{
  "_id": "6a1efa7ab401979e7341873b",
  "Package": "SMITIDstruct",
  "Type": "Package",
  "Encoding": "UTF-8",
  "Title": "Data Structure and Manipulations Tool for Host and Viral\nPopulation",
  "Version": "0.0.5",
  "Date": "2019-06-14",
  "Authors@R": "c(person(\"Jean-Francois\", \"Rey\", role = c(\"aut\", \"cre\"), email = \"jean-francois.rey@inra.fr\"))",
  "Author": "Jean-Francois Rey [aut, cre]",
  "Maintainer": "Jean-Francois Rey <jean-francois.rey@inra.fr>",
  "Description": "Statistical Methods for Inferring Transmissions of\nInfectious Diseases from deep sequencing data (SMITID). It\nallow sequence-space-time host and viral population data\nstorage, indexation and querying.",
  "License": "GPL (>= 2) | file LICENSE",
  "BuildVignettes": "true",
  "NeedsCompilation": "no",
  "Biarch": "true",
  "URL": "https://informatique-mia.inra.fr/biosp/anr-smitid-project,\nhttps://gitlab.paca.inra.fr/SMITID/structR",
  "BugReports": "https://gitlab.paca.inra.fr/SMITID/structR/issues",
  "DependsNote": "BioC (>= 3.0)",
  "ImportsNote": "BioC (>= 3.0), Recommended: Biostrings",
  "Collate": "'Class-Host.R' 'Class-ViralPop.R' 'Methods-Host.R'\n'Methods-ViralPop.R' 'Methods-time.R' 'SMITIDstruct.R' 'demo.R'\n'diversity.R' 'index.R'",
  "RoxygenNote": "6.1.1",
  "Packaged": {
    "Date": "2026-05-18 15:23:27 UTC",
    "User": "root"
  },
  "Config/pak/sysreqs": "libabsl-dev cmake libgdal-dev gdal-bin libgeos-dev\nlibssl-dev libproj-dev libsqlite3-dev libudunits2-dev\nzlib1g-dev",
  "Repository": "https://cranhaven.r-universe.dev",
  "Date/Publication": "2026-05-18 06:02:00 UTC",
  "RemoteUrl": "https://github.com/cranhaven/cranhaven.r-universe.dev",
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  "_updates": [
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  "_tags": [],
  "_topics": [
    "archived",
    "packages",
    "r-universe"
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  "_stars": 5,
  "_contributors": [
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      "user": "henrikbengtsson",
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    "description": "CRANhaven - Repository for Recently Archived CRAN Packages"
  },
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    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/SMITIDstruct"
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  "_devurl": "https://github.com/cranhaven/cranhaven.r-universe.dev",
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  "_rbuild": "4.6.0",
  "_assets": [
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    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/SMITIDstruct.html",
    "manual.pdf"
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  "_releases": [
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    },
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      "date": "2019-03-08"
    },
    {
      "version": "0.0.5",
      "date": "2019-06-17"
    }
  ],
  "_exports": [
    "addHost",
    "addViralObs",
    "concatViralPop",
    "createAViralPop",
    "createHost",
    "createIndex",
    "demo.SMITIDstruct.run",
    "diversity.pDistance",
    "diversity.sfs",
    "getCov",
    "getDate",
    "getDiversity.pDistance",
    "getDiversity.sfs",
    "getInfosByHostAndTime",
    "getStates",
    "getTimeLine",
    "getTimestamp",
    "getTransmissionTree",
    "is.juliendate",
    "is.StringDate",
    "is.timestamp",
    "isInCode",
    "loadCoords",
    "loadCovs",
    "loadHost",
    "loadStates",
    "loadTree",
    "loadTreeDF",
    "loadViralObs",
    "loadViralPop",
    "loadViralPopSet",
    "mergeCode",
    "plotDiversity.pDistance",
    "plotDiversity.sfs",
    "simulateStates"
  ],
  "_help": [
    {
      "page": "SMITIDstruct-package",
      "title": "Data Structure and Manipulation Tool for Host and Viral Population",
      "topics": [
        "SMITIDstruct-package",
        "SMITIDstruct",
        "_PACKAGE"
      ]
    },
    {
      "page": "addcode",
      "title": "addcode",
      "topics": [
        "addcode"
      ]
    },
    {
      "page": "addHost",
      "title": "addHost",
      "topics": [
        "addHost"
      ]
    },
    {
      "page": "addIndex",
      "title": "addIndex",
      "topics": [
        "addIndex"
      ]
    },
    {
      "page": "addViralObs",
      "title": "addViralObs",
      "topics": [
        "addViralObs"
      ]
    },
    {
      "page": "alleleCount",
      "title": "alleleCount",
      "topics": [
        "alleleCount"
      ]
    },
    {
      "page": "concatViralPop",
