epiverse-trace / epiverse-trace/finalsize

Function to calculate dominant eigenvector of next generation matrix

Open
#216 0 comments 0 reactions 0 assignees View on GitHub
Dominant language
R
Stars
15
Forks
6
PR merge metrics
No merged PRs in 30d

Description

As well as `r_eff()` for effective R (i.e. the dominant eigenvalue of the next generation matrix), it can be useful to have a complementary function that calculates the dominant eigenvector, which indicates the expected distribution of new infections across multiple transmission generations (i.e. once any transient distribution of introduced infections has faded).

This would make it possible to produce plots like the below from [Klepac et al (2020)](https://www.medrxiv.org/content/10.1101/2020.02.16.20023754v2), which can be used for planning and situational awareness (e.g. if observed incidence does/doesn't match expectations of what transmission driven by physical contact would produce).

bbc_eigenvector

Contributor guide

Open the contributing guide

Research direction

Start by locating r_eff() and the code that constructs the next generation matrix, then determine how its dominant eigenvalue is calculated. Add a complementary function that returns the dominant eigenvector and verify that it represents the expected distribution of new infections across transmission generations.

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
42/100

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.