RDocumentation
Moon
Learn R
Search all packages and functions
⚠️
There's a newer version (0.9.100) of this package.
Take me there.
taxize (version 0.7.4)
Taxonomic Information from Around the Web
Description
Interacts with a suite of web 'APIs' for taxonomic tasks, such as verifying species names, and getting taxonomic 'hierarchies'.
Copy Link
Copy
Link to current version
Version
Version
0.9.100
0.9.99
0.9.98
0.9.97
0.9.96
0.9.95
0.9.94
0.9.93
0.9.92
0.9.91
0.9.9
0.9.8
0.9.7
0.9.6
0.9.5
0.9.4
0.9.3
0.8.9
0.8.8
0.8.4
0.8.0
0.7.9
0.7.8
0.7.6
0.7.5
0.7.4
0.7.0
0.6.6
0.6.2
0.6.0
0.5.2
0.4.0
0.3.0
0.2.2
0.2.0
0.1.8
0.1.5
0.1.0
0.0.6
0.0.5
0.0.4
0.0.3
0.0.2
0.0.1
Down Chevron
Install
install.packages('taxize')
Monthly Downloads
27,574
Version
0.7.4
License
MIT + file LICENSE
Issues
55
Pull Requests
1
Stars
262
Forks
58
Repository
https://github.com/ropensci/taxize
Maintainer
Scott Chamberlain
Last Published
March 9th, 2016
Functions in taxize (0.7.4)
Search functions
iucn_getname
Get any matching IUCN species names
downstream
Retrieve the downstream taxa for a given taxon name or ID.
get_boldid
Get the BOLD (Barcode of Life) code for a search term.
gni_details
Search for taxonomic name details using the Global Names Index.
genbank2uid
Get NCBI taxonomy UID from GenBankID
tp_summary
Return summary data a taxon name with a given id.
apg_families
MOBOT family names
class2tree
Convert list of classifications to a tree.
get_tpsid
Get the NameID codes from Tropicos for taxonomic names.
getcoremetadatafromtsn
Get core metadata from tsn
apg_orders
MOBOT order names
col_classification
Search Catalogue of Life for taxonomic classifications.
gethierarchydownfromtsn
Get hierarchy down from tsn
getunacceptabilityreasonfromtsn
Returns the unacceptability reason, if any, for the TSN.
ncbi_search
Search for gene sequences available for taxa from NCBI.
comm2sci
Get scientific names from common names.
eol_invasive
Search for presence of taxonomic names in EOL invasive species databases.
getglobalspeciescompletenessfromtsn
Get global species completeness from tsn
gettaxonomicranknamefromtsn
Returns the kingdom and rank information for the TSN.
col_children
Search Catalogue of Life for for direct children of a particular taxon.
getlsidfromtsn
Gets the unique LSID for the TSN, or an empty result if there is no match.
eol_dataobjects
Given the identifier for a data object, return all metadata about the object
getacceptednamesfromtsn
Get accepted names from tsn
getitistermsfromcommonname
Get itis terms from common names
gbif_name_usage
Lookup details for specific names in all taxonomies in GBIF.
getreviewyearfromtsn
Returns the review year for the TSN.
getjurisdictionoriginvalues
Get jurisdiction origin values
gettsnfromlsid
Gets the TSN corresponding to the LSID, or an empty result if there is no match.
sci2comm
Get common names from scientific names.
ipni_search
Search for names in the International Plant Names Index (IPNI).
getfullhierarchyfromtsn
Get full hierarchy from tsn
itis_name
Get taxonomic names for a given taxonomic name query.
itis_refs
Get references related to a ITIS TSN.
tnrs
Phylotastic Taxonomic Name Resolution Service.
getpublicationsfromtsn
Returns a list of the pulications used for the TSN.
children
Retrieve immediate children taxa for a given taxon name or ID.
getgeographicvalues
Get all possible geographic values
getfullrecordfromtsn
Get full record from TSN.
gni_parse
Parse scientific names using EOL's name parser.
col_downstream
Use Catalogue of Life to get downstream taxa to a given taxonomic level.
classification
Retrieve the taxonomic hierarchy for a given taxon ID.
getjurisdictionvalues
Get possible jurisdiction values
getparenttsnfromtsn
Returns the parent TSN for the entered TSN.
