Bayesian inference of outbreak dynamics based on epidemiological and genetic information.

Documentation for package ‘outbreaker’ version 1.0-1

as.igraph.simOutbreak	Simulation of pathogen genotypes during disease outbreaks
as.igraph.tTree	Simple transmission tree from outreaber's output
findMutations.tTree	Simple transmission tree from outreaber's output
get.incid	Derive reproduction numbers from outbreak's outputs
get.R	Derive reproduction numbers from outbreak's outputs
get.Rt	Derive reproduction numbers from outbreak's outputs
get.tTree	Simple transmission tree from outreaber's output
labels.simOutbreak	Simulation of pathogen genotypes during disease outbreaks
outbreaker	Outbreaker
outbreaker.parallel	Outbreaker
plot.simOutbreak	Simulation of pathogen genotypes during disease outbreaks
plot.tTree	Simple transmission tree from outreaber's output
plotChains	Plot outbreaker's results
plotOutbreak	Plot outbreaker's results
print.simOutbreak	Simulation of pathogen genotypes during disease outbreaks
selectChains	Select 'good' runs from independent MCMC chains
simOutbreak	Simulation of pathogen genotypes during disease outbreaks
simOutbreak-class	Simulation of pathogen genotypes during disease outbreaks
toyOutbreak	Toy outbreak dataset used to illustrate outbreaker
transGraph	Plot outbreaker's results
tTree	Simple transmission tree from outreaber's output
[.simOutbreak	Simulation of pathogen genotypes during disease outbreaks