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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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@sbfnk sbfnk commented Jan 18, 2023 •
edited by seabbs
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Attempts to resurrect #307 as work in progress. Copying text from there:

This PR is meant to supersede #213 and #214. It

Things left to do:

  • expose and document the model options and ensure the stan model options are set consistently
  • Update the README so that it works.
  • Remove backcalc_opts() from all input
  • Remove rt_opts() from all input
  • Move generation_time_opts() inside of process_opts() as an argument.
  • Check postprocessing works as expected
  • Check that all examples and docs work as expected
  • Document model based on update specification
  • Get passing CRAN check if not already
  • more extensive testing
  • update NEWS

@sbfnk sbfnk mentioned this pull request Jan 27, 2023
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@seabbs seabbs force-pushed the update_growth_and_generation branch from 40709d2 to 8fe772a Compare January 27, 2023 14:05
@seabbs seabbs mentioned this pull request Jan 27, 2023
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Base automatically changed from develop to main April 27, 2023 08:36
@sbfnk sbfnk force-pushed the update_growth_and_generation branch from 1e5e88c to 998cadd Compare July 4, 2023 20:01
@sbfnk sbfnk mentioned this pull request Jul 18, 2023
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@sbfnk sbfnk mentioned this pull request Oct 30, 2023
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@sbfnk sbfnk force-pushed the main branch 2 times, most recently from 7568882 to 23229a8 Compare February 19, 2024 20:09
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sbfnk commented Feb 21, 2024

To do for being able to revisit this:

  • rebase to main
  • reduce the number of models to 2 (growth rate model is the same as renewal model with fixed generation time of 1)
    and then go back to the items in the original issue

This was referenced Mar 12, 2024
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@sbfnk sbfnk added this to the CRAN v1.5 release milestone Mar 29, 2024
@sbfnk sbfnk force-pushed the main branch 4 times, most recently from 3b7431c to 6a52995 Compare May 3, 2024 19:32
seabbs and others added 7 commits May 17, 2024 08:05
@seabbs @sbfnk
make infection seeding a function
b1bb3e5
@seabbs @sbfnk
update naming and extract seeding
bd2e9cc
@sbfnk
implement different model types
fb795b9 
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.
@seabbs @sbfnk
simplify infection model and fix bug in usage of growth rate (keep ev…
8b5d379 
…erything on the log scale as long as possible)
@seabbs @sbfnk
check all models compile
bf4c906
@seabbs @sbfnk
update documentation
a43ccaf
@sbfnk
fix rebase errors
e543808
@sbfnk sbfnk force-pushed the update_growth_and_generation branch from 998cadd to e543808 Compare May 17, 2024 07:05
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EpiNow2 v2.0.0
Status: Todo
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