[R-sig-phylo] follow up for lambda transform - query: how to use an existing covariance matrix directly in a gls procedure in R?

Hi all, I forgot to copy my reply to Luke to the list - here's another solution in case the question crops up again. Cheers, David Begin forwarded message: Date: 20 July 2011 11:57:46 GMT+01:00 To: Luke Matthews matth...@mednetworks.commailto:matth...@mednetworks.com Subject: Re:

Re: [R-sig-phylo] follow up for lambda transform - query: how to use an existing covariance matrix directly in a gls procedure in R?

Hi Liam and all, Thanks Liam for the helpful code, which does get me part way there. I would like to estimate lambda actually as part of the regression, just as in a pgls. So, one solution would be to build an optimizer around your code, which I think would work but probably is not the most

Re: [R-sig-phylo] follow up for lambda transform - query: how to use an existing covariance matrix directly in a gls procedure in R?

Hi Luke. For a fixed value of lambda this is very easy. For this example, you would just do: library(ape) data(bird.orders) dat-data.frame(y=rnorm(23),x=rnorm(23)) rownames(dat)-bird.orders$tip.label mat-vcv(bird.orders,cor=TRUE) # following Blomberg to here lambda-0.75 # for instance