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 |