RRphylo (version 3.0.0)

namesCompare: Checking species names for misspelling and synonyms

Description

The function cross-references two vectors of species names checking for possible synonyms, misspelled names, and genus-species or species-subspecies correspondence.

Usage

namesCompare(vec1,vec2,proportion=0.15,
  focus=c("genus","subspecies","epithet","misspelling"))

Value

The function returns a list including (according to focus):

$genus if vec1 includes genera names which miss specific epithet, this object lists all the species in vec2

belonging to each of the genera.

$subspecies if vec1 includes subspecies (i.e. two epithets after genus name), this object lists species in vec2

possibly corresponding to each of the subspecies.

$epithet lists species with matching epithets as possible synonyms.

$misspelling lists possible misspelled names. For each proposed mismatched names pair the proportion of characters in the

vec1 differing from the string in vec2 is returned.

Arguments

vec1, vec2

a vector of species names. Genus names only are also allowed. Generic name and specific epithet must be separated by '_'. Note that vec2 is used as the reference. Incomplete or suspicious names are better placed in vec1 (see example below).

proportion

the maximum proportion of different characters between any vec1-vec2 names pair to consider it a possible misspelling.

focus

one or more of "genus", "subspecies", "epithet", "misspelling". See Values for details.

Author

Silvia Castiglione, Carmela Serio, Antonella Esposito

Examples

if (FALSE) {
names(DataFelids$statefel)->nams.fel
nams.fel[c(19,12,37,80,43)]<-c("Puma_yagouaroundi","Felis_manul","Catopuma",
                           "Pseudaelurus","Panthera_zdansky")
nams<-nams.fel[-81]

namesCompare(nams,names(DataFelids$statefel))->nc1
namesCompare(names(DataFelids$statefel),nams)->nc2
}