API for phybreak
Analysis of Outbreaks with Sequence Data

Global functions
AvianFluH7N7_2003 Man page
FMD_2001 Man page
FMD_2007 Man page
M_tuberculosis_2013 Man page
accept.pbe Source code
build.pbe Source code
burnin.phybreak Man page Source code
copy2pbe0 Source code
copy2pbe1 Source code
cycleYN Source code
destroy.pbe Source code
distmatrix_phybreak Source code
edmondsiterative 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
lik.coaltimes Source code
lik.gentimes Source code
lik.sampletimes Source code
likseq Source code
likseqenv Source code
logLik.phybreak Man page Source code
make_nodehostsparents Source code
makenodehp Source code
makephyloparset Source code
makephyloparsets Source code
maketransplot Source code
mcctree Source code
mpcinfector Source code
mtcctree Source code
nfarray Source code
nflist Source code
nthsample Source code
obkData2phybreak Source code
pathtocycle 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
postinfector Source code
prepare.pbe Source code
propose.pbe Source code
ptr Source code
rankhostsforplot Source code
removetransnodes Source code
rinfectors Source code
rinftimes Source code
sample.phybreak Man page 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
sim.phybreak Man page Source code
sim.phylotree Source code
sim.sequences 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
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
whichgeneration Source code
phybreak documentation built on July 30, 2017, 5:02 p.m.