phytools: ratebystate – R documentation

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ratebystate

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 an object of class "ratebystate" 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.