Package: taxadb 0.3.0

Carl Boettiger

taxadb: A High-Performance Taxonomic Database Interface

Provides fast access to many commonly used taxonomic authorities in a uniform Darwin Core format. Tables are read directly from versioned Parquet snapshots, streamed from cloud storage or from a local copy, and queried with familiar 'dplyr' verbs.

Authors:Carl Boettiger [aut, cre], Kari Norman [aut], Jorrit Poelen [aut], Scott Chamberlain [aut], Noam Ross [ctb], Mattia Ghilardi [ctb]

taxadb_0.3.0.tar.gz
taxadb_0.3.0.zip(r-4.7-any)taxadb_0.3.0.zip(r-4.6-any)taxadb_0.3.0.zip(r-4.5-any)
taxadb_0.3.0.tgz(r-4.6-any)taxadb_0.3.0.tgz(r-4.5-any)
taxadb_0.3.0.tar.gz(r-4.7-any)taxadb_0.3.0.tar.gz(r-4.6-any)
taxadb_0.3.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
taxadb/json (API)

# Install 'taxadb' in R:

install.packages('taxadb', repos = c('https://ropensci.r-universe.dev', 'https://cloud.r-project.org'))

Reviews:rOpenSci Software Review #344

Bug tracker:https://github.com/ropensci/taxadb/issues

On CRAN:

6.90 score 44 stars 2 packages 922 downloads 38 exports 24 dependencies

Last updated from:e933f95674 (on master). Checks:10 OK. Indexed: yes.

Target	Result	Time
linux-devel	OK	178
pkgdown docs	OK	186
source / vignettes	OK	252
linux-release	OK	148
macos-release	OK	126
macos-oldrel	OK	121
windows-devel	OK	2821
windows-release	OK	3126
windows-oldrel	OK	2914
wasm-release	OK	123

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

Dependencies:blob cli cpp11 DBI dbplyr dplyr duckdb generics glue lifecycle magrittr pillar pkgconfig purrr R6 rlang stringi stringr tibble tidyr tidyselect utf8 vctrs withr

Name Providers and schema used in taxadb

Rendered fromdata-sources.Rmdusingknitr::rmarkdown

Last update: 2026-08-30
Started: 2020-01-24

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Name providers available for a given version	available_providers
Versions of the taxadb data available	available_versions
Rebuild the Catalogue of Life snapshot	build_col
Where build inputs and outputs are kept	build_dir
Rebuild the FishBase or SeaLifeBase snapshot	build_fishbase
Rebuild the GBIF backbone snapshot	build_gbif
Rebuild the ITIS snapshot	build_itis
Rebuild the NCBI Taxonomy snapshot	build_ncbi
Rebuild the Open Tree Taxonomy snapshot	build_ott
Clean taxonomic names	clean_names
common name starts with	common_contains
common name starts with	common_starts_with
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).	filter_by
Look up taxonomic information by common name	filter_common
Return a taxonomic table matching the requested ids	filter_id
Look up taxonomic information by scientific name	filter_name
Get all members (descendants) of a given rank level	filter_rank
Match names that start or contain a specified text string	fuzzy_filter
get_ids	get_ids
get_names	get_names
The most recent taxadb snapshot version	latest_version
List the taxonomic snapshots available from the taxadb repository	list_snapshots
return all taxa in which scientific name contains the text provided	name_contains
scientific name starts with	name_starts_with
Return a reference to a given table in the taxadb database	taxa_tbl
Show the local taxadb directory	taxadb_dir
Describe the taxonomic name providers	taxadb_provider_info
Providers taxadb can rebuild	taxadb_providers
The taxadb data repository	taxadb_repo
Locate the Parquet files backing a taxadb table	taxadb_uri
Rebuild taxadb snapshots from the providers	td_build
Connect to the taxadb database	td_connect
Create a local taxadb database	td_create
Disconnect from the taxadb database.	td_disconnect
Install a local copy of a taxadb snapshot	td_download
Describe a built snapshot	td_manifest
Check a taxadb table against the taxadb Darwin Core rules	td_validate
Write the metadata published with a snapshot	td_write_metadata