taxize (version 0.7.0)

resolve: 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 b

...

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

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())