Hi Andy,
Your diagnostic seems correct: this is due to the convergence of the
likelihoods towards 0, then underflow occurs. Log-transformation doesn't
seem a solution here, and I don't see an obvious solution. If anybody
has a suggestion, that will be welcome. I'll try to explore some
possibilities.
EP
Le 06.06.2009 01:14, Andy Raduski a écrit :
Hi Everyone,
I have a problem with the ace function in the ape package. The same
problem appears whether or not I use Emmanuel Paradis' "patch" posted on
this discussion group recently.
Specifically, