Simulates two characters under a model in which the rate of one depends on the state of the other.
sim.ratebystate(tree, sig2x=1, sig2y=1, beta=c(0,1), ...)This function returns a matrix.
phylogenetic tree.
variance of the Brownian process of evolution for x, \(\sigma_x^2\).
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 traitgram ("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.
Liam Revell liam.revell@umb.edu
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.
Revell, L. J. (2024) phytools 2.0: an updated R ecosystem for phylogenetic comparative methods (and other things). PeerJ, 12, e16505.
fastBM, ratebystate