Inference of Transmission Tree from a Dated Phylogeny

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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