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    "hmean",
    "InflMat",
    "invDistWeighting",
    "isDivergent",
    "isLinear",
    "isTree",
    "isUnderEdge",
    "isUnderVertex",
    "labels<-",
    "locate",
    "model.data",
    "molEvolSim",
    "nedge",
    "PEM",
    "pemlm",
    "PEMweights",
    "Psquare",
    "purge.median",
    "purge.terminal",
    "randomGraph",
    "reorderGraph",
    "rm.edge",
    "rm.vertex",
    "show.sequence",
    "simulateSequence",
    "simulateTrait",
    "traitEvolSim",
    "weighted.hmean",
    "write.fasta"
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    {
      "page": "MPSEM-package",
      "title": "Modelling Phylogenetic Signals using Eigenvector Maps",
      "topics": [
        "MPSEM-package"
      ]
    },
    {
      "page": "concatenate",
      "title": "Sequence Concatenation",
      "topics": [
        "concatenate"
      ]
    },
    {
      "page": "dstGraph",
      "title": "Distance-Based Directed Graph",
      "topics": [
        "dstGraph"
      ]
    },
    {
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      "title": "Class and Method for Directed Graphs",
      "topics": [
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        "as.graph.phylo",
        "as.phylo.graph",
        "geometry.graph",
        "geometry<-.graph",
        "graph-class",
        "locate.graph",
        "nedge.graph",
        "plot.graph",
        "print.graph"
      ]
    },
    {
      "page": "graph-functions",
      "title": "MPSEM Graph Manipulation Functions",
      "topics": [
        "add.edge",
        "add.vertex",
        "graph",
        "graph-functions",
        "rm.edge",
        "rm.vertex"
      ]
    },
    {
      "page": "graph-purge",
      "title": "MPSEM Graph Purging Functions",
      "topics": [
        "graph-purge",
        "purge.median",
        "purge.terminal"
      ]
    },
    {
      "page": "graph-utils",
      "title": "Graph Utility Functions",
      "topics": [
        "getConnected",
        "getMedian",
        "getNonConnected",
        "getOrigin",
        "getTerminal",
        "graph-utils",
        "graphDist",
        "isDivergent",
        "isLinear",
        "isTree",
        "reorderGraph"
      ]
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    {
      "page": "graphModplot",
      "title": "Graph Plot Editor",
      "topics": [
        "graphModplot"
      ]
    },
    {
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      "topics": [
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        "hmean",
        "weighted.hmean"
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      "title": "Influence Matrix",
      "topics": [
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        "edge<-.InflMat",
        "edgenames.InflMat",
        "edgenames<-.InflMat",
        "InflMat",
        "inflMat",
        "InflMat-class",
        "nedge.InflMat",
        "print.InflMat"
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      "title": "Inverse Distance Weighting",
      "topics": [
        "invDistWeighting"
      ]
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      "page": "lm-utils",
      "title": "Linear Modelling Utility Functions",
      "topics": [
        "lm-utils",
        "model.data",
        "Psquare",
        "utils"
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    {
      "page": "molEvolSim",
      "title": "Molecular Evolution Simulator",
      "topics": [
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        "drawDNASequence",
        "drawEvolRate",
        "molEvolSim",
        "simulateSequence"
      ]
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    {
      "page": "MPSEM-generics",
      "title": "Generic Function (Methods)",
      "topics": [
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        "edge",
        "edge.graph",
        "edge<-",
        "edge<-.graph",
        "edgenames",
        "edgenames.graph",
        "edgenames<-",
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        "evolution.model",
        "geometry",
        "geometry<-",
        "labels<-",
        "locate",
        "MPSEM-generics",
        "nedge"
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      "page": "PEM-class",
      "title": "Class and Methods for Phylogenetic Eigenvector Maps (PEM)",
      "topics": [
        "as.data.frame.PEM",
        "as.matrix.PEM",
        "evolution.model.PEM",
        "PEM",
        "PEM-class",
        "predict.PEM",
        "print.PEM",
        "update.PEM"
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      "title": "Phylogenetic Eigenvector Maps",
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        "PEMweights"
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      "title": "Utility Function for Phylogenetic Eigenvector Maps",
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        "isUnderVertex",
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      "topics": [
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        "simulateTrait",
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      "title": "Write Sequences to a FASTA Text File",
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      "filename": "PEM_with_MPSEM.html",
      "title": "A phylogenetic modelling tutorial using Phylogenetic Eigenvector Maps (PEM) as implemented in R package MPSEM",
      "author": "Guillaume Guénard",
      "engine": "knitr::rmarkdown",
      "headings": [
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        "The Phylogenetic eigenvector maps (PEM) expression",
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        "Calculating PEM",
        "Edge weighting function",
        "Phylogenetic graph",
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