ape: is.monophyletic – R documentation

Pricing

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

Get Started for Free

Documentation

ape

is.monophyletic

Is Group Monophyletic

Description

This function tests whether a list of tip labels is monophyletic on a given tree.

Usage

is.monophyletic(phy, tips, reroot = !is.rooted(phy), plot = FALSE, ...)

Arguments

`phy`	a phylogenetic tree description of class `"phylo"`.
`tips`	a vector of mode numeric or character specifying the tips to be tested.
`reroot`	a logical. If `FALSE`, then the input tree is not unrooted before the test.
`plot`	a logical. If `TRUE`, then the tree is plotted with the specified group `tips` highlighted.
`...`	further arguments passed to `plot`.

Details

If phy is rooted, the test is done on the rooted tree, otherwise the tree is first unrooted, then arbitrarily rerooted, in order to be independent on the current position of the root. That is, the test asks if tips could be monophyletic given any favourably rooting of phy.

If phy is unrooted the test is done on an unrooted tree, unless reroot = FALSE is specified.

If tip labels in the list tips are given as characters, they need to be spelled as in the object phy.

Value

TRUE or FALSE.

Author(s)

Johan Nylander jnylander@users.sourceforge.net

Examples

## Test one monophyletic and one paraphyletic group on the bird.orders tree
    ## Not run: data("bird.orders")
    ## Not run: is.monophyletic(phy = bird.orders, tips = c("Ciconiiformes", "Gruiformes"))
    ## Not run: is.monophyletic(bird.orders, c("Passeriformes", "Ciconiiformes", "Gruiformes"))

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