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Develop #343

Merged
merged 60 commits into from
Jan 31, 2023
Merged

Develop #343

merged 60 commits into from
Jan 31, 2023

Commits on Nov 18, 2022

  1. add more flexibility with delays (#305)

    @sbfnk
    sbfnk authored Nov 18, 2022
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Commits on Nov 23, 2022

  1. documentation fixes and deprecation warning (#335)

    @sbfnk
    sbfnk authored Nov 23, 2022
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Commits on Nov 24, 2022

  1. fixes to small issues introduced by PR #305 (#336)

    @sbfnk
    sbfnk authored Nov 24, 2022
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Commits on Dec 9, 2022

  1. upper bound frac_obs by 1 (#340)

    @sbfnk
    sbfnk authored Dec 9, 2022
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Commits on Jan 18, 2023

  1. Merge branch 'main' into develop

    @seabbs
    seabbs authored Jan 18, 2023
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  2. Documentation: Fix report_plots example

    @seabbs
    seabbs committed Jan 18, 2023
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  3. merge changes from main

    @seabbs
    seabbs committed Jan 18, 2023
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  4. Merge branch 'main' into develop

    @seabbs
    seabbs committed Jan 18, 2023
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  5. Catch change in max delay definition in report_cases()

    @seabbs
    seabbs committed Jan 18, 2023
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Commits on Jan 19, 2023

  1. Merge branch 'main' into develop

    @seabbs
    seabbs committed Jan 19, 2023
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  2. Hotfix: Fix estimate_infections() example for truncation which did no… 

    …t use the new dist input
    @seabbs
    seabbs committed Jan 19, 2023
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Commits on Jan 20, 2023

  1. Merge changes from main

    @seabbs
    seabbs committed Jan 20, 2023
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Commits on Jan 23, 2023

  1. update news file to use categories

    @seabbs
    seabbs committed Jan 23, 2023
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  2. update news

    @seabbs
    seabbs committed Jan 23, 2023
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  3. Tests: Add tests for stan convolution functions

    @seabbs
    seabbs committed Jan 23, 2023
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  4. Feature: Add fixed argument to get_dist functions

    @seabbs
    seabbs committed Jan 23, 2023
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  5. Documentation: Make new left truncation clearer

    @seabbs
    seabbs committed Jan 23, 2023
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  6. Package: Surface reversing of PMF to happen once and explicitly vs wi… 

    …thin multiple function calls
    @seabbs
    seabbs committed Jan 23, 2023
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  7. Package: Check code compilation and reset testing for CI

    @seabbs
    seabbs committed Jan 23, 2023
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  8. Documnetation: Make sure fixed is documented in all get_dist children

    @seabbs
    seabbs committed Jan 23, 2023
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  9. Tests: Add generation_time_opts test that should pas

    @seabbs
    seabbs committed Jan 23, 2023
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  10. move synthetic validation to its own folder

    @seabbs
    seabbs committed Jan 23, 2023
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  11. Tests: Add a synthetic recovery test for estimate_secondary (prevalen… 

    …ce currently failing)
    @seabbs
    seabbs committed Jan 23, 2023
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  12. Package: Review estimate_secondary code

    @seabbs
    seabbs committed Jan 23, 2023
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  13. Package: Clean up not currently generated syntethic validation figures

    @seabbs
    seabbs committed Jan 23, 2023
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  14. Package: Add support for passing generation time distribution to gene… 

    …ration_time_opts as a list
    @seabbs
    seabbs committed Jan 23, 2023
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  15. Package: Use rev_ to indicate reversed PMFs and catch reverse induced… 

    … renewal bug
    @seabbs
    seabbs committed Jan 23, 2023
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  16. Package: Add random walk + stationary GP to synthetic recovery

    @seabbs
    seabbs committed Jan 23, 2023
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Commits on Jan 24, 2023

  1. Package: Fix synthetic validation

    @seabbs
    seabbs committed Jan 24, 2023
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  2. Package: First pass at vector of delay mean lower bounds - depends on… 

    … passing -Inf being allowed
    @seabbs
    seabbs committed Jan 24, 2023
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  3. Package: Use reals vs ints for lower bounds of course

