evolve.phylo

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Ancestral Character Simulation

Simulate the (independent) evolution of one or several continuous characters along a given phylogenetic tree under a homogeneous Brownian model.

Keywords
models
Usage
evolve.phylo(phy, value, var)
Arguments
phy
an object of class 'phylo' with branch lengths.
value
ancestral states, one by character. The (optional) names of this vector will be used as character names.
var
the variance of each character.
Details

Let x be a continuous character. If it evolves according to a Brownian model, its value at time t follows a normal law with mean x0 and variance t*sigma_x, where x0 is the value of the character at time 0, and sigma_x is the 'inner' variance of the character. The evolution of a continuous character is performed by letting the character evolve on each branch, from its ancestral root state. The final state of a branch is the ancestral states of the daughter branches, and so on.

Value

  • An object of class 'ancestral', inheriting from the 'phylo' class. The following components are added:
  • node.charactera data.frame with node ids as rownames and one column by character, containing all the inner node values for each character.
  • tip.charactera data.frame with tip ids as rownames and one column by character, containing all the tip values for each character.

See Also

plot.ancestral, ace

Aliases
  • evolve.phylo
Examples
data(bird.orders)
x <- rep(0, 5)
names(x) <- c("A", "B", "C", "D", "E")
anc1 <- evolve.phylo(bird.orders, x, 1)
anc2 <- evolve.phylo(bird.orders, x, 1)
cor(anc1$tip.character, anc2$tip.character)
Documentation reproduced from package ape, version 2.1-1, License: GPL (>= 2)

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