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Right Truncation in NSSP Demo #17

Merged
merged 36 commits into from
Oct 2, 2024
Merged

Right Truncation in NSSP Demo #17

merged 36 commits into from
Oct 2, 2024

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damonbayer
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@damonbayer damonbayer commented Sep 18, 2024 •
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This PR enables model fitting with right-truncation estimates provided by NNH.

damonbayer and others added 27 commits September 13, 2024 19:41
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git ignore private data
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update rprofile for VAP dev
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bump renv.lock
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add priors
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prep_data checkin
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activate.R whitespace
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add generation_interval_pmf
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fix names of pmfs
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save test data in json
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Merge branch 'dmb_nssp_demo' of https://github.com/CDCgov/pyrenew-cov…
5a2454b 
…id-wastewater into dmb_nssp_demo
@damonbayer
move priors
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fit_model
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add post_process.R
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update for correct data source
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re-arrange set_host_device_count
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prep all data
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use argparse
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Merge branch 'dmb_nssp_demo' of https://github.com/CDCgov/pyrenew-cov…
0fc7f03 
…id-wastewater into dmb_nssp_demo
@damonbayer
fit all models
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create all figures
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Merge branch 'dmb_nssp_demo' of https://github.com/CDCgov/pyrenew-cov…
3ba78a9 
…id-wastewater into dmb_nssp_demo
@damonbayer
revise fit all models script
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remove unused post processing code
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use mid step
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first pass at right_truncation_offset
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right truncation working
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correct for new fit data
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@damonbayer damonbayer changed the base branch from main to dmb_nssp_demo September 20, 2024 19:16
@damonbayer damonbayer marked this pull request as ready for review September 20, 2024 19:18
Base automatically changed from dmb_nssp_demo to main September 27, 2024 15:05
An error occurred while trying to automatically change base from dmb_nssp_demo to main September 27, 2024 15:05
dylanhmorris
dylanhmorris requested changes Sep 27, 2024
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@dylanhmorris dylanhmorris left a comment

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Looks very good. Thanks @damonbayer. A few minor things.

pyrenew_covid_wastewater/hosp_only_ww_right_truncation_model.py Outdated Show resolved Hide resolved
pyrenew_covid_wastewater/hosp_only_ww_right_truncation_model.py Outdated Show resolved Hide resolved
pyrenew_covid_wastewater/hosp_only_ww_right_truncation_model.py Outdated Show resolved Hide resolved
pyrenew_covid_wastewater/hosp_only_ww_right_truncation_model.py Outdated Show resolved Hide resolved
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Thanks @dylanhmorris. Will address your comments and probably merge this back into the original model with optional right truncation.

@damonbayer damonbayer mentioned this pull request Oct 1, 2024
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@damonbayer damonbayer merged commit 165753f into main Oct 2, 2024
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@damonbayer damonbayer deleted the dmb_right_truncation branch October 2, 2024 20:27
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@sbidari sbidari Awaiting requested review from sbidari sbidari is a code owner

@dylanhmorris dylanhmorris Awaiting requested review from dylanhmorris dylanhmorris is a code owner

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