A B C D E F G I L N P R S T U V
taxize-package | Taxonomic Information from Around the Web |
apg | Get APG names |
apgFamilies | Get APG names |
apgOrders | Get APG names |
apg_families | MOBOT family names |
apg_lookup | Lookup in the APGIII taxonomy and replace family names |
apg_orders | MOBOT order names |
as.boldid | Get the BOLD (Barcode of Life) code for a search term. |
as.boldid.boldid | Get the BOLD (Barcode of Life) code for a search term. |
as.boldid.character | Get the BOLD (Barcode of Life) code for a search term. |
as.boldid.data.frame | Get the BOLD (Barcode of Life) code for a search term. |
as.boldid.list | Get the BOLD (Barcode of Life) code for a search term. |
as.boldid.numeric | Get the BOLD (Barcode of Life) code for a search term. |
as.colid | Get the Catalogue of Life ID from taxonomic names. |
as.colid.character | Get the Catalogue of Life ID from taxonomic names. |
as.colid.colid | Get the Catalogue of Life ID from taxonomic names. |
as.colid.data.frame | Get the Catalogue of Life ID from taxonomic names. |
as.colid.list | Get the Catalogue of Life ID from taxonomic names. |
as.data.frame.boldid | Get the BOLD (Barcode of Life) code for a search term. |
as.data.frame.colid | Get the Catalogue of Life ID from taxonomic names. |
as.data.frame.eolid | Get the EOL ID from Encyclopedia of Life from taxonomic names. |
as.data.frame.gbifid | Get the GBIF backbone taxon ID from taxonomic names. |
as.data.frame.nbnid | Get the UK National Biodiversity Network ID from taxonomic names. |
as.data.frame.tpsid | Get the NameID codes from Tropicos for taxonomic names. |
as.data.frame.tsn | Get the TSN code for a search term. |
as.data.frame.ubioid | Get the uBio id for a search term |
as.data.frame.uid | Get the UID codes from NCBI for taxonomic names. |
as.eolid | Get the EOL ID from Encyclopedia of Life from taxonomic names. |
as.eolid.character | Get the EOL ID from Encyclopedia of Life from taxonomic names. |
as.eolid.data.frame | Get the EOL ID from Encyclopedia of Life from taxonomic names. |
as.eolid.eolid | Get the EOL ID from Encyclopedia of Life from taxonomic names. |
as.eolid.list | Get the EOL ID from Encyclopedia of Life from taxonomic names. |
as.eolid.numeric | Get the EOL ID from Encyclopedia of Life from taxonomic names. |
as.gbifid | Get the GBIF backbone taxon ID from taxonomic names. |
as.gbifid.character | Get the GBIF backbone taxon ID from taxonomic names. |
as.gbifid.data.frame | Get the GBIF backbone taxon ID from taxonomic names. |
as.gbifid.gbifid | Get the GBIF backbone taxon ID from taxonomic names. |
as.gbifid.list | Get the GBIF backbone taxon ID from taxonomic names. |
as.gbifid.numeric | Get the GBIF backbone taxon ID from taxonomic names. |
as.nbnid | Get the UK National Biodiversity Network ID from taxonomic names. |
as.nbnid.character | Get the UK National Biodiversity Network ID from taxonomic names. |
as.nbnid.data.frame | Get the UK National Biodiversity Network ID from taxonomic names. |
as.nbnid.list | Get the UK National Biodiversity Network ID from taxonomic names. |
as.nbnid.nbnid | Get the UK National Biodiversity Network ID from taxonomic names. |
as.tpsid | Get the NameID codes from Tropicos for taxonomic names. |
as.tpsid.character | Get the NameID codes from Tropicos for taxonomic names. |
as.tpsid.data.frame | Get the NameID codes from Tropicos for taxonomic names. |
as.tpsid.list | Get the NameID codes from Tropicos for taxonomic names. |
as.tpsid.numeric | Get the NameID codes from Tropicos for taxonomic names. |
as.tpsid.tpsid | Get the NameID codes from Tropicos for taxonomic names. |
as.tsn | Get the TSN code for a search term. |
as.tsn.character | Get the TSN code for a search term. |
as.tsn.data.frame | Get the TSN code for a search term. |
as.tsn.list | Get the TSN code for a search term. |
as.tsn.numeric | Get the TSN code for a search term. |
as.tsn.tsn | Get the TSN code for a search term. |
as.ubioid | Get the uBio id for a search term |
as.ubioid.character | Get the uBio id for a search term |
as.ubioid.data.frame | Get the uBio id for a search term |
