R: Label Management

label2table {ape} | R Documentation

## Label Management

### Description

These functions work on a vector of character strings storing bi- or trinomial species names, typically “Genus_species_subspecies”.

### Usage

    label2table(x, sep = NULL, as.is = FALSE)
    stripLabel(x, species = FALSE, subsp = TRUE, sep = NULL)
    abbreviateGenus(x, genus = TRUE, species = FALSE, sep = NULL)

### Arguments

`x` | a vector of mode character.
`sep` | the separator (a single character) between the taxonomic levels (see details).
`as.is` | a logical specifying whether to convert characters into factors (like in `read.table`).
`species, subsp, genus` | a logical specifying whether the taxonomic level is concerned by the operation.

### Details

`label2table` returns a data frame with three columns named “genus”, “species”, and “subspecies” (with `NA` if the level is missing).

`stripLabel` deletes the subspecies names from the input. If `species = TRUE`, the species names are also removed, thus returning only the genus names.

`abbreviateGenus` abbreviates the genus names keeping only the first letter. If `species = TRUE`, the species names are abbreviated.

By default, these functions try to guess what is the separator between the genus, species and/or subspecies names. If an underscore is present in the input, then this character is assumed to be the separator; otherwise, a space. If this does not work, you can specify `sep` to its appropriate value.

### Value

A vector of mode character or a data frame.

### Author(s)

Emmanuel Paradis

### See Also

`makeLabel`, `makeNodeLabel`, `mixedFontLabel`

### Examples

    x <- c("Panthera_leo", "Panthera_pardus", "Panthera_onca", "Panthera_uncia",
           "Panthera_tigris_altaica", "Panthera_tigris_amoyensis")
    label2table(x)
    stripLabel(x)
    stripLabel(x, TRUE)
    abbreviateGenus(x)
    abbreviateGenus(x, species = TRUE)
    abbreviateGenus(x, genus = FALSE, species = TRUE)

[Package ape version 5.0 Index]