tnrs: Search the Phylotastic Taxonomic Name Resolution Service.

Description

Match taxonomic names using the Taxonomic Name Resolution Service (TNRS). Returns score of the matched name, and whether it was accepted or not.

Usage

tnrs(query = NA, source_ = NULL, code = NULL,
    getpost = "POST", sleep = 0, splitby = NULL,
    verbose = TRUE)

Arguments

query

Quoted taxonomic names to search in a vector (character).

source_

Specify the source you want to match names against. Defaults to just retrieve data from all sources. Options: NCBI, iPlant_TNRS, or MSW3.

code

Nomenclatural code. One of: ICZN (zoological), ICN (algae, fungi, and plants), ICNB (bacteria), ICBN (botanical), ICNCP (cultivated plants), ICTV (viruses)

getpost

Use GET or POST method to send the query. If you have more than say 50 species or so in your query, you should probably use POST.

sleep

Numer of seconds by which to pause between calls. Defaults to 0 seconds. Use when doing many calls in a for loop ar lapply type call.

splitby

Number by which to split species list for querying the TNRS.

verbose

Verbosity or not (default TRUE)

Value

data.frame of results from TNRS plus the name submitted.

Details

If there is no match in the Taxosaurus database, nothing is returned, so youwill not get anything back for non matches.

Examples

Run this code

# Default, uses GET curl method, you can't specify any other parameters when
using GET
mynames <- c("Panthera tigris", "Neotamias minimus", "Magnifera indica")
tnrs(query = mynames, source="NCBI")

# Specifying the source to match against
mynames <- c("Helianthus annuus", "Poa annua")
tnrs(query = mynames, source_ = "iPlant_TNRS")

# Specifying the nomenclatural code to match against
mynames <- c("Helianthus annuus", "Poa annua")
tnrs(query = mynames, code = "ICBN")

# You can specify multiple sources, by comma-separating them
mynames <- c("Panthera tigris", "Eutamias minimus", "Magnifera indica",
"Humbert humbert")
tnrs(query = mynames, source_ = "NCBI,MSW3")

# Using POST method, especially useful when you have a lot of species
mynames <- c("Panthera tigris", "Eutamias minimus", "Magnifera indica",
   "Humbert humbert", "Helianthus annuus", "Pinus contorta", "Poa annua",
   "Abies magnifica", "Rosa california", "Festuca arundinace",
   "Mimulus bicolor", "Sorbus occidentalis","Madia sativa", "Thymopsis
   thymodes", "Bartlettia scaposa")
tnrs(mynames, getpost="POST", source_ = "NCBI")

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