Re: [R-sig-phylo] pic() vs gls()

2011-07-14 Thread ppiras
Hi all, Citing http://www.r-phylo.org/wiki/HowTo/Ancestral_State_Reconstruction: Using Felsenstein's (1985) phylogenetic independent contrasts (pic); This is also a Brownian-motion based estimator, but it only takes descendants of each node into account in reconstructing the state at that node.

Re: [R-sig-phylo] pic() vs gls()

2011-07-14 Thread Joe Felsenstein
Paolo Piras wrote -- Citing http://www.r-phylo.org/wiki/HowTo/Ancestral_State_Reconstruction: Using Felsenstein's (1985) phylogenetic independent contrasts (pic); This is also a Brownian-motion based estimator, but it only takes descendants of each node into account in reconstructing the state

Re: [R-sig-phylo] pic() vs gls()

2011-07-14 Thread Theodore Garland Jr
of Joe Felsenstein [j...@gs.washington.edu] Sent: Thursday, July 14, 2011 6:35 AM To: ppi...@uniroma3.it Cc: r-sig-phylo Subject: Re: [R-sig-phylo] pic() vs gls() Paolo Piras wrote -- Citing http://www.r-phylo.org/wiki/HowTo/Ancestral_State_Reconstruction: Using Felsenstein's (1985) phylogenetic

[R-sig-phylo] pic() vs gls()

2011-07-13 Thread Nicholas Mason
Dear R-sig-phylo users,I have a question regarding comparative analyses of contrasts done with the functions fitContinuous() and pic() compared to using PGLS (using the gls() function).From my understanding the first method involving pic() below fits alpha (estimated using fitContinuous()) to each

Re: [R-sig-phylo] pic() vs gls()

2011-07-13 Thread Liam J. Revell
Hi Nick. For your first (simple) problem, I believe you want to do: read.csv(file=Mason_data.csv,row.names=1)-smdata Regarding the more complicated issue, the problem of non-independence in linear regression comes in the residual error of the model. Thus, you should fit a correlation