taxize v0.9.91

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Taxonomic Information from Around the Web

Interacts with a suite of web 'APIs' for taxonomic tasks, such as getting database specific taxonomic identifiers, verifying species names, getting taxonomic hierarchies, fetching downstream and upstream taxonomic names, getting taxonomic synonyms, converting scientific to common names and vice versa, and more.

Readme

taxize

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taxize allows users to search over many taxonomic data sources for species names (scientific and common) and download up and downstream taxonomic hierarchical information - among other things.

The taxize book => https://taxize.dev

The functions in the package that hit a specific API have a prefix and suffix separated by an underscore. They follow the format of service_whatitdoes. For example, gnr_resolve uses the Global Names Resolver API to resolve species names. General functions in the package that don't hit a specific API don't have two words separated by an underscore, e.g., classification.

You need API keys for Encyclopedia of Life (EOL), Tropicos, IUCN, and NatureServe.

SOAP

Note that a few data sources require SOAP web services, which are difficult to support in R across all operating systems. These include: Pan-European Species directories Infrastructure and Mycobank. Data sources that use SOAP web services have been moved to taxizesoap at https://github.com/ropensci/taxizesoap.

Currently implemented in taxize

Souce Function prefix API Docs API key
Encylopedia of Life eol link link
Taxonomic Name Resolution Service tnrs "api.phylotastic.org/tnrs" none
Integrated Taxonomic Information Service itis link none
Global Names Resolver gnr link none
Global Names Index gni link none
IUCN Red List iucn link link
Tropicos tp link link
Theplantlist dot org tpl ** none
Catalogue of Life col link none
National Center for Biotechnology Information ncbi none none
CANADENSYS Vascan name search API vascan link none
International Plant Names Index (IPNI) ipni none none
Barcode of Life Data Systems (BOLD) bold link none
National Biodiversity Network (UK) nbn link none
Index Fungorum fg none none
EU BON eubon link none
Index of Names (ION) ion link none
Open Tree of Life (TOL) tol link none
World Register of Marine Species (WoRMS) worms link none
NatureServe natserv link link
Wikipedia wiki link none
Kew's Plants of the World pow none none

**: There are none! We suggest using TPL and TPLck functions in the taxonstand package. We provide two functions to get bulk data: tpl_families and tpl_get.

***: There are none! The function scrapes the web directly.

May be in taxize in the future...

See the datasources tag in the issue tracker


Installation

Stable version from CRAN

install.packages("taxize")

Development version from GitHub

Windows users install Rtools first.

install.packages("remotes")
remotes::install_github("ropensci/taxize")
library('taxize')

Get unique taxonomic identifier from NCBI

Alot of taxize revolves around taxonomic identifiers. Because, as you know, names can be a mess (misspelled, synonyms, etc.), it's better to get an identifier that a particular data source knows about, then we can move forth acquiring more fun taxonomic data.

uids <- get_uid(c("Chironomus riparius", "Chaetopteryx"))
#> ══  2 queries  ═══════════════
#> ✔  Found:  Chironomus+riparius
#> ✔  Found:  Chaetopteryx
#> ══  Results  ═════════════════
#> 
#> ● Total: 2 
#> ● Found: 2 
#> ● Not Found: 0

Retrieve classifications

Classifications - think of a species, then all the taxonomic ranks up from that species, like genus, family, order, class, kingdom.

out <- classification(uids)
lapply(out, head)
#> $`315576`
#>                 name         rank     id
#> 1 cellular organisms      no rank 131567
#> 2          Eukaryota superkingdom   2759
#> 3       Opisthokonta      no rank  33154
#> 4            Metazoa      kingdom  33208
#> 5          Eumetazoa      no rank   6072
#> 6          Bilateria      no rank  33213
#> 
#> $`492549`
#>                 name         rank     id
#> 1 cellular organisms      no rank 131567
#> 2          Eukaryota superkingdom   2759
#> 3       Opisthokonta      no rank  33154
#> 4            Metazoa      kingdom  33208
#> 5          Eumetazoa      no rank   6072
#> 6          Bilateria      no rank  33213

