API for TransPhylo
Inference of Transmission Tree from a Dated Phylogeny

Global functions
.computeHost	Source code
.glueTrees	Source code
TransPhylo	Man page
TransPhylo-package	Man page
as.mcmc.resTransPhylo	Man page Source code
coalescent	Source code
computeMatTDist	Man page Source code
computeMatWIW	Man page Source code
consTTree	Man page Source code
convertToCoda	Man page Source code
dateLastSample	Man page Source code
extractCTree	Man page Source code
extractPTree	Man page Source code
extractTTree	Man page Source code
getGenerationTimeDist	Man page Source code
getGenerationTimes	Source code
getIncidentCases	Man page Source code Source code
getInfectionTimeDist	Man page Source code
getInfectionTimes	Source code
getNumberUnsampled	Source code
getOffspringDist	Man page Source code
getOmegaR	Source code
getOmegabarR	Source code
getSamplingTimeDist	Man page Source code
getTTreeDistInfo	Source code
inferTTree	Man page Source code
infer_multittree_share_param	Man page Source code
log_subtract_exp	Source code
log_sum_exp	Source code
log_sum_exp_vec	Source code
makeCTreeFromPTree	Man page Source code
makeTTree	Man page Source code
medTTree	Man page Source code
move1	Source code
move2	Source code
move3	Source code
networkPlot	Source code
phyloFromPTree	Man page Source code
plot.ctree	Man page Source code
plot.ptree	Man page Source code
plot.resTransPhylo	Man page Source code
plot.ttree	Man page Source code
plotCTree	Man page Source code
plotTTree	Man page Source code
plotTTree2	Man page Source code
plotTraces	Man page Source code
print.ctree	Man page Source code
print.ptree	Man page Source code
print.resTransPhylo	Man page Source code
print.ttree	Man page Source code
probPTreeGivenTTree	Man page Source code
probPTreeGivenTTreeR	Man page Source code
probSubtree	Source code
probSubtreeLinear	Source code
probSubtreeR	Source code
probTTree	Man page Source code
probTTreeR	Man page Source code
proposal	Source code
ptreeFromPhylo	Man page Source code
rexpT	Source code
selectTTree	Man page Source code
seqML	Source code
simulateOutbreak	Man page Source code
summary.resTransPhylo	Man page Source code
treeAdd	Source code
treeRem	Source code
wbar	Source code
withinhost	Source code
withinhostLinear	Source code
wstar_rootFinderR	Source code