    @seabbs
    seabbs committed Jan 24, 2023
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  4. Package: Arrggh vectorised lower bounds are not in stan 2.21

    @seabbs
    seabbs committed Jan 24, 2023
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  5. Documentation: Refresh docs style

    @seabbs
    seabbs committed Jan 24, 2023
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  6. Package: Update namespace

    @seabbs
    seabbs committed Jan 24, 2023
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  7. Package: Restyle code and docs

    @seabbs
    seabbs committed Jan 24, 2023
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  8. Package: Add use of delays_lp for generation time and define truncate… 

    …d prior for distributions
    @seabbs
    seabbs committed Jan 24, 2023
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  9. Model: Use delays_lp for truncation and generation time to properly s… 

    …upport multiple dists etc
    @seabbs
    seabbs committed Jan 24, 2023
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  10. Model: Catch missinng changes for truncation in estimate_secondary

    @seabbs
    seabbs committed Jan 24, 2023
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  11. Bug: Fix edge case when using mixed distributions so that seeding tim… 

    …e is correctly calculated
    @seabbs
    seabbs committed Jan 24, 2023
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  12. Docmentation: Refresh README

    @seabbs
    seabbs committed Jan 24, 2023
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  13. Bug: Fix edge case where generation_time_opts was ignoring max from g… 

    …et_generation_time
    @seabbs
    seabbs committed Jan 24, 2023
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  14. Model: Drop numeric stabilisation in convolve

    @seabbs
    seabbs committed Jan 24, 2023
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  15. Bug: Update if/else to check for max in generation_time_opts when loo… 

    …king to use max arg
    @seabbs
    seabbs committed Jan 24, 2023
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  16. Documentation: Refresh docs

    @seabbs
    seabbs committed Jan 24, 2023
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  17. Tests: Fix tests failing due to PR changes

    @seabbs
    seabbs committed Jan 24, 2023
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  18. Documentation: Move frac_obs change into breaking changes section of … 

    …news
    @seabbs
    seabbs committed Jan 24, 2023
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  19. Documentation: Check everything is included in pkgdown:

    @seabbs
    seabbs committed Jan 24, 2023
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Commits on Jan 25, 2023

  1. update synthetic validation

    @sbfnk
    sbfnk committed Jan 25, 2023
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  2. Documentation: URL check and spelling

    @seabbs
    seabbs committed Jan 25, 2023
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  3. Merge branch 'develop' of https://github.com/epiforecasts/EpiNow2 int… 

    …o develop
    @seabbs
    seabbs committed Jan 25, 2023
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Commits on Jan 27, 2023

  1. Update R/create.R 

    Co-authored-by: Sebastian Funk <[email protected]>
    @seabbs @sbfnk
    seabbs and sbfnk authored Jan 27, 2023
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  2. Update README.Rmd 

    Co-authored-by: Sebastian Funk <[email protected]>
    @seabbs @sbfnk
    seabbs and sbfnk authored Jan 27, 2023
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  3. Update R/create.R 

    Co-authored-by: Sebastian Funk <[email protected]>
    @seabbs @sbfnk
    seabbs and sbfnk authored Jan 27, 2023
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  4. Update R/estimate_truncation.R 

    Co-authored-by: Sebastian Funk <[email protected]>
    @seabbs @sbfnk
    seabbs and sbfnk authored Jan 27, 2023
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  5. Update R/create.R 

    Co-authored-by: Sebastian Funk <[email protected]>
    @seabbs @sbfnk
    seabbs and sbfnk authored Jan 27, 2023
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  6. Update NEWS.md 

    Co-authored-by: Sebastian Funk <[email protected]>
    @seabbs @sbfnk
    seabbs and sbfnk authored Jan 27, 2023
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Commits on Jan 30, 2023

  1. clarify connection between forecast_ and simulate_ secondary

    @seabbs
    seabbs committed Jan 30, 2023
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  2. update news to remove reference to improved run times

    @seabbs
    seabbs committed Jan 30, 2023
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  3. refresh documentation

    @seabbs
    seabbs committed Jan 30, 2023
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  4. update CRAN comments after window devel check

    @seabbs
    seabbs committed Jan 30, 2023
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