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Add plots for wastewater concentrations #382

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sbidari
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@sbidari sbidari commented Mar 10, 2025

Adds plots of wastewater concentration to the postprocessing steps.

Summary of changes:

  • preprocessing of wastewater data to ensure lab_site_index ordered by population size
  • Updates process_state_forecast.R, make_forecast_figure.R and plot_and_save_state_forecast.R to handle new variables
  • Adds NWSS data and associated variable column lab_site_index to pipelines/prep_data.py
  • Update pipelines/score_forecast.R and pipelines/timeseries_forecast.R to handle lab_site_index column appropriately

…-generate-plots-for-predictedobserved-site-level-wastewater-concentration
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codecov bot commented Mar 10, 2025

Codecov Report

Attention: Patch coverage is 8.00000% with 92 lines in your changes missing coverage. Please review.

Project coverage is 30.16%. Comparing base (6b4f986) to head (f16acd1).
Report is 1 commits behind head on main.

Files with missing lines Patch % Lines
hewr/R/process_state_forecast.R 8.97% 71 Missing ⚠️
hewr/R/make_forecast_figure.R 0.00% 11 Missing ⚠️
pipelines/prep_data.py 20.00% 4 Missing ⚠️
pyrenew_hew/pyrenew_hew_model.py 0.00% 3 Missing ⚠️
hewr/R/directory_utils.R 0.00% 2 Missing ⚠️
pipelines/prep_eval_data.py 0.00% 1 Missing ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##             main     #382      +/-   ##
==========================================
- Coverage   30.58%   30.16%   -0.43%     
==========================================
  Files          26       26              
  Lines        1942     1986      +44     
==========================================
+ Hits          594      599       +5     
- Misses       1348     1387      +39     
Flag Coverage Δ
hewr 34.02% <7.69%> (-1.53%) ⬇️
pipelines 14.35% <16.66%> (ø)
pyrenew_hew 42.24% <0.00%> (-0.07%) ⬇️

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@sbidari sbidari force-pushed the 370-generate-plots-for-predictedobserved-site-level-wastewater-concentration branch from 31f5fb8 to 1b0ed66 Compare March 12, 2025 19:22
sbidari added 2 commits March 17, 2025 17:54
…tewater-concentration' of https://github.com/CDCgov/pyrenew-hew into 370-generate-plots-for-predictedobserved-site-level-wastewater-concentration
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@damonbayer damonbayer left a comment

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Thanks @sbidari! Some changes requested.

sbidari and others added 7 commits March 17, 2025 15:39
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@damonbayer damonbayer left a comment

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Thanks @sbidari! I tried some minor modifications to clean up the plot saving, but I was unsuccessful. Going to save it for #388

@damonbayer damonbayer enabled auto-merge (squash) March 18, 2025 17:51
@damonbayer damonbayer merged commit 2e9f9f7 into main Mar 18, 2025
37 of 39 checks passed
@damonbayer damonbayer deleted the 370-generate-plots-for-predictedobserved-site-level-wastewater-concentration branch March 18, 2025 18:03
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Generate plots for predicted/observed site level wastewater concentration
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