TPLck2: Modified version of 'TPLck' indicating the number of homonyms...

In frmunoz/TreeGhats: Taxonomic name resolution and phylogeny generator for Western Ghats trees

Modified version of TPLck indicating the number of homonyms of a taxon name

Description

A modified version of the TPLck function from package Taxonstand. The function basically provides the same information than TPLck, but further keeps track of homonyms. Although a warning message indicates in TPLck when there are several homonyms, the function returns the first homonym in alphabetic order only. TPLck2 returns the number of homonyms for a given taxon name.

Usage

TPLck2(sp, corr = TRUE, diffchar = 2, max.distance = 1, infra = TRUE, abbrev = TRUE,
version = "1.1", encoding = "UTF-8")

Arguments

sp	a character vector specifying the input taxon, i.e. genus and specific epithet and, potentially, author name and infraspecific abbreviation and epithet.
corr	logical. If TRUE (default), spelling errors are corrected (only) in the specific and infraspecific epithets prior to taxonomic standardization.
diffchar	a number indicating the maximum difference between the number of characters in corrected and original taxon names. Not used if corr = FALSE.
max.distance	a number indicating the maximum distance allowed for a match in agrep when performing corrections of spelling errors in specific epithets. Not used if corr = FALSE.
infra	logical. If TRUE (default), infraspecific epithets are used to match taxon names in TPL.
abbrev	logical. If 'TRUE' (default), abbreviations (aff., cf., subsp., var.) and their variants are removed prior to taxonomic standardization.
version	a character vector indicating whether to connect to the newest version of TPL (1.1) or to the older one (1.0). Default to "1.1".
encoding	encoding to be assumed for input strings from TPL website; defaults to "UTF-8" (see read.csv and Encoding).

Details

TPLck2 overcomes two issues in TPLck. First, valid homonyms (i.e., a name for a taxon that is identical in spelling to another such name, but belongs to a different taxon) cannot be identified. Second, if the infraspecific epithet does not match any of the infraspecific epithets considered in TPL, then the first accepted name with no infraspecific epithet is selected as the best match. If all names provided by TPL have infraspecific epithets and are all synonyms (e.g. Pottia starkeana), then there is no best match and the output will match the original name.

Value

The function return an object of class data.frame including the same elements than those provided by TPLck, plus the element $Homonym indicating the number of homonyms if any. The value of $Homonym is NA if there is no homonym.

Author(s)

V. Raevel, adapted from Luis Cayuela & Jari Oksanen

See Also

TPLck

Examples

## Not run: 
Taxonstand::TPLck("Acacia sundra") 
test <- TPLck2("Acacia sundra") 
test

## End(Not run)

frmunoz/TreeGhats documentation built on July 29, 2022, 5:21 a.m.