{
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  "Package": "plantTracker",
  "Title": "Extract Demographic and Competition Data from Fine-Scale Maps",
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  "Date": "2026-01-09",
  "Authors@R": "c(\nperson(\"Alice\", \"Stears\", , \"alice.e.stears@gmail.com\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-1325-6641\")),\nperson(\"Jared\", \"Studyvin\", , \"studyvin@uwyo.edu\", role = \"aut\"),\nperson(\"David\", \"Atkins\", , \"datkins8@uwyo.edu\", role = \"aut\")\n)",
  "Author": "Alice Stears [aut, cre]\n(<https://orcid.org/0000-0002-1325-6641>), Jared Studyvin\n[aut], David Atkins [aut]",
  "Maintainer": "Alice Stears <alice.e.stears@gmail.com>",
  "Description": "Extracts growth, survival, and local neighborhood density\ninformation from repeated, fine-scale maps of organism\noccurrence. Further information about this package can be found\nin our journal article, \"plantTracker: An R package to\ntranslate maps of plant occurrence into demographic data\"\npublished in 2022 in Methods in Ecology and Evolution (Stears,\net al., 2022) <doi:10.1111/2041-210X.13950>.",
  "License": "MIT + file LICENSE",
  "URL": "https://github.com/aestears/plantTracker",
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  "Repository": "https://aestears.r-universe.dev",
  "Date/Publication": "2026-04-30 22:12:38 UTC",
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    "spatial"
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    "aggregateByGenet",
    "checkDat",
    "drawQuadMap",
    "getBasalAreas",
    "getLambda",
    "getNeighbors",
    "getRecruits",
    "groupByGenet",
    "trackSpp"
  ],
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      "name": "grasslandData",
      "title": "Chart Quadrat Dataset for grassland species in MT and AZ An example dataset that contains data from mapped plant chart quadrats. Each row is an observation of one plant.",
      "object": "grasslandData",
      "class": [
        "sf",
        "data.frame"
      ],
      "fields": [
        "Species",
        "Clone",
        "Seedling",
        "Stems",
        "Basal",
        "Type",
        "Site",
        "Quad",
        "Year",
        "sp_code_4",
        "sp_code_6",
        "Area",
        "geometry"
      ],
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    },
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      "object": "grasslandInventory",
      "class": [
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      ],
      "fields": [],
      "table": false,
      "tojson": true
    }
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    {
      "page": "plantTracker-package",
      "title": "Extract Demographic and Competition Data from Fine-Scale Maps",
      "topics": [
        "plantTracker-package",
        "plantTracker"
      ]
    },
    {
      "page": "aggregateByGenet",
      "title": "aggregateByGenet",
      "topics": [
        "aggregateByGenet"
      ]
    },
    {
      "page": "assign",
      "title": "Tracks genets through time",
      "topics": [
        "assign"
      ]
    },
    {
      "page": "checkDat",
      "title": "checkDat",
      "topics": [
        "checkDat"
      ]
    },
    {
      "page": "drawQuadMap",
      "title": "Create maps of a quadrat over time",
      "topics": [
        "drawQuadMap"
      ]
    },
    {
      "page": "getBasalAreas",
      "title": "Calculates basal area for each species in a quadrat",
      "topics": [
        "getBasalAreas"
      ]
    },
    {
      "page": "getLambda",
      "title": "Calculates lambda, the population growth rate, for each species in a quadrat based on changes in basal cover.",
      "topics": [
        "getLambda"
      ]
    },
    {
      "page": "getNeighbors",
      "title": "Calculates local neighborhood density around each individual in a mapped dataset",
      "topics": [
        "getNeighbors"
      ]
    },
    {
      "page": "getRecruits",
      "title": "Calculates the number of recruits of each species per year in each quadrat",
      "topics": [
        "getRecruits"
      ]
    },
    {
      "page": "grasslandData",
      "title": "Chart Quadrat Dataset for grassland species in MT and AZ An example dataset that contains data from mapped plant chart quadrats. Each row is an observation of one plant.",
      "topics": [
        "grasslandData"
      ]
    },
    {
      "page": "grasslandInventory",
      "title": "A dataset indicating sampling years for the grasslandData example dataset",
      "topics": [
        "grasslandInventory"
      ]
    },
    {
      "page": "groupByGenet",
      "title": "Group polygon observations together into a 'genet' based on proximity",
      "topics": [
        "groupByGenet"
      ]
    },
    {
      "page": "trackSpp",
      "title": "Tracks genets through time for multiple species and sites",
      "topics": [
        "trackSpp"
      ]
    }
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      "filename": "Suggested_plantTracker_Workflow.html",
      "title": "Suggested plantTracker Workflow",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "1. Prepare data",
        "1.1 The dat data frame must . . .",
        "1.1.1 Get your data into the sf data format",
        "1.2 The inv list must . . .",
        "1.3 Check the inv and dat arguments  using checkDat()",
        "2 Track individuals through time using trackSpp()",
        "2.1 Function arguments",
        "2.2 Function output",
        "3 Calculate local neighborhood density using getNeighbors()",
        "3.1 Function options and arguments",
        "3.2 Function outputs",
        "4 Next steps"
      ],
      "created": "2021-07-27 20:41:29",
      "modified": "2026-01-09 21:56:12",
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      "source": "Using_the_plantTracker_trackSpp_function.Rmd",
      "filename": "Using_the_plantTracker_trackSpp_function.html",
      "title": "Using the plantTracker trackSpp() function",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "1 Input data",
        "3.3 Assign age and recruitment data to first year",
        "3.4 Compare sequential years of data to track individuals through time",
        "3.4.1 Is there a gap between year i-1 and year i?",
        "3.4.2 Get data for year i",
        "3.4.3 Are there any observations in the \"previous\" year (inv[i-1])?",
        "3.4.4 Add a buffer around the \"previous\" year data",
        "3.4.5 Are there actually any observations in the \"current\" year (inv[i])?",
        "3.4.6 Store observations as \"ghosts\" to compare to data from the next year (inv[i+1]) during the next iteration of the loop.",
        "3.4.7 Are there any overlaps between polygons in tempPreviousYear and tempCurrentYear?",
        "3.4.8 Compare the overlap between tempPreviousYear and tempCurrentYear to assign trackIDs.",
        "3.4.9 Flag any suspect observations",
        "3.4.10 Separate the \"ghosts\" and the new recruits from the \"parent\" and \"child\" data frames",
        "3.4.11 Store the resulting demographic data",
        "3.4.12 Get ready for the next iteration of the loop",
        "4 Prepare the trackSpp() results to be returned!",
        "4.1 Aggregate the results by genet",
        "4.2 Informative messages",
        "5 Examples"
      ],
      "created": "2021-10-12 20:36:01",
      "modified": "2025-10-28 22:27:50",
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