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Dataframe constructor script for scoring #403

Merged
merged 7 commits into from
Jul 28, 2024
Merged

Dataframe constructor script for scoring #403

merged 7 commits into from
Jul 28, 2024

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SamuelBrand1
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This PR makes a parallel dataframe creator to the analysis dataframe used to make figs 1 and 2. This dataframe has the CRPS scores for the various target processes mentioned in #401 .

NB: this PR uses summarise_crps again to address a missing feature of #401 in combination with out pipeline. The missing feature is that we are not aiming to do inference on infection generating processes DirectInfections and ExpGrowth for mis-specified GI means (because this does not affect the simulation of these processes). This gets addressed in the same way as it was for creating the analysis dataframe by for these IGPs iterating over the GI scenarios.

This does not close #402 , but contributes the underlying dataframe that we can build a visualisation from.

@SamuelBrand1 SamuelBrand1 requested a review from seabbs July 25, 2024 22:04
@SamuelBrand1 SamuelBrand1 linked an issue Jul 25, 2024 that may be closed by this pull request
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Try this Pull Request!

Open Julia and type:

import Pkg
Pkg.activate(temp=true)
Pkg.add(url="https://github.com/CDCgov/Rt-without-renewal", rev="402-fig-3-code", subdir="EpiAware")
using EpiAware

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codecov-commenter commented Jul 25, 2024

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 93.57%. Comparing base (2b816a8) to head (128d037).

Additional details and impacted files
@@           Coverage Diff           @@
##             main     #403   +/-   ##
=======================================
  Coverage   93.57%   93.57%           
=======================================
  Files          54       54           
  Lines         560      560           
=======================================
  Hits          524      524           
  Misses         36       36           

☔ View full report in Codecov by Sentry.
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seabbs
seabbs previously approved these changes Jul 26, 2024
@seabbs seabbs enabled auto-merge July 26, 2024 09:57
@seabbs seabbs disabled auto-merge July 28, 2024 13:30
@seabbs seabbs merged commit 2e30981 into main Jul 28, 2024
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@seabbs seabbs deleted the 402-fig-3-code branch July 28, 2024 13:30
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Fig 3 code.
3 participants