{
  "_id": "6a21e33fcd65a98ecbd41b45",
  "Package": "zooper",
  "Title": "Download and Integrate Zooplankton Datasets from the Upper San\nFrancisco Estuary",
  "Version": "2.5.0.9000",
  "Date": "2019-12-13",
  "Authors@R": "c(person(given = c(\"Samuel\", \"M\"),\nfamily = \"Bashevkin\",\nrole = c(\"aut\", \"cre\"),\nemail = \"sam.bashevkin@waterboards.ca.gov\",\ncomment = c(ORCID = \"0000-0001-7406-7089\")),\nperson(given = \"Rosemary\",\nfamily = \"Hartman\",\nrole = c(\"aut\"),\nemail = \"Rosemary.Hartman@water.ca.gov\",\ncomment = c(ORCID = \"0000-0002-0642-183X\")),\nperson(given = \"Karrin\",\nfamily = \"Alstad\",\nrole = c(\"aut\"),\nemail = \"Karrin.Alstad@wildlife.ca.gov\"),\nperson(given = \"Catarina\",\nfamily = \"Pien\",\nrole = c(\"aut\"),\nemail = \"cpien@usbr.gov\",\ncomment = c(ORCID = \"0000-0003-4427-6300\")))",
  "Description": "This package downloads and integrates zooplankton datasets\nfrom the Sacramento San Joaquin Delta. Datasets are manipulated\ninto a consistent format and bound together, then differences\nin taxonomic resolution among datasets are resolved using one\nof two methods, depending on whether the user wishes to analyze\ncommunity or taxa-specific trends.  Ancillary environmental\ndata are retained in the final dataset. Users can also filter\nthe dataset by a number of parameters.",
  "License": "GPL-3",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "LazyDataCompression": "xz",
  "URL": "https://github.com/InteragencyEcologicalProgram/zooper",
  "BugReports": "https://github.com/InteragencyEcologicalProgram/zooper/issues",
  "RoxygenNote": "7.3.3",
  "Language": "en-US",
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  "Config/pak/sysreqs": "libicu-dev libxml2-dev libssl-dev libx11-dev",
  "Repository": "https://sbashevkin.r-universe.dev",
  "Date/Publication": "2026-06-04 19:20:46 UTC",
  "RemoteUrl": "https://github.com/InteragencyEcologicalProgram/zooper",
  "RemoteRef": "HEAD",
  "RemoteSha": "2e1a7368bd82311fe494c8ea428811958c5b276f",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-06-04 20:28:55 UTC",
    "User": "root"
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  "Author": "Samuel M Bashevkin [aut, cre] (ORCID:\n<https://orcid.org/0000-0001-7406-7089>),\nRosemary Hartman [aut] (ORCID: <https://orcid.org/0000-0002-0642-183X>),\nKarrin Alstad [aut],\nCatarina Pien [aut] (ORCID: <https://orcid.org/0000-0003-4427-6300>)",
  "Maintainer": "Samuel M Bashevkin <sam.bashevkin@waterboards.ca.gov>",
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  "_created": "2026-06-04T20:28:55.000Z",
  "_published": "2026-06-04T20:42:39.541Z",
  "_distro": "noble",
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      "title": "Macro zooplankton length-weight equations",
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        "Carbon_mass_micrograms"
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      "table": true,
      "tojson": true
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      ],
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      "table": false,
      "tojson": true
    },
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      "title": "Taxonomic crosswalk among datasets",
      "object": "crosswalk",
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        "EMP_Meso",
        "EMP_Macro",
        "EMP_Lengths",
        "STN_Meso",
        "STN_Macro",
        "FMWT_Meso",
        "FMWT_Macro",
        "twentymm_Meso",
        "FRP_Meso",
        "FRP_Macro",
        "YBFMP",
        "LI_Meso",
        "LI_Micro",
        "DOP_Meso",
        "DOP_Macro",
        "Lifestage",
        "Taxname",
        "Level",
        "Phylum",
        "Class",
        "Order",
        "Family",
        "Genus",
        "Species",
        "Intro",
        "EMPstart",
        "EMPend",
        "FMWTstart",
        "FMWTend",
        "twentymmstart",
        "twentymmend",
        "twentymmstart2",
        "DOPstart",
        "DOPend",
        "FRPstart",
        "FRPend"
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      "rows": 471,
      "table": true,
      "tojson": true
    },
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      "name": "startDates",
      "title": "Start dates",
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        "SizeClass",
        "Startdate"
      ],
      "rows": 14,
      "table": true,
      "tojson": true
    },
    {
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      "object": "stations",
      "class": [
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        "tbl",
        "data.frame"
      ],
      "fields": [
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        "Station",
        "Latitude",
        "Longitude"
      ],
      "rows": 399,
      "table": true,
      "tojson": true
    },
    {
      "name": "stationsEMPEZ",
      "title": "EMP EZ Station locations",
      "object": "stationsEMPEZ",
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        "data.frame"
      ],