      "title": "concatViralPop",
      "topics": [
        "concatViralPop"
      ]
    },
    {
      "page": "createAViralPop",
      "title": "createAViralPop",
      "topics": [
        "createAViralPop"
      ]
    },
    {
      "page": "createHost",
      "title": "createHost",
      "topics": [
        "createHost"
      ]
    },
    {
      "page": "createIndex",
      "title": "createIndex",
      "topics": [
        "createIndex"
      ]
    },
    {
      "page": "demo.SMITIDstruct.run",
      "title": "demo.SMITIDstruct.run",
      "topics": [
        "demo.SMITIDstruct.run"
      ]
    },
    {
      "page": "diversity.pDistance",
      "title": "diversity.pDistance",
      "topics": [
        "diversity.pDistance"
      ]
    },
    {
      "page": "diversity.sfs",
      "title": "diversity.sfs",
      "topics": [
        "diversity.sfs"
      ]
    },
    {
      "page": "getCov",
      "title": "getCov",
      "topics": [
        "getCov"
      ]
    },
    {
      "page": "getDate",
      "title": "getDate",
      "topics": [
        "getDate"
      ]
    },
    {
      "page": "getDiversity.pDistance",
      "title": "getDiversity.pDistance",
      "topics": [
        "getDiversity.pDistance"
      ]
    },
    {
      "page": "getDiversity.sfs",
      "title": "getDiversity.sfs",
      "topics": [
        "getDiversity.sfs"
      ]
    },
    {
      "page": "getInfosByHostAndTime",
      "title": "getInfosByHostAndTime",
      "topics": [
        "getInfosByHostAndTime"
      ]
    },
    {
      "page": "getStates",
      "title": "getStates",
      "topics": [
        "getStates"
      ]
    },
    {
      "page": "getTimeLine",
      "title": "getTimeLine",
      "topics": [
        "getTimeLine"
      ]
    },
    {
      "page": "getTimestamp",
      "title": "getTimestamp",
      "topics": [
        "getTimestamp"
      ]
    },
    {
      "page": "getTransmissionTree",
      "title": "getTransmissionTree",
      "topics": [
        "getTransmissionTree"
      ]
    },
    {
      "page": "Host",
      "title": "Class Host",
      "topics": [
        "Host",
        "Host-class"
      ]
    },
    {
      "page": "is.juliendate",
      "title": "is.juliendate",
      "topics": [
        "is.juliendate"
      ]
    },
    {
      "page": "is.StringDate",
      "title": "is.StringDate",
      "topics": [
        "is.StringDate"
      ]
    },
    {
      "page": "is.timestamp",
      "title": "is.timestamp",
      "topics": [
        "is.timestamp"
      ]
    },
    {
      "page": "isInCode",
      "title": "isInCode",
      "topics": [
        "isInCode"
      ]
    },
    {
      "page": "loadCoords",
      "title": "loadCoords",
      "topics": [
        "loadCoords"
      ]
    },
    {
      "page": "loadCovs",
      "title": "loadCovs",
      "topics": [
        "loadCovs"
      ]
    },
    {
      "page": "loadHost",
      "title": "loadHost",
      "topics": [
        "loadHost"
      ]
    },
    {
      "page": "loadStates",
      "title": "loadStates",
      "topics": [
        "loadStates"
      ]
    },
    {
      "page": "loadTree",
      "title": "loadTree",
      "topics": [
        "loadTree"
      ]
    },
    {
      "page": "loadTreeDF",
      "title": "loadTreeDF",
      "topics": [
        "loadTreeDF"
      ]
    },
    {
      "page": "loadViralObs",
      "title": "loadViralObs",
      "topics": [
        "loadViralObs"
      ]
    },
    {
      "page": "loadViralPop",
      "title": "loadViralPop",
      "topics": [
        "loadViralPop"
      ]
    },
    {
      "page": "loadViralPopSet",
      "title": "loadViralPopSet",
      "topics": [
        "loadViralPopSet"
      ]
    },
    {
      "page": "mergeCode",
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      ]
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        "plotDiversity.pDistance"
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    },
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      "title": "plotDiversity.sfs",
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      "page": "setStates",
      "title": "setStates",
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        "setStates"
      ]
    },
    {
      "page": "simulateStates",
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      "topics": [
        "simulateStates"
      ]
    },
    {
      "page": "ViralPop-class",
      "title": "Class ViralPop",
      "topics": [
        "ViralPop",
        "ViralPop-class"
      ]
    }
  ],
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