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switch to directly calculated growth rate and extend model options, take 2 #345

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switch to directly calculated growth rate and extend model options, take 2 #345

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+505 −195

Commits on May 17, 2024

  1. make infection seeding a function

    @seabbs @sbfnk
    seabbs authored and sbfnk committed May 17, 2024
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  2. update naming and extract seeding

    @seabbs @sbfnk
    seabbs authored and sbfnk committed May 17, 2024
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  3. implement different model types 

    implements suggestions by @hsbadr

See
#213 (comment)
#213 (comment)
#213 (comment)

For now not implementing comparison to the approximate growth rate as
this seems quite a specific use case that could also be done outside the
stan model.

Also not implementing any approximate growth rate from seeding time -
instead minimum seeding time is now set to 1, so the last seeding time
is used to calculate the first growth rate.
    @sbfnk
    sbfnk committed May 17, 2024
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  4. simplify infection model and fix bug in usage of growth rate (keep ev… 

    …erything on the log scale as long as possible)
    @seabbs @sbfnk
    seabbs authored and sbfnk committed May 17, 2024
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  5. check all models compile

    @seabbs @sbfnk
    seabbs authored and sbfnk committed May 17, 2024
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  6. update documentation

    @seabbs @sbfnk
    seabbs authored and sbfnk committed May 17, 2024
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  7. fix rebase errors

    @sbfnk
    sbfnk committed May 17, 2024
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