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"Package": "taxadb",
"Version": "0.3.0",
"Title": "A High-Performance Taxonomic Database Interface",
"Description": "Provides fast access to many commonly used taxonomic\nauthorities in a uniform Darwin Core format. Tables are read\ndirectly from versioned Parquet snapshots, streamed from cloud\nstorage or from a local copy, and queried with familiar 'dplyr'\nverbs.",
"Authors@R": "c(\nperson(\"Carl\", \"Boettiger\", , \"cboettig@gmail.com\", c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-1642-628X\")),\nperson(\"Kari\", \"Norman\", role= \"aut\",\ncomment = c(ORCID = \"0000-0002-2029-2325\")),\nperson(\"Jorrit\", \"Poelen\", role =\"aut\",\ncomment = c(ORCID=\"0000-0003-3138-4118\")),\nperson(\"Scott\", \"Chamberlain\", role =\"aut\",\ncomment = c(ORCID=\"0000-0003-1444-9135\")),\nperson(\"Noam\", \"Ross\", , \"ross@ecohealthalliance.org\", role =\"ctb\",\ncomment = c(ORCID = \"0000-0002-2136-0000\")),\nperson(\"Mattia\", \"Ghilardi\", role =\"ctb\",\ncomment = c(ORCID = \"0000-0001-9592-7252\"))\n)",
"License": "MIT + file LICENSE",
"Encoding": "UTF-8",
"ByteCompile": "true",
"Roxygen": "list(markdown = TRUE)",
"Language": "en-US",
"VignetteBuilder": "knitr",
"URL": ",\n",
"BugReports": "https://github.com/ropensci/taxadb/issues",
"Config/roxygen2/version": "8.0.0",
"Config/pak/sysreqs": "libicu-dev xz-utils",
"Repository": "https://ropensci.r-universe.dev",
"Date/Publication": "2026-08-30 19:26:18 UTC",
"RemoteUrl": "https://github.com/ropensci/taxadb",
"RemoteRef": "master",
"RemoteSha": "e933f9567417c014dab0a6166d2f4f76f8f30409",
"NeedsCompilation": "no",
"Packaged": {
"Date": "2026-09-29 12:55:26 UTC",
"User": "root"
},
"Author": "Carl Boettiger [aut, cre] (ORCID:\n),\nKari Norman [aut] (ORCID: ),\nJorrit Poelen [aut] (ORCID: ),\nScott Chamberlain [aut] (ORCID:\n),\nNoam Ross [ctb] (ORCID: ),\nMattia Ghilardi [ctb] (ORCID: )",
"Maintainer": "Carl Boettiger ",
"_user": "ropensci",
"_type": "src",
"_file": "taxadb_0.3.0.tar.gz",
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"_created": "2026-09-29T12:55:26.000Z",
"_published": "2026-09-29T13:48:31.321Z",
"_jobs": [
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"_buildurl": "https://github.com/r-universe/ropensci/actions/runs/36570920365",
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"_upstream": "https://github.com/ropensci/taxadb",
"_commit": {
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"author": "Carl Boettiger ",
"committer": "GitHub ",
"message": "Stop giving provider URLs to the CRAN URL check (#126)\n\nThe incoming check on the 0.3.0 submission reported https://www.itis.gov/\nas a 404 from inst/doc/data-sources.html. The URL is correct -- it serves\n200 from every network, user agent and method tried -- so the 404 came from\nITIS's own CDN. That does not help: a chance 404 during the incoming check\nroutes the submission to manual review and costs a round trip with the\nmaintainers, whatever the page actually serves.\n\nSo the vignette no longer names a URL for any provider. The table names\neach one, and the home page, licence and preferred citation come from\ntaxadb_provider_info() at runtime, where the check does not resolve them.\n\nThe ITIS citation is bibliographic rather than its DOI on purpose: a bare\ndoi: in a vignette *is* harvested and resolved (two already are, from the\nsame file), and doi:10.5066/F7KH0KBK redirects to www.itis.gov, so citing\nthe DOI would have inherited the same flakiness.\n\nTwo links that were genuinely dead, which the check never sees but users\ndo, are fixed in passing: itis.gov/what_itis.html was renamed (citation.html\nis the page stating CC0), and the Catalogue of Life citation pointed at\ndoi.org/10.48580/dfz8, which is gone -- COL mints a DOI per release, so any\npinned one rots.\n\nThe new url-check workflow runs urlchecker monthly against the built\npackage, so inst/doc HTML exists to check, and against the provider URLs\nheld in R strings. It tolerates the 403s that GBIF, FishBase and\nSeaLifeBase return to automated clients, and rechecks once before failing,\nsince a single hiccup is the thing being defended against rather than a\nreason to go red. It stays off the pull request path for the same reason.",
"time": 1788117978
},
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"email": "cboettig@gmail.com",
"login": "cboettig",
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"uuid": 222586
},
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"version": ">= 4.0",
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},
{
"package": "DBI",
"role": "Imports"
