TransPhylo-package      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
