Hi Lara,
A few responses in-line below, hope they're helpful. In general averaging
over trees to estimate parameters sounds great, a couple hurdles.
On Tue, Oct 12, 2010 at 5:08 PM, Lara Poplarski wrote:
> Dear List,
>
> I am new to R, and hope someone can kindly help with the following
> task.
Dear List,
I am new to R, and hope someone can kindly help with the following
task. I have a Bayesian sample of trees in nexus format and discrete
data; example trees and data are at the bottom of the email. I would
like to use fitDiscrete in geiger to estimate parameter lambda for all
variables.
Actually, the function residuals.gls calculates 3 different types of
residuals: "response" or raw residuals, "pearson" or standardized
residuals, and "normalized" residuals. For diagnostic purposes, you
probably want the normalized residuals. The default is the "response"
residuals (although t
Hi Jan:
Yes. gls() returns an object of class gls which contains a vector
containing the residuals as one of its components.
So for instance you might compute:
>
result<-gls(y~x,data=test.data,correlation=corPagel(phy=tree,value=1,fixed=FALSE))
in which case:
> result$residuals
contains the
Dear R-sig-phylo members,
for some analyses I used the gls and gnls functions (package "nlme") and
controlled for phylogenetic effects by the phylogenetic correlation
structure "corPagel" provided by the ape-package. My question is, is
there a possibility to get the transformed residuals (phylo