},
{
"package": "duckdb",
"role": "Imports"
},
{
"package": "tibble",
"role": "Imports"
},
{
"package": "dplyr",
"role": "Imports"
},
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"package": "dbplyr",
"role": "Imports"
},
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"package": "rlang",
"role": "Imports"
},
{
"package": "magrittr",
"role": "Imports"
},
{
"package": "stringi",
"role": "Imports"
},
{
"package": "spelling",
"role": "Suggests"
},
{
"package": "testthat",
"role": "Suggests"
},
{
"package": "curl",
"role": "Suggests"
},
{
"package": "knitr",
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},
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},
{
"package": "crayon",
"role": "Suggests"
},
{
"package": "withr",
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}
],
"_owner": "ropensci",
"_selfowned": true,
"_usedby": 2,
"_updates": [
{
"week": "2026-35",
"n": 13
}
],
"_tags": [],
"_stars": 44,
"_contributors": [
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"user": "cboettig",
"count": 486,
"uuid": 222586
},
{
"user": "karinorman",
"count": 127,
"uuid": 9221037
},
{
"user": "maelle",
"count": 3,
"uuid": 8360597
},
{
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"count": 2,
"uuid": 47717037
},
{
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"count": 1,
"uuid": 5583057
},
{
"user": "kguidonimartins",
"count": 1,
"uuid": 8163542
},
{
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}
],
"_userbio": {
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"type": "organization",
"name": "rOpenSci",
"followers": 1157,
"description": "Tools and R Packages for Open Science"
},
"_downloads": {
"count": 922,
"source": "https://cranlogs.r-pkg.org/downloads/total/last-month/taxadb"
},
"_devurl": "https://github.com/ropensci/taxadb",
"_searchresults": 0,
"_metadata": {
"review": {
"id": 344,
"status": "reviewed",
"version": "0.0.1",
"organization": "rOpenSci Software Review",
"url": "https://github.com/ropensci/software-review/issues/344"
},
"ropensci_category": "taxonomy"
},
"_rbuild": "4.6.1",
"_assets": [
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"extra/citation.html",
"extra/citation.json",
"extra/citation.txt",
"extra/contents.json",
"extra/manual.pdf",
"extra/NEWS.html",
"extra/NEWS.txt",
"extra/readme.html",
"extra/readme.md",
"extra/taxadb.html",
"LICENSE"
],
"_homeurl": "https://github.com/ropensci/taxadb",
"_realowner": "ropensci",
"_cranurl": true,
"_releases": [
{
"version": "0.1.0",
"date": "2020-02-19"
},
{
"version": "0.1.1",
"date": "2021-02-25"
},
{
"version": "0.1.2",
"date": "2021-03-15"
},
{
"version": "0.1.3",
"date": "2021-04-27"
},
{
"version": "0.1.4",
"date": "2022-03-05"
},
{
"version": "0.1.5",
"date": "2022-05-03"
},
{
"version": "0.1.6",
"date": "2022-09-14"
},
{
"version": "0.2.0",
"date": "2023-02-14"
},
{
"version": "0.2.1",
"date": "2023-03-09"
},
{
"version": "0.3.0",
"date": "2026-09-08"
}
],
"_exports": [
"available_providers",
"available_versions",
"build_col",
"build_dir",
"build_fishbase",
"build_gbif",
"build_itis",
"build_ncbi",
"build_ott",
"clean_names",
"common_contains",
"common_starts_with",
"filter_by",
"filter_common",
"filter_id",
"filter_name",
"filter_rank",
"fuzzy_filter",
"get_ids",
"get_names",
"latest_version",
"list_snapshots",
"name_contains",
"name_starts_with",
"taxa_tbl",
"taxadb_dir",
"taxadb_provider_info",
"taxadb_providers",
"taxadb_repo",
"taxadb_uri",
"td_build",
"td_connect",
"td_create",
"td_disconnect",
"td_download",
"td_manifest",
"td_validate",
"td_write_metadata"
],
"_help": [
{
"page": "available_providers",
"title": "Name providers available for a given version",
"topics": [
"available_providers"
]
},
{
"page": "available_versions",
"title": "Versions of the taxadb data available",
"topics": [
"available_versions"
]
},
{
"page": "build_col",
"title": "Rebuild the Catalogue of Life snapshot",
"concept": [
"build"
],
"topics": [
"build_col"
]
},
{
"page": "build_dir",
"title": "Where build inputs and outputs are kept",
"topics": [
"build_dir"
]
},
{
"page": "build_fishbase",
"title": "Rebuild the FishBase or SeaLifeBase snapshot",
"concept": [
"build"
],
"topics": [
"build_fishbase"
]
},
{
"page": "build_gbif",
"title": "Rebuild the GBIF backbone snapshot",
"concept": [
"build"
],
"topics": [
"build_gbif"
]
},
{
"page": "build_itis",
"title": "Rebuild the ITIS snapshot",
"concept": [
"build"
],
"topics": [
"build_itis"
]
},
{
"page": "build_ncbi",
"title": "Rebuild the NCBI Taxonomy snapshot",
"concept": [
"build"
],
"topics": [
"build_ncbi"
]
},
{
"page": "build_ott",
"title": "Rebuild the Open Tree Taxonomy snapshot",
