taxize (version 0.9.100.1)

resolve: Resolve names from different data sources

Description

Resolve names from iPlant's name resolver, and the Global Names Resolver (GNR)

Usage

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

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.

Arguments

sci

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

db

Source to check names against. One of iplant 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).

query

Deprecated, see sci

...

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

Examples

if (FALSE) {
resolve(sci=c("Helianthus annuus", "Homo sapiens"))
resolve(sci="Quercus keloggii", db='gnr')
resolve(sci=c("Helianthus annuus", "Homo sapiens"), db=c('iplant', 'gnr'))
resolve(sci="Quercus keloggii", db=c('iplant', 'gnr'))

# 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')
)

# pass in curl options
resolve(sci="Qercuss", db = "iplant", verbose = TRUE)
}