tp_accnames
Return all accepted names for a taxon name with a given id.
gnr_resolve
Resolve names using Global Names Resolver.
gnr_datasources
Get data sources for the Global Names Resolver.
getothersourcesfromtsn
Returns a list of the other sources used for the TSN.
eol_pages
Search for pages in EOL database using a taxonconceptID.
rankagg
Aggregate data by given taxonomic rank
getcoveragefromtsn
Get coverge from tsn
getsynonymnamesfromtsn
Returns a list of the synonyms (if any) for the TSN.
getcommonnamesfromtsn
Get common names from tsn
ncbi_getbyname
Retrieve gene sequences from NCBI by taxon name and gene names.
gethierarchyupfromtsn
Get hierarchy up from tsn
getvernacularlanguages
Provides a list of the unique languages used in the vernacular table.
itis_terms
Get ITIS terms, i.e., tsn's, authors, common names, and scientific names.
ion
ION - Index to Organism Names
iplant_resolve
iPlant name resolution
tp_dist
Return all distribution records for for a taxon name with a given id.
itis_acceptname
Retrieve accepted TSN (with accepted name).
get_uid
Get the UID codes from NCBI for taxonomic names.
eol_hierarchy
Retrieve the taxonomic hierarchy from given EOL taxonID.
plantNames
Vector of plant species (genus - specific epithet) names from ThePlantList
taxize_capwords
Capitalize the first letter of a character string.
theplantlist
Lookup-table for family, genus, and species names for ThePlantList
itis_lsid
Get kingdom names
getkey
Function to get API key.
taxize_ldfast
Replacement function for ldply that should be faster in all cases.
ubio_classification_search
This function will return ClassificationBankIDs (hierarchiesIDs) that refer to the given NamebankID
phylomatic_format
Get family names to make Phylomatic input object, and output input string to Phylomatic for use in the function phylomatic_tree.
getranknames
Provides a list of all the unique rank names contained in the database and their kingdom and rank ID values.
iucn_id
Get an ID for a IUCN listed taxon
tp_namereferences
Return all reference records for for a taxon name with a given id.
gbif_parse
Parse taxon names using the GBIF name parser.
eol_search
Search for terms in EOL database.
status_codes
Get HTTP status codes
get_nbnid
Get the UK National Biodiversity Network ID from taxonomic names.
apg
Get APG names
itis_downstream
Retrieve all taxa names or TSNs downstream in hierarchy from given TSN.
gettsnbyvernacularlanguage
Get tsn by vernacular language
getdescription
Get description of the ITIS service
itis_kingdomnames
Get kingdom names
itis_native
Get jurisdiction data, i.e., native or not native in a region.
searchforanymatchpaged
Search for any matched page
ncbi_getbyid
Retrieve gene sequences from NCBI by accession number.
nbn_classification
Search UK National Biodiversity Network database for taxonomic classification
bold_search
Search Barcode of Life for taxonomic IDs
tnrs_sources
TNRS sources
taxize-package
Taxonomic Information from Around the Web
searchbyscientificname
Search by scientific name
get_genes_avail
Retrieve gene sequences from NCBI by accession number.
get_genes
Retrieve gene sequences from NCBI by accession number.
iucn_summary
Get a summary from the IUCN Red List
gbif_downstream
Retrieve all taxa names downstream in hierarchy for GBIF
searchforanymatch
Search for any match
getanymatchcount
Get any match count.
tpl_get
Get The Plant List csv files.
get_eolid
Get the EOL ID from Encyclopedia of Life from taxonomic names.
lowest_common
Retrieve the lowest common taxon and rank for a given taxon name or ID
getitisterms
Get itis terms from common names
get_colid
Get the Catalogue of Life ID from taxonomic names.
nbn_search
Search UK National Biodiversity Network database
scrapenames
Resolve names using Global Names Recognition and Discovery.
tax_agg
Aggregate species data to given taxonomic rank
getkingdomnamefromtsn
Get kingdom names from tsn
ubio_id
Search uBio by namebank ID.
ubio_synonyms
Search uBio for taxonomic synonyms by hierarchiesID.
