resolve {taxize}R Documentation

Resolve names from different data sources

Description

Resolve names from iPlant's name resolver, the Taxonomic Name Resolution Service (TNRS), and the Global Names Resolver (GNR)

Usage

resolve(query, db = "gnr", ...)

Arguments

query

Vector of one or more taxonomic names (common names not supported)

db

Source to check names against. One of iplant, tnrs, or gnr. Default: gnr Note that each taxonomic data source has their own identifiers, so that if you provide the wrong db value for the identifier you could get a result, but it will likely be wrong (not what you were expecting).

...

Curl options passed on to GET or POST. In addition, further named args passed on to each respective function. See examples

Value

A list with length equal to length of the db parameter (number of sources requested), with each element being a data.frame or list with results from that source.

Examples

## Not run: 
resolve(query=c("Helianthus annuus", "Homo sapiens"))
resolve(query="Quercus keloggii", db='gnr')
resolve(query=c("Helianthus annuus", "Homo sapiens"), db='tnrs')
resolve(query=c("Helianthus annuus", "Homo sapiens"), db=c('iplant', 'gnr'))
resolve(query="Quercus keloggii", db=c('iplant', 'gnr'))
resolve(query="Quercus keloggii", db=c('iplant', 'gnr', 'tnrs'))

# pass in options specific to each source
resolve("Helianthus annuus", db = 'gnr', preferred_data_sources = c(3, 4))
resolve("Helianthus annuus", db = 'iplant', retrieve = 'best')
identical(
 resolve("Helianthus annuus", db = 'iplant', retrieve = 'best')$iplant,
 iplant_resolve("Helianthus annuus", retrieve = 'best')
)
mynames <- c("Helianthus annuus", "Pinus contorta", "Poa annua",
   "Abies magnifica", "Rosa california")
resolve(mynames, db = 'tnrs', source = "NCBI")
resolve(mynames, db = 'tnrs', source = "iPlant_TNRS")
identical(
 resolve(mynames, db = 'tnrs', source = "iPlant_TNRS")$tnrs,
 tnrs(mynames, source = "iPlant_TNRS")
)

# pass in curl options
library("httr")
resolve(query="Qercuss", db = "iplant", config=verbose())
res <- resolve(query=c("Helianthus annuus", "Homo sapiens"), config=progress())

## End(Not run)
[Package taxize version 0.9.3 Index]