R: Conduct simulation of state dependent rate variation

sim.ratebystate {phytools}

R Documentation

Conduct simulation of state dependent rate variation

Description

This function attempts to simulate two characters under a model in which the rate of evolution for the second (y) depends on the states for the first x. See ratebystate for more details.

Usage

sim.ratebystate(tree, sig2x=1, sig2y=1, beta=c(0,1), ...)

Arguments

`tree`	phylogenetic tree.
`sig2x`	variance of the Brownian process of evolution for `x`.
`sig2y`	variance of the Brownian process of evolution for `y` when `x-min(x)==1` (for `logarithm=FALSE`) or `x==0` (for `logarithm=TRUE`).
`beta`	intercept and slope of the relationship between the value of `x` and the Brownian rate in `y`.
`...`	optional arguments which include `method` (`"by.node"` or `"by.branch"` indicating whether to assume the rate varies as a function of the node state or the mean branch state); `plot`, a logical value indicating whether or not to plot a phenogram with the branches used for simulation of `y` after rescaling by the state of `x`; and `logarithm`, a logical value indicating whether or not simulate changes in the variance of Brownian evolution for `y` as an additive `logarithm=FALSE` or multiplicative function of `x`. The default is `logarithm=FALSE`.

Value

This function returns a matrix.

Author(s)

Liam Revell liam.revell@umb.edu

References

Revell, L. J. (2012) phytools: An R package for phylogenetic comparative biology (and other things). Methods Ecol. Evol., 3, 217-223.