ape: label2table – R documentation

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label2table

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

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)

ape

Analyses of Phylogenetics and Evolution

v5.5

GPL-2 | GPL-3

Authors

Emmanuel Paradis [aut, cre, cph] (<https://orcid.org/0000-0003-3092-2199>), Simon Blomberg [aut, cph] (<https://orcid.org/0000-0003-1062-0839>), Ben Bolker [aut, cph] (<https://orcid.org/0000-0002-2127-0443>), Joseph Brown [aut, cph] (<https://orcid.org/0000-0002-3835-8062>), Santiago Claramunt [aut, cph] (<https://orcid.org/0000-0002-8926-5974>), Julien Claude [aut, cph] (<https://orcid.org/0000-0002-9267-1228>), Hoa Sien Cuong [aut, cph], Richard Desper [aut, cph], Gilles Didier [aut, cph] (<https://orcid.org/0000-0003-0596-9112>), Benoit Durand [aut, cph], Julien Dutheil [aut, cph] (<https://orcid.org/0000-0001-7753-4121>), RJ Ewing [aut, cph], Olivier Gascuel [aut, cph], Thomas Guillerme [aut, cph] (<https://orcid.org/0000-0003-4325-1275>), Christoph Heibl [aut, cph] (<https://orcid.org/0000-0002-7655-3299>), Anthony Ives [aut, cph] (<https://orcid.org/0000-0001-9375-9523>), Bradley Jones [aut, cph] (<https://orcid.org/0000-0003-4498-1069>), Franz Krah [aut, cph] (<https://orcid.org/0000-0001-7866-7508>), Daniel Lawson [aut, cph] (<https://orcid.org/0000-0002-5311-6213>), Vincent Lefort [aut, cph], Pierre Legendre [aut, cph] (<https://orcid.org/0000-0002-3838-3305>), Jim Lemon [aut, cph], Guillaume Louvel [aut, cph] (<https://orcid.org/0000-0002-7745-0785>), Eric Marcon [aut, cph] (<https://orcid.org/0000-0002-5249-321X>), Rosemary McCloskey [aut, cph] (<https://orcid.org/0000-0002-9772-8553>), Johan Nylander [aut, cph], Rainer Opgen-Rhein [aut, cph], Andrei-Alin Popescu [aut, cph], Manuela Royer-Carenzi [aut, cph], Klaus Schliep [aut, cph] (<https://orcid.org/0000-0003-2941-0161>), Korbinian Strimmer [aut, cph] (<https://orcid.org/0000-0001-7917-2056>), Damien de Vienne [aut, cph] (<https://orcid.org/0000-0001-9532-5251>)

Initial release

2021-04-24