ratebystate {phytools} R Documentation

## Method for investigating the rate of one trait as a function of the state of another

### Description

This function attempts to ask if the rate of a continuous character, `y`, depends on the state of a separate continuous trait, `x`. This is accomplished by regressing the squared contrasts in `y` on the branch or node ancestral estimates of `x`.

### Usage

```ratebystate(tree, x, y, nsim=100, corr=c("pearson","spearman"), ...)
```

### Arguments

 `tree` phylogenetic tree. `x` a continuous character - the dependent variable in the model. `y` a second continuous trait - the response variable. `nsim` number of simulations for hypothesis testing. `corr` correlation method to use. Same as in `cor`. `...` optional arguments which include `sim.method` (`"fastBM"` or `"sim.corrs"`; see `fastBM` and `sim.corrs`); `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); `message` - a logical value indicating whether or not to return `corr` and `method`; finally `logarithm` - indicating whether or not to fit a model in which the variance of Brownian evolution in `y` changes as a multiplicative function of `x`. The default is `logarithm=FALSE`.

### Value

This function returns a list with up to the following four elements:

 `beta` value of the regression coefficient for square of the contrasts in `y` regressed on the ancestral or branch-wise estimated states for `x`. `r` correlation coefficient for `corr=corr`. `corr` string giving the value of `corr`. `method` string giving the value of `method`.

### 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.

`fastAnc`, `pic`