resolve
Resolve names from different data sources
rank_ref
Lookup-table for IDs of taxonomic ranks
eubon
EU BON taxonomy
tp_namedistributions
Return all distribution records for for a taxon name with a given id.
getcurrencyfromtsn
Get currency from tsn
tp_acceptednames
Return all accepted names for a taxon name with a given id.
tp_synonyms
Return all synonyms for a taxon name with a given id.
getcommentdetailfromtsn
Get comment detail from TSN
getdatedatafromtsn
Get date data from tsn
getjurisdictionaloriginfromtsn
Get jurisdictional origin from tsn
get_ids
Retrieve taxonomic identifiers for a given taxon name.
getitistermsfromscientificname
Get itis terms from scientific names
getfullrecordfromlsid
Returns the full ITIS record for the TSN in the LSID, found by comparing the TSN in the search key to the TSN field. Returns an empty result set if there is no match or the TSN is invalid.
getexpertsfromtsn
Get expert information for the TSN.
gettaxonauthorshipfromtsn
Returns the author information for the TSN.
ncbi_get_taxon_summary
NCBI taxon information from uids
itis_hierarchy
ITIS hierarchy
get_seqs
Retrieve gene sequences from NCBI by accession number.
getkingdomnames
Get all possible kingdom names
getscientificnamefromtsn
Returns the scientific name for the TSN. Also returns the component parts (names and indicators) of the scientific name.
getcredibilityratingfromtsn
Get credibility rating from tsn
names_list
Get a random vector of species names.
gettaxonomicusagefromtsn
Returns the usage information for the TSN.
iucn_status
Extractor functions for
iucn
-class.
tax_rank
Get rank for a given taxonomic name.
tp_refs
Return all reference records for for a taxon name with a given id.
vascan_search
Search the CANADENSYS Vascan API.
taxize-defunct
Defunct functions in taxize
plantminer
Search for taxonomy data from Plantminer.com
gni_search
Search for taxonomic names using the Global Names Index.
phylomatic_tree
Query Phylomatic for a phylogenetic tree.
searchbycommonname
Search for tsn by common name
tpl_families
Get The Plant List families.
ncbi_children
Search NCBI for children of a taxon
tp_classification
Return all synonyms for a taxon name with a given id.
nbn_synonyms
Return all synonyms for a taxon name with a given id from NBN
tpl_search
A light wrapper around the taxonstand fxn to call Theplantlist.org database.
ubio_search
This function will return NameBankIDs that match given search terms
ping
Ping an API used in taxize to see if it's working.
tp_search
Search Tropicos by scientific name, common name, or Tropicos ID.
upstream
Retrieve the upstream taxa for a given taxon name or ID.
col_search
Search Catalogue of Life for taxonomic IDs
get_ubioid
Get the uBio id for a search term
getgeographicdivisionsfromtsn
Get geographic divisions from tsn
ubio_ping
uBio ping
get_gbifid
Get the GBIF backbone taxon ID from taxonomic names.
get_tsn
Get the TSN code for a search term.
getcredibilityratings
Get possible credibility ratings
getlastchangedate
Provides the date the ITIS database was last updated.
itis_searchcommon
Searches common name and acts as thin wrapper around
searchbycommonnamebeginswith
and
searchbycommonnameendswith
gisd_isinvasive
Check invasive species status for a set of species from GISD database
fungorum
Index Fungorum
searchbycommonnameendswith
Search for tsn by common name ending with
getrecordfromlsid
Gets the partial ITIS record for the TSN in the LSID, found by comparing the TSN in the search key to the TSN field. Returns an empty result set if there is no match or the TSN is invalid.
itis_getrecord
Get full ITIS record for one or more ITIS TSN's or lsid's.
taxize_cite
Get citations and licenses for data sources used in taxize
itis-api
Low level functions for working with the ITIS API.
ubio_classification
uBio classification
plantGenusNames
Vector of plant genus names from ThePlantList
searchbycommonnamebeginswith
Search for tsn by common name beginning with
synonyms
Retrieve synonyms from various sources given input taxonomic names or identifiers.
tax_name
Get taxonomic names for a given rank.
itis_taxrank
Retrieve taxonomic rank name from given TSN.
apg_lookup
Lookup in the APGIII taxonomy and replace family names