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.

`fastBM`, `ratebystate`