{ "_id": "69e9d87ac5259ad4cda3ffe8", "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 ", "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(), 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": "2026-04-23 08:25:25 UTC", "User": "root" }, "MD5sum": "6761283d6887e3befef55a58c30e9cc9", "_user": "ropensci", "_type": "src", "_file": "neotoma_1.7.7.tar.gz", "_fileid": "f072d134dbbbb5d372f46a273aeef1c3982c2d638f32184c7654c470c77415a0", "_filesize": 2470188, "_sha256": "f072d134dbbbb5d372f46a273aeef1c3982c2d638f32184c7654c470c77415a0", "_created": "2026-04-23T08:25:25.000Z", "_published": "2026-04-23T08:29:46.895Z", "_distro": "noble", "_jobs": [ { "job": 72658619230, "time": 199, "config": "linux-devel-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "6597163620" }, { "job": 72658619320, "time": 208, "config": "linux-release-x86_64", "r": "4.5.3", "check": "NOTE", "artifact": "6597166297" }, { "job": 72658619275, "time": 107, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "6597137717" }, { "job": 72658619262, "time": 152, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "6597150339" }, { "job": 72658138061, "time": 159, "config": "pkgdown", "r": "4.5.2", "check": "OK", "artifact": "6597093111" }, { "job": 72658138064, "time": 207, "config": "source", "r": "4.5.3", "check": "OK", "artifact": "6597106453" }, { "job": 72658619276, "time": 156, "config": "wasm-release", "r": "4.5.1", "check": "OK", "artifact": "6597151246" }, { "job": 72658619261, "time": 138, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "6597146184" }, { "job": 72658619263, "time": 135, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "6597145316" }, { "job": 72658619271, "time": 128, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "6597143332" } ], "_buildurl": "https://github.com/r-universe/ropensci/actions/runs/24824855071", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/ropensci/neotoma", "_commit": { "id": "fd935c440bb5809502bb3d41c034af0ce7a45ecc", "author": "Simon ", "committer": "GitHub ", "message": "Update README.md\n\nAdded deprecation note.", "time": 1669835266 }, "_maintainer": { "name": "Simon J. Goring", "email": "goring@wisc.edu", "login": "simongoring", "uuid": 1619126 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 2.10", "role": "Depends" }, { "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": [ { "user": "simongoring", "count": 593, "uuid": 1619126 }, { "user": "gavinsimpson", "count": 131, "uuid": 514696 }, { "user": "sckott", "count": 44, "uuid": 577668 }, { "user": "karthik", "count": 21, "uuid": 138494 }, { "user": "andydawson", "count": 5, "uuid": 3595715 }, { "user": "stevenysw", "count": 2, "uuid": 14078330 } ], "_userbio": { "uuid": 1200269, "type": "organization", "name": "rOpenSci", "description": "Tools and R Packages for Open Science" }, "_downloads": { "count": 6, "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": 141, "_metadata": { "ropensci_category": "data-access" }, "_rbuild": "4.5.3", "_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", "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", "date": "2016-08-19" }, { "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": [ 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