Immediate children

Get immediate children of Salmo. In this case, Salmo is a genus, so this gives species within the genus.

children("Salmo", db = 'ncbi')
#> $Salmo
#>    childtaxa_id                   childtaxa_name childtaxa_rank
#> 1       2304090                  Salmo abanticus        species
#> 2       2126688              Salmo ciscaucasicus        species
#> 3       1509524  Salmo marmoratus x Salmo trutta        species
#> 4       1484545 Salmo cf. cenerinus BOLD:AAB3872        species
#> 5       1483130               Salmo zrmanjaensis        species
#> 6       1483129               Salmo visovacensis        species
#> 7       1483128                Salmo rhodanensis        species
#> 8       1483127                 Salmo pellegrini        species
#> 9       1483126                     Salmo opimus        species
#> 10      1483125                Salmo macedonicus        species
#> 11      1483124                Salmo lourosensis        species
#> 12      1483123                   Salmo labecula        species
#> 13      1483122                  Salmo farioides        species
#> 14      1483121                      Salmo chilo        species
#> 15      1483120                     Salmo cettii        species
#> 16      1483119                  Salmo cenerinus        species
#> 17      1483118                   Salmo aphelios        species
#> 18      1483117                    Salmo akairos        species
#> 19      1201173               Salmo peristericus        species
#> 20      1035833                   Salmo ischchan        species
#> 21       700588                     Salmo labrax        species
#> 22       602068                    Salmo caspius     subspecies
#> 23       237411              Salmo obtusirostris        species
#> 24       235141              Salmo platycephalus        species
#> 25       234793                    Salmo letnica        species
#> 26        62065                  Salmo ohridanus        species
#> 27        33518                 Salmo marmoratus        species
#> 28        33516                    Salmo fibreni        species
#> 29        33515                     Salmo carpio        species
#> 30         8032                     Salmo trutta        species
#> 31         8030                      Salmo salar        species
#> 
#> attr(,"class")
#> [1] "children"
#> attr(,"db")
#> [1] "ncbi"

Downstream children to a rank

Get all species in the genus Apis

downstream(as.tsn(154395), db = 'itis', downto = 'species', mesages = FALSE)
#> $`154395`
#>      tsn parentname parenttsn          taxonname rankid rankname
#> 1 154396       Apis    154395     Apis mellifera    220  species
#> 2 763550       Apis    154395 Apis andreniformis    220  species
#> 3 763551       Apis    154395        Apis cerana    220  species
#> 4 763552       Apis    154395       Apis dorsata    220  species
#> 5 763553       Apis    154395        Apis florea    220  species
#> 6 763554       Apis    154395 Apis koschevnikovi    220  species
#> 7 763555       Apis    154395   Apis nigrocincta    220  species
#> 
#> attr(,"class")
#> [1] "downstream"
#> attr(,"db")
#> [1] "itis"

Upstream taxa

Get all genera up from the species Pinus contorta (this includes the genus of the species, and its co-genera within the same family).

upstream("Pinus contorta", db = 'itis', upto = 'Genus', mesages = FALSE)
#> ══  1 queries  ═══════════════
#> ✔  Found:  Pinus contorta
#> ══  Results  ═════════════════
#> 
#> ● Total: 1 
#> ● Found: 1 
#> ● Not Found: 0
#> $`Pinus contorta`
#>      tsn parentname parenttsn   taxonname rankid rankname
#> 1  18031   Pinaceae     18030       Abies    180    genus
#> 2  18033   Pinaceae     18030       Picea    180    genus
#> 3  18035   Pinaceae     18030       Pinus    180    genus
#> 4 183396   Pinaceae     18030       Tsuga    180    genus
#> 5 183405   Pinaceae     18030      Cedrus    180    genus
#> 6 183409   Pinaceae     18030       Larix    180    genus
#> 7 183418   Pinaceae     18030 Pseudotsuga    180    genus
#> 8 822529   Pinaceae     18030  Keteleeria    180    genus
#> 9 822530   Pinaceae     18030 Pseudolarix    180    genus
#> 
#> attr(,"class")
#> [1] "upstream"
#> attr(,"db")
#> [1] "itis"

