# Inference of Transmission Tree from a Dated Phylogeny

## Documentation for package ‘TransPhylo’ version 1.4.5

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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
plotTraces | Plot MCMC traces
plotTTree | Plot a transmission tree in a detailed format
plotTTree2 | Plot a transmission tree in an economic format
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
TransPhylo | Inference of Transmission Tree from a Dated Phylogeny