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Simulate infections #557

Merged
merged 24 commits into from
Feb 20, 2024
Merged

Simulate infections #557

merged 24 commits into from
Feb 20, 2024

Commits on Feb 20, 2024

  1. simulate infections function

    @sbfnk
    sbfnk committed Feb 20, 2024
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  2. add test

    @sbfnk
    sbfnk committed Feb 20, 2024
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  3. we always need initial infections

    @sbfnk
    sbfnk committed Feb 20, 2024
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  4. add missing truncation

    @sbfnk
    sbfnk committed Feb 20, 2024
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  5. swap check for seeding time

    @sbfnk
    sbfnk committed Feb 20, 2024
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  6. update extract function to work with simulations

    @sbfnk
    sbfnk committed Feb 20, 2024
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  7. add news item

    @sbfnk
    sbfnk committed Feb 20, 2024
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  8. fix typo 

    Co-authored-by: James Azam <[email protected]>
    @sbfnk @jamesmbaazam
    sbfnk and jamesmbaazam committed Feb 20, 2024
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  9. add more tests

    @sbfnk
    sbfnk committed Feb 20, 2024
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  10. correctly index infections when no delay

    @sbfnk
    sbfnk committed Feb 20, 2024
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  11. generation times are now zero-indexed

    @sbfnk
    sbfnk committed Feb 20, 2024
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  12. ensure overdispersion is fixed

    @sbfnk
    sbfnk committed Feb 20, 2024
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  13. improve checks in simulate_infections

    @sbfnk
    sbfnk committed Feb 20, 2024
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  14. expand simulate_infections documentation

    @sbfnk
    sbfnk committed Feb 20, 2024
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  15. add simulate_infections snapshot test

    @sbfnk
    sbfnk committed Feb 20, 2024
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  16. add backend argument

    @sbfnk
    sbfnk committed Feb 20, 2024
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  17. use simpler Poisson for example

    @sbfnk
    sbfnk committed Feb 20, 2024
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  18. single comment hash for package style

    @sbfnk
    sbfnk committed Feb 20, 2024
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  19. re-render documentation

    @sbfnk
    sbfnk committed Feb 20, 2024
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  20. add reviewer 

    Co-authored-by: James Azam <[email protected]>
    @sbfnk @jamesmbaazam
    sbfnk and jamesmbaazam committed Feb 20, 2024
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  21. only extract frac_obs if obs_scale_sd exists

    @sbfnk
    sbfnk committed Feb 20, 2024
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  22. Apply suggestions from code review 

    Co-authored-by: James Azam <[email protected]>
    @sbfnk @jamesmbaazam
    sbfnk and jamesmbaazam committed Feb 20, 2024
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  23. add deprecation context and re-render doc

    @sbfnk
    sbfnk committed Feb 20, 2024
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  24. improve documentation

    @sbfnk
    sbfnk committed Feb 20, 2024
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