All functions 


Inference of Transmission Tree from a Dated Phylogeny 

Convert to coda mcmc format 

Build a matrix indicating for each pairs of individuals how many intermediates there are in the transmission chain 

Build a matrix of probability of who infected whom from a MCMC output 

Build a consensus transmission tree from a MCMC output 

Convert to coda mcmc format 

Return the date of last sample from a ttree or ctree or ptree 

Return the combined tree corresponding to a given iteration of the TransPhylo results 

Extracts phylogenetic tree from a combined phylogenetic/transmission tree 

Extracts transmission tree from a combined phylogenetic/transmission tree 

Extract and return realised generation time distribution 

Returns and/or plot numbers of sampled and unsampled cases over time 

Extract and return distribution of infection time of given sampled case(s) 

Extract and return offspring distribution of given sampled case(s) 

Extract and return realised sampling time distribution 

Infer transmission tree given a phylogenetic tree 

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". 

Create a transmission tree compatible with the provided phylogenetic tree 

Simulate a transmission tree 

Return the medoid from a MCMC output 

Converts a phylogenetic tree into an ape phylo object 

Plotting for ctree 

Plotting for ptree 

Plotting for resTransPhylo 

Plotting for ttree 

Plot both phylogenetic and transmission trees using colors on the phylogeny 

Plot a transmission tree in a detailed format 

Plot a transmission tree in an economic format 

Plot MCMC traces 

Print function for ctree objects 

Print function for ptree objects 

Print function for resTransPhylo objects 

Print function for ttree objects 

Calculate the probability of a phylogenetic tree given a transmission tree 

Calculate the probability of a phylogenetic tree given a transmission tree 

Calculates the logprobability of a transmission tree 

Calculates the logprobability of a transmission tree 

Converts an ape phylo object into a phylogenetic tree 

Select the most representative transmission tree from a MCMC output 

Simulate an outbreak 

Summary function for resTransPhylo objects 