phytools (version 0.1-9)

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)

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 lambda.

fixed

logical value indicating whether or not lambda should be fixed.

h0

null hypothesis for beta. Defaults to 1.0. Note that a null hypothesis of 0.0 is not allowed.

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.

Details

Optionally jointly estimates lambda if method="lambda". Likelihood optimization of lambda is performed using optimize on the interval (0,1).

See Also

phyl.pca, phyl.resid