epiverse-trace / epiverse-trace/simulist

add argument to configure a incubation time

Open
#253 2 comments 0 reactions 0 assignees View on GitHub
Dominant language
R
Stars
11
Forks
1
Avg merge
3d 1h
Merged PRs (30d)
2

Description

Currently, the date of infection is equal to the date of symptoms onset.

epidemic curves can be used to infer the probable date of exposure (if known incubation period), or calculate the incubation period (if data of exposure is known). Including the incubation period in the configuration could help use {simulist} for outbreak investigation of point source or extended source epidemics

https://github.com/epiverse-trace/simulist/blob/c9e56966a8993066e55c08c06638903a9716d9cf/R/sim_internal.R#L59

Contributor guide

Open the contributing guide

Research direction

Start at R/sim_internal.R#L59, where the issue identifies the current relationship between infection and symptom-onset dates. Determine how configuration is passed into the simulation and how incubation time should affect those dates; done means users can configure an incubation period and use the resulting line list for point-source or extended-source outbreak investigation.

Written by the indexing model from the issue text.

Assessment

Tech stack
r
Domain
data
Issue type
Feature
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
35/100

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.