A taxonomic toolbelt for R
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README.md

taxize

Build Status Build status codecov.io rstudio mirror downloads cran version

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 tutorial is can be found at https://ropensci.org/tutorials/taxize.html.

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), and Tropicos.

SOAP

Note that a few data sources require SOAP web services, which are difficult to support in R across all operating systems. These include: World Register of Marine Species, Pan-European Species directories Infrastructure , and Mycobank, so far. Data sources that use SOAP web services have been moved to a new package called taxizesoap. Find it 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 none
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 link none
Barcode of Life Data Systems (BOLD) bold link none
National Biodiversity Network (UK) nbn link none
Index Fungorum fg link none
EU BON eubon link none
Index of Names (ION) ion link none

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

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

May be in taxize in the future...

See the newdatasource tag in the issue tracker

Tutorial

For more examples see the tutorial

Installation

Stable version from CRAN

install.packages("taxize")

Development version from GitHub

Windows users install Rtools first.

install.packages("devtools")
devtools::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 sources knows about, then we can move forth acquiring more fun taxonomic data.

uids <- get_uid(c("Chironomus riparius", "Chaetopteryx"))

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       1509524  Salmo marmoratus x Salmo trutta        species
#> 2       1484545 Salmo cf. cenerinus BOLD:AAB3872        species
#> 3       1483130               Salmo zrmanjaensis        species
#> 4       1483129               Salmo visovacensis        species
#> 5       1483128                Salmo rhodanensis        species
#> 6       1483127                 Salmo pellegrini        species
#> 7       1483126                     Salmo opimus        species
#> 8       1483125                Salmo macedonicus        species
#> 9       1483124                Salmo lourosensis        species
#> 10      1483123                   Salmo labecula        species
#> 11      1483122                  Salmo farioides        species
#> 12      1483121                      Salmo chilo        species
#> 13      1483120                     Salmo cettii        species
#> 14      1483119                  Salmo cenerinus        species
#> 15      1483118                   Salmo aphelios        species
#> 16      1483117                    Salmo akairos        species
#> 17      1201173               Salmo peristericus        species
#> 18      1035833                   Salmo ischchan        species
#> 19       700588                     Salmo labrax        species
#> 20       237411              Salmo obtusirostris        species
#> 21       235141              Salmo platycephalus        species
#> 22       234793                    Salmo letnica        species
#> 23        62065                  Salmo ohridanus        species
#> 24        33518                 Salmo marmoratus        species
#> 25        33516                    Salmo fibreni        species
#> 26        33515                     Salmo carpio        species
#> 27         8032                     Salmo trutta        species
#> 28         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("Apis", db = 'itis', downto = 'Species', verbose = FALSE)
#> $Apis
#>      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', verbose=FALSE)
#> $`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")
#> $`Acer drummondii`
#>   sub_tsn                    acc_name acc_tsn                    syn_name
#> 1  183671 Acer rubrum var. drummondii  526853 Acer rubrum ssp. drummondii
#> 2  183671 Acer rubrum var. drummondii  526853             Acer drummondii
#> 3  183671 Acer rubrum var. drummondii  526853          Rufacer drummondii
#>   syn_tsn
#> 1   28730
#> 2  183671
#> 3  183672

Get taxonomic IDs from many sources

get_ids(names="Salvelinus fontinalis", db = c('itis', 'ncbi'), verbose=FALSE)
#> $itis
#> Salvelinus fontinalis 
#>              "162003" 
#> attr(,"match")
#> [1] "found"
#> attr(,"multiple_matches")
#> [1] FALSE
#> attr(,"pattern_match")
#> [1] FALSE
#> attr(,"uri")
#> [1] "http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=162003"
#> attr(,"class")
#> [1] "tsn"
#> 
#> $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] "http://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)
#> $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] "http://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`
#>   ptaxonversionkey    searchmatchtitle    rank  namestatus
#> 1 NBNSYS0000027573 Chironomus riparius species Recommended
#> 2 NHMSYS0001718042   Elaphrus riparius species Recommended
#> 3 NBNSYS0000023345   Paederus riparius species Recommended
#> 
#> $nbn$`Pinus contorta`
#>   ptaxonversionkey               searchmatchtitle       rank  namestatus
#> 1 NHMSYS0000494848   Pinus contorta var. contorta    variety Recommended
#> 2 NBNSYS0000004786                 Pinus contorta    species Recommended
#> 3 NHMSYS0000494848 Pinus contorta subsp. contorta subspecies Recommended
#> 
#> 
#> attr(,"class")
#> [1] "ids"

Common names from scientific names

sci2comm('Helianthus annuus', db = 'itis')
#> $`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] "Ursus thibetanus"            "Ursus thibetanus"           
#> [7] "Chiropotes satanas"

Lowest common rank among taxa

spp <- c("Sus scrofa", "Homo sapiens", "Nycticebus coucang")
lowest_common(spp, db = "ncbi")
#>             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] "http://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] "http://www.ncbi.nlm.nih.gov/taxonomy/315567"
#> [2] "http://www.ncbi.nlm.nih.gov/taxonomy/3339"  
#> [3] "http://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 http://www.ncbi.nlm.nih.gov/taxonomy/315567
#> 2   http://www.ncbi.nlm.nih.gov/taxonomy/3339
#> 3   http://www.ncbi.nlm.nih.gov/taxonomy/9696

Contributors

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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