R: Abbreviates a Botanical or Zoological Latin Name into an...

make.cepnames {vegan} | R Documentation

## Abbreviates a Botanical or Zoological Latin Name into an Eight-character Name

### 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 `abbreviate`d 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))

[Package vegan version 2.4-3 Index]