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