as.ubioid.list | Get the uBio id for a search term |
as.ubioid.numeric | Get the uBio id for a search term |
as.ubioid.ubioid | Get the uBio id for a search term |
as.uid | Get the UID codes from NCBI for taxonomic names. |
as.uid.character | Get the UID codes from NCBI for taxonomic names. |
as.uid.data.frame | Get the UID codes from NCBI for taxonomic names. |
as.uid.list | Get the UID codes from NCBI for taxonomic names. |
as.uid.numeric | Get the UID codes from NCBI for taxonomic names. |
as.uid.uid | Get the UID codes from NCBI for taxonomic names. |
bold_ping | Ping an API used in taxize to see if it's working. |
bold_search | Search Barcode of Life for taxonomic IDs |
cbind.classification | Retrieve the taxonomic hierarchy for a given taxon ID. |
cbind.classification_ids | Retrieve the taxonomic hierarchy for a given taxon ID. |
children | Retrieve immediate children taxa for a given taxon name or ID. |
children.colid | Retrieve immediate children taxa for a given taxon name or ID. |
children.default | Retrieve immediate children taxa for a given taxon name or ID. |
children.ids | Retrieve immediate children taxa for a given taxon name or ID. |
children.tsn | Retrieve immediate children taxa for a given taxon name or ID. |
children.uid | Retrieve immediate children taxa for a given taxon name or ID. |
class2tree | Convert list of classifications to a tree. |
classification | Retrieve the taxonomic hierarchy for a given taxon ID. |
classification.colid | Retrieve the taxonomic hierarchy for a given taxon ID. |
classification.default | Retrieve the taxonomic hierarchy for a given taxon ID. |
classification.eolid | Retrieve the taxonomic hierarchy for a given taxon ID. |
classification.gbifid | Retrieve the taxonomic hierarchy for a given taxon ID. |
classification.ids | Retrieve the taxonomic hierarchy for a given taxon ID. |
classification.nbnid | Retrieve the taxonomic hierarchy for a given taxon ID. |
classification.tpsid | Retrieve the taxonomic hierarchy for a given taxon ID. |
classification.tsn | Retrieve the taxonomic hierarchy for a given taxon ID. |
classification.uid | Retrieve the taxonomic hierarchy for a given taxon ID. |
col_children | Search Catalogue of Life for for direct children of a particular taxon. |
col_downstream | Use Catalogue of Life to get downstream taxa to a given taxonomic level. |
col_ping | Ping an API used in taxize to see if it's working. |
col_search | Search Catalogue of Life for taxonomic IDs |
comm2sci | Get scientific names from common names. |
defunct | Defunct functions in taxize |
downstream | Retrieve the downstream taxa for a given taxon name or ID. |
downstream.colid | Retrieve the downstream taxa for a given taxon name or ID. |
downstream.default | Retrieve the downstream taxa for a given taxon name or ID. |
downstream.gbifid | Retrieve the downstream taxa for a given taxon name or ID. |
downstream.ids | Retrieve the downstream taxa for a given taxon name or ID. |
downstream.tsn | Retrieve the downstream taxa for a given taxon name or ID. |
eol_dataobjects | Given the identifier for a data object, return all metadata about the object |
eol_pages | Search for pages in EOL database using a taxonconceptID. |
eol_ping | Ping an API used in taxize to see if it's working. |
eol_search | Search for terms in EOL database. |
eubon | EU BON taxonomy |
fg_all_updated_names | Index Fungorum |
fg_author_search | Index Fungorum |
fg_deprecated_names | Index Fungorum |
fg_epithet_search | Index Fungorum |
fg_name_by_key | Index Fungorum |
fg_name_full_by_lsid | Index Fungorum |
fg_name_search | Index Fungorum |
fg_ping | Ping an API used in taxize to see if it's working. |
fungorum | Index Fungorum |
gbif_downstream | Retrieve all taxa names downstream in hierarchy for GBIF |
gbif_name_usage | Lookup details for specific names in all taxonomies in GBIF. |
gbif_parse | Parse taxon names using the GBIF name parser. |
gbif_ping | Ping an API used in taxize to see if it's working. |
genbank2uid | Get NCBI taxonomy UID from GenBankID |
get_boldid | Get the BOLD (Barcode of Life) code for a search term. |
