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  "Package": "quadcleanR",
  "Title": "Cleanup and Visualization of Quadrat Data",
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  "Authors@R": "person(\"Dominique\", \"Maucieri\", role = c(\"aut\", \"cre\"), email = \"dominiquemaucieri@gmail.com\",\ncomment = c(ORCID = \"0000-0003-1849-2472\"))",
  "Description": "A tool that can be customized to aid in the clean up of\necological data collected using quadrats and can crop quadrats\nto ensure comparability between quadrats collected under\ndifferent methodologies.",
  "License": "GPL (>= 3)",
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  "Date/Publication": "2022-10-18 22:55:59 UTC",
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    "User": "root"
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  "Author": "Dominique Maucieri [aut, cre] (ORCID:\n<https://orcid.org/0000-0003-1849-2472>)",
  "Maintainer": "Dominique Maucieri <dominiquemaucieri@gmail.com>",
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  "_created": "2026-10-11T09:53:13.000Z",
  "_published": "2026-10-11T10:11:58.485Z",
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    "categorize",
    "change_names",
    "change_values",
    "cover_calc",
    "crop_area",
    "keep_rm",
    "rm_chr",
    "sample_size",
    "sum_cols",
    "usable_obs",
    "visualize_app"
  ],
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      "title": "Labelset for Corals",
      "object": "coral_labelset",
      "class": [
        "data.frame"
      ],
      "fields": [
        "short_name",
        "full_name",
        "taxonomic_name",
        "functional_group",
        "life_history"
      ],
      "rows": 134,
      "table": true,
      "tojson": true
    },
    {
      "name": "corals",
      "title": "Simple Coral Quadrat Data",
      "object": "corals",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Field.Season",
        "Site",
        "Quadrat",
        "AcCor",
        "AcDig",
        "AcroTab",
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        "Lepta",
        "Sinu",
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        "Lobph",
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        "Unc",
        "SHAD"
      ],
      "rows": 1355,
      "table": true,
      "tojson": true
    },
    {
      "name": "environmental_data",
      "title": "Sample Environmental Data for Cleaning Vignettes",
      "object": "environmental_data",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Site",
        "HD_Cat",
        "HD_Cont",
        "NPP",
        "WE",
        "Region",
        "WaveEnergy"
      ],
      "rows": 40,
      "table": true,
      "tojson": true
    },
    {
      "name": "final_cleaned",
      "title": "Final cleaned quadrat data",
      "object": "final_cleaned",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Field.Season",
        "TimeBlock",
        "Site",
        "Quadrat",
        "HD_Cat",
        "HD_Cont",
        "NPP",
        "WE",
        "Region",
        "WaveEnergy",
        "Taxonomic_Name",
        "functional_group",
        "life_history",
        "prop_cover"
      ],
      "rows": 15772,
      "table": true,
      "tojson": true
    },
    {
      "name": "softcoral_annotations",
      "title": "Sample Annotation Data for Cropping Vignette",
      "object": "softcoral_annotations",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Name",
        "Row",
        "Column",
        "Label"
      ],
      "rows": 454900,
      "table": true,
      "tojson": true
    },
    {
      "name": "softcoral_LQuads",
      "title": "Sample Quadrat Data (1m by 1m)",
      "object": "softcoral_LQuads",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Image.ID",
        "Image.name",
        "Annotation.status",
        "Points",
        "AcCor",
        "AcDig",
        "Acr_arb",
        "Acrop",
        "AcroTab",
        "Astreo",
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        "B_Astre",
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        "B_Echin",
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        "B_Favia",
        "B_FaviaM",
        "B_FaviaS",
        "B_FaviaSt",
        "B_Favites",
        "B_FavPent",
        "B_Fung",
        "BGard",
        "B_GonEd",
        "B_Herpo",
        "B_HYDNO",
        "B_HyExe",
        "BlAcro.Cor",
        "B_Lepta",
        "B_Lepto",
        "Blisop",
        "B_Lobo",
        "BlTurbFol",
        "B_MOEN",
        "B_MOFO",
        "B_Monta",
        "B_Monti",
        "B_Oxyp",
        "B_Paly",
        "B_PaveDUER",
        "B_Pavona",
        "B_PEYDO",
        "B_Plat",
        "B_PMEAN",
        "B_Pocillo",
        "B_Porit",
        "B_Psam",
        "B_PVAR",
        "B_Sando",
        "B_UnkCoral",
        "Cirr",
        "COSC",
        "ECHIN",
        "Fav",
        "FavHal",
        "Favia",
        "FaviaM",
        "FaviaS",
        "FaviaSt",
        "FavPent",
        "Fung",
        "Gardin",
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        "Plat",
        "Plero",
        "PMEAN",
        "Pocill",
        "Porit",
        "Psam",
        "PVAR",
        "Sando",
        "Tuba",
        "TURB",
        "UnkCoral",
        "ANEM",
        "B_Clad",
        "B_Sinu",
        "Clad",
        "EncBry",
        "EUR",
        "HYDCO",
        "Hydra",
        "Mille",
        "MOBI",
        "Sarco",
        "SECO",
        "Sinu",
        "Sponge",
        "Stylas",
        "UnkTUN",
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        "Lobph",