Get synonyms

synonyms("Acer drummondii", db="itis")
#> ══  1 queries  ═══════════════
#> ✔  Found:  Acer drummondii
#> ══  Results  ═════════════════
#> 
#> ● Total: 1 
#> ● Found: 1 
#> ● Not Found: 0
#> $`Acer drummondii`
#>   sub_tsn                    acc_name acc_tsn
#> 1  183671 Acer rubrum var. drummondii  526853
#> 2  183671 Acer rubrum var. drummondii  526853
#> 3  183671 Acer rubrum var. drummondii  526853
#>                      acc_author                        syn_author
#> 1 (Hook. & Arn. ex Nutt.) Sarg. (Hook. & Arn. ex Nutt.) E. Murray
#> 2 (Hook. & Arn. ex Nutt.) Sarg.             Hook. & Arn. ex Nutt.
#> 3 (Hook. & Arn. ex Nutt.) Sarg.     (Hook. & Arn. ex Nutt.) Small
#>                      syn_name syn_tsn
#> 1 Acer rubrum ssp. drummondii   28730
#> 2             Acer drummondii  183671
#> 3          Rufacer drummondii  183672
#> 
#> attr(,"class")
#> [1] "synonyms"
#> attr(,"db")
#> [1] "itis"

Get taxonomic IDs from many sources

get_ids(names="Salvelinus fontinalis", db = c('itis', 'ncbi'), mesages = FALSE)
#> ══  1 queries  ═══════════════
#> ✔  Found:  Salvelinus fontinalis
#> ══  Results  ═════════════════
#> 
#> ● Total: 1 
#> ● Found: 1 
#> ● Not Found: 0
#> ══  1 queries  ═══════════════
#> ✔  Found:  Salvelinus+fontinalis
#> ══  Results  ═════════════════
#> 
#> ● Total: 1 
#> ● Found: 1 
#> ● Not Found: 0
#> $itis
#> Salvelinus fontinalis 
#>              "162003" 
#> attr(,"class")
#> [1] "tsn"
#> attr(,"match")
#> [1] "found"
#> attr(,"multiple_matches")
#> [1] FALSE
#> attr(,"pattern_match")
#> [1] FALSE
#> attr(,"uri")
#> [1] "https://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=162003"
#> 
#> $ncbi
#> Salvelinus fontinalis 
#>                "8038" 
#> attr(,"class")
#> [1] "uid"
#> attr(,"match")
#> [1] "found"
#> attr(,"multiple_matches")
#> [1] FALSE
#> attr(,"pattern_match")
#> [1] FALSE
#> attr(,"uri")
#> [1] "https://www.ncbi.nlm.nih.gov/taxonomy/8038"
#> 
#> attr(,"class")
#> [1] "ids"

You can limit to certain rows when getting ids in any get_*() functions

get_ids(names="Poa annua", db = "gbif", rows=1)
#> ══  1 queries  ═══════════════
#> ✔  Found:  Poa annua
#> ══  Results  ═════════════════
#> 
#> ● Total: 1 
#> ● Found: 1 
#> ● Not Found: 0
#> $gbif
#> Poa annua 
#> "2704179" 
#> attr(,"class")
#> [1] "gbifid"
#> attr(,"match")
#> [1] "found"
#> attr(,"multiple_matches")
#> [1] TRUE
#> attr(,"pattern_match")
#> [1] FALSE
#> attr(,"uri")
#> [1] "https://www.gbif.org/species/2704179"
#> 
#> attr(,"class")
#> [1] "ids"

