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  "Package": "STraTUS",
  "Title": "Enumeration and Uniform Sampling of Transmission Trees for a\nKnown Phylogeny",
  "Version": "1.1.2",
  "Authors@R": "c(person(\"Matthew\", \"Hall\", email = \"matthew.hall@bdi.ox.ac.uk\", role = c(\"aut\", \"cre\")), person(\"Caroline\", \"Colijn\", role = c(\"ctb\")))",
  "Author": "Matthew Hall [aut, cre], Caroline Colijn [ctb]",
  "Maintainer": "Matthew Hall <matthew.hall@bdi.ox.ac.uk>",
  "Description": "For a single, known pathogen phylogeny, provides functions\nfor enumeration of the set of compatible epidemic transmission\ntrees, and for uniform sampling from that set. Optional\narguments allow for incomplete sampling with a known number of\nmissing individuals, multiple sampling, and known infection\ntime limits. Always assumed are a complete transmission\nbottleneck and no superinfection or reinfection. See Hall and\nColijn (2019) <doi:10.1093/molbev/msz058> for methodology.",
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  "URL": "http://github.com/mdhall272/STraTUS/",
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  "Repository": "https://mdhall272.r-universe.dev",
  "Date/Publication": "2024-10-23 13:36:45 UTC",
  "RemoteUrl": "https://github.com/mdhall272/stratus",
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    "draw.incompletely.sampled",
    "sample.partial.tt",
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    "tt.generator"
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      "page": "build.edgelist",
      "title": "For a sample, produce the transmission tree as a 'igraph' object",
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      "title": "For a sample with no unsampled hosts, draw the annotated phylogeny using 'ggtree'",
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      "page": "draw.incompletely.sampled",
      "title": "For a sample with or without unsampled hosts, draw the annotated phylogeny using 'ggtree'",
      "topics": [
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    {
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      "title": "Resample the subtree rooted at any tree node, keeping the annotations for the rest of the tree fixed",
      "topics": [
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    {
      "page": "sample.tt",
      "title": "Sample one or more transmission trees uniformly",
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