Resolving Names via TNRS

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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

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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

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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)