Hello,
after a discussion with Brian (see [R-sig-phylo] corDISC binary coding
problems, 04/15) I used the method from Ives and Garland (2010),
which is implemented in the R package phylolm.
The problem is, that the likelihood estimator does not converge.
Here is my code:
fit <- phyloglm(rot.fill ~ Acrogymnospermae + Magnoliophyta,
data=dat, phy=data$phy, method = "logistic_IG10", btol=20,
log.alpha.bound = 4, start.beta=NULL, start.alpha=NULL)
And the warning message:
In phyloglm(rot.fill ~ Acrogymnospermae + Magnoliophyta, data = dat, :
phyloglm failed to converge.
So the function produces an output but the results are not reliable since the
global maximum is very likely not reached...
I set the btol value to 20 by try and error-increasing (which I don’t really
understand since I thought the bounds converge to 0 and 1 at about btol=10 ??)
Now I have to find suitable start.beta and start.alpha values. But I have no
clue how to approach them. Can anyone help?
Why doesn’t phyloglm has a option for iterating starting values?
All the Best,
Franz
Franz Krah
Personal Webpage: http://franzkrah.github.io <http://franzkrah.github.io/>
University: http://www.biodiv.wzw.tum.de/index.php?id=18
<http://www.biodiv.wzw.tum.de/index.php?id=18>
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