Tony,
gls() fits the model by ML or REML (the default), and the parameters in
the correlation structure (e.g., lambda) are estimated if needed or
specified.
Cheers,
Emmanuel
Anthony R Ives wrote on 21/04/2011 17:45:
Emmanuel,
I don't know gls, so I'd have to look at this. Technically,
This is mostly directed towards Dr. Paradis, but here goes.
I realize that ape computes the Felsenstein contrasts that incorporate
Felsenstein's within species variance.
However, does anyone have code in R for doing the complete method proposed by
Felsenstein, including the likelihood ratio
