ape: c.phylo – R documentation

Pricing

Become an expert in R — Interactive courses, Cheat Sheets, certificates and more!

Get Started for Free

Documentation

ape

c.phylo

Building Lists of Trees

Description

These functions help to build lists of trees of class "multiPhylo".

Usage

## S3 method for class 'phylo'
c(..., recursive = TRUE)
## S3 method for class 'multiPhylo'
c(..., recursive = TRUE)
.compressTipLabel(x, ref = NULL)
.uncompressTipLabel(x)

Arguments

`...`	one or several objects of class `"phylo"` and/or `"multiPhylo"`.
`recursive`	see details.
`x`	an object of class `"phylo"` or `"multiPhylo"`.
`ref`	an optional vector of mode character to constrain the order of the tips. By default, the order from the first tree is used.

Details

These c methods check all the arguments, and return by default a list of single trees unless some objects are not trees or lists of trees, in which case recursive is switched to FALSE and a warning message is given. If recursive = FALSE, the objects are simply concatenated into a list. Before ape 4.0, recursive was always set to FALSE.

.compressTipLabel transforms an object of class "multiPhylo" by checking that all trees have the same tip labels and renumbering the tips in the edge matrix so that the tip numbers are also the same taking the first tree as the reference (duplicated labels are not allowed). The returned object has a unique vector of tip labels (attr(x, "TipLabel")).

.uncompressTipLabel does the reverse operation.

Value

An object of class "multiPhylo".

Author(s)

Emmanuel Paradis

Examples

x <- c(rtree(4), rtree(2))
x
y <- c(rtree(4), rtree(4))
z <- c(x, y)
z
print(z, TRUE)
try(.compressTipLabel(x)) # error
a <- .compressTipLabel(y)
.uncompressTipLabel(a) # back to y
## eventually compare str(a) and str(y)

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