R: Phylogenetic reduced major axis (RMA) regression

phyl.RMA {phytools}

R Documentation

Phylogenetic reduced major axis (RMA) regression

Description

This function performs phylogenetic RMA regression.

Usage

phyl.RMA(x, y, tree, method="BM", lambda=NULL, fixed=FALSE, h0=1.0)

Arguments

`x`	vector with names.
`y`	vector with names.
`tree`	a phylogenetic tree in `"phylo"` format.
`method`	method to obtain the correlation structure: can be `"BM"` or `"lambda"`.
`lambda`	value of `lambda` for fixed λ.
`fixed`	logical value indicating whether or not λ should be optimized using likelihood.
`h0`	null hypothesis for `beta`. Defaults to 1.0. Note that a null hypothesis of 0.0 is not allowed.

Details

Optionally jointly estimates lambda if method="lambda". Likelihood optimization of lambda is performed using optimize on the interval (0,1). Note that some statistician think there is never a condition in which a reduced-major-axis regression should be used.

Value

A list with the following components:

`RMA.beta`	a vector of RMA regression coefficients.
`V`	a VCV matrix for the traits.
`lambda`	fitted value of lambda (`method="lambda"` only).
`logL`	log-likelihood (`method="lambda"` only).
`test`	a vector containing results for hypothesis tests on `beta`.
`resid`	a vector of residuals for `y` given `x`.

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.