taxize v0.9.99

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Taxonomic Information from Around the Web

Interacts with a suite of web 'APIs' for taxonomic tasks, such as getting database specific taxonomic identifiers, verifying species names, getting taxonomic hierarchies, fetching downstream and upstream taxonomic names, getting taxonomic synonyms, converting scientific to common names and vice versa, and more.

Readme

taxize

Project Status: Active – The project has reached a stable, usable state and is being actively developed. cran checks R-CMD-check codecov rstudio mirror downloads cran version

taxize allows users to search over many taxonomic data sources for species names (scientific and common) and download up and downstream taxonomic hierarchical information - among other things.

The taxize book: https://taxize.dev

Package documentation: https://docs.ropensci.org/taxize/

Installation

Stable version from CRAN

install.packages("taxize")

Development version from GitHub

Windows users install Rtools first.

install.packages("remotes")
remotes::install_github("ropensci/taxize")
library('taxize')

Screencast

Contributing

See our CONTRIBUTING document.

Road map

Check out our milestones to see what we plan to get done for each version.

Meta

  • Please report any issues or bugs.
  • License: MIT
  • Get citation information for taxize in R doing citation(package = 'taxize')
  • Please note that this package is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.

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Functions in taxize

Name Description
apg Get APG names
get_natservid Get NatureServe taxonomic ID for a taxon name
eol_search Search for terms in EOL database.
eol_pages Search for pages in EOL database using a taxonconceptID.
get_nbnid Get the UK National Biodiversity Network ID from taxonomic names.
get_uid Get the UID codes from NCBI for taxonomic names.
get_wiki Get the page name for a Wiki taxon
genbank2uid Get NCBI taxonomy UID from GenBankID
gni_details Search for taxonomic name details using the Global Names Index
itis_downstream Retrieve all taxa names or TSNs downstream in hierarchy from given TSN.
gni_parse Parse scientific names using EOL's name parser.
get_gbifid Get the GBIF backbone taxon ID from taxonomic names.
itis_getrecord Get full ITIS record for one or more ITIS TSN's or lsid's.
ncbi_getbyid Retrieve gene sequences from NCBI by accession number.
ping Ping an API used in taxize to see if it's working.
ncbi_get_taxon_summary NCBI taxon information from uids
apg_orders MOBOT order names
apg_lookup Lookup in the APGIII taxonomy and replace family names
downstream Retrieve the downstream taxa for a given taxon name or ID.
class2tree Convert a list of classifications to a tree.
plantGenusNames Vector of plant genus names from ThePlantList
gbif_downstream Retrieve all taxa names downstream in hierarchy for GBIF
eol_dataobjects Given the identifier for a data object, return all metadata about the object
classification Retrieve the taxonomic hierarchy for a given taxon ID.
eubon DEFUNCT
synonyms Retrieve synonyms from various sources given input taxonomic names or identifiers
get_genes Retrieve gene sequences from NCBI by accession number.
get_tsn Get the TSN code for a search term.
get_ubioid Get the uBio id for a search term
bold_children Barcode of Life taxonomic children
eubon_search EUBON taxonomy search
get_id_details Details on get_*() functions
get_genes_avail Retrieve gene sequences from NCBI by accession number.
eubon_capabilities EUBON capabilities
fungorum Index Fungorum
bold_downstream Retrieve all taxa names downstream in hierarchy for BOLD
eubon_children EUBON children
eol_invasive Search for presence of taxonomic names in EOL invasive species databases.
eol_hierarchy Retrieve the taxonomic hierarchy from given EOL taxonID.
eubon_hierarchy EUBON hierarchy
gni_search Search for taxonomic names using the Global Names Index
itis_hierarchy ITIS hierarchy
gbif_name_usage Lookup details for specific names in all taxonomies in GBIF.
get_seqs Retrieve gene sequences from NCBI by accession number.
get_pow Get Kew's Plants of the World code for a taxon
itis_native Get jurisdiction data, i.e., native or not native in a region.
gnr_datasources Global Names Resolver Data Sources
iucn_status Extractor functions for iucn-class.
itis_refs Get references related to a ITIS TSN.
iucn_summary Get a summary from the IUCN Red List
tax_agg Aggregate species data to given taxonomic rank
theplantlist Lookup-table for family, genus, and species names for ThePlantList
tnrs Phylotastic Taxonomic Name Resolution Service.
gn_parse Parse scientific names using Global Names Parser
ipni_search Search for names in the International Plant Names Index (IPNI).
gisd_isinvasive Check invasive species status for a set of species from GISD database
itis_kingdomnames Get kingdom names
nbn_classification Search UK National Biodiversity Network database for taxonomic classification
names_list Get a random vector of species names.
pow_lookup Lookup taxa in Kew's Plants of the World
itis_acceptname Retrieve accepted TSN and name
pow_search Search Kew's Plants of the World
get_tolid Get the OTT id for a search term
get_tpsid Get the NameID codes from Tropicos for taxonomic names.
id2name Taxonomic IDs to taxonomic names
gnr_resolve Resolve names using Global Names Resolver
ncbi_downstream Retrieve all taxa names downstream in hierarchy for NCBI