Furthermore, you can just back all ids if that's your jam with the get_*_() functions (all get_*() functions with additional _ underscore at end of function name)

get_ids_(c("Chironomus riparius", "Pinus contorta"), db = 'nbn', rows=1:3)
#> $nbn
#> $nbn$`Chironomus riparius`
#>               guid      scientificName    rank taxonomicStatus
#> 1 NBNSYS0000027573 Chironomus riparius species        accepted
#> 2 NHMSYS0001718585  Hypnoidus riparius species        accepted
#> 3 NBNSYS0000023573    Quedius riparius species        accepted
#> 
#> $nbn$`Pinus contorta`
#>               guid                scientificName    rank taxonomicStatus
#> 1 NBNSYS0000004786                Pinus contorta species        accepted
#> 2 NHMSYS0000494848  Pinus contorta var. contorta variety        accepted
#> 3 NHMSYS0000494858 Pinus contorta var. murrayana variety        accepted
#> 
#> 
#> attr(,"class")
#> [1] "ids"

Common names from scientific names

sci2comm('Helianthus annuus', db = 'itis')
#> ══  1 queries  ═══════════════
#> ✔  Found:  Helianthus annuus
#> ══  Results  ═════════════════
#> 
#> ● Total: 1 
#> ● Found: 1 
#> ● Not Found: 0
#> $`Helianthus annuus`
#> [1] "common sunflower" "sunflower"        "wild sunflower"  
#> [4] "annual sunflower"

Scientific names from common names

comm2sci("black bear", db = "itis")
#> $`black bear`
#> [1] "Ursus americanus luteolus"   "Ursus americanus"           
#> [3] "Ursus americanus"            "Ursus americanus americanus"
#> [5] "Chiropotes satanas"          "Ursus thibetanus"           
#> [7] "Ursus thibetanus"

Lowest common rank among taxa

spp <- c("Sus scrofa", "Homo sapiens", "Nycticebus coucang")
lowest_common(spp, db = "ncbi")
#> ══  3 queries  ═══════════════
#> ✔  Found:  Sus+scrofa
#> ✔  Found:  Homo+sapiens
#> ✔  Found:  Nycticebus+coucang
#> ══  Results  ═════════════════
#> 
#> ● Total: 3 
#> ● Found: 3 
#> ● Not Found: 0
#>             name        rank      id
#> 21 Boreoeutheria below-class 1437010

Coerce codes to taxonomic id classes

numeric to uid

as.uid(315567)
#> [1] "315567"
#> attr(,"class")
#> [1] "uid"
#> attr(,"match")
#> [1] "found"
#> attr(,"multiple_matches")
#> [1] FALSE
#> attr(,"pattern_match")
#> [1] FALSE
#> attr(,"uri")
#> [1] "https://www.ncbi.nlm.nih.gov/taxonomy/315567"

list to uid

as.uid(list("315567", "3339", "9696"))
#> [1] "315567" "3339"   "9696"  
#> attr(,"class")
#> [1] "uid"
#> attr(,"match")
#> [1] "found" "found" "found"
#> attr(,"multiple_matches")
#> [1] FALSE FALSE FALSE
#> attr(,"pattern_match")
#> [1] FALSE FALSE FALSE
#> attr(,"uri")
#> [1] "https://www.ncbi.nlm.nih.gov/taxonomy/315567"
#> [2] "https://www.ncbi.nlm.nih.gov/taxonomy/3339"  
#> [3] "https://www.ncbi.nlm.nih.gov/taxonomy/9696"

Coerce taxonomic id classes to a data.frame

out <- as.uid(c(315567, 3339, 9696))
(res <- data.frame(out))
#>      ids class match multiple_matches pattern_match
#> 1 315567   uid found            FALSE         FALSE
#> 2   3339   uid found            FALSE         FALSE
#> 3   9696   uid found            FALSE         FALSE
#>                                            uri
#> 1 https://www.ncbi.nlm.nih.gov/taxonomy/315567
#> 2   https://www.ncbi.nlm.nih.gov/taxonomy/3339
#> 3   https://www.ncbi.nlm.nih.gov/taxonomy/9696

Screencast

Contributing

See our CONTRIBUTING document.

