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taxize (version 0.7.0)
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'.
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Install
install.packages('taxize')
Monthly Downloads
26,874
Version
0.7.0
License
MIT + file LICENSE
Issues
53
Pull Requests
1
Stars
260
Forks
62
Repository
https://github.com/ropensci/taxize
Maintainer
Scott Chamberlain
Last Published
November 30th, 2015
Functions in taxize (0.7.0)
Search functions
genbank2uid
Get NCBI taxonomy UID from GenBankID
get_uid
Get the UID codes from NCBI for taxonomic names.
apg
Get APG names
gbif_downstream
Retrieve all taxa names downstream in hierarchy for GBIF
getcommonnamesfromtsn
Get common names from tsn
col_classification
Search Catalogue of Life for taxonomic classifications.
getkingdomnames
Get all possible kingdom names
get_genes
Retrieve gene sequences from NCBI by accession number.
get_tpsid
Get the NameID codes from Tropicos for taxonomic names.
get_seqs
Retrieve gene sequences from NCBI by accession number.
getfullrecordfromtsn
Get full record from TSN.
apg_orders
MOBOT order names
getparenttsnfromtsn
Returns the parent TSN for the entered TSN.
itis_native
Get jurisdiction data, i.e., native or not native in a region.
classification
Retrieve the taxonomic hierarchy for a given taxon ID.
get_ubioid
Get the uBio id for a search term
gni_details
Search for taxonomic name details using the Global Names Index.
class2tree
Convert list of classifications to a tree.
get_gbifid
Get the GBIF backbone taxon ID from taxonomic names.
col_search
Search Catalogue of Life for taxonomic IDs
getglobalspeciescompletenessfromtsn
Get global species completeness from tsn
col_downstream
Use Catalogue of Life to get downstream taxa to a given taxonomic level.
getexpertsfromtsn
Get expert information for the TSN.
gettaxonauthorshipfromtsn
Returns the author information for the TSN.
getpublicationsfromtsn
Returns a list of the pulications used for the TSN.
get_genes_avail
Retrieve gene sequences from NCBI by accession number.
getcoveragefromtsn
Get coverge from tsn
eol_search
Search for terms in EOL database.
getlsidfromtsn
Gets the unique LSID for the TSN, or an empty result if there is no match.
gethierarchyupfromtsn
Get hierarchy up from tsn
getothersourcesfromtsn
Returns a list of the other sources used for the TSN.
iucn_id
Get an ID for a IUCN listed taxon
getitistermsfromcommonname
Get itis terms from common names
eubon
EU BON taxonomy
getdescription
Get description of the ITIS service
eol_dataobjects
Given the identifier for a data object, return all metadata about the object
getcurrencyfromtsn
Get currency from tsn
eol_pages
Search for pages in EOL database using a taxonconceptID.
apg_lookup
Lookup in the APGIII taxonomy and replace family names
getranknames
Provides a list of all the unique rank names contained in the database and their kingdom and rank ID values.
eol_hierarchy
Retrieve the taxonomic hierarchy from given EOL taxonID.
getjurisdictionaloriginfromtsn
Get jurisdictional origin from tsn
getitisterms
Get itis terms from common names
getkey
Function to get API key.
get_ids
Retrieve taxonomic identifiers for a given taxon name.
getfullhierarchyfromtsn
Get full hierarchy from tsn
gbif_name_usage
Lookup details for specific names in all taxonomies in GBIF.
sci2comm
Get common names from scientific names.
searchbycommonname
Search for tsn by common name
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.
col_children
Search Catalogue of Life for for direct children of a particular taxon.
gbif_parse
Parse taxon names using the GBIF name parser.
apg_families
MOBOT family names
getcoremetadatafromtsn
Get core metadata from tsn
nbn_search
Search UK National Biodiversity Network database
ncbi_getbyname
Retrieve gene sequences from NCBI by taxon name and gene names.
getkingdomnamefromtsn
Get kingdom names from tsn
children
Retrieve immediate children taxa for a given taxon name or ID.
getgeographicdivisionsfromtsn
Get geographic divisions from tsn
theplantlist
Lookup-table for family, genus, and species names for ThePlantList
nbn_synonyms
Return all synonyms for a taxon name with a given id from NBN
ubio_synonyms
Search uBio for taxonomic synonyms by hierarchiesID.
getunacceptabilityreasonfromtsn
Returns the unacceptability reason, if any, for the TSN.
synonyms
Retrieve synonyms from various sources given input taxonomic names or identifiers.
ncbi_search
Search for gene sequences available for taxa from NCBI.
gettaxonomicranknamefromtsn
Returns the kingdom and rank information for the TSN.
getacceptednamesfromtsn
Get accepted names from tsn
taxize-defunct
Defunct functions in taxize
getcredibilityratings
Get possible credibility ratings
iucn_getname
Get any matching IUCN species names
tax_rank
Get rank for a given taxonomic name.
gnr_datasources
Get data sources for the Global Names Resolver.
searchforanymatchpaged
Search for any matched page
iplant_resolve
iPlant name resolution
tnrs_sources
TNRS sources
itis_acceptname
Retrieve accepted TSN (with accepted name).
getdatedatafromtsn
Get date data from tsn
get_nbnid
Get the UK National Biodiversity Network ID from taxonomic names.
tp_search
Search Tropicos by scientific name, common name, or Tropicos ID.
vascan_search
Search the CANADENSYS Vascan API.
taxize-package
Taxonomic Information from Around the Web
getjurisdictionoriginvalues
Get jurisdiction origin values
tpl_search
A light wrapper around the taxonstand fxn to call Theplantlist.org database.
