This function performs phylogenetic RMA regression.
phyl.RMA(x, y, tree, method="BM", lambda=NULL, fixed=FALSE, h0=1.0)
# S3 method for phyl.RMA
coef(object, ...)
# S3 method for phyl.RMA
plot(x, ...)vector with names. In the case of the S3 plot method x is an object of class "phyl.RMA".
vector with names.
a phylogenetic tree in "phylo" format.
method to obtain the correlation structure: can be "BM" or "lambda".
value of lambda for fixed \(\lambda\).
logical value indicating whether or not \(\lambda\) should be optimized using likelihood.
null hypothesis for beta. Defaults to 1.0. Note that a null hypothesis of 0.0 is not allowed.
for coef method, an object of class "phyl.RMA".
optional arguments for S3 methods.
An object of class "phyl.RMA" consisting of a list with the following components:
a vector of RMA regression coefficients.
a VCV matrix for the traits.
fitted value of \(\lambda\) (method="lambda" only).
log-likelihood (method="lambda" only).
a vector containing results for hypothesis tests on beta.
a vector of residuals for y given x.
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.
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.