Contributors

Alphebetical

Code Contributors

All Contributors!

Collected via GitHub Issues - this list honors all contributions, whether code or not.

Alphebetical

afkoeppel - ahhurlbert - albnd - Alectoria - andzandz11 - antagomir - arendsee - ArielGreiner - arw36 - ashenkin - ashiklom - benjaminschwetz - benmarwick - bomeara - bw4sz - cboettig - cdeterman - ChrKoenig - chuckrp - clarson2191 - claudenozeres - cmzambranat - cparsania - daattali - DanielGMead - DarrenObbard - davharris - davidvilanova - diogoprov - dlebauer - dlenz1 - dschlaep - EDiLD - edwbaker - emhart - eregenyi - fdschneider - fgabriel1891 - fischhoff - fmichonneau - fozy81 - gedankenstuecke - GISKid - git-og - glaroc - gpli - gustavobio - hlapp - ibartomeus - Ironholds - jangorecki - jarioksa - jebyrnes - jimmyodonnell - johnbaums - jonmcalder - josephwb - jsgosnell - jwilk - kamapu - karthik - katrinleinweber - KevCaz - kgturner - kmeverson - Koalha - ljvillanueva - maelle - Markus2015 - mcsiple - MikkoVihtakari - millerjef - miriamgrace - MK212 - mpnelsen - MUSEZOOLVERT - nate-d-olson - nmatzke - npch - paternogbc - patperu - pederengelstad - philippi - pmarchand1 - PrincessPi314 - pssguy - raredd - rec3141 - Rekyt - RodgerG - rossmounce - sariya - scelmendorf - sckott - SimonGoring - snsheth - snubian - Squiercg - taddallas - tdjames1 - tmkurobe - toczydlowski - tpaulson1 - tpoisot - vijaybarve - wcornwell - willpearse - wpetry - yhg926 - zachary-foster

Road map

Check out our milestones to see what we plan to get done for each version.

Meta

  • Please report any issues or bugs.
  • License: MIT
  • Get citation information for taxize in R doing citation(package = 'taxize')
  • Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.

