{
  "_id": "6a39080f3efcd9bda444695a",
  "Package": "neotoma",
  "Type": "Package",
  "Title": "Access to the Neotoma Paleoecological Database Through R",
  "Version": "1.7.7",
  "Date": "2022-09-13",
  "Encoding": "UTF-8",
  "Author": "Simon J. Goring [aut, cre], Gavin L. Simpson [aut], Jeremiah P.\nMarsicek [ctb], Karthik Ram [aut], Luke Sosalla [ctb]",
  "Authors@R": "c(person(given = c(\"Simon\", \"J.\"), family = \"Goring\",\nrole = c(\"aut\", \"cre\"), email = \"goring@wisc.edu\"),\nperson(given = c(\"Gavin\", \"L.\"), family = \"Simpson\", role = \"aut\"),\nperson(given = c(\"Jeremiah\", \"P.\"), family = \"Marsicek\", role = \"ctb\"),\nperson(given = \"Karthik\", family = \"Ram\", role = \"aut\"),\nperson(given = \"Luke\", family = \"Sosalla\", role = \"ctb\"))",
  "Maintainer": "Simon J. Goring <goring@wisc.edu>",
  "Description": "NOTE: This package is deprecated. Please use the neotoma2\npackage described at https://github.com/NeotomaDB/neotoma2.\nAccess paleoecological datasets from the Neotoma\nPaleoecological Database using the published API\n(<http://wnapi.neotomadb.org/>), only containing datasets\nuploaded prior to June 2020.  The functions in this package\naccess various pre-built API functions and attempt to return\nthe results from Neotoma in a usable format for researchers and\nthe public.",
  "License": "MIT + file LICENSE",
  "URL": "https://docs.ropensci.org/neotoma,\nhttps://github.com/ropensci/neotoma",
  "BugReports": "https://github.com/ropensci/neotoma/issues",
  "RoxygenNote": "7.2.1",
  "Config/pak/sysreqs": "libabsl-dev cmake libgdal-dev gdal-bin libgeos-dev\nmake libicu-dev libpng-dev libuv1-dev libxml2-dev libssl-dev\nlibproj-dev libsqlite3-dev libudunits2-dev",
  "Repository": "https://ropensci.r-universe.dev",
  "Date/Publication": "2022-11-30 19:07:46 UTC",
  "RemoteUrl": "https://github.com/ropensci/neotoma",
  "RemoteRef": "master",
  "RemoteSha": "fd935c440bb5809502bb3d41c034af0ce7a45ecc",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-06-22 09:51:51 UTC",
    "User": "root"
  },
  "MD5sum": "72264dcb3991b568fab0990ae0035808",
  "_user": "ropensci",
  "_type": "src",
  "_file": "neotoma_1.7.7.tar.gz",
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  "_created": "2026-06-22T09:51:51.000Z",
  "_published": "2026-06-22T10:01:51.086Z",
  "_distro": "noble",
  "_jobs": [
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  "_buildurl": "https://github.com/r-universe/ropensci/actions/runs/27944099727",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/ropensci/neotoma",
  "_commit": {
    "id": "fd935c440bb5809502bb3d41c034af0ce7a45ecc",
    "author": "Simon <simon.j.goring@gmail.com>",
    "committer": "GitHub <noreply@github.com>",
    "message": "Update README.md\n\nAdded deprecation note.",
    "time": 1669835266
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  "_maintainer": {
    "name": "Simon J. Goring",
    "email": "goring@wisc.edu",
    "login": "simongoring",
    "description": "Assistant Scientist at the University of Wisconsin-Madison\nAdjunct Professor at the University of British Columbia.",
    "uuid": 1619126
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 2.10",
      "role": "Depends"
    },
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      "package": "plyr",
      "role": "Imports"
    },
    {
      "package": "reshape2",
      "role": "Imports"
    },
    {
      "package": "jsonlite",
      "role": "Imports"
    },
    {
      "package": "httr",
      "role": "Imports"
    },
    {
      "package": "xml2",
      "role": "Imports"
    },
    {
      "package": "analogue",
      "role": "Imports"
    },
    {
      "package": "leaflet",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "sf",
      "role": "Imports"
    },
    {
      "package": "assertthat",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    }
  ],
  "_owner": "ropensci",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [],
  "_tags": [],
  "_topics": [
    "neotoma",
    "neotoma-apis",
    "neotoma-database",
    "nsf",
    "paleoecology"
  ],
  "_stars": 31,
  "_contributors": [
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    },
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    },
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    },
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    "type": "organization",
    "name": "rOpenSci",
    "followers": 1100,
    "description": "Tools and R Packages for Open Science"
  },
  "_downloads": {
    "count": 55,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/neotoma"
  },
  "_mentions": 1,
