WorldFlora (version 1.14-5)

WFO.prepare: Prepare a data set for analysis with WFO.match

Description

The main function of WFO.prepare attempts to split a list of species names with naming authorities in different fields of botanical names and authorities.

Usage

WFO.prepare(spec.data = NULL, spec.full="spec.full",
    squish = TRUE, spec.name.nonumber = TRUE,
        spec.name.sub = TRUE, 
        sub.pattern = c(" sp[.] A", " sp[.] B", " sp[.] C", " sp[.]", " spp[.]", " pl[.]",
            " indet[.]", " ind[.]", " gen[.]", " g[.]", " fam[.]", " nov[.]", " prox[.]", 
            " cf[.]", " aff[.]", " s[.]s[.]", " s[.]l[.]", 
            " p[.]p[.]", " p[.] p[.]", "[?]", " inc[.]", " stet[.]", "Ca[.]", 
            "nom[.] cons[.]", "nom[.] dub[.]", " nom[.] err[.]", " nom[.] illeg[.]", 
            " nom[.] inval[.]", " nom[.] nov[.]", " nom[.] nud[.]", " nom[.] obl[.]", 
            " nom[.] prot[.]", " nom[.] rej[.]", " nom[.] supp[.]", " sensu auct[.]"),  
    genus.2.flag = TRUE, species.2.flag = TRUE, 
    punctuation.flag = TRUE, pointless.flag = TRUE,
    trinomial = c("cultivar.", "f.", "sect.", "subf.", "subg.", 
        "subsp.", "subvar.", "var.",
        "CULTIVAR.",  "SECT.", "SUBF.", "SUBG.", "SUBSP.", "SUBVAR.", "VAR."),
    authors.ending.f=c("Aiton f.", "Baker f.", "Bak. f.", "Burm. f.", 
                       "Cheng f.", "Chrtek f.", 
                       "De Marco f.", "Fang f.", "Ferry f.", "Forsyth f.", 
                       "Forster f.", "Fraser f.", "G.Don f.", "Haller f.",
                       "Hallier f.", "Hook. f.", "Hooker f.", "Hsueh f.", 
                       "J.Kickx f.", "J. Kickx f.", "Keng f.", 
                       "Kickx f.", "Klokov f.", "Koster f.",
                       "Liou f.", "L. f.", "Ma f.", "Mikan f.",
                       "Occhioni f.", "Rchb. f.", 
                       "Schultes f.", "Schult. f.", "Stapf f."),
    verbose = TRUE, counter = 1000)
    
WFO.preprepare(spec.data=NULL, spec.full="spec.full",
    trinomial.first="subsp.", trinomial.second="var.")

Value

The function splits names in the botanical name and the naming authority.

Arguments

spec.data

A data.frame containing variables with species names. In case that a character vector is provided, then this vector will be converted to a data.frame

spec.full

Name of the column with full taxonomic names.

squish

If TRUE, remove repeated whitespace and white space from the start and end of the submitted full name via str_squish.

spec.name.nonumber

If TRUE, then submitted spec.full that contain numbers will be interpreted as genera, only matching the first word.

spec.name.sub

If TRUE, then delete sections of the spec.full that match the sub.pattern.

sub.pattern

Sections of the spec.full to be deleted

genus.2.flag

Flag first part of the names with only 2 characters.

species.2.flag

Flag second part of the names with only 2 characters.

punctuation.flag

Flag if the retained plant name has punctuation characters.

pointless.flag

Flag if the retained plant name has sub.pattern without the point.

trinomial

Descriptors for trinomial names. In case a trinomial name is expected, the species name will be obtained from the first two words and the two words starting with the trinomial descriptor.

authors.ending.f

Author names that end with ' f.', not confuse the function about trinomials with 'f.', indicating 'filius' ('son of').

verbose

Give details on the process.

counter

Progress on the process is reported by multiples of this counter.

trinomial.first

Pattern to split species name in different columns.

trinomial.second

Second pattern to split species name in different columns.

Author

Roeland Kindt (World Agroforestry)

Details

Function WFO.prepare splits submitted names into the botanical name ('spec.name') and the naming authority ('Authorship'). When the submitted name contains section between brackets that are not at the beginning of the naming authority, these sections will be removed. Function WFO.preprepare was designed to deal with situations where author names are given at species and infra-specific levels (see examples).

Examples

if (FALSE) {
WFO.prepare("Terminalia superba Engl. & Diels (**) (In review)")
WFO.prepare("Sorbus aucuparia subsp. praemorsa (Guss.) Nyman")
WFO.prepare("Ormosia aff. coarctata Jackson")
WFO.prepare("Ormosia aff coarctata Jackson")
WFO.prepare("Ormosia /coarctata Jackson")
WFO.prepare("Qualea TMG 148 Aubl.")
# Note that the sub.pattern is ' cf.'
WFO.prepare("cf Myrcia M1")
# Dealing with author names that end with ' f.' ('filius')
WFO.prepare("Malveopsis scabrosum Stapf f.")

# Using preprepare to deal with authorities at multiple levels
WFO.preprepare("Agave deserti Engelm. subsp. simplex Gentry")
WFO.preprepare("Zoysia matrella (L.) Merr. var. pacifica Goudsw.")

test.name <- paste0("Agastache pallidiflora (A. Heller) Rydb.",
  " subsp. neomexicana (Briq.) Lint & Epling",
  " var. havardii (A. Gray) R.W. Sanders")
WFO.preprepare(test.name)
}