ape: rTraitMult – R documentation

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rTraitMult

Multivariate Character Simulation

Description

This function simulates the evolution of a multivariate set of traits along a phylogeny. The calculation is done recursively from the root.

Usage

rTraitMult(phy, model, p = 1, root.value = rep(0, p), ancestor = FALSE,
           asFactor = NULL, trait.labels = paste("x", 1:p, sep = ""), ...)

Arguments

`phy`	an object of class `"phylo"`.
`model`	a function specifying the model (see details).
`p`	an integer giving the number of traits.
`root.value`	a numeric vector giving the values at the root.
`ancestor`	a logical value specifying whether to return the values at the nodes as well (by default, only the values at the tips are returned).
`asFactor`	the indices of the traits that are returned as factors (discrete traits).
`trait.labels`	a vector of mode character giving the names of the traits.
`...`	further arguments passed to `model` if it is a function.

Details

The model is specified with an R function of the form foo(x, l) where x is a vector of the traits of the ancestor and l is the branch length. Other arguments may be added. The function must return a vector of length p.

Value

A data frame with p columns whose names are given by trait.labels and row names taken from the labels of the tree.

Author(s)

Emmanuel Paradis

Examples

## correlated evolution of 2 continuous traits:
mod <- function(x, l) {
    y1 <- rnorm(1, x[1] + 0.5*x[2], 0.1)
    y2 <- rnorm(1, 0.5*x[1] + x[2], 0.1)
    c(y1, y2)
}
set.seed(11)
tr <- makeNodeLabel(rcoal(20))
x <- rTraitMult(tr, mod, 2, ancestor = TRUE)
op <- par(mfcol = c(2, 1))
plot(x, type = "n")
text(x, labels = rownames(x), cex = 0.7)
oq <- par(mar = c(0, 1, 0, 1), xpd = TRUE)
plot(tr, font = 1, cex = 0.7)
nodelabels(tr$node.label, cex = 0.7, adj = 1)
par(c(op, oq))

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