  "_devurl": "https://github.com/ropensci/neotoma",
  "_pkgdown": "https://docs.ropensci.org/neotoma",
  "_searchresults": 117,
  "_metadata": {
    "ropensci_category": "data-access"
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  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/neotoma.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "LICENSE",
    "manual.pdf"
  ],
  "_realowner": "ropensci",
  "_cranurl": false,
  "_releases": [
    {
      "version": "1.2-0",
      "date": "2015-05-03"
    },
    {
      "version": "1.3.0",
      "date": "2015-05-29"
    },
    {
      "version": "1.3.1",
      "date": "2015-07-14"
    },
    {
      "version": "1.3.2",
      "date": "2015-07-15"
    },
    {
      "version": "1.3.3",
      "date": "2015-08-22"
    },
    {
      "version": "1.4.0",
      "date": "2015-09-25"
    },
    {
      "version": "1.5.0",
      "date": "2016-02-29"
    },
    {
      "version": "1.5.1",
      "date": "2016-05-06"
    },
    {
      "version": "1.6.0",
      "date": "2016-07-27"
    },
    {
      "version": "1.6.1",
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    },
    {
      "version": "1.6.2",
      "date": "2016-09-22"
    },
    {
      "version": "1.7.0",
      "date": "2017-06-21"
    },
    {
      "version": "1.7.2",
      "date": "2018-09-26"
    },
    {
      "version": "1.7.4",
      "date": "2019-01-05"
    }
  ],
  "_exports": [
    "ages",
    "bind",
    "browse",
    "compile_downloads",
    "compile_taxa",
    "counts",
    "depths",
    "get_chroncontrol",
    "get_closest",
    "get_contact",
    "get_dataset",
    "get_download",
    "get_geochron",
    "get_publication",
    "get_site",
    "get_table",
    "get_taxa",
    "param_check",
    "plot_leaflet",
    "read_bacon",
    "read.tilia",
    "taxa",
    "write_agefile"
  ],
  "_datasets": [
    {
      "name": "pollen.equiv",
      "title": "A table to convert the pollen taxa identified by investigators to standardized lists.",
      "object": "pollen.equiv",
      "file": "pollen.equiv.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "taxon",
        "taxon.id",
        "P25",
        "WS64",
        "WhitmoreFull",
        "WhitmoreSmall",
        "type",
        "cf"
      ],
      "rows": 9030,
      "table": true,
      "tojson": true
    },
    {
      "name": "taxon.list",
      "title": "Neotoma taxon list",
      "object": "taxon.list",
      "file": "taxon.list.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Valid",
        "ValidatorID",
        "TaxonName",
        "RecDateModified",
        "TaxonCode",
        "Author",
        "Notes",
        "PublicationID",
        "TaxonID",
        "TaxaGroupID",
        "HigherTaxonID",
        "Extinct",
        "ValidateDate",
        "RecDateCreated"
      ],
      "rows": 37075,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "ages",
      "title": "Access proxy age data",
      "topics": [
        "ages",
        "ages.download",
        "ages.download_list"
      ]
    },
    {
      "page": "bind",
      "title": "Function to bind objects together into a longer object.",
      "topics": [
        "bind"
      ]
    },
    {
      "page": "browse",
      "title": "Open a browser window to display a Neotoma dataset within the Neotoma Explorer",
      "topics": [
        "browse"
      ]
    },
    {
      "page": "browse.dataset",
      "title": "Open a browser window to display a Neotoma dataset within the Neotoma Explorer",
      "topics": [
        "browse.dataset"
      ]
    },
    {
      "page": "browse.dataset_list",
      "title": "Open a browser window to display a Neotoma dataset within the Neotoma Explorer",
      "topics": [
        "browse.dataset_list"
      ]
    },
    {
      "page": "browse.default",
      "title": "Open a browser window to display a Neotoma dataset within the Neotoma Explorer",
      "topics": [
        "browse.default"
      ]
    },
    {
      "page": "browse.download",
      "title": "Open a browser window to display a Neotoma dataset within the Neotoma Explorer",
      "topics": [
        "browse.download"
      ]
    },
    {
      "page": "browse.download_list",
      "title": "Open a browser window to display a Neotoma dataset within the Neotoma Explorer",
      "topics": [
        "browse.download_list"
      ]
    },
    {
      "page": "compile_downloads",
      "title": "Compile download objects",
      "topics": [
        "compile_downloads"
      ]
    },
    {
      "page": "compile_taxa",
      "title": "Function to convert assemblage taxa to standardized lists.",
      "topics": [
        "compile_taxa"
      ]
    },
