switch to directly calculated growth rate and extend model options #307

sbfnk · 2022-07-27T16:10:13Z

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

finalises the work commenced in Standardises generation of infections #214 to support three different models
merges Standardises generation of infections #214 into Update growth calculation #213 and implements most of the suggestions made there by @hsbadr
rebases Update growth calculation #213 onto current master
works with default options and a simple example (the README)

Things left to do:

expose and document the model options and ensure the stan model options are set consistently
more extensive testing
update NEWS

sbfnk · 2023-01-18T10:27:15Z

Any reason this work in progress shouldn't continue?

sbfnk mentioned this pull request Jul 27, 2022

Update growth calculation #213

Closed

sbfnk changed the title ~~switch to directly calculated growth rate~~ switch to directly calculated growth rate and extend model options Jul 27, 2022

sbfnk mentioned this pull request Jul 27, 2022

Standardises generation of infections #214

Closed

sbfnk mentioned this pull request Sep 22, 2022

Fit to multiple time series and fold in secondary model #313

Closed

sbfnk force-pushed the update_growth_and_generation branch 2 times, most recently from 2393a20 to dbbef42 Compare October 14, 2022 19:09

seabbs force-pushed the main branch from 3e43d35 to a619107 Compare October 16, 2022 22:44

seabbs closed this Jan 18, 2023

seabbs force-pushed the update_growth_and_generation branch from dbbef42 to d51c207 Compare January 18, 2023 10:09

sbfnk mentioned this pull request Jan 18, 2023

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

Draft

11 tasks

Provide feedback