Package: taxizedb 0.3.2

Tamás Stirling

taxizedb: Offline Access to Taxonomic Databases

Download taxonomic databases, convert them into 'SQLite' format, and query them locally for fast, reliable, and reproducible access to taxonomic data.

Authors:Scott Chamberlain [aut], Zebulun Arendsee [aut], Tamás Stirling [ctb, cre]

taxizedb_0.3.2.tar.gz
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taxizedb.pdf |taxizedb.html✨
taxizedb/json (API)
NEWS

# Install 'taxizedb' in R:

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

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

Pkgdown site:https://docs.ropensci.org

On CRAN:

itis taxize taxonomic-databases taxonomy

6.07 score 32 stars 1 packages 101 scripts 32 downloads 30 exports 42 dependencies

Last updated 27 days ago from:6438f8a6de (on master). Checks:11 OK. Indexed: yes.

Target	Result	Total time
linux-devel-x86_64	OK	152
pkgdown docs	OK	158
source / vignettes	OK	192
linux-release-x86_64	OK	149
macos-release-arm64	OK	123
macos-oldrel-arm64	OK	118
windows-devel	OK	107
windows-release	OK	106
windows-oldrel	OK	114
wasm-release	OK	113
wasm-oldrel	OK	182

Exports:children classification db_download_col db_download_gbif db_download_itis db_download_ncbi db_download_tpl db_download_wfo db_download_wikidata db_load_col db_load_gbif db_load_itis db_load_ncbi db_load_tpl db_load_wikidata db_path downstream name2taxid sql_collect src_col src_gbif src_itis src_ncbi src_tpl src_wfo src_wikidata taxa_at taxid2name taxid2rank tdb_cache

Dependencies:bit bit64 blob cachem cli clipr cpp11 crayon curl DBI dbplyr digest dplyr fastmap generics glue hms hoardr lifecycle magrittr memoise pillar pkgconfig plogr prettyunits progress purrr R6 rappdirs readr rlang RSQLite stringi stringr tibble tidyr tidyselect tzdb utf8 vctrs vroom withr

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
taxizedb	taxizedb-package taxizedb
Retrieve immediate descendents of a taxon	children
Retrieve the taxonomic hierarchies from local database	classification
Download taxonomic databases	db_download db_download_col db_download_gbif db_download_itis db_download_ncbi db_download_tpl db_download_wfo db_download_wikidata
Load taxonomic databases	db_load-defunct db_load_col db_load_gbif db_load_itis db_load_ncbi db_load_tpl db_load_wikidata
database path	db_path
Retrieve all taxa descending from a vector of taxa	downstream
Convert species names to taxon IDs	name2taxid
Query and get data back into a data.frame	sql_collect
src - dplyr src objects	src_col src_gbif src_itis src_ncbi src_taxizedb src_tpl src_wfo src_wikidata
Get taxa at specific scientific ranks	taxa_at
Convert taxon IDs to scientific names	taxid2name
Convert taxon IDs to scientific ranks	taxid2rank
Caching	tdb_cache