"concept": [
"build"
],
"topics": [
"build_ott"
]
},
{
"page": "clean_names",
"title": "Clean taxonomic names",
"topics": [
"clean_names"
]
},
{
"page": "common_contains",
"title": "common name starts with",
"topics": [
"common_contains"
]
},
{
"page": "common_starts_with",
"title": "common name starts with",
"topics": [
"common_starts_with"
]
},
{
"page": "filter_by",
"title": "Creates a data frame with column name given by 'by', and values given by the vector 'x', and then uses this table to do a filtering join, joining on the 'by' column to return all rows matching the 'x' values (scientificNames, taxonIDs, etc).",
"concept": [
"filter_by"
],
"topics": [
"filter_by"
]
},
{
"page": "filter_common",
"title": "Look up taxonomic information by common name",
"concept": [
"filter_by"
],
"topics": [
"filter_common"
]
},
{
"page": "filter_id",
"title": "Return a taxonomic table matching the requested ids",
"concept": [
"filter_by"
],
"topics": [
"filter_id"
]
},
{
"page": "filter_name",
"title": "Look up taxonomic information by scientific name",
"concept": [
"filter_by"
],
"topics": [
"filter_name"
]
},
{
"page": "filter_rank",
"title": "Get all members (descendants) of a given rank level",
"concept": [
"filter_by"
],
"topics": [
"filter_rank"
]
},
{
"page": "fuzzy_filter",
"title": "Match names that start or contain a specified text string",
"topics": [
"fuzzy_filter"
]
},
{
"page": "get_ids",
"title": "get_ids",
"concept": [
"get"
],
"topics": [
"get_ids"
]
},
{
"page": "get_names",
"title": "get_names",
"concept": [
"get"
],
"topics": [
"get_names"
]
},
{
"page": "latest_version",
"title": "The most recent taxadb snapshot version",
"topics": [
"latest_version"
]
},
{
"page": "list_snapshots",
"title": "List the taxonomic snapshots available from the taxadb repository",
"topics": [
"list_snapshots"
]
},
{
"page": "name_contains",
"title": "return all taxa in which scientific name contains the text provided",
"topics": [
"name_contains"
]
},
{
"page": "name_starts_with",
"title": "scientific name starts with",
"topics": [
"name_starts_with"
]
},
{
"page": "taxa_tbl",
"title": "Return a reference to a given table in the taxadb database",
"topics": [
"taxa_tbl"
]
},
{
"page": "taxadb_dir",
"title": "Show the local taxadb directory",
"topics": [
"taxadb_dir"
]
},
{
"page": "taxadb_provider_info",
"title": "Describe the taxonomic name providers",
"topics": [
"taxadb_provider_info"
]
},
{
"page": "taxadb_providers",
"title": "Providers taxadb can rebuild",
"topics": [
"taxadb_providers"
]
},
{
"page": "taxadb_repo",
"title": "The taxadb data repository",
"topics": [
"taxadb_repo"
]
},
{
"page": "taxadb_uri",
"title": "Locate the Parquet files backing a taxadb table",
"topics": [
"taxadb_uri"
]
},
{
"page": "td_build",
"title": "Rebuild taxadb snapshots from the providers",
"topics": [
"td_build"
]
},
{
"page": "td_connect",
"title": "Connect to the taxadb database",
"topics": [
"td_connect"
]
},
{
"page": "td_create",
"title": "Create a local taxadb database",
"topics": [
"td_create"
]
},
{
"page": "td_disconnect",
"title": "Disconnect from the taxadb database.",
"topics": [
"td_disconnect"
]
},
{
"page": "td_download",
"title": "Install a local copy of a taxadb snapshot",
"topics": [
"td_download"
]
},
{
"page": "td_manifest",
"title": "Describe a built snapshot",
"topics": [
"td_manifest"
]
},
{
"page": "td_validate",
"title": "Check a taxadb table against the taxadb Darwin Core rules",
"topics": [
"td_validate"
]
},
{
"page": "td_write_metadata",
"title": "Write the metadata published with a snapshot",
"topics": [
"td_write_metadata"
]
}
],
"_pkglogo": "https://github.com/ropensci/taxadb/raw/master/man/figures/logo.svg",
"_readme": "https://github.com/ropensci/taxadb/raw/master/README.md",
"_rundeps": [
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"cli",
"cpp11",
"DBI",
"dbplyr",
"dplyr",
"duckdb",
"generics",
"glue",
"lifecycle",
"magrittr",
"pillar",
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"rlang",
"stringi",
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"_vignettes": [
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"source": "data-sources.Rmd",
"filename": "data-sources.html",
"title": "Name Providers and schema used in taxadb",
"author": "Carl Boettiger, Kari Norman",
"engine": "knitr::rmarkdown",
"headings": [
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"Conventions",
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"Data Processing",
"Data Versioning",
"Archival versions"
],
"created": "2020-01-24 18:10:03",
"modified": "2026-08-30 19:26:18",
"commits": 12
}
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