All functions

TransPhylo-package TransPhylo

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