmorris commented Jan 7, 2025

Major change

  • Create helper RVs for the latent infection process and the three observation processes, and produce a PyrenewHEWModel

Minor changes

  • Tweak some variable names for clarity, rename PyrenewHEWModel class to title case to accord with general Python class naming conventions.

@dylanhmorris dylanhmorris marked this pull request as ready for review January 7, 2025 16:38
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codecov bot commented Jan 7, 2025

Codecov Report

Attention: Patch coverage is 0% with 94 lines in your changes missing coverage. Please review.

Project coverage is 15.87%. Comparing base (1fb4c2e) to head (9bdf638).
Report is 1 commits behind head on main.

Files with missing lines Patch % Lines
pyrenew_hew/pyrenew_hew_model.py 0.00% 85 Missing ⚠️
pipelines/build_pyrenew_model.py 0.00% 9 Missing ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##             main     #277      +/-   ##
==========================================
- Coverage   16.48%   15.87%   -0.62%     
==========================================
  Files          21       21              
  Lines        1480     1537      +57     
==========================================
  Hits          244      244              
- Misses       1236     1293      +57     
Flag Coverage Δ
hewr 47.68% <ø> (ø)
pipelines 0.00% <0.00%> (ø)
pyrenew_hew 1.65% <0.00%> (-0.24%) ⬇️

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@sbidari sbidari left a comment

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Looks good to me!

@dylanhmorris dylanhmorris merged commit 5d790b7 into main Jan 7, 2025
13 of 15 checks passed
@dylanhmorris dylanhmorris deleted the dhm-fit-nhsn branch January 7, 2025 19:30
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2 participants