taxize v0.1.5

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Taxonomic information from around the web.

Taxonomic information from around the web. This package interacts with a suite of web APIs for taxonomic tasks, such as verifying species names, getting taxonomic hierarchies, and verifying name spelling.

Functions in taxize

Name Description
gbif_parse Parse taxon names using the GBIF name parser.
eol_hierarchy Retrieve the taxonomic hierarchy from given EOL taxonID.
getcredibilityratings Get possible credibility ratings
getcoveragefromtsn Get coverge from tsn
getpublicationsfromtsn Returns a list of the pulications used for the TSN.
get_tsn Get the TSN code for a search term.
getglobalspeciescompletenessfromtsn Get global species completeness from tsn
get_genes_avail Retrieve gene sequences available for a species from NCBI.
searchbycommonnamebeginswith Search for tsn by common name beginning with
classification Retrieve the taxonomic hierarchy for a given taxon ID.
getdatedatafromtsn Get date data from tsn
getothersourcesfromtsn Returns a list of the other sources used for the TSN.
collapse_double_root Function to collapse a double phylogenetic tree root
gettaxonauthorshipfromtsn Returns the author information for the TSN.
eol_search Search for terms in EOL database.
apg_families Lookup-table for APGIII family names
col_search Search Catalogue of Life for taxonomic IDs
get_seqs Retrieve nucleotide sequences from NCBI.
getscientificnamefromtsn Returns the scientific name for the TSN. Also returns the component parts (names and indicators) of the scientific name.
getgeographicvalues Get all possible geographic values
getfullrecordfromtsn Get full record from TSN.
gettaxonomicusagefromtsn Returns the usage information for the TSN.
getcredibilityratingfromtsn Get credibility rating from tsn
getcommentdetailfromtsn Get comment detail from TSN
ifelsedata Function to parse xml data, decode strings, and return NULL if logical is zero.
getgeographicdivisionsfromtsn Get geographic divisions from tsn
getvernacularlanguages Provides a list of the unique languages used in the vernacular table.
mssg Print a message if verbose is TRUE, but don't if FALSE
itis_downstream Retrieve all taxa names or TSNs downstream in hierarchy from given TSN.
getunacceptabilityreasonfromtsn Returns the unacceptability reason, if any, for the TSN.
rankagg Aggregate data by given taxonomic rank
getkingdomnames Get all possible kingdom names
getdescription Get description of the ITIS service
getjurisdictionaloriginfromtsn Get jurisdictional origin from tsn
getanymatchcount Get any match count.
gisd_isinvasive Check invasive species status for a set of species from GISD database
itis_searchcommon Searches common name and acts as thin wrapper around searchbycommonnamebeginswith and searchbycommonnameendswith
itis_hierarchy Get hierarchies from TSN values, full, upstream only, or immediate downstream only
get_tpsid Get the NameID codes from Tropicos for taxonomic names.
getsynonymnamesfromtsn Returns a list of the synonyms (if any) for the TSN.
col_downstream Use Catalogue of Life to get downstream taxa to a given taxonomic level.
get_genes Retrieve gene sequences from NCBI by accession number.
getitistermsfromcommonname Get itis terms from common names
iucn_status Extractor functions for iucn-class.
itis_lsid Get kingdom names.
get_uid Get the UID codes from NCBI for taxonomic names.
tpl_families Get The Plant List families.
getjurisdictionvalues Get possible jurisdiction values
getlsidfromtsn Gets the unique LSID for the TSN, or an empty result if there is no match.
getacceptednamesfromtsn Get accepted names from tsn
plantGenusNames Vector of 793 genus names of plants
itis_phymat_format Get family names to make Phylomatic input object, and output input string to Phylomatic for use in the function phylomatic_tree.
eol_pages Search for pages in EOL database using a taxonconceptID.
gnr_resolve Resolve names using Global Names Resolver.
plantminer Search for taxonomy data from Plantminer.com
itis_refs Get references related to a ITIS TSN.
tpl_get Get The Plant List csv files.
colldouble Function to to do things
eol_invasive Search for presence of taxonomic names in EOL invasive species databases.
gettsnfromlsid Gets the TSN corresponding to the LSID, or an empty result if there is no match.
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.
eol_ping Ping EOL API to see if it's working.
gethierarchyupfromtsn Get hierarchy up from tsn
getkingdomnamefromtsn Get kingdom names from tsn
getcoremetadatafromtsn Get core metadata from tsn
gettsnbyvernacularlanguage Retrieve accepted TSN (with accepted name)
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.
get_eolid Get the EOL ID from Encyclopedia of Life from taxonomic names.
rank_ref Lookup-table for IDs of taxonomic ranks
get_colid Get the Catalogue of Life ID from taxonomic names.
searchbycommonname Search for tsn by common name
itis_getrecord Get full ITIS record for one or more ITIS TSN's or lsid's.
searchforanymatch Search for any match
searchbyscientificname Search by scientific name
gni_parse Parse scientific names using EOL's name parser.
itis_kingdomnames Get kingdom names.
plantNames Vector of 1,182 species names of plants
tnrs Search the Phylotastic Taxonomic Name Resolution Service.
tax_rank Get rank for a given taxonomic name.
taxize_capwords Capitalize the first letter of a character string.
