phyl.RMA: Phylogenetic reduced major axis (RMA) regression

Description Usage Arguments Details Value Author(s) References See Also

View source: R/phyl.RMA.R

Description

This function performs phylogenetic RMA regression.

Usage

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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 beta. 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 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.

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 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 [email protected]

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.

See Also

phyl.cca, phyl.pca, phyl.resid


phytools documentation built on Nov. 17, 2017, 6:24 a.m.