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taxize (version 0.7.5)
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
0.7.5
License
MIT + file LICENSE
Issues
55
Pull Requests
1
Stars
262
Forks
58
Repository
https://github.com/ropensci/taxize
Maintainer
Scott Chamberlain
Last Published
April 6th, 2016
Functions in taxize (0.7.5)
Search functions
col_search
Search Catalogue of Life for taxonomic IDs
bold_search
Search Barcode of Life for taxonomic IDs
getunacceptabilityreasonfromtsn
Returns the unacceptability reason, if any, for the TSN.
getfullhierarchyfromtsn
Get full hierarchy from tsn
getdatedatafromtsn
Get date data from tsn
fungorum
Index Fungorum
get_ids
Retrieve taxonomic identifiers for a given taxon name.
getlsidfromtsn
Gets the unique LSID for the TSN, or an empty result if there is no match.
get_seqs
Retrieve gene sequences from NCBI by accession number.
eol_hierarchy
Retrieve the taxonomic hierarchy from given EOL taxonID.
gethierarchyupfromtsn
Get hierarchy up from tsn
getkingdomnamefromtsn
Get kingdom names from tsn
eol_pages
Search for pages in EOL database using a taxonconceptID.
getjurisdictionoriginvalues
Get jurisdiction origin values
gbif_name_usage
Lookup details for specific names in all taxonomies in GBIF.
apg_lookup
Lookup in the APGIII taxonomy and replace family names
apg
Get APG names
gbif_parse
Parse taxon names using the GBIF name parser.
children
Retrieve immediate children taxa for a given taxon name or ID.
gethierarchydownfromtsn
Get hierarchy down from tsn
eol_dataobjects
Given the identifier for a data object, return all metadata about the object
itis_downstream
Retrieve all taxa names or TSNs downstream in hierarchy from given TSN.
getglobalspeciescompletenessfromtsn
Get global species completeness from tsn
getkingdomnames
Get all possible kingdom names
getanymatchcount
Get any match count.
gettsnfromlsid
Gets the TSN corresponding to the LSID, or an empty result if there is no match.
get_tpsid
Get the NameID codes from Tropicos for taxonomic names.
col_classification
Search Catalogue of Life for taxonomic classifications.
iucn_summary
Get a summary from the IUCN Red List
getcoremetadatafromtsn
Get core metadata from tsn
ipni_search
Search for names in the International Plant Names Index (IPNI).
genbank2uid
Get NCBI taxonomy UID from GenBankID
eol_search
Search for terms in EOL database.
gni_parse
Parse scientific names using EOL's name parser.
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.
phylomatic_tree
Query Phylomatic for a phylogenetic tree.
comm2sci
Get scientific names from common names.
eol_invasive
Search for presence of taxonomic names in EOL invasive species databases.
getvernacularlanguages
Provides a list of the unique languages used in the vernacular table.
getpublicationsfromtsn
Returns a list of the pulications used for the TSN.
searchbycommonname
Search for tsn by common name
tnrs_sources
TNRS sources
gettaxonomicranknamefromtsn
Returns the kingdom and rank information for the TSN.
apg_orders
MOBOT order names
iplant_resolve
iPlant name resolution
get_eolid
Get the EOL ID from Encyclopedia of Life from taxonomic names.
get_ubioid
Get the uBio id for a search term
sci2comm
Get common names from scientific names.
get_boldid
Get the BOLD (Barcode of Life) code for a search term.
getcoveragefromtsn
Get coverge from tsn
get_uid
Get the UID codes from NCBI for taxonomic names.
plantminer
Search for taxonomy data from Plantminer.com
getitistermsfromcommonname
Get itis terms from common names
class2tree
Convert list of classifications to a tree.
ncbi_getbyname
Retrieve gene sequences from NCBI by taxon name and gene names.
getcommonnamesfromtsn
Get common names from tsn
tp_refs
Return all reference records for for a taxon name with a given id.
names_list
Get a random vector of species names.
gettaxonomicusagefromtsn
Returns the usage information for the TSN.
getexpertsfromtsn
Get expert information for the TSN.
getkey
Function to get API key.
ncbi_children
Search NCBI for children of a taxon
col_children
Search Catalogue of Life for for direct children of a particular taxon.
tp_classification
Return all synonyms for a taxon name with a given id.
getdescription
Get description of the ITIS service
getgeographicvalues
Get all possible geographic values
getcommentdetailfromtsn
Get comment detail from TSN
get_colid
Get the Catalogue of Life ID from taxonomic names.
gettaxonauthorshipfromtsn
Returns the author information for the TSN.
ion
ION - Index to Organism Names
getacceptednamesfromtsn
Get accepted names from tsn
itis_searchcommon
Searches common name and acts as thin wrapper around
searchbycommonnamebeginswith
and
searchbycommonnameendswith
rankagg
Aggregate data by given taxonomic rank
synonyms
Retrieve synonyms from various sources given input taxonomic names or identifiers.
tp_dist
Return all distribution records for for a taxon name with a given id.
searchbycommonnameendswith
Search for tsn by common name ending with
taxize-defunct
Defunct functions in taxize
get_genes
Retrieve gene sequences from NCBI by accession number.
nbn_synonyms
Return all synonyms for a taxon name with a given id from NBN
getsynonymnamesfromtsn
Returns a list of the synonyms (if any) for the TSN.
tp_accnames
Return all accepted names for a taxon name with a given id.
eubon
EU BON taxonomy
tp_namedistributions
Return all distribution records for for a taxon name with a given id.
itis-api
Low level functions for working with the ITIS API.
