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taxize (version 0.7.6)
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
27,574
Version
0.7.6
License
MIT + file LICENSE
Issues
55
Pull Requests
1
Stars
262
Forks
58
Repository
https://github.com/ropensci/taxize
Maintainer
Scott Chamberlain
Last Published
May 11th, 2016
Functions in taxize (0.7.6)
Search functions
children
Retrieve immediate children taxa for a given taxon name or ID.
eol_hierarchy
Retrieve the taxonomic hierarchy from given EOL taxonID.
getitistermsfromscientificname
Get itis terms from scientific names
gbif_name_usage
Lookup details for specific names in all taxonomies in GBIF.
apg_lookup
Lookup in the APGIII taxonomy and replace family names
get_nbnid
Get the UK National Biodiversity Network ID from taxonomic names.
apg
Get APG names
getvernacularlanguages
Provides a list of the unique languages used in the vernacular table.
get_colid
Get the Catalogue of Life ID from taxonomic names.
get_ids
Retrieve taxonomic identifiers for a given taxon name.
get_ubioid
Get the uBio id for a search term
fungorum
Index Fungorum
getjurisdictionvalues
Get possible jurisdiction values
searchforanymatchpaged
Search for any matched page
classification
Retrieve the taxonomic hierarchy for a given taxon ID.
comm2sci
Get scientific names from common names.
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
getcredibilityratingfromtsn
Get credibility rating from tsn
genbank2uid
Get NCBI taxonomy UID from GenBankID
get_genes
Retrieve gene sequences from NCBI by accession number.
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.
col_search
Search Catalogue of Life for taxonomic IDs
getcoveragefromtsn
Get coverge from tsn
gettaxonauthorshipfromtsn
Returns the author information for the TSN.
col_children
Search Catalogue of Life for for direct children of a particular taxon.
eol_invasive
Search for presence of taxonomic names in EOL invasive species databases.
searchbycommonnamebeginswith
Search for tsn by common name beginning with
gnr_resolve
Resolve names using Global Names Resolver.
getkingdomnamefromtsn
Get kingdom names from tsn
getexpertsfromtsn
Get expert information for the TSN.
gettaxonomicusagefromtsn
Returns the usage information for the TSN.
downstream
Retrieve the downstream taxa for a given taxon name or ID.
getanymatchcount
Get any match count.
get_boldid
Get the BOLD (Barcode of Life) code for a search term.
get_tpsid
Get the NameID codes from Tropicos for taxonomic names.
col_downstream
Use Catalogue of Life to get downstream taxa to a given taxonomic level.
eol_search
Search for terms in EOL database.
getreviewyearfromtsn
Returns the review year for the TSN.
nbn_synonyms
Return all synonyms for a taxon name with a given id from NBN
tp_refs
Return all reference records for for a taxon name with a given id.
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.
bold_search
Search Barcode of Life for taxonomic IDs
itis_searchcommon
Searches common name and acts as thin wrapper around
searchbycommonnamebeginswith
and
searchbycommonnameendswith
getjurisdictionoriginvalues
Get jurisdiction origin values
get_genes_avail
Retrieve gene sequences from NCBI by accession number.
get_eolid
Get the EOL ID from Encyclopedia of Life from taxonomic names.
getjurisdictionaloriginfromtsn
Get jurisdictional origin from tsn
get_seqs
Retrieve gene sequences from NCBI by accession number.
tp_synonyms
Return all synonyms for a taxon name with a given id.
getlsidfromtsn
Gets the unique LSID for the TSN, or an empty result if there is no match.
itis_hierarchy
ITIS hierarchy
sci2comm
Get common names from scientific names.
class2tree
Convert list of classifications to a tree.
getparenttsnfromtsn
Returns the parent TSN for the entered TSN.
get_gbifid
Get the GBIF backbone taxon ID from taxonomic names.
getitistermsfromcommonname
Get itis terms from common names
gethierarchydownfromtsn
Get hierarchy down from tsn
getcredibilityratings
Get possible credibility ratings
getkey
Function to get API key.
getlastchangedate
Provides the date the ITIS database was last updated.
itis_terms
Get ITIS terms, i.e., tsn's, authors, common names, and scientific names.
searchbycommonnameendswith
Search for tsn by common name ending with
names_list
Get a random vector of species names.
ipni_search
Search for names in the International Plant Names Index (IPNI).
getothersourcesfromtsn
Returns a list of the other sources used for the TSN.
itis_getrecord
Get full ITIS record for one or more ITIS TSN's or lsid's.
iucn_summary
Get a summary from the IUCN Red List
ncbi_search
Search for gene sequences available for taxa from NCBI.
itis-api
Low level functions for working with the ITIS API.
status_codes
Get HTTP status codes
ncbi_children
Search NCBI for children of a taxon
getranknames
Provides a list of all the unique rank names contained in the database and their kingdom and rank ID values.
apg_families
MOBOT family names
tpl_families
Get The Plant List families.
ion
ION - Index to Organism Names
getunacceptabilityreasonfromtsn
Returns the unacceptability reason, if any, for the TSN.
nbn_search
Search UK National Biodiversity Network database
col_classification
Search Catalogue of Life for taxonomic classifications.
searchbycommonname
Search for tsn by common name
getcommonnamesfromtsn
Get common names from tsn
getcurrencyfromtsn
Get currency from tsn
phylomatic_format
Get family names to make Phylomatic input object, and output input string to Phylomatic for use in the function phylomatic_tree.