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Functions in taxize

Name Description
downstream Retrieve the downstream taxa for a given taxon name or ID.
classification Retrieve the taxonomic hierarchy for a given taxon ID.
eubon DEFUNCT
gni_search Search for taxonomic names using the Global Names Index
get_iucn Get a IUCN Redlist taxon
get_wiki Get the page name for a Wiki taxon
eol_pages Search for pages in EOL database using a taxonconceptID.
get_natservid Get NatureServe taxonomic ID for a taxon name
get_wormsid Get Worms ID for a taxon name
eubon_capabilities EUBON capabilities
eol_dataobjects Given the identifier for a data object, return all metadata about the object
get_ubioid Get the uBio id for a search term
comm2sci Get scientific names from common names.
fungorum Index Fungorum
get_uid Get the UID codes from NCBI for taxonomic names.
get_genes_avail Retrieve gene sequences from NCBI by accession number.
col_search_paginate col_search wrapper to iterate to get more than default results
eubon_search EUBON taxonomy search
get_genes Retrieve gene sequences from NCBI by accession number.
col_downstream Use Catalogue of Life to get downstream taxa to a given taxonomic level
eol_hierarchy Retrieve the taxonomic hierarchy from given EOL taxonID.
eol_invasive Search for presence of taxonomic names in EOL invasive species databases.
eubon_children EUBON children
eubon_hierarchy EUBON hierarchy
iucn_status Extractor functions for iucn-class.
ipni_search Search for names in the International Plant Names Index (IPNI).
itis_acceptname Retrieve accepted TSN and name
gnr_datasources Global Names Resolver Data Sources
iucn_summary Get a summary from the IUCN Red List
ncbi_downstream Retrieve all taxa names downstream in hierarchy for NCBI
ncbi_children Search NCBI for children of a taxon
progressor methods for preparing/printing info for prompts for get_* functions
rank_ref Lookup-table for IDs of taxonomic ranks
get_id_details Details on get_*() functions
eol_search Search for terms in EOL database.
gnr_resolve Resolve names using Global Names Resolver
iplant_resolve iPlant name resolution
get_ids Retrieve taxonomic identifiers for a given taxon name.
itis_hierarchy ITIS hierarchy
ion ION - Index to Organism Names
get_tsn Get the TSN code for a search term.
get_tpsid Get the NameID codes from Tropicos for taxonomic names.
itis_kingdomnames Get kingdom names
id2name Taxonomic IDs to taxonomic names
itis_native Get jurisdiction data, i.e., native or not native in a region.
gbif_parse Parse taxon names using the GBIF name parser.
tp_summary Return summary data a taxon name with a given id.
resolve Resolve names from different data sources
theplantlist Lookup-table for family, genus, and species names for ThePlantList
tp_classification Return all synonyms for a taxon name with a given id.
rankagg Aggregate data by given taxonomic rank
tp_accnames Return all accepted names for a taxon name with a given id.
taxon_state Keep track of queries in get_* functions
upstream Retrieve the upstream taxa for a given taxon name or ID.
tp_search Search Tropicos by scientific name, common name, or Tropicos ID.
vascan_search Search the CANADENSYS Vascan API.
genbank2uid Get NCBI taxonomy UID from GenBankID
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_seqs Retrieve gene sequences from NCBI by accession number.
itis_refs Get references related to a ITIS TSN.
getkey Function to get API key.
iucn_id Get an ID for a IUCN listed taxon
gisd_isinvasive Check invasive species status for a set of species from GISD database
itis_downstream Retrieve all taxa names or TSNs downstream in hierarchy from given TSN.
get_tolid Get the OTT id for a search term
names_list Get a random vector of species names.
itis_getrecord Get full ITIS record for one or more ITIS TSN's or lsid's.
iucn_getname Get any matching IUCN species names
nbn_classification Search UK National Biodiversity Network database for taxonomic classification
pow_lookup Lookup taxa in Kew's Plants of the World
limited_print Print a subset of a character vector
tax_agg Aggregate species data to given taxonomic rank
synonyms Retrieve synonyms from various sources given input taxonomic names or identifiers
ncbi_search Search for gene sequences available for taxa from NCBI.
ncbi_getbyname Retrieve gene sequences from NCBI by taxon name and gene names.
itis_terms Get ITIS terms, i.e., tsn's, authors, common names, and scientific names.
plantminer Search for taxonomy data from Plantminer.com
plantNames Vector of plant species (genus - specific epithet) names from ThePlantList
itis_taxrank Retrieve taxonomic rank name from given TSN.
pow_search Search Kew's Plants of the World
ubio_classification uBio classification
