TNRS: Resolving Names via TNRS

In rPlant: Interface to the Agave API

Description

The function ResolveNames interacts with the TNRS server at iPlant that uses fuzzy name matching to find standardized taxonomic plant names. GetPhylotasticToken is similar, but can be used for animal taxa as well, since it also utilizes the NCBI and ITIS databases. GetPhylotasticToken returns a unique token that can be checked online or using the RetrieveTNRSNames function. CompareTNRS will compare the original list of names to the returned TNRS names to see which names changed.

Usage

ResolveNames(names, max.per.call=100, verbose=TRUE) 
GetPhylotasticToken(names, max.per.call=100, verbose=TRUE) 
RetrieveTNRSNames(names, token, source=c("iPlant_TNRS", "NCBI"),
                  match.threshold=0.5, verbose=FALSE)
CompareNames(old.names, new.names, verbose=TRUE)

Arguments

names	Vector of names to be resolved via TNRS
max.per.call	The number of names to submit at a time, default is 100
verbose	Optional screen output that displays all of the results from the api
token	Unique identifier from the GetPhylotasticToken function used to retrieve names
source	Which source to utilize to check names
match.threshold	Threshold to accept new name
old.names	Original names
new.names	Returned TNRS names

Value

Vector of taxonomic names for ResolveNames and RetrieveTNRSNames. Unique identifier (=token) for GetPhylotasticToken

Examples

data(DNA.fasta)
speciesNames <- names(DNA.fasta)

#Taxonomic name checking by iPlant TNRS
## Not run: TNRSspeciesNames <- ResolveNames(speciesNames, 100, verbose=F)

#Taxonomic name checking by Phylotastic Taxosaurus
token <- GetPhylotasticToken(speciesNames)
TNRSSpeciesNames <- RetrieveTNRSNames(speciesNames, token, "NCBI")
CompareNames(speciesNames, TNRSSpeciesNames, verbose=TRUE)

rPlant documentation built on April 14, 2017, 6:03 p.m.