R: Resolve names from different data sources

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 0.9.0 Index]