    {
      "page": "counts",
      "title": "Access proxy count data",
      "topics": [
        "counts",
        "counts.download",
        "counts.download_list"
      ]
    },
    {
      "page": "depths",
      "title": "Extracts the depth values from a `download` object",
      "topics": [
        "depths",
        "depths.default",
        "depths.download",
        "depths.download_list"
      ]
    },
    {
      "page": "download",
      "title": "A class for download objects.",
      "topics": [
        "download"
      ]
    },
    {
      "page": "get_chroncontrol",
      "title": "Function to return chronological control tables used to build age models.",
      "topics": [
        "get_chroncontrol"
      ]
    },
    {
      "page": "get_chroncontrol.dataset",
      "title": "Function to return chronological control tables from a 'dataset'.",
      "topics": [
        "get_chroncontrol.dataset"
      ]
    },
    {
      "page": "get_chroncontrol.dataset_list",
      "title": "Function to return chronological control tables from a 'dataset_list'.",
      "topics": [
        "get_chroncontrol.dataset_list"
      ]
    },
    {
      "page": "get_chroncontrol.default",
      "title": "Function to return chronological control tables from a chronologic ID.",
      "topics": [
        "get_chroncontrol.default"
      ]
    },
    {
      "page": "get_chroncontrol.download",
      "title": "Function to return chronological control tables from a 'download' object.",
      "topics": [
        "get_chroncontrol.download"
      ]
    },
    {
      "page": "get_chroncontrol.download_list",
      "title": "Function to return chronological control tables from a 'download_list' object.",
      "topics": [
        "get_chroncontrol.download_list"
      ]
    },
    {
      "page": "get_closest",
      "title": "Find the closest dataset records to a site, dataset or long/lat pair in Neotoma",
      "topics": [
        "get_closest"
      ]
    },
    {
      "page": "get_contact",
      "title": "Get contact information.",
      "topics": [
        "get_contact"
      ]
    },
    {
      "page": "get_dataset",
      "title": "Obtain dataset information from the Neotoma Paleoecological Database or an existing object.",
      "topics": [
        "get_dataset"
      ]
    },
    {
      "page": "get_dataset.default",
      "title": "Obtain dataset information from the Neotoma Paleoecological Database or an existing object.",
      "topics": [
        "get_dataset.default"
      ]
    },
    {
      "page": "get_dataset.download",
      "title": "Obtain dataset information from an existing 'download' object.",
      "topics": [
        "get_dataset.download"
      ]
    },
    {
      "page": "get_dataset.download_list",
      "title": "Obtain dataset information from a 'download_list'.",
      "topics": [
        "get_dataset.download_list"
      ]
    },
    {
      "page": "get_dataset.geochronologic",
      "title": "Obtain dataset information from an object of class 'geochronologic'.",
      "topics": [
        "get_dataset.geochronologic"
      ]
    },
    {
      "page": "get_dataset.geochronologic_list",
      "title": "Obtain dataset information from an object of class 'geochronologic_list'.",
      "topics": [
        "get_dataset.geochronologic_list"
      ]
    },
    {
      "page": "get_dataset.integer",
      "title": "Obtain dataset information from a vector of dataset IDs.",
      "topics": [
        "get_dataset.integer"
      ]
    },
    {
      "page": "get_dataset.numeric",
      "title": "Obtain dataset information from a vector of dataset IDs.",
      "topics": [
        "get_dataset.numeric"
      ]
    },
    {
      "page": "get_dataset.site",
      "title": "Obtain dataset information from an existing 'site' object.",
      "topics": [
        "get_dataset.site"
      ]
    },
    {
      "page": "get_download",
      "title": "Function to return full download records using 'site's, 'dataset's, or dataset IDs.",
      "topics": [
        "get_download"
      ]
    },
    {
      "page": "get_download.dataset",
      "title": "Function to return full download records using a 'dataset'.",
      "topics": [
        "get_download.dataset"
      ]
    },
    {
      "page": "get_download.dataset_list",
      "title": "Function to return full download records using a 'dataset_list'.",
      "topics": [
        "get_download.dataset_list"
      ]
    },
    {
      "page": "get_download.default",
      "title": "Function to return full download records using 'numeric' dataset IDs.",
      "topics": [
        "get_download.default"
