Function reference • TransPhylo

All functions
`TransPhylo-package` `TransPhylo`	Inference of Transmission Tree from a Dated Phylogeny
`as.mcmc.resTransPhylo()`	Convert to coda mcmc format
`computeMatTDist()`	Build a matrix indicating for each pairs of individuals how many intermediates there are in the transmission chain
`computeMatWIW()`	Build a matrix of probability of who infected whom from a MCMC output
`consTTree()`	Build a consensus transmission tree from a MCMC output
`convertToCoda()`	Convert to coda mcmc format
`dateLastSample()`	Return the date of last sample from a ttree or ctree or ptree
`extractCTree()`	Return the combined tree corresponding to a given iteration of the TransPhylo results
`extractPTree()`	Extracts phylogenetic tree from a combined phylogenetic/transmission tree
`extractTTree()`	Extracts transmission tree from a combined phylogenetic/transmission tree
`getGenerationTimeDist()`	Extract and return realised generation time distribution
`getIncidentCases()`	Returns and/or plot numbers of sampled and unsampled cases over time
`getInfectionTimeDist()`	Extract and return distribution of infection time of given sampled case(s)
`getOffspringDist()`	Extract and return offspring distribution of given sampled case(s)
`getSamplingTimeDist()`	Extract and return realised sampling time distribution
`inferTTree()`	Infer transmission tree given a phylogenetic tree
`infer_multittree_share_param()`	Simultaneously infer transmission trees given phylogenetic trees User can specify any subset of parameters that will be shared by providing a character vector of parameter names to the argument "share".
`makeCTreeFromPTree()`	Create a transmission tree compatible with the provided phylogenetic tree
`makeTTree()`	Simulate a transmission tree
`medTTree()`	Return the medoid from a MCMC output
`phyloFromPTree()`	Converts a phylogenetic tree into an ape phylo object
`plot(<ctree>)`	Plotting for ctree
`plot(<ptree>)`	Plotting for ptree
`plot(<resTransPhylo>)`	Plotting for resTransPhylo
`plot(<ttree>)`	Plotting for ttree
`plotCTree()`	Plot both phylogenetic and transmission trees using colors on the phylogeny
`plotTTree()`	Plot a transmission tree in a detailed format
`plotTTree2()`	Plot a transmission tree in an economic format
`plotTraces()`	Plot MCMC traces
`print(<ctree>)`	Print function for ctree objects
`print(<ptree>)`	Print function for ptree objects
`print(<resTransPhylo>)`	Print function for resTransPhylo objects
`print(<ttree>)`	Print function for ttree objects
`probPTreeGivenTTree()`	Calculate the probability of a phylogenetic tree given a transmission tree
`probPTreeGivenTTreeR()`	Calculate the probability of a phylogenetic tree given a transmission tree
`probTTree()`	Calculates the log-probability of a transmission tree
`probTTreeR()`	Calculates the log-probability of a transmission tree
`ptreeFromPhylo()`	Converts an ape phylo object into a phylogenetic tree
`selectTTree()`	Select the most representative transmission tree from a MCMC output
`simulateOutbreak()`	Simulate an outbreak
`summary(<resTransPhylo>)`	Summary function for resTransPhylo objects

Reference

All functions