ape: compute.brlen – R documentation

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ape

compute.brlen

Branch Lengths Computation

Description

This function computes branch lengths of a tree using different methods.

Usage

compute.brlen(phy, method = "Grafen", power = 1, ...)

Arguments

`phy`	an object of class `phylo` representing the tree.
`method`	the method to be used to compute the branch lengths; this must be one of the followings: (i) `"Grafen"` (the default), (ii) a numeric vector, or (iii) a function.
`power`	The power at which heights must be raised (see below).
`...`	further argument(s) to be passed to `method` if it is a function.

Details

Grafen's (1989) computation of branch lengths: each node is given a ‘height’, namely the number of leaves of the subtree minus one, 0 for leaves. Each height is scaled so that root height is 1, and then raised at power 'rho' (> 0). Branch lengths are then computed as the difference between height of lower node and height of upper node.

If one or several numeric values are provided as method, they are recycled if necessary. If a function is given instead, further arguments are given in place of ... (they must be named, see examples).

Zero-length branches are not treated as multichotomies, and thus may need to be collapsed (see di2multi).

Value

An object of class phylo with branch lengths.

Author(s)

Julien Dutheil dutheil@evolbio.mpg.de and Emmanuel Paradis

References

Grafen, A. (1989) The phylogenetic regression. Philosophical Transactions of the Royal society of London. Series B. Biological Sciences, 326, 119–157.

Examples

data(bird.orders)
plot(compute.brlen(bird.orders, 1))
plot(compute.brlen(bird.orders, runif, min = 0, max = 5))
layout(matrix(1:4, 2, 2))
plot(compute.brlen(bird.orders, power=1), main=expression(rho==1))
plot(compute.brlen(bird.orders, power=3), main=expression(rho==3))
plot(compute.brlen(bird.orders, power=0.5), main=expression(rho==0.5))
plot(compute.brlen(bird.orders, power=0.1), main=expression(rho==0.1))
layout(1)

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