gni_search Search for taxonomic names using the Global Names Index.
itis_taxrank Retrieve taxonomic rank name from given TSN.
ubio_synonyms Search uBio by namebank ID.
itis_native Get jurisdiction data, i.e., native or not native in a region.
gnr_datasources Get data sources for the Global Names Resolver.
sci2comm Get common names from scientific names.
getkey Function to get API key.
getxml_syns Function to parse xml data and decode strings
apg_lookup Lookup in the APGII taxonomy and replace family names.
tp_namedistributions Return all distribution records for for a taxon name with a given id.
col_children Search Catalogue of Life for for direct children of a particular taxon.
tp_namereferences Return all reference records for for a taxon name with a given id.
itis_ping Ping the ITIS API to see if it's working.
taxize-package Taxnomic search and phylogeny retrieval.
ubio_id Search uBio by namebank ID.
iucn_getname Get any matching IUCN species names
ubio_classification_search This function will return all ClassificationBank data pertaining to a particular ClassificationBankID
iucn_summary Get a summary from the IUCN Red List.
getitistermsfromscientificname Get itis terms from scientific names
searchbycommonnameendswith Search for tsn by common name ending with
tp_classification Return all synonyms for a taxon name with a given id.
getjurisdictionoriginvalues Get jurisdiction origin values
getranknames Provides a list of all the unique rank names contained in the database and their kingdom and rank ID values.
tax_name Get taxonomic names for a given rank.
gettaxonomicranknamefromtsn Returns the kingdom and rank information for the TSN.
itis_terms Get ITIS terms, i.e., tsn's, authors, common names, and scientific names.
tnrs_sources Get sources for the Phylotastic Taxonomic Name Resolution Service.
getexpertsfromtsn Get expert information for the TSN.
tax_agg Aggregate species data to given taxonomic rank
tp_synonyms Return all synonyms for a taxon name with a given id.
tp_acceptednames Return all accepted names for a taxon name with a given id.
col_classification Search Catalogue of Life for taxonomic classifications.
apg_orders Lookup-table for APGIII order names
comm2sci Get scientific names from common names.
get_ids Retrieve taxonomic identifiers for a given taxon name.
eol_dataobjects Given the identifier for a data object, return all metadata about the object.
getfullhierarchyfromtsn Get full hierarchy from tsn
names_list Get a random vector of species names.
tp_summary Return summary data a taxon name with a given id.
getcurrencyfromtsn Get currency from tsn
ubio_classification This function will return all ClassificationBank data pertaining to a particular ClassificationBankID
getreviewyearfromtsn Returns the review year for the TSN.
gni_details Search for taxonomic name details using the Global Names Index.
searchforanymatchpaged Search for any matched page
getcommonnamesfromtsn Get common names from tsn
phylomatic_tree Format tree string, submit to Phylomatic, get newick or nexml tree.
synonyms Retrieve synonyms from various sources given input taxonomic names or identifiers.
tp_search Search Tropicos by scientific name, common name, or Tropicos ID.
ubio_search This function will return NameBankIDs that match given search terms
gethierarchydownfromtsn Get hierarchy down from tsn
getitisterms Get itis terms from common names
getparenttsnfromtsn Returns the parent TSN for the entered TSN.
ldfast Replacement function for ldply that should be faster in all cases.
itis_name Get taxonomic names for a given taxonomic name query.
getlastchangedate Provides the date the ITIS database was last updated.
getxmldata Function to parse xml data and decode strings
itis_acceptname Retrieve accepted TSN (with accepted name).
tpl_search A light wrapper around the taxonstand fxn to call Theplantlist.org database.
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Date 2013-11-18
License CC0
URL https://ropensci.github.com/taxize_
BugReports https://github.com/ropensci/taxize_/issues
LazyLoad yes
LazyData yes
VignetteBuilder knitr
Collate 'classification.R' 'get_tsn.R' 'gnr_datasources.R' 'gni_search.R' 'gni_details.R' 'iucn_summary.R' 'get_uid.R' 'plantminer.R' 'eol_hierarchy.R' 'eol_ping.R' 'eol_search.R' 'gnr_resolve.R' 'get_seqs.R' 'taxize-package.R' 'itis_acceptname.R' 'itis_phymat_format.R' 'itis_taxrank.R' 'eol_pages.R' 'tp_acceptednames.R' 'tp_namedistributions.R' 'tp_namereferences.R' 'tp_summary.R' 'tp_synonyms.R' 'zzz.R' 'get_genes_avail.R' 'tpl_search.r' 'tpl_get.r' 'itis_downstream.R' 'eol_dataobjects.R' 'col_children.R' 'col_classification.R' 'gisd_isinvasive.R' 'itis_name.R' 'tax_name.R' 'col_downstream.R' 'get_genes.R' 'tnrs_sources.r' 'tnrs.R' 'itis.R' 'apg_lookup.R' 'tax_rank.R' 'gni_parse.R' 'iucn_getname.R' 'rankagg.R' 'tax_agg.R' 'tpl_families.r' 'names_list.r' 'startup.R' 'taxize_capwords.r' 'ubio_id.R' 'ubio_classification.R' 'ubio_search.R' 'ubio_classification_search.R' 'ubio_synonyms.R' 'eol_invasive.R' 'get_tpsid.R' 'synonyms.R' 'tp_search.R' 'get_eolid.R' 'col_search.R' 'get_colid.R' 'tp_classification.R' 'get_ids.R' 'comm2sci.R' 'sci2comm.R' 'phylomatic_tree.R' 'gbif_parse.R' 'itis_getrecord.R' 'itis_ping.R' 'itis_refs.R' 'itis_kingdomnames.R' 'itis_lsid.R' 'itis_native.R' 'itis_hierarchy.R' 'itis_terms.R'
Packaged 2013-11-19 01:11:45 UTC; scottmac2
NeedsCompilation no
Repository CRAN
Date/Publication 2013-11-19 07:38:04

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