Inference of Transmission Tree from a Dated Phylogeny
Convert to coda mcmc format
Build a matrix indicating for each pairs of individuals how many inter...
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 Tra...
Extracts phylogenetic tree from a combined phylogenetic/transmission t...
Extracts transmission tree from a combined phylogenetic/transmission t...
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 cas...
Extract and return offspring distribution of given sampled case(s)
Extract and return realised sampling time distribution
Simultaneously infer transmission trees given phylogenetic trees User ...
Infer transmission tree given a phylogenetic tree
Create a transmission tree compatible with the provided phylogenetic t...
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 phyl...
Plot MCMC traces
Plot a transmission tree in a detailed format
Plot a transmission tree in an economic format
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 ...
Calculate the probability of a phylogenetic tree given a transmission ...
Calculates the log-probability of a transmission tree
Calculates the log-probability 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
Inference of Transmission Tree from a Dated Phylogeny
Inference of transmission tree from a dated phylogeny. Includes methods to simulate and analyse outbreaks. The methodology is described in Didelot et al. (2014) <doi:10.1093/molbev/msu121>, Didelot et al. (2017) <doi:10.1093/molbev/msw275>.