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TransPhylo-package
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Inference of Transmission Tree from a Dated Phylogeny |
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as.mcmc.resTransPhylo()
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Convert to coda mcmc format |
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computeMatTDist()
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Build a matrix indicating for each pairs of individuals how many intermediates there are in the transmission chain |
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computeMatWIW()
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Build a matrix of probability of who infected whom from a MCMC output |
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consTTree()
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Build a consensus transmission tree from a MCMC output |
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convertToCoda()
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Convert to coda mcmc format |
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dateLastSample()
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Return the date of last sample from a ttree or ctree or ptree |
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extractCTree()
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Return the combined tree corresponding to a given iteration of the TransPhylo results |
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extractPTree()
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Extracts phylogenetic tree from a combined phylogenetic/transmission tree |
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extractTTree()
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Extracts transmission tree from a combined phylogenetic/transmission tree |
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getGenerationTimeDist()
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Extract and return realised generation time distribution |
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getIncidentCases()
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Returns and/or plot numbers of sampled and unsampled cases over time |
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getInfectionTimeDist()
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Extract and return distribution of infection time of given sampled case(s) |
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getOffspringDist()
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Extract and return offspring distribution of given sampled case(s) |
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getSamplingTimeDist()
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Extract and return realised sampling time distribution |
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inferTTree()
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Infer transmission tree given a phylogenetic tree |
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infer_multittree_share_param()
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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". |
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makeCTreeFromPTree()
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Create a transmission tree compatible with the provided phylogenetic tree |
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makeTTree()
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Simulate a transmission tree |
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medTTree()
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Return the medoid from a MCMC output |
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phyloFromPTree()
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Converts a phylogenetic tree into an ape phylo object |
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plot(<ctree>)
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Plotting for ctree |
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plot(<ptree>)
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Plotting for ptree |
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plot(<resTransPhylo>)
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Plotting for resTransPhylo |
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plot(<ttree>)
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Plotting for ttree |
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plotCTree()
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Plot both phylogenetic and transmission trees using colors on the phylogeny |
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plotTTree()
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Plot a transmission tree in a detailed format |
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plotTTree2()
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Plot a transmission tree in an economic format |
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plotTraces()
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Plot MCMC traces |
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print(<ctree>)
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Print function for ctree objects |
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print(<ptree>)
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Print function for ptree objects |
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print(<resTransPhylo>)
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Print function for resTransPhylo objects |
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print(<ttree>)
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Print function for ttree objects |
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probPTreeGivenTTree()
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Calculate the probability of a phylogenetic tree given a transmission tree |
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probPTreeGivenTTreeR()
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Calculate the probability of a phylogenetic tree given a transmission tree |
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probTTree()
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Calculates the log-probability of a transmission tree |
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probTTreeR()
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Calculates the log-probability of a transmission tree |
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ptreeFromPhylo()
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Converts an ape phylo object into a phylogenetic tree |
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selectTTree()
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Select the most representative transmission tree from a MCMC output |
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simulateOutbreak()
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Simulate an outbreak |
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summary(<resTransPhylo>)
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Summary function for resTransPhylo objects |