WFO.acceptable.match: Check for fuzzy matches that can be acceptable based on...

In WorldFlora: Standardize Plant Names According to World Flora Online Taxonomic Backbone

Check for fuzzy matches that can be acceptable based on gender notations

Description

The function checks whether submitted and match names only differ by ending by -um, -us or -a. An extra check is done to accept differences that result from having 'ii' instead of 'i' in the submitted and matched name. An optional check ignores differences in vowels.

Usage

    WFO.acceptable.match(x, spec.name="spec.name",
      no.vowels=FALSE)

Arguments

x	Output for WFO.match, WFO.match.fuzzyjoin or WFO.match.one.
spec.name	Name of taxon submitted for matching.
no.vowels	Accept results if only vowels differ between submitted and matched name.

Details

The function was initially developed to check for changes in gender notations.

In new versions, also the following differences in species names are judged to be acceptable:

- hybrid and non-hybrid names (eg, Sorbus avonensis - Sorbus xavonensis)

- i vs. j (eg, Syzygium naiadum - Syzygium najadum)

- tt vs. t (eg, Ficus scott-elliottii - Ficus scott-elliotii)

- ll vs. l (eg, Garcinia moseleyana - Garcinia moselleyana)

- rr vs. r (eg, Hymenodictyon perrieri - Hymenodictyon perieri)

- mm vs. m (eg, Monteverdia schummaniana - Monteverdia schumanniana)

- nn vs. n (eg, Pyrus tamamschiannae - Pyrus tamamschianae)

- ff vs. f (eg, Dendropanax langsdorfii - Dendropanax langsdorffii)

- hh vs. h (eg, Gmelina leichardtii - Gmelina leichhardtii)

- dd vs. d (eg, Miconia buddlejoides - Miconia budlejoides)

- is vs. e (eg, Decarydendron ranomafanensis - Decarydendron ranomafanense)

- dt vs. d (eg, Stadtmannia acuminata - Stadmania acuminata)

Value

The function returns a logical vector that indicates whether names could be acceptable.

Author(s)

Roeland Kindt (World Agroforestry)

Examples

## Not run: 

data(WFO.example)

spec.test <- data.frame(spec.name=c("Faidherbia albida", "Acacia albida",
  "Faidherbia albidum", "Faidherbia albidus",
  "Faidherbia albiida",
  "Prunus africanus", "Prunos africanea",
  "Prunus afrocaneus", "Prunus afrocaneos"))

match1 <- WFO.match.fuzzyjoin(spec.data=spec.test, WFO.data=WFO.example,
  fuzzydist.max = 6)
match1[, c("spec.name", "scientificName")]

# check for gender differences (and ii - i)
WFO.acceptable.match(match1)

# ignore differences in vowels
WFO.acceptable.match(match1, no.vowels=TRUE)

accepted.cases <- WFO.acceptable.match(match1, no.vowels=TRUE)
match1.accepted <- match1[accepted.cases == TRUE, ]
match1.notaccepted <- match1[accepted.cases == FALSE, ]

## End(Not run)

WorldFlora documentation built on Sept. 11, 2024, 8:24 p.m.