CDCgov/PyRenew

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Python package for multi-signal Bayesian renewal modeling with JAX and NumPyro.

Stars: 29
Forks: 9
Open beginner issues: 0
Indexed issues: 63
Avg merge: 9d 9h
Merged PRs (30d): 8

Dominant language: Python
License: Apache-2.0
Last GitHub push: Sep 18, 2026
Latest indexed: Sep 20, 2026
Contributing guide: No contributing guide
Code of conduct: No code of conduct
Beginner labels: No beginner labels indexed

Beginner friendly Everything

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63 open issues indexed

Update MultiSignalModel API to allow for time-varying ascertainment Open

model pyrenew

Difficulty 3/5 1-2 days Newbie friendliness 68/100

CDCgov/PyRenew#890 · Opened Sep 20, 2026
Posterior prediction, forecasting, and output handling tutorial Open

Difficulty 3/5 1-2 days Newbie friendliness 68/100

CDCgov/PyRenew#877 · 1 comment · Opened Aug 31, 2026
`InfectionsWithFeedback` docstring has incorrect feedback sign Open

documentation

CDCgov/PyRenew#854 · 1 reaction · 1 assignee · Opened Jul 10, 2026
Add `LogitNormalVariable` as pre-specified RV Open

Difficulty 3/5 1-2 days Newbie friendliness 74/100

CDCgov/PyRenew#853 · Opened Jul 10, 2026
Add "RatioLinkedAscertainment" component Open

model

CDCgov/PyRenew#852 · 1 assignee · Opened Jul 10, 2026
Explore new numpyro transforms for parameterizing Temporal Processes Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

CDCgov/PyRenew#849 · 1 reaction · Opened Jul 6, 2026
Consider re-writing innovation-based parameterizations of key stochastic processes as `numpyro.Distributions` Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

CDCgov/PyRenew#833 · Opened Jun 4, 2026
Update to use NumPyro support for zero-mean Negative Binomials and add tests Open

CDCgov/PyRenew#830 · 2 comments · 1 reaction · 2 assignees · Opened May 19, 2026
Consider deprecating `DeterministicVariable` in favor of Delta distribtions Open

Difficulty 4/5 3-5 days Newbie friendliness 38/100

CDCgov/PyRenew#780 · Opened Apr 10, 2026
Refactor bundled example dataset interface Open

Difficulty 4/5 3-5 days Newbie friendliness 42/100

CDCgov/PyRenew#767 · 1 comment · Opened Apr 3, 2026
Latent Processes appear twice in documentation Open

Difficulty 3/5 1-2 days Newbie friendliness 48/100

CDCgov/PyRenew#760 · Opened Mar 26, 2026
Migrate docs to Zensical Open

Difficulty 4/5 3-5 days Newbie friendliness 42/100

CDCgov/PyRenew#750 · 2 comments · Opened Mar 12, 2026
Remove metaclass module Open

Difficulty 3/5 1-2 days Newbie friendliness 55/100

CDCgov/PyRenew#743 · 3 comments · Opened Mar 10, 2026
add meaningful unit test for right truncation Open

Difficulty 3/5 1-2 days Newbie friendliness 45/100

CDCgov/PyRenew#719 · 1 comment · Opened Feb 19, 2026
Support prediction vectors shorter than the right-truncation PMF in `compute_prop_already_reported` Open

Difficulty 3/5 1-2 days Newbie friendliness 42/100

CDCgov/PyRenew#714 · Opened Feb 18, 2026
Add Hilbert Space Gaussian Processes Approximation as a Temporal Process Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

CDCgov/PyRenew#700 · 3 comments · 2 reactions · Opened Feb 11, 2026
Try `show_submodules: true` in all modules Open

Difficulty 2/5 1-3 hours Newbie friendliness 55/100

CDCgov/PyRenew#691 · Opened Feb 9, 2026
Initial deviations in hierarchical infections should be configurable, not fixed. Open

CDCgov/PyRenew#680 · 1 assignee · Opened Feb 6, 2026
Make `noise` a module rather than a submodule of `observation` Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

CDCgov/PyRenew#656 · Opened Jan 28, 2026
Consider making `CountNoise` and `MeasurementNoise` subclasses of an overall abstract `Noise` class Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

CDCgov/PyRenew#655 · Opened Jan 28, 2026
add `support` attribute to RandomVariable Open

model pyrenew

Difficulty 3/5 1-2 days Newbie friendliness 35/100

CDCgov/PyRenew#638 · 1 comment · 1 reaction · Opened Dec 17, 2025
ODE based stepping compatible with `jax.lax.scan` Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

CDCgov/PyRenew#619 · Opened Nov 12, 2025
NumPyro Censored Distributions Open

CDCgov/PyRenew#609 · 2 comments · 4 reactions · 1 assignee · Opened Oct 8, 2025
Refactor code repetition in the time module Open

CDCgov/PyRenew#606 · 1 assignee · Opened Oct 7, 2025
✨ Set up Copilot instructions Open

