phytools: phyl.RMA – R documentation

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phytools

phyl.RMA

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)
## S3 method for class 'phyl.RMA'
coef(object, ...)
## S3 method for class 'phyl.RMA'
plot(x, ...)

Arguments

`x`	vector with names. In the case of the S3 `plot` method `x` is an object of class `"phyl.RMA"`.
`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 β. Defaults to 1.0. Note that a null hypothesis of 0.0 is not allowed.
`object`	for `coef` method, an object of class `"phyl.RMA"`.
`...`	optional arguments for S3 methods.

Details

Optionally jointly estimates λ if method="lambda". Likelihood optimization of λ 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.

The statistical hypothesis testing is based on Clarke (1980; reviewed in McArdle 1988), which differs from some other implementations of non-phylogenetic major axis regression in R.

Value

An object of class "phyl.RMA" consisting of 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 λ (`method="lambda"` only).
`logL`	log-likelihood (`method="lambda"` only).
`test`	a vector containing results for hypothesis tests on β.
`resid`	a vector of residuals for `y` given `x`.

Author(s)

Liam Revell liam.revell@umb.edu

References

Clarke, M. R. B. (1980) The reduced major axis of a bivariate sample. Biometrika, 67, 441-446.

McArdle, B. H. (1988) The structural relationship: Regression in biology. Can. J. Zool., 66, 2329-2339.

Revell, L. J. (2012) phytools: An R package for phylogenetic comparative biology (and other things). Methods Ecol. Evol., 3, 217-223.