get_boldid_ | Get the BOLD (Barcode of Life) code for a search term. |
get_colid | Get the Catalogue of Life ID from taxonomic names. |
get_colid_ | Get the Catalogue of Life ID from taxonomic names. |
get_eolid | Get the EOL ID from Encyclopedia of Life from taxonomic names. |
get_eolid_ | Get the EOL ID from Encyclopedia of Life from taxonomic names. |
get_gbifid | Get the GBIF backbone taxon ID from taxonomic names. |
get_gbifid_ | Get the GBIF backbone taxon ID from taxonomic names. |
get_ids | Retrieve taxonomic identifiers for a given taxon name. |
get_ids_ | Retrieve taxonomic identifiers for a given taxon name. |
get_nbnid | Get the UK National Biodiversity Network ID from taxonomic names. |
get_nbnid_ | Get the UK National Biodiversity Network ID from taxonomic names. |
get_tpsid | Get the NameID codes from Tropicos for taxonomic names. |
get_tpsid_ | Get the NameID codes from Tropicos for taxonomic names. |
get_tsn | Get the TSN code for a search term. |
get_tsn_ | Get the TSN code for a search term. |
get_ubioid | Get the uBio id for a search term |
get_ubioid_ | Get the uBio id for a search term |
get_uid | Get the UID codes from NCBI for taxonomic names. |
get_uid_ | Get the UID codes from NCBI for taxonomic names. |
gni_details | Search for taxonomic name details using the Global Names Index. |
gni_parse | Parse scientific names using EOL's name parser. |
gni_search | Search for taxonomic names using the Global Names Index. |
gnr_datasources | Get data sources for the Global Names Resolver. |
gnr_resolve | Resolve names using Global Names Resolver. |
ion | ION - Index to Organism Names |
iplant_resolve | iPlant name resolution |
ipni_ping | Ping an API used in taxize to see if it's working. |
ipni_search | Search for names in the International Plant Names Index (IPNI). |
itis-api | Low level functions for working with the ITIS API. |
itis_acceptname | Retrieve accepted TSN and name |
itis_downstream | Retrieve all taxa names or TSNs downstream in hierarchy from given TSN. |
itis_getrecord | Get full ITIS record for one or more ITIS TSN's or lsid's. |
itis_hierarchy | ITIS hierarchy |
itis_kingdomnames | Get kingdom names |
itis_lsid | Get kingdom names |
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. |
itis_ping | Ping an API used in taxize to see if it's working. |
itis_refs | Get references related to a ITIS TSN. |
itis_searchcommon | Searches common name and acts as thin wrapper around 'searchbycommonnamebeginswith' and 'searchbycommonnameendswith' |
itis_taxrank | Retrieve taxonomic rank name from given TSN. |
itis_terms | Get ITIS terms, i.e., tsn's, authors, common names, and scientific names. |
iucn_getname | Get any matching IUCN species names |
iucn_id | Get an ID for a IUCN listed taxon |
iucn_status | Extractor functions for 'iucn'-class. |
iucn_status.iucn | Get a summary from the IUCN Red List |
iucn_summary | Get a summary from the IUCN Red List |
iucn_summary_id | Get a summary from the IUCN Red List |
lowest_common | Retrieve the lowest common taxon and rank for a given taxon name or ID |
lowest_common.default | Retrieve the lowest common taxon and rank for a given taxon name or ID |
lowest_common.gbifid | Retrieve the lowest common taxon and rank for a given taxon name or ID |
lowest_common.tsn | Retrieve the lowest common taxon and rank for a given taxon name or ID |
lowest_common.uid | Retrieve the lowest common taxon and rank for a given taxon name or ID |
names_list | Get a random vector of species names. |
nbn_classification | Search UK National Biodiversity Network database for taxonomic classification |
nbn_ping | Ping an API used in taxize to see if it's working. |
nbn_search | Search UK National Biodiversity Network database |
nbn_synonyms | Return all synonyms for a taxon name with a given id from NBN |
ncbi_children | Search NCBI for children of a taxon |
ncbi_get_taxon_summary | NCBI taxon information from uids |
ncbi_ping | Ping an API used in taxize to see if it's working. |
phylomatic_format | Get family names to make Phylomatic input object, and output input string to Phylomatic for use in the function phylomatic_tree. |
