Analysis of Outbreaks with Sequence Data


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Documentation for package ‘phybreak’ version 0.2.0

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AvianFluH7N7_2003 Avian influenza (H7N7) epidemic
burnin.phybreak MCMC updating of a phybreak-object.
FMD_2001 Foot-and-Mouth Disease outbreak (2001)
FMD_2007 Foot-and-Mouth Disease outbreak (2007)
get.mcmc Accessing a phybreak object
get.multiPhylo Accessing a phybreak object
get.parameters Accessing a phybreak object
get.phybreak Accessing a phybreak object
get.phylo Accessing a phybreak object
get.seqdata Accessing a phybreak object
get.tree Accessing a phybreak object
infectorsets Sampled infectors for each host in a phybreak-object.
logLik.phybreak Log-likelihood of a phybreak-object.
M_tuberculosis_2013 Mycobacterium tuberculosis outbreak
phybreak Create a phybreak-object from data and prior distributions.
phybreakdata Create a phybreakdata-object from raw data.
phylotree Maximum clade credibility tree.
plot.phybreak Plotting a phybreak object.
plot.phybreakdata Plotting a phybreakdata object.
plotPhylo Plotting a phybreak object phylogenetic tree.
plotTrans Plotting a phybreak object transmission tree.
sample.phybreak Sampling from a phybreak MCMC-chain.
sim.phybreak Outbreak simulation.
thin_phybreak Remove posterior samples from a phybreak-object.
transtree Create a consensus transmission tree.