getlastchangedate
Provides the date the ITIS database was last updated.
gettsnfromlsid
Gets the TSN corresponding to the LSID, or an empty result if there is no match.
tp_summary
Return summary data a taxon name with a given id.
taxize_ldfast
Replacement function for ldply that should be faster in all cases.
status_codes
Get HTTP status codes
itis-api
Low level functions for working with the ITIS API.
ubio_ping
uBio ping
gni_parse
Parse scientific names using EOL's name parser.
phylomatic_format
Get family names to make Phylomatic input object, and output input string to Phylomatic for use in the function phylomatic_tree.
ubio_id
Search uBio by namebank ID.
searchforanymatch
Search for any match
itis_taxrank
Retrieve taxonomic rank name from given TSN.
ncbi_get_taxon_summary
NCBI taxon information from uids
iucn_status
Extractor functions for
iucn
-class.
tp_dist
Return all distribution records for for a taxon name with a given id.
itis_terms
Get ITIS terms, i.e., tsn's, authors, common names, and scientific names.
gisd_isinvasive
Check invasive species status for a set of species from GISD database
gettaxonomicusagefromtsn
Returns the usage information for the TSN.
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.
gnr_resolve
Resolve names using Global Names Resolver.
getgeographicvalues
Get all possible geographic values
phylomatic_tree
Query Phylomatic for a phylogenetic tree.
itis_name
Get taxonomic names for a given taxonomic name query.
upstream
Retrieve the upstream taxa for a given taxon name or ID.
searchbycommonnameendswith
Search for tsn by common name ending with
getcommentdetailfromtsn
Get comment detail from TSN
itis_searchcommon
Searches common name and acts as thin wrapper around
searchbycommonnamebeginswith
and
searchbycommonnameendswith
itis_getrecord
Get full ITIS record for one or more ITIS TSN's or lsid's.
getanymatchcount
Get any match count.
searchbyscientificname
Search by scientific name
ncbi_children
Search NCBI for children of a taxon
itis_lsid
Get kingdom names
itis_refs
Get references related to a ITIS TSN.
ipni_search
Search for names in the International Plant Names Index (IPNI).
iucn_summary
Get a summary from the IUCN Red List
tp_acceptednames
Return all accepted names for a taxon name with a given id.
gni_search
Search for taxonomic names using the Global Names Index.
plantminer
Search for taxonomy data from Plantminer.com
nbn_classification
Search UK National Biodiversity Network database for taxonomic classification
itis_hierarchy
ITIS hierarchy
itis_kingdomnames
Get kingdom names
tnrs
Phylotastic Taxonomic Name Resolution Service.
rankagg
Aggregate data by given taxonomic rank
getjurisdictionvalues
Get possible jurisdiction values
tp_classification
Return all synonyms for a taxon name with a given id.
tp_namereferences
Return all reference records for for a taxon name with a given id.
ubio_classification_search
This function will return ClassificationBankIDs (hierarchiesIDs) that refer to the given NamebankID
tpl_get
Get The Plant List csv files.
tp_refs
Return all reference records for for a taxon name with a given id.
getsynonymnamesfromtsn
Returns a list of the synonyms (if any) for the TSN.
rank_ref
Lookup-table for IDs of taxonomic ranks
tp_synonyms
Return all synonyms for a taxon name with a given id.
scrapenames
Resolve names using Global Names Recognition and Discovery.
ncbi_getbyid
Retrieve gene sequences from NCBI by accession number.
tax_name
Get taxonomic names for a given rank.
taxize_capwords
Capitalize the first letter of a character string.
ubio_search
This function will return NameBankIDs that match given search terms
tp_accnames
Return all accepted names for a taxon name with a given id.
plantNames
Vector of plant species (genus - specific epithet) names from ThePlantList
taxize_cite
Get citations and licenses for data sources used in taxize
resolve
Resolve names from different data sources
ubio_classification
uBio classification
plantGenusNames
Vector of plant genus names from ThePlantList
tp_namedistributions
Return all distribution records for for a taxon name with a given id.
get_colid
Get the Catalogue of Life ID from taxonomic names.
comm2sci
Get scientific names from common names.
downstream
Retrieve the downstream taxa for a given taxon name or ID.
gethierarchydownfromtsn
Get hierarchy down from tsn
getscientificnamefromtsn
Returns the scientific name for the TSN. Also returns the component parts (names and indicators) of the scientific name.
getreviewyearfromtsn
Returns the review year for the TSN.
ion
ION - Index to Organism Names
itis_downstream
Retrieve all taxa names or TSNs downstream in hierarchy from given TSN.
names_list
Get a random vector of species names.
searchbycommonnamebeginswith
Search for tsn by common name beginning with
bold_search
Search Barcode of Life for taxonomic IDs
eol_invasive
Search for presence of taxonomic names in EOL invasive species databases.
fungorum
Index Fungorum
get_boldid
Get the BOLD (Barcode of Life) code for a search term.
get_eolid
Get the EOL ID from Encyclopedia of Life from taxonomic names.
get_tsn
Get the TSN code for a search term.
getcredibilityratingfromtsn
Get credibility rating from tsn
getitistermsfromscientificname
Get itis terms from scientific names
getvernacularlanguages
Provides a list of the unique languages used in the vernacular table.
tax_agg
Aggregate species data to given taxonomic rank
gettsnbyvernacularlanguage
Get tsn by vernacular language
tpl_families
Get The Plant List families.
ping
Ping an API used in taxize to see if it's working.