phytools (version 0.2-40)

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 optimized using likelihood.

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