Bayesian Reconstruction of Disease Outbreaks by Combining Epidemiologic and Genomic Data

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Documentation for package ‘outbreaker’ version 1.1-8

Help Pages

as.igraph.simOutbreak Simulation of pathogen genotypes during disease outbreaks
as.igraph.tTree Simple transmission tree from outreaber's output
disperse Simulation of pathogen genotypes during disease outbreaks
fakeOutbreak Toy outbreak dataset used to illustrate outbreaker
findMutations.tTree Simple transmission tree from outreaber's output
get.incid Derive reproduction numbers from outbreak's outputs
get.mu Derive mutation rate estimation 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: disease outbreak reconstruction using genetic data
outbreaker.package outbreaker: disease outbreak reconstruction using epidemiological and genetic data
outbreaker.parallel Outbreaker: disease outbreak reconstruction using genetic data
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
simulated outbreak dataset 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