API for phybreak
Analysis of Outbreaks with Sequence Data
| Global functions | |
|---|---|
| .accept.pbe | Source code |
| .build.pbe | Source code |
| .copy2pbe0 | Source code |
| .copy2pbe1 | Source code |
| .cycleYN | Source code |
| .destroy.pbe | Source code |
| .edmondsiterative | Source code |
| .infarray | Source code |
| .inflist | Source code |
| .lik.coaltimes | Source code |
| .lik.gentimes | Source code |
| .lik.sampletimes | Source code |
| .likseq | Source code |
| .likseqenv | Source code |
| .makephyloparset | Source code |
| .makephyloparsets | Source code |
| .mcctree | Source code |
| .mpcinfector | Source code |
| .mtcctree | Source code |
| .pathtocycle | Source code |
| .postinfector | Source code |
| .prepare.pbe | Source code |
| .propose.pbe | Source code |
| .ptr | Source code |
| .rinfectors | Source code |
| .rinftimes | Source code |
| .samplecoaltimes | Source code |
| .sampleextracoaltime | Source code |
| .sampleextraupnode | Source code |
| .sampletopology | Source code |
| .sctwh3 | Source code |
| .sim.additionalsamples | Source code |
| .sim.outbreak | Source code |
| .sim.outbreak.size | Source code |
| .transtreecount | Source code |
| .transtreeedmonds | Source code |
| .update.mG | Source code |
| .update.mS | Source code |
| .update.mu | Source code |
| .update.wh | Source code |
| .updatehost | Source code |
| .updatehost.keepphylo | Source code |
| .updatehost.topology | Source code |
| AvianFluH7N7_2003 | Man page |
| FMD_2001 | Man page |
| FMD_2007 | Man page |
| M_tuberculosis_2013 | Man page |
| burnin.phybreak | Man page Source code |
| distmatrix_phybreak | Source code |
| get.mcmc | Man page Source code |
| get.multiPhylo | Man page Source code |
| get.parameters | Man page Source code |
| get.phybreak | Man page |
| get.phylo | Man page Source code |
| get.seqdata | Man page Source code |
| get.tree | Man page Source code |
| graphicalparameters | Source code |
| infectorsets | Man page Source code |
| logLik.phybreak | Man page Source code |
| make_nodehostsparents | Source code |
| makenodehp | Source code |
| maketransplot | Source code |
| nthsample | Source code |
| obkData2phybreak | Source code |
| phybreak | Man page Source code |
| phybreak2phylo | Source code |
| phybreak2trans | Source code |
| phybreakdata | Man page Source code |
| phylotree | Man page Source code |
| plot.phybreak | Man page Source code |
| plot.phybreakdata | Man page Source code |
| plotPhylo | Man page Source code |
| plotTrans | Man page Source code |
| rankhostsforplot | Source code |
| removetransnodes | Source code |
| sample.phybreak | Man page Source code |
| sim.phybreak | Man page Source code |
| testargumentsclass_phybreak | Source code |
| testdataclass_phybreak | Source code |
| testfortree_phybreak | Source code |
| thin_phybreak | Man page Source code |
| transphylo2phybreak | Source code |
| transtree | Man page Source code |
| whichgeneration | Source code |