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      "rows": 4106,
      "table": true,
      "tojson": true
    },
    {
      "name": "softcoral_SQuads",
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      ],
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      "rows": 2522,
      "table": true,
      "tojson": true
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  ],
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    {
      "page": "add_data",
      "title": "Add data to existing data frame.",
      "topics": [
        "add_data"
      ]
    },
    {
      "page": "categorize",
      "title": "Categorize data based on contents of a column",
      "topics": [
        "categorize"
      ]
    },
    {
      "page": "change_names",
      "title": "Change names of columns",
      "topics": [
        "change_names"
      ]
    },
    {
      "page": "change_values",
      "title": "Change values within a column",
      "topics": [
        "change_values"
      ]
    },
    {
      "page": "coral_labelset",
      "title": "Labelset for Corals",
      "topics": [
        "coral_labelset"
      ]
    },
    {
      "page": "corals",
      "title": "Simple Coral Quadrat Data",
      "topics": [
        "corals"
      ]
    },
    {
      "page": "cover_calc",
      "title": "Calculate species cover",
      "topics": [
        "cover_calc"
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    },
    {
      "page": "crop_area",
      "title": "Crop quadrats based on area",
      "topics": [
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    },
    {
      "page": "environmental_data",
      "title": "Sample Environmental Data for Cleaning Vignettes",
      "topics": [
        "environmental_data"
      ]
    },
    {
      "page": "final_cleaned",
      "title": "Final cleaned quadrat data",
      "topics": [
        "final_cleaned"
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    {
      "page": "keep_rm",
      "title": "Keep or remove rows and columns from data frame",
      "topics": [
        "keep_rm"
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    {
      "page": "rm_chr",
      "title": "Remove characters from data frame",
      "topics": [
        "rm_chr"
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    },
    {
      "page": "sample_size",
      "title": "Calculate sample sizes",
      "topics": [
        "sample_size"
      ]
    },
    {
      "page": "softcoral_annotations",
      "title": "Sample Annotation Data for Cropping Vignette",
      "topics": [
        "softcoral_annotations"
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    },
    {
      "page": "softcoral_LQuads",
      "title": "Sample Quadrat Data (1m by 1m)",
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        "softcoral_LQuads"
      ]
    },
    {
      "page": "softcoral_SQuads",
      "title": "Sample Quadrat Data (0.6m by 0.9m)",
      "topics": [
        "softcoral_SQuads"
      ]
    },
    {
      "page": "sum_cols",
      "title": "Sum columns based on matching names",
      "topics": [
        "sum_cols"
      ]
    },
    {
      "page": "usable_obs",
      "title": "Extract usable observations",
      "topics": [
        "usable_obs"
      ]
    },
    {
      "page": "visualize_app",
      "title": "Visualize cleaned data",
      "topics": [
        "visualize_app"
      ]
    }
  ],
  "_pkglogo": "https://github.com/dominiquemaucieri/quadcleanr/raw/HEAD/man/figures/logo.png",
  "_readme": "https://github.com/dominiquemaucieri/quadcleanr/raw/HEAD/README.md",
  "_rundeps": [
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  "_vignettes": [
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      "source": "cleaning_cropping_coral.Rmd",
      "filename": "cleaning_cropping_coral.html",
      "title": "Cleaning and Cropping Quadrat Data from CoralNet",
      "engine": "knitr::rmarkdown",
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        "Exploration"
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      "title": "Cleaning Quadrat Data from CoralNet",
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      "headings": [
        "Introduction",
        "Cleaning the Data",
        "Exploration"
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      "modified": "2022-09-02 17:38:36",
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      "source": "function_examples.Rmd",
      "filename": "function_examples.html",
      "title": "Simple Examples of Functions",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Cleaning Functions",
        "1. change_names()",
        "2. change_values()",
        "3. keep_rm()",
        "4. rm_chr()",
        "5. sum_cols()",
        "Adding Functions",
        "1. add_data()",
        "2. categorize()",
        "Processing Functions",
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        "2. crop_area()",
        "3. usable_obs()",
        "Assessing Functions",
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      "created": "2022-08-31 18:31:19",
      "modified": "2022-10-13 22:47:51",
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      "source": "cropping.Rmd",
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      "title": "Why to Crop Quadrats by Area",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Randomized Data",
        "Coral Data",
        "References"
      ],
      "created": "2022-02-19 00:17:37",
      "modified": "2022-04-18 20:13:20",
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