taxon-state Last taxon state object from a get_* function call
taxize_options taxon state options
tnrs_sources TNRS sources
tnrs Phylotastic Taxonomic Name Resolution Service.
scrapenames Resolve names using Global Names Recognition and Discovery.
sci2comm Get common names from scientific names.
ubio_classification_search This function will return ClassificationBankIDs (hierarchiesIDs) that refer to the given NamebankID
col_search Search Catalogue of Life for taxonomic IDs
gbif_downstream Retrieve all taxa names downstream in hierarchy for GBIF
gbif_name_usage Lookup details for specific names in all taxonomies in GBIF.
taxize-package Taxonomic Information from Around the Web
nbn_search Search UK National Biodiversity Network
get_eolid Get the EOL ID from Encyclopedia of Life from taxonomic names.
lowest_common Retrieve the lowest common taxon and rank for a given taxon name or ID
nbn_synonyms Return all synonyms for a taxon name with a given id from NBN
taxize_capwords Capitalize the first letter of a character string.
ping Ping an API used in taxize to see if it's working.
plantGenusNames Vector of plant genus names from ThePlantList
get_pow Get Kew's Plants of the World code for a taxon
get_gbifid Get the GBIF backbone taxon ID from taxonomic names.
get_nbnid Get the UK National Biodiversity Network ID from taxonomic names.
iucn_summary_id DEFUNCT
key_helpers Helpers to set up authentication for the different providers.
itis_name Get taxonomic names for a given taxonomic name query.
gni_parse Parse scientific names using EOL's name parser.
species_plantarum_binomials Species names from Species Plantarum
itis_lsid Get TSN from LSID
gni_details Search for taxonomic name details using the Global Names Index
worms_downstream Retrieve all taxa names downstream in hierarchy for WORMS
status_codes Get HTTP status codes
taxize-defunct Defunct functions in taxize
tp_namedistributions Return all distribution records for for a taxon name with a given id.
taxize-authentication taxize authentication
tp_dist Return all distribution records for for a taxon name with a given id.
ncbi_get_taxon_summary NCBI taxon information from uids
phylomatic_format Get family names to make Phylomatic input object, and output input string to Phylomatic for use in the function phylomatic_tree.
ncbi_getbyid Retrieve gene sequences from NCBI by accession number.
phylomatic_tree Query Phylomatic for a phylogenetic tree.
tp_synonyms Return all synonyms for a taxon name with a given id.
tol_resolve Resolve names using Open Tree of Life (OTL) resolver
tax_name Get taxonomic names for a given rank
tpl_families Get The Plant List families.
tp_acceptednames Return all accepted names for a taxon name with a given id.
ubio_id Search uBio by namebank ID.
ubio_search This function will return NameBankIDs that match given search terms
tax_rank Get rank for a given taxonomic name.
taxize_cite Get citations and licenses for data sources used in taxize
taxize_ldfast Replacement function for ldply that should be faster in all cases.
ubio_synonyms Search uBio for taxonomic synonyms by hierarchiesID.
ubio_ping uBio ping
tp_namereferences Return all reference 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.
tpl_get Get The Plant List csv files.
tpl_search A light wrapper around the taxonstand fxn to call Theplantlist.org database.
col_classification Search Catalogue of Life for taxonomic classifications.
apg Get APG names
children Retrieve immediate children taxa for a given taxon name or ID.
col_children Search Catalogue of Life for for direct children of a particular taxon.
apg_lookup Lookup in the APGIII taxonomy and replace family names
apg_families MOBOT family names
class2tree Convert a list of classifications to a tree.
bold_search Search Barcode of Life for taxonomic IDs
apg_orders MOBOT order names
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Vignettes of taxize

Name
name_cleaning.Rmd
taxize_case_study.Rmd
taxize_infotable.Rmd
taxize_vignette.Rmd
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Details

License MIT + file LICENSE
URL https://docs.ropensci.org/taxize (website), https://github.com/ropensci/taxize (devel), https://taxize.dev (user manual)
BugReports https://github.com/ropensci/taxize/issues
LazyLoad yes
LazyData true
VignetteBuilder knitr
Encoding UTF-8
Language en-US
RoxygenNote 6.1.1
X-schema.org-applicationCategory Taxonomy
X-schema.org-keywords taxonomy, biology, nomenclature, JSON, API, web, api-client, identifiers, species, names
X-schema.org-isPartOf https://ropensci.org
NeedsCompilation no
Packaged 2019-11-15 00:11:30 UTC; sckott
Repository CRAN
Date/Publication 2019-11-15 11:40:02 UTC

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