search

idem-lab / epiwave.pipelines

0 stars 3 forks source link

find a better incubation period dist #18

Closed AugustHao closed 8 months ago

AugustHao commented 11 months ago

the current one is too concentrated

smwindecker commented 10 months ago

Check what is available in Epiparams package. If that is not available, Freya says find a good paper from within the metaanalysis - and use that one. Currently function only works with "Omicron" strain.

For generic package, clean up so that it is reasonable for variaous uses.

smwindecker commented 10 months ago

option 1: exemplar parameters for GI and IP for variety of pathogens option 2: user specify

interface with epiparams

AugustHao commented 10 months ago

also for the time being can use M Plank's https://www.medrxiv.org/content/10.1101/2023.08.14.23294060v1.full.pdf

AugustHao commented 10 months ago

Michael's group used this: Weibull with mean 2.9 days and standard deviation 2.0 days

estimated by this paper https://www.eurosurveillance.org/content/10.2807/1560-7917.ES.2022.27.6.2200042

seems reasonably reliable, can sub in this for now

AugustHao commented 8 months ago

done but should reopen when epiparams updates