sim.ratebystate {phytools}R Documentation

Conduct simulation of state dependent rate variation


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.


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



phylogenetic tree.


variance of the Brownian process of evolution for x.


variance of the Brownian process of evolution for y when x-min(x)==1 (for logarithm=FALSE) or x==0 (for logarithm=TRUE).


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.


This function returns a matrix.


Liam Revell


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

See Also

fastBM, ratebystate

[Package phytools version 0.4-60 Index]