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        "Station",
        "Latitude",
        "Longitude"
      ],
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      "table": true,
      "tojson": true
    },
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      "name": "undersampled",
      "title": "Taxa undersampled in each size class",
      "object": "undersampled",
      "class": [
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        "tbl",
        "data.frame"
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        "Lifestage"
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      "table": true,
      "tojson": true
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        "data.frame"
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        "Lifestage",
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        "Phylum",
        "Class",
        "Order",
        "Family",
        "Genus",
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        "Temperature",
        "BottomDepth",
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        "Tide",
        "TowType",
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        "TurbidityNTU",
        "pH",
        "DO",
        "Microcystis",
        "Year",
        "TurbidityFNU",
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        "SalBott",
        "Latitude",
        "Longitude"
      ],
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    {
      "page": "biomass_macro",
      "title": "Macro zooplankton length-weight equations",
      "topics": [
        "biomass_macro"
      ]
    },
    {
      "page": "biomass_mesomicro",
      "title": "Meso and Micro zooplankton average biomass values",
      "topics": [
        "biomass_mesomicro"
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    },
    {
      "page": "Commontaxer",
      "title": "Detect common taxonomic names across all source datasets",
      "topics": [
        "Commontaxer"
      ]
    },
    {
      "page": "completeTaxaList",
      "title": "All taxonomic names",
      "topics": [
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      "page": "crosswalk",
      "title": "Taxonomic crosswalk among datasets",
      "topics": [
        "crosswalk"
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      "page": "LCD_Taxa",
      "title": "Apply LCD approach for \"Taxa\" option",
      "topics": [
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    {
      "page": "SourceTaxaKeyer",
      "title": "Unique taxa by lifestage combinations present in each source and size class",
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      "title": "Start dates",
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      "topics": [
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      "title": "EMP EZ Station locations",
      "topics": [
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      "page": "Taxnamefinder",
      "title": "Finds all of the lowest-level (i.e. counted) taxonomic names within a vector of taxa",
      "topics": [
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    },
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      "title": "Detect dates when a species was not counted",
      "topics": [
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    },
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      "page": "undersampled",
      "title": "Taxa undersampled in each size class",
      "topics": [
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    },
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      "page": "zoop_urls",
      "title": "Extract latest EDI files This function extracts the latest version of a zooplankton EDI package and the list of files from that package",
      "topics": [
        "zoop_urls"
      ]
    },
    {
      "page": "Zoopbiomass",
      "title": "Convert CPUE to biomass This function converts zooplankton CPUE to carbon biomass (Carbon biomass per unit effort (mug/ m^{3})) for taxa with conversion equations.",
      "topics": [
        "Zoopbiomass"
      ]
    },
    {
      "page": "zoopComb",
      "title": "Combined zooplankton dataset",
      "topics": [
        "zoopComb"
      ]
    },
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        "Zoopdownloader"
      ]
    },
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      "page": "zoopEnvComb",
      "title": "Environmental data",
      "topics": [
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      ]
    },
    {
      "page": "zooper",
      "title": "zooper: A package for integrating zooplankton datasets from the Sacramento San Joaquin Delta",
      "topics": [
        "zooper-package",
        "zooper"
      ]
    },
    {
      "page": "Zoopsynther",
      "title": "Integrates zooplankton datasets collected by the Interagency Ecological Program from the Sacramento-San Joaquin Delta",
      "topics": [
        "Zoopsynther"
      ]
    }
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