Learn R Programming
⚠️There's a newer version (1.1-8) of this package.Take me there.

outbreaker (version 1.1-6)

Bayesian Reconstruction of Disease Outbreaks by Combining Epidemiologic and Genomic Data

Description

Bayesian reconstruction of disease outbreaks using epidemiological and genetic information.

Copy Link

Version

Install

install.packages('outbreaker')

Monthly Downloads

11

Version

1.1-6

License

GPL (>= 2)

Maintainer

Thibaut Jombart

Last Published

September 11th, 2015

Functions in outbreaker (1.1-6)

reproduction numbers

Derive reproduction numbers from outbreak's outputs
Mutation rate estimation

Derive mutation rate estimation from outbreak's outputs
outbreaker

Outbreaker: disease outbreak reconstruction using genetic data
simple outbreak simulator

Simulation of pathogen genotypes during disease outbreaks
select MCMC chains

Select 'good' runs from independent MCMC chains
simulated outbreak dataset

Toy outbreak dataset used to illustrate outbreaker
outbreaker graphics

Plot outbreaker's results
consensus ancestries

Simple transmission tree from outreaber's output