Man pages for donkeyshot/phybreak
Analysis of Outbreaks with Sequence Data

AvianFluH7N7_2003Avian influenza (H7N7) epidemic
burnin_phybreakMCMC updating of a phybreak-object.
c.phybreakCombine mcmc-chains of phybreak-objects.
ESSEffective sample size
FMD_2001Foot-and-Mouth Disease outbreak (2001)
FMD_2007Foot-and-Mouth Disease outbreak (2007)
get_phybreakExtracting from a phybreak object
infectorsetsSampled infectors for each host in a phybreak-object.
logLik.phybreakLog-likelihood of a phybreak-object.
M_tuberculosis_2013Mycobacterium tuberculosis outbreak
phybreakCreate a phybreak-object from data and prior distributions.
phybreakdataCreate a phybreakdata-object from raw data.
phylotreeMaximum clade credibility tree.
plot.phybreakPlotting a phybreak object.
plot.phybreakdataPlotting a phybreakdata object.
plotPhyloPlotting a phybreak object phylogenetic tree.
plotTransPlotting a phybreak or phybreakdata transmission tree.
print.phybreakDescription of phybreak object.
quantile.phybreakQuantiles of sampled parameter values.
sample_phybreakSampling from a phybreak MCMC-chain.
sim_phybreakOutbreak simulation.
thin.phybreakRemove posterior samples from a phybreak-object.
transtreeCreate a consensus transmission tree.
donkeyshot/phybreak documentation built on Aug. 16, 2018, noon