taxize_cite
Get citations and licenses for data sources used in taxize
tax_rank
Get rank for a given taxonomic name.
getothersourcesfromtsn
Returns a list of the other sources used for the TSN.
getjurisdictionvalues
Get possible jurisdiction values
gnr_resolve
Resolve names using Global Names Resolver.
getcurrencyfromtsn
Get currency from tsn
getjurisdictionaloriginfromtsn
Get jurisdictional origin from tsn
itis_native
Get jurisdiction data, i.e., native or not native in a region.
getranknames
Provides a list of all the unique rank names contained in the database and their kingdom and rank ID values.
itis_taxrank
Retrieve taxonomic rank name from given TSN.
plantGenusNames
Vector of plant genus names from ThePlantList
rank_ref
Lookup-table for IDs of taxonomic ranks
col_downstream
Use Catalogue of Life to get downstream taxa to a given taxonomic level.
itis_lsid
Get kingdom names
itis_acceptname
Retrieve accepted TSN (with accepted name).
phylomatic_format
Get family names to make Phylomatic input object, and output input string to Phylomatic for use in the function phylomatic_tree.
get_nbnid
Get the UK National Biodiversity Network ID from taxonomic names.
gisd_isinvasive
Check invasive species status for a set of species from GISD database
ncbi_getbyid
Retrieve gene sequences from NCBI by accession number.
tol_resolve
Resolve names using Open Tree of Life resolver
status_codes
Get HTTP status codes
getgeographicdivisionsfromtsn
Get geographic divisions from tsn
itis_name
Get taxonomic names for a given taxonomic name query.
itis_getrecord
Get full ITIS record for one or more ITIS TSN's or lsid's.
searchforanymatchpaged
Search for any matched page
nbn_search
Search UK National Biodiversity Network database
searchbycommonnamebeginswith
Search for tsn by common name beginning with
plantNames
Vector of plant species (genus - specific epithet) names from ThePlantList
taxize_ldfast
Replacement function for ldply that should be faster in all cases.
searchforanymatch
Search for any match
apg_families
MOBOT family names
gbif_downstream
Retrieve all taxa names downstream in hierarchy for GBIF
resolve
Resolve names from different data sources
tpl_families
Get The Plant List families.
tp_acceptednames
Return all accepted names for a taxon name with a given id.
tax_agg
Aggregate species data to given taxonomic rank
iucn_status
Extractor functions for
iucn
-class.
ubio_synonyms
Search uBio for taxonomic synonyms by hierarchiesID.
gnr_datasources
Get data sources for the Global Names Resolver.
get_genes_avail
Retrieve gene sequences from NCBI by accession number.
iucn_id
Get an ID for a IUCN listed taxon
itis_hierarchy
ITIS hierarchy
tnrs
Phylotastic Taxonomic Name Resolution Service.
theplantlist
Lookup-table for family, genus, and species names for ThePlantList
getcredibilityratingfromtsn
Get credibility rating from tsn
itis_terms
Get ITIS terms, i.e., tsn's, authors, common names, and scientific names.
tp_namereferences
Return all reference records for for a taxon name with a given id.
gni_search
Search for taxonomic names using the Global Names Index.
getitistermsfromscientificname
Get itis terms from scientific names
classification
Retrieve the taxonomic hierarchy for a given taxon ID.
tpl_search
A light wrapper around the taxonstand fxn to call Theplantlist.org database.
tax_name
Get taxonomic names for a given rank.
ubio_search
This function will return NameBankIDs that match given search terms
itis_refs
Get references related to a ITIS TSN.
ubio_id
Search uBio by namebank ID.
gni_details
Search for taxonomic name details using the Global Names Index.
getcredibilityratings
Get possible credibility ratings
ubio_classification
uBio classification
tpl_get
Get The Plant List csv files.
tp_search
Search Tropicos by scientific name, common name, or Tropicos ID.
ncbi_get_taxon_summary
NCBI taxon information from uids
ubio_classification_search
This function will return ClassificationBankIDs (hierarchiesIDs) that refer to the given NamebankID
lowest_common
Retrieve the lowest common taxon and rank for a given taxon name or ID
get_tsn
Get the TSN code for a search term.
upstream
Retrieve the upstream taxa for a given taxon name or ID.
itis_kingdomnames
Get kingdom names
tp_summary
Return summary data a taxon name with a given id.
getitisterms
Get itis terms from common names
nbn_classification
Search UK National Biodiversity Network database for taxonomic classification
getreviewyearfromtsn
Returns the review year for the TSN.
searchbyscientificname
Search by scientific name
taxize-package
Taxonomic Information from Around the Web
ubio_ping
uBio ping
ping
Ping an API used in taxize to see if it's working.
tp_synonyms
Return all synonyms for a taxon name with a given id.
downstream
Retrieve the downstream taxa for a given taxon name or ID.
getfullrecordfromtsn
Get full record from TSN.
iucn_getname
Get any matching IUCN species names
get_gbifid
Get the GBIF backbone taxon ID from taxonomic names.
gettsnbyvernacularlanguage
Get tsn by vernacular language
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.
getlastchangedate
Provides the date the ITIS database was last updated.
getscientificnamefromtsn
Returns the scientific name for the TSN. Also returns the component parts (names and indicators) of the scientific name.
vascan_search
Search the CANADENSYS Vascan API.
scrapenames
Resolve names using Global Names Recognition and Discovery.
getparenttsnfromtsn
Returns the parent TSN for the entered TSN.
taxize_capwords
Capitalize the first letter of a character string.
ncbi_search
Search for gene sequences available for taxa from NCBI.