ncbi_children Search NCBI for children of a taxon
itis_lsid Get TSN from LSID
lowest_common Retrieve the lowest common taxon and rank for a given taxon name or ID
itis_name Get taxonomic names for a given taxonomic name query.
phylomatic_format Get family names to make Phylomatic input object, and output input string to Phylomatic for use in the function phylomatic_tree.
itis_taxrank Retrieve taxonomic rank name from given TSN.
limited_print Print a subset of a character vector
phylomatic_tree Query Phylomatic for a phylogenetic tree.
itis_terms Get ITIS terms, i.e., tsn's, authors, common names, and scientific names.
key_helpers Helpers to set up authentication for the different providers.
ncbi_getbyname Retrieve gene sequences from NCBI by taxon name and gene names.
taxon-state Last taxon state object from a get_* function call
iucn_summary_id DEFUNCT
ncbi_search Search for gene sequences available for taxa from NCBI.
tp_summary Return summary data a taxon name with a given id.
tp_synonyms Return all synonyms for a taxon name with a given id.
plantNames Vector of plant species (genus - specific epithet) names from ThePlantList
rank_ref Lookup-table for IDs of taxonomic ranks
tp_namedistributions Return all distribution records for for a taxon name with a given id.
tp_namereferences Return all reference records for for a taxon name with a given id.
taxon_state Keep track of queries in get_* functions
bold_search Search Barcode of Life for taxonomic IDs
species_plantarum_binomials Species names from Species Plantarum
plantminer Search for taxonomy data from Plantminer.com
rank_ref_zoo Lookup-table for IDs of taxonomic ranks (WoRMS)
rankagg Aggregate data by given taxonomic rank
resolve Resolve names from different data sources
tax_name Get taxonomic names for a given rank
tpl_get Get The Plant List csv files.
tpl_families Get The Plant List families.
ubio_ping uBio ping
ubio_search This function will return NameBankIDs that match given search terms
status_codes Get HTTP status codes
children Retrieve immediate children taxa for a given taxon name or ID.
taxize_capwords Capitalize the first letter of a character string.
tax_rank Get rank for a given taxonomic name.
taxize-authentication taxize authentication
get_boldid Get the BOLD (Barcode of Life) code for a search term.
get_ids Retrieve taxonomic identifiers for a given taxon name.
col-defunct COL defunct functions
get_eolid Get the EOL ID from Encyclopedia of Life from taxonomic names.
comm2sci Get scientific names from common names.
get_iucn Get a IUCN Redlist taxon
taxize_cite Get citations and licenses for data sources used in taxize
get_wormsid Get Worms ID for a taxon name
getkey Function to get API key.
ion ION - Index to Organism Names
taxize_ldfast Replacement function for ldply that should be faster in all cases.
tnrs_sources TNRS sources
tp_search Search Tropicos by scientific name, common name, or Tropicos ID.
tp_refs Return all reference records for for a taxon name with a given id.
taxize-defunct Defunct functions in taxize
tol_resolve Resolve names using Open Tree of Life (OTL) resolver
taxize_options taxon state options
tp_classification Return all synonyms for a taxon name with a given id.
use_eol-defunct use eol
tp_acceptednames Return all accepted names for a taxon name with a given id.
iplant_resolve iPlant name resolution
vascan_search Search the CANADENSYS Vascan API.
tp_accnames Return all accepted names for a taxon name with a given id.
upstream Retrieve the upstream taxa for a given taxon name or ID.
ubio_synonyms Search uBio for taxonomic synonyms by hierarchiesID.
tpl_search A light wrapper around the taxonstand fxn to call Theplantlist.org database.
ubio_classification uBio classification
tp_dist Return all distribution records for for a taxon name with a given id.
worms_downstream Retrieve all taxa names downstream in hierarchy for WORMS
worrms_ranks WORMS ranks
iucn_id Get an ID for a IUCN listed taxon
iucn_getname Get any matching IUCN species names
nbn_synonyms Return all synonyms for a taxon name with a given id from NBN
progressor methods for preparing/printing info for prompts for get_* functions
pow_synonyms Lookup synonyms in Kew's Plants of the World
nbn_search Search UK National Biodiversity Network
scrapenames Resolve names using Global Names Recognition and Discovery.
sci2comm Get common names from scientific names.
taxize-package Taxonomic Information from Around the Web
taxize-params taxize parameters
ubio_classification_search This function will return ClassificationBankIDs (hierarchiesIDs) that refer to the given NamebankID
ubio_id Search uBio by namebank ID.
apg_families MOBOT family names
gbif_parse Parse taxon names using the GBIF name parser.
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Details

License MIT + file LICENSE
URL https://docs.ropensci.org/taxize/ (website), https://github.com/ropensci/taxize (devel), https://taxize.dev (user manual)
BugReports https://github.com/ropensci/taxize/issues
LazyLoad yes
LazyData true
Encoding UTF-8
Language en-US
RoxygenNote 7.1.1
X-schema.org-applicationCategory Taxonomy
X-schema.org-keywords taxonomy, biology, nomenclature, JSON, API, web, api-client, identifiers, species, names
X-schema.org-isPartOf https://ropensci.org
NeedsCompilation no
Packaged 2020-10-30 00:50:09 UTC; sckott
Repository CRAN
Date/Publication 2020-10-30 05:50:02 UTC

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