phylomatic_tree | Query Phylomatic for a phylogenetic tree. |
ping | Ping an API used in taxize to see if it's working. |
plantGenusNames | Vector of plant genus names from ThePlantList |
plantminer | Search for taxonomy data from Plantminer.com |
plantNames | Vector of plant species (genus - specific epithet) names from ThePlantList |
plot.classtree | Convert list of classifications to a tree. |
print.classtree | Convert list of classifications to a tree. |
print.tax_agg | Aggregate species data to given taxonomic rank |
rankagg | Aggregate data by given taxonomic rank |
rank_ref | Lookup-table for IDs of taxonomic ranks |
rbind.classification | Retrieve the taxonomic hierarchy for a given taxon ID. |
rbind.classification_ids | Retrieve the taxonomic hierarchy for a given taxon ID. |
resolve | Resolve names from different data sources |
sci2comm | Get common names from scientific names. |
sci2comm.default | Get common names from scientific names. |
sci2comm.tsn | Get common names from scientific names. |
sci2comm.uid | Get common names from scientific names. |
scrapenames | Resolve names using Global Names Recognition and Discovery. |
status_codes | Get HTTP status codes |
synonyms | Retrieve synonyms from various sources given input taxonomic names or identifiers. |
synonyms.colid | Retrieve synonyms from various sources given input taxonomic names or identifiers. |
synonyms.default | Retrieve synonyms from various sources given input taxonomic names or identifiers. |
synonyms.ids | Retrieve synonyms from various sources given input taxonomic names or identifiers. |
synonyms.nbnid | Retrieve synonyms from various sources given input taxonomic names or identifiers. |
synonyms.tpsid | Retrieve synonyms from various sources given input taxonomic names or identifiers. |
synonyms.tsn | Retrieve synonyms from various sources given input taxonomic names or identifiers. |
taxize | Taxonomic Information from Around the Web |
taxize-defunct | Defunct functions in taxize |
taxize_capwords | Capitalize the first letter of a character string. |
taxize_cite | Get citations and licenses for data sources used in taxize |
tax_agg | Aggregate species data to given taxonomic rank |
tax_name | Get taxonomic names for a given rank |
tax_rank | Get rank for a given taxonomic name. |
theplantlist | Lookup-table for family, genus, and species names for ThePlantList |
tnrs | Phylotastic Taxonomic Name Resolution Service. |
tnrs_sources | TNRS sources |
tol_resolve | Resolve names using Open Tree of Life resolver |
tpl_families | Get The Plant List families. |
tpl_get | Get The Plant List csv files. |
tpl_search | A light wrapper around the taxonstand fxn to call Theplantlist.org database. |
tp_accnames | Return all accepted names for a taxon name with a given id. |
tp_dist | Return all distribution records for for a taxon name with a given id. |
tp_refs | Return all reference records for for a taxon name with a given id. |
tp_search | Search Tropicos by scientific name, common name, or Tropicos ID. |
tp_summary | Return summary data a taxon name with a given id. |
tp_synonyms | Return all synonyms for a taxon name with a given id. |
tropicos_ping | Ping an API used in taxize to see if it's working. |
ubio_classification | uBio classification |
ubio_classification_search | This function will return ClassificationBankIDs (hierarchiesIDs) that refer to the given NamebankID |
ubio_id | Search uBio by namebank ID. |
ubio_ping | uBio ping |
ubio_search | This function will return NameBankIDs that match given search terms |
ubio_synonyms | Search uBio for taxonomic synonyms by hierarchiesID. |
upstream | Retrieve the upstream taxa for a given taxon name or ID. |
upstream.colid | Retrieve the upstream taxa for a given taxon name or ID. |
upstream.default | Retrieve the upstream taxa for a given taxon name or ID. |
upstream.ids | Retrieve the upstream taxa for a given taxon name or ID. |
upstream.tsn | Retrieve the upstream taxa for a given taxon name or ID. |
vascan_ping | Ping an API used in taxize to see if it's working. |
vascan_search | Search the CANADENSYS Vascan API. |