      ]
    },
    {
      "page": "get_download.site",
      "title": "Function to return full download records using a 'site'.",
      "topics": [
        "get_download.site"
      ]
    },
    {
      "page": "get_geochron",
      "title": "Function to return geochronological data from records.",
      "topics": [
        "get_geochron"
      ]
    },
    {
      "page": "get_publication",
      "title": "A function to get publications for sites or datasets in the Neotoma Database using the API.",
      "topics": [
        "get_publication"
      ]
    },
    {
      "page": "get_publication.dataset",
      "title": "A function to get publications for datasets in the Neotoma Database using the API.",
      "topics": [
        "get_publication.dataset"
      ]
    },
    {
      "page": "get_publication.dataset_list",
      "title": "A function to get publications for dataset_lists in the Neotoma Database using the API.",
      "topics": [
        "get_publication.dataset_list"
      ]
    },
    {
      "page": "get_publication.default",
      "title": "A function to get publications for sites or datasets in the Neotoma Database using the API.",
      "topics": [
        "get_publication.default"
      ]
    },
    {
      "page": "get_publication.download",
      "title": "A function to get publications for downloads in the Neotoma Database using the API.",
      "topics": [
        "get_publication.download"
      ]
    },
    {
      "page": "get_publication.download_list",
      "title": "A function to get publications for datasets in the Neotoma Database using the API.",
      "topics": [
        "get_publication.download_list"
      ]
    },
    {
      "page": "get_site",
      "title": "Return Site Information.",
      "topics": [
        "get_site"
      ]
    },
    {
      "page": "get_site.dataset",
      "title": "Return Site Information from a numeric list of site ids.",
      "topics": [
        "get_site.dataset"
      ]
    },
    {
      "page": "get_site.dataset_list",
      "title": "Return Site Information from a 'dataset_list'",
      "topics": [
        "get_site.dataset_list"
      ]
    },
    {
      "page": "get_site.default",
      "title": "Return Site Information.",
      "topics": [
        "get_site.default"
      ]
    },
    {
      "page": "get_site.download",
      "title": "Return Site Information from a 'download'",
      "topics": [
        "get_site.download"
      ]
    },
    {
      "page": "get_site.download_list",
      "title": "Return Site Information from a 'download_list'",
      "topics": [
        "get_site.download_list"
      ]
    },
    {
      "page": "get_site.geochronologic",
      "title": "Return Site Information from a 'geochronologic'",
      "topics": [
        "get_site.geochronologic"
      ]
    },
    {
      "page": "get_site.geochronologic_list",
      "title": "Return Site Information from a 'geochronologic_list'",
      "topics": [
        "get_site.geochronologic_list"
      ]
    },
    {
      "page": "get_site.integer",
      "title": "Return Site Information from a vector of integers.",
      "topics": [
        "get_site.integer"
      ]
    },
    {
      "page": "get_site.numeric",
      "title": "Return Site information from a vector of numeric elements.",
      "topics": [
        "get_site.numeric"
      ]
    },
    {
      "page": "get_table",
      "title": "Get Neotoma value tables.",
      "topics": [
        "get_table"
      ]
    },
    {
      "page": "get_taxa",
      "title": "Get taxon information from Neotoma.",
      "topics": [
        "get_taxa"
      ]
    },
    {
      "page": "gp.table",
      "title": "A list of all the geopolitical entities in the Neotoma database.",
      "topics": [
        "gp.table"
      ]
    },
    {
      "page": "plot_leaflet",
      "title": "Leaflet plots for neotoma data.",
      "topics": [
        "plot_leaflet"
      ]
    },
    {
      "page": "pollen.equiv",
      "title": "A table to convert the pollen taxa identified by investigators to standardized lists.",
      "topics": [
        "pollen.equiv"
      ]
    },
    {
      "page": "read_bacon",
      "title": "Function to read in defined Bacon outputs.",
      "topics": [
        "read_bacon"
      ]
    },
    {
      "page": "read.tilia",
      "title": "Read proxy data from Tilia TLX files",
      "topics": [
        "read.tilia"
      ]
    },
    {
      "page": "Stratiplot.download",
      "title": "Palaeoecological stratigraphic diagrams",
      "topics": [
        "Stratiplot.download"
      ]
    },
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