Man pages for xavierdidelot/TransPhylo
Inference of Transmission Tree under a Within-Host Evolution Model

computeMatTDistBuild a matrix indicating for each pairs of individuals how...
computeMatWIWBuild a matrix of probability of who infected whom from a...
consTTreeBuild a consensus transmission tree from a MCMC output
convertToCodaConvert to coda mcmc format
extractPTreeExtracts phylogenetic tree from a combined...
extractTTreeExtracts transmission tree from a combined...
getGenerationTimeDistExtract and return realised generation time distribution
getIncidentCasesReturns and/or plot numbers of sampled and unsampled cases...
getInfectionTimeDistExtract and return distribution of infection time of a given...
getSamplingTimeDistExtract and return realised sampling time distribution
infer_multittree_share_paramSimultaneously infer transmission trees given phylogenetic...
inferTTreeInfer transmission tree given a phylogenetic tree
makeCtreeFromPTreeCreate a transmission tree compatible with the provided...
makeTTreeSimulate a transmission tree
phyloFromPTreeConverts a phylogenetic tree into an ape phylo object
plotCTreePlot both phylogenetic and transmission trees using colors on...
plotTracesPlot MCMC traces
plotTTreePlot a transmission tree
plotTTree2Plot a transmission tree in an economic format
probPTreeGivenTTreeCalculate the probability of a phylogenetic tree given a...
probTTreeCalculates the log-probability of a transmission tree
probTTreeRCalculates the log-probability of a transmission tree
ptreeFromPhyloConverts an ape phylo object into a phylogenetic tree
selectTTreeSelect the most representative transmission tree from a MCMC...
simulateOutbreakSimulate an outbreak
TransPhyloInference of Transmission Tree under a Within-Host Evolution...
xavierdidelot/TransPhylo documentation built on Dec. 14, 2018, 5:24 p.m.