make.cepnames: Abbreviates a Botanical or Zoological Latin Name into an...

In vegan: Community Ecology Package

Description

A standard CEP name has four first letters of the generic name and four first letters of the specific epithet of a Latin name. The last epithet, that may be a subspecific name, is used in the current function. If the name has only one component, it is abbreviated to eight characters (see abbreviate). The returned names are made unique with function make.unique which adds numbers to the end of CEP names if needed.

Usage

make.cepnames(names, seconditem = FALSE)

Arguments

names	The names to be formatted into CEP names.
seconditem	Take always the second item of the original name to the abbreviated name instead of the last original item (default).

Details

Cornell Ecology Programs (CEP) used eight-letter abbreviations for species and site names. In species, the names were formed by taking four first letters of the generic name and four first letters of the specific or subspecific epithet. The current function first makes valid R names using make.names, and then splits these into elements. The CEP name is made by taking the four first letters of the first element, and four first letters of the last (default) or the second element (with seconditem = TRUE). If there was only one name element, it is abbreviated to eight letters. Finally, the names are made unique which may add numbers to duplicated names.

The CEP names were originally used, because old FORTRAN IV did not have CHARACTER data type, but text had to be stored in numerical variables, which in popular computers could hold four characters. In modern times, there is no reason for this limitation, but ecologists are used to these names, and they may be practical to avoid congestion in ordination plots.

Value

Function returns CEP names.

Note

The function is simpleminded and rigid. You must write a better one if you need.

Author(s)

Jari Oksanen

See Also

make.names, strsplit, substring, paste, abbreviate.

Examples

make.cepnames(c("Aa maderoi", "Poa sp.", "Cladina rangiferina",
"Cladonia cornuta", "Cladonia cornuta var. groenlandica",
"Cladonia rangiformis", "Bryoerythrophyllum"))
data(BCI)
colnames(BCI) <- make.cepnames(colnames(BCI))

Example output

Loading required package: permute
Loading required package: lattice
This is vegan 2.5-4
[1] "Aamade"     "Poasp"      "Cladrang"   "Cladcorn"   "Cladgroe"  
[6] "Cladrang.1" "Bryrythr"  

vegan documentation built on May 2, 2019, 5:51 p.m.