resolve {taxize}

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, ...)

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

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(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)

## End(Not run)