getpublicationsfromtsn
Returns a list of the pulications used for the TSN.
getglobalspeciescompletenessfromtsn
Get global species completeness from tsn
apg_orders
MOBOT order names
gisd_isinvasive
Check invasive species status for a set of species from GISD database
iucn_id
Get an ID for a IUCN listed taxon
getfullrecordfromtsn
Get full record from TSN.
gethierarchyupfromtsn
Get hierarchy up from tsn
getkingdomnames
Get all possible kingdom names
itis_refs
Get references related to a ITIS TSN.
searchforanymatch
Search for any match
taxize-package
Taxonomic Information from Around the Web
gnr_datasources
Get data sources for the Global Names Resolver.
gni_details
Search for taxonomic name details using the Global Names Index.
ping
Ping an API used in taxize to see if it's working.
plantNames
Vector of plant species (genus - specific epithet) names from ThePlantList
iucn_getname
Get any matching IUCN species names
ubio_classification_search
This function will return ClassificationBankIDs (hierarchiesIDs) that refer to the given NamebankID
phylomatic_tree
Query Phylomatic for a phylogenetic tree.
taxize-defunct
Defunct functions in taxize
gettaxonomicranknamefromtsn
Returns the kingdom and rank information for the TSN.
itis_acceptname
Retrieve accepted TSN (with accepted name).
gettsnfromlsid
Gets the TSN corresponding to the LSID, or an empty result if there is no match.
tnrs_sources
TNRS sources
tax_agg
Aggregate species data to given taxonomic rank
resolve
Resolve names from different data sources
getgeographicvalues
Get all possible geographic values
ncbi_getbyname
Retrieve gene sequences from NCBI by taxon name and gene names.
getcoremetadatafromtsn
Get core metadata from tsn
vascan_search
Search the CANADENSYS Vascan API.
tp_acceptednames
Return all accepted names for a taxon name with a given id.
theplantlist
Lookup-table for family, genus, and species names for ThePlantList
ubio_search
This function will return NameBankIDs that match given search terms
synonyms
Retrieve synonyms from various sources given input taxonomic names or identifiers.
ubio_classification
uBio classification
ubio_synonyms
Search uBio for taxonomic synonyms by hierarchiesID.
searchbyscientificname
Search by scientific name
tnrs
Phylotastic Taxonomic Name Resolution Service.
ncbi_getbyid
Retrieve gene sequences from NCBI by accession number.
nbn_classification
Search UK National Biodiversity Network database for taxonomic classification
tax_name
Get taxonomic names for a given rank.
plantGenusNames
Vector of plant genus names from ThePlantList
itis_lsid
Get kingdom names
plantminer
Search for taxonomy data from Plantminer.com
getdescription
Get description of the ITIS service
tp_classification
Return all synonyms for a taxon name with a given id.
tpl_search
A light wrapper around the taxonstand fxn to call Theplantlist.org database.
ubio_id
Search uBio by namebank ID.
itis_downstream
Retrieve all taxa names or TSNs downstream in hierarchy from given TSN.
lowest_common
Retrieve the lowest common taxon and rank for a given taxon name or ID
rankagg
Aggregate data by given taxonomic rank
getscientificnamefromtsn
Returns the scientific name for the TSN. Also returns the component parts (names and indicators) of the scientific name.
tp_namereferences
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.
tp_summary
Return summary data a taxon name with a given id.
itis_name
Get taxonomic names for a given taxonomic name query.
itis_native
Get jurisdiction data, i.e., native or not native in a region.
gni_search
Search for taxonomic names using the Global Names Index.
getgeographicdivisionsfromtsn
Get geographic divisions from tsn
taxize_capwords
Capitalize the first letter of a character string.
tol_resolve
Resolve names using Open Tree of Life resolver
iucn_status
Extractor functions for
iucn
-class.
tp_dist
Return all distribution records for for a taxon name with a given id.
tp_search
Search Tropicos by scientific name, common name, or Tropicos ID.
tp_namedistributions
Return all distribution records for for a taxon name with a given id.
eubon
EU BON taxonomy
tp_accnames
Return all accepted names for a taxon name with a given id.
scrapenames
Resolve names using Global Names Recognition and Discovery.
tpl_get
Get The Plant List csv files.
tax_rank
Get rank for a given taxonomic name.
iplant_resolve
iPlant name resolution
taxize_cite
Get citations and licenses for data sources used in taxize
upstream
Retrieve the upstream taxa for a given taxon name or ID.
ncbi_get_taxon_summary
NCBI taxon information from uids
gbif_parse
Parse taxon names using the GBIF name parser.
get_tsn
Get the TSN code for a search term.
get_uid
Get the UID codes from NCBI for taxonomic names.
getdatedatafromtsn
Get date data from tsn
getfullhierarchyfromtsn
Get full hierarchy from tsn
getitisterms
Get itis terms from common names
gettsnbyvernacularlanguage
Get tsn by vernacular language
gni_parse
Parse scientific names using EOL's name parser.
itis_taxrank
Retrieve taxonomic rank name from given TSN.
eol_pages
Search for pages in EOL database using a taxonconceptID.
taxize_ldfast
Replacement function for ldply that should be faster in all cases.
ubio_ping
uBio ping
itis_kingdomnames
Get kingdom names
rank_ref
Lookup-table for IDs of taxonomic ranks
getacceptednamesfromtsn
Get accepted names from tsn
getcommentdetailfromtsn
Get comment detail from TSN