as.mcmc.resTransPhylo | Convert to coda mcmc format |
computeMatTDist | Build a matrix indicating for each pairs of individuals how... |
computeMatWIW | Build a matrix of probability of who infected whom from a... |
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... |
extractPTree | Extracts phylogenetic tree from a combined... |
extractTTree | Extracts transmission tree from a combined... |
getGenerationTimeDist | Extract and return realised generation time distribution |
getIncidentCases | Returns and/or plot numbers of sampled and unsampled cases... |
getInfectionTimeDist | Extract and return distribution of infection time of given... |
getOffspringDist | Extract and return offspring distribution of given sampled... |
getSamplingTimeDist | Extract and return realised sampling time distribution |
infer_multittree_share_param | Simultaneously infer transmission trees given phylogenetic... |
inferTTree | Infer transmission tree given a phylogenetic tree |
makeCtreeFromPTree | Create a transmission tree compatible with the provided... |
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 |
plotCTree | Plot both phylogenetic and transmission trees using colors on... |
plot.ptree | Plotting for ptree |
plot.resTransPhylo | Plotting for resTransPhylo |
plotTraces | Plot MCMC traces |
plot.ttree | Plotting for ttree |
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... |
probPTreeGivenTTreeR | Calculate the probability of a phylogenetic tree given a... |
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... |
simulateOutbreak | Simulate an outbreak |
summary.resTransPhylo | Summary function for resTransPhylo objects |
TransPhylo-package | Inference of Transmission Tree from a Dated Phylogeny |
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