CDCgov/PyRenew#576 · 1 reaction · 1 assignee · Opened Sep 9, 2025
Tracer-aware argument checking Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

CDCgov/PyRenew#495 · 1 reaction · Opened Apr 1, 2025
DiscretePMF type Open

CDCgov/PyRenew#490 · 5 comments · 1 assignee · Opened Feb 28, 2025
Vectorize `r_approx_from_R` Open

Difficulty 3/5 1-2 days Newbie friendliness 42/100

CDCgov/PyRenew#486 · Opened Feb 26, 2025
Make `daily_to_weekly` multidimensional Open

Difficulty 3/5 1-2 days Newbie friendliness 45/100

CDCgov/PyRenew#485 · Opened Feb 26, 2025
Simplify infection initialization API Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

CDCgov/PyRenew#479 · Opened Jan 7, 2025
Should pyrenew's default MCMC sampler backend be numpyro's bundled NUTS sampler? Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

CDCgov/PyRenew#466 · 3 comments · Opened Oct 1, 2024
Review and clean up `developer_documentation.md` Open

documentation

Difficulty 1/5 1-3 hours Newbie friendliness 35/100

CDCgov/PyRenew#462 · 1 comment · Opened Sep 29, 2024
Have edit links for dynamically-generated documentation pages point to their source files Open

documentation

Difficulty 3/5 1-2 days Newbie friendliness 35/100

CDCgov/PyRenew#459 · Opened Sep 26, 2024
Longer running infection feedback process Open

pyrenew

Difficulty 5/5 Over a week Newbie friendliness 30/100

CDCgov/PyRenew#458 · Opened Sep 25, 2024
DRYify input validation Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

CDCgov/PyRenew#452 · 1 comment · Opened Sep 18, 2024
Helper functions for broadcasting / shape checking / etc for multi-dim arrays with time as first dimension Open

Difficulty 5/5 Over a week Newbie friendliness 15/100

CDCgov/PyRenew#451 · Opened Sep 18, 2024
`InfectionsWithFeedback` requires `gen_int` and `inf_feedback_pmf` to be of same length Open

CDCgov/PyRenew#447 · 1 comment · 2 reactions · 1 assignee · Opened Sep 16, 2024
Tutorial / Model Demonstrating limitations of `scan` with `numpyro.plate` Open

tutorial

CDCgov/PyRenew#444 · 1 comment · 4 reactions · 2 assignees · Opened Sep 12, 2024
Parallelize quarto rendering of tutorials in CI Open

developer documentation

Difficulty 4/5 3-5 days Newbie friendliness 28/100

CDCgov/PyRenew#434 · 1 comment · Opened Sep 6, 2024
Clean Up `InfectionInitializationMethod` and `InfectionInitializationProcess` Open

clean up

Difficulty 4/5 3-5 days Newbie friendliness 30/100

CDCgov/PyRenew#433 · 1 comment · Opened Sep 5, 2024
Standardize variable names for conditional probabilities and delay distributions Open

clean up

Difficulty 3/5 1-2 days Newbie friendliness 45/100

CDCgov/PyRenew#410 · 1 reaction · Opened Aug 22, 2024
Deprecate `record` for `DeterministicVariable`s Open

clean up

CDCgov/PyRenew#407 · 3 comments · 1 reaction · 1 assignee · Opened Aug 22, 2024
Standard check function for "integer greater than value" Open

clean up testing

Difficulty 3/5 1-2 days Newbie friendliness 42/100

CDCgov/PyRenew#403 · 1 reaction · Opened Aug 21, 2024
Automatically wrap long docstrings Open

developer

Difficulty 4/5 3-5 days Newbie friendliness 28/100

CDCgov/PyRenew#396 · Opened Aug 19, 2024
Tests for `InfectionsWithFeedback` class Open

testing

Difficulty 3/5 1-2 days Newbie friendliness 45/100

CDCgov/PyRenew#394 · 3 comments · Opened Aug 19, 2024
Explore fitting models with `bayeux` algorithms Open

discussion pyrenew

Difficulty 5/5 Over a week Newbie friendliness 20/100

CDCgov/PyRenew#361 · 1 comment · 1 reaction · Opened Aug 5, 2024
Consider incorporating `numpyro-oop` Open

discussion

Difficulty 5/5 Over a week Newbie friendliness 20/100

CDCgov/PyRenew#355 · 1 comment · 1 reaction · Opened Aug 1, 2024
Review the need for `Null*` instances of RVs. Open

clean up discussion

CDCgov/PyRenew#314 · 1 comment · 1 assignee · Opened Jul 24, 2024
Should `DeterministicVariable` be able to have an arbitrary `pytree` as their `vars` value? Open

discussion

Difficulty 5/5 Over a week Newbie friendliness 25/100

CDCgov/PyRenew#308 · Opened Jul 24, 2024
Document convention of preferring named arguments even for mandatory (positional) args Open

discussion documentation

CDCgov/PyRenew#298 · 2 comments · 1 reaction · 1 assignee · Opened Jul 23, 2024

CDCgov/PyRenew

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