ape: rTraitCont – R documentation

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rTraitCont

Continuous Character Simulation

Description

This function simulates the evolution of a continuous character along a phylogeny. The calculation is done recursively from the root. See Paradis (2012, pp. 232 and 324) for an introduction.

Usage

rTraitCont(phy, model = "BM", sigma = 0.1, alpha = 1, theta = 0,
           ancestor = FALSE, root.value = 0, ...)

Arguments

`phy`	an object of class `"phylo"`.
`model`	a character (either `"BM"` or `"OU"`) or a function specifying the model (see details).
`sigma`	a numeric vector giving the standard-deviation of the random component for each branch (can be a single value).
`alpha`	if `model = "OU"`, a numeric vector giving the strength of the selective constraint for each branch (can be a single value).
`theta`	if `model = "OU"`, a numeric vector giving the optimum for each branch (can be a single value).
`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).
`root.value`	a numeric giving the value at the root.
`...`	further arguments passed to `model` if it is a function.

Details

There are three possibilities to specify model:

"BM":a Browian motion model is used. If the arguments sigma has more than one value, its length must be equal to the the branches of the tree. This allows to specify a model with variable rates of evolution. You must be careful that branch numbering is done with the tree in “postorder” order: to see the order of the branches you can use: tr <- reorder(tr, "po"); plor(tr); edgelabels(). The arguments alpha and theta are ignored.
"OU":an Ornstein-Uhlenbeck model is used. The above indexing rule is used for the three parameters sigma, alpha, and theta. This may be interesting for the last one to model varying phenotypic optima. The exact updating formula from Gillespie (1996) are used which are reduced to BM formula if alpha = 0.
A function:it must be of the form foo(x, l) where x is the trait of the ancestor and l is the branch length. It must return the value of the descendant. The arguments sigma, alpha, and theta are ignored.

Value

A numeric vector with names taken from the tip labels of phy. If ancestor = TRUE, the node labels are used if present, otherwise, “Node1”, “Node2”, etc.

Author(s)

Emmanuel Paradis

References

Gillespie, D. T. (1996) Exact numerical simulation of the Ornstein-Uhlenbeck process and its integral. Physical Review E, 54, 2084–2091.

Paradis, E. (2012) Analysis of Phylogenetics and Evolution with R (Second Edition). New York: Springer.

Examples

data(bird.orders)
rTraitCont(bird.orders) # BM with sigma = 0.1
### OU model with two optima:
tr <- reorder(bird.orders, "postorder")
plot(tr)
edgelabels()
theta <- rep(0, Nedge(tr))
theta[c(1:4, 15:16, 23:24)] <- 2
## sensitive to 'alpha' and 'sigma':
rTraitCont(tr, "OU", theta = theta, alpha=.1, sigma=.01)
### an imaginary model with stasis 0.5 time unit after a node, then
### BM evolution with sigma = 0.1:
foo <- function(x, l) {
    if (l <= 0.5) return(x)
    x + (l - 0.5)*rnorm(1, 0, 0.1)
}
tr <- rcoal(20, br = runif)
rTraitCont(tr, foo, ancestor = TRUE)
### a cumulative Poisson process:
bar <- function(x, l) x + rpois(1, l)
(x <- rTraitCont(tr, bar, ancestor = TRUE))
plot(tr, show.tip.label = FALSE)
Y <- x[1:20]
A <- x[-(1:20)]
nodelabels(A)
tiplabels(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