Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Add helper data PyrenewHEWData class to hold input data to PyrenewHewModels #283

Merged
merged 38 commits into from
Jan 18, 2025
Merged

Add helper data PyrenewHEWData class to hold input data to PyrenewHewModels #283

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
38 commits
Select commit Hold shift + click to select a range
a4e5bbb
Split up main call into sample helper functions
dylanhmorris Jan 6, 2025
ff2d629
Correct names in function calls
dylanhmorris Jan 6, 2025
ac306ff
Fix missing arg
dylanhmorris Jan 6, 2025
37b3357
fix missing self in fn defn
dylanhmorris Jan 6, 2025
a52719f
Clean up admissions placeholder
dylanhmorris Jan 6, 2025
ca882fc
Add some conditionals to the observation process
dylanhmorris Jan 6, 2025
a266f2f
Add assignments of other sampled quantities
dylanhmorris Jan 6, 2025
559d29f
Modularize model in prep for real admissions data
dylanhmorris Jan 7, 2025
c180f4f
Merge branch 'main' into dhm-fit-nhsn
dylanhmorris Jan 7, 2025
32ba7d0
Checkpoint commit
dylanhmorris Jan 7, 2025
9bdf638
Merge branch 'main' into dhm-fit-nhsn
dylanhmorris Jan 7, 2025
e1a860f
Merge branch 'dhm-fit-nhsn' into dhm-fit-to-real-data
dylanhmorris Jan 7, 2025
c9e8cac
Make models day-of-week aware (needed for epiweekly obs)
dylanhmorris Jan 7, 2025
8f175f3
Add helper data class
dylanhmorris Jan 8, 2025
b036195
Merge branch 'main' into dhm-fit-to-real-data
dylanhmorris Jan 8, 2025
7517a33
Remove old demo
dylanhmorris Jan 8, 2025
2cfefdd
Fix missing close parenthesis, run precommit
dylanhmorris Jan 8, 2025
813bfc2
Fix incorrectly added parenthesis
dylanhmorris Jan 8, 2025
44716fe
Fix upgrade issue with pygit2 by holding at 1.16.0 for now
dylanhmorris Jan 8, 2025
8584cbe
Try fitting Pyrenew-HE
dylanhmorris Jan 8, 2025
0a21be7
Merge branch 'main' into dhm-fit-to-real-data
dylanhmorris Jan 8, 2025
376469a
Use mmwr epiweek function
dylanhmorris Jan 13, 2025
43bda9d
Fix type hint for dict
dylanhmorris Jan 13, 2025
7e24656
Comment priors
dylanhmorris Jan 13, 2025
d239a47
Unpin and update pygit2
dylanhmorris Jan 14, 2025
ff6b55e
Merge branch 'main' into dhm-fit-to-real-data
dylanhmorris Jan 17, 2025
e0651d1
Use dictionaries and filter(None) for dates
dylanhmorris Jan 17, 2025
4c88194
Update pyrenew_hew/pyrenew_hew_model.py
dylanhmorris Jan 17, 2025
a0cd3a8
Update pyrenew_hew/pyrenew_hew_model.py
dylanhmorris Jan 17, 2025
1aa327a
IEDR/IHR conditional logic
dylanhmorris Jan 17, 2025
c108adf
Standardize nomenclature
dylanhmorris Jan 17, 2025
26cc2d3
Fix missing import
dylanhmorris Jan 17, 2025
c3040ad
deterministic module
dylanhmorris Jan 17, 2025
5eb688c
Use fact that latent infections now has an n_initialization_points at…
dylanhmorris Jan 18, 2025
b672c39
access attribute correctly
dylanhmorris Jan 18, 2025
0d03fd0
Tweak prior assignment to handle new exactly one ihr prior check
dylanhmorris Jan 18, 2025
001e292
Update test
dylanhmorris Jan 18, 2025
4131e81
Fix bug introduced by copy/paste
dylanhmorris Jan 18, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
386 changes: 0 additions & 386 deletions demos/hosp_only_ww_model/data/fit_hosp_only/stan_data.json
View file
Open in desktop

This file was deleted.

137 changes: 0 additions & 137 deletions demos/hosp_only_ww_model/model_comp.qmd
View file
Open in desktop

This file was deleted.

122 changes: 0 additions & 122 deletions demos/hosp_only_ww_model/pyrenew_hew_model.qmd
View file
Open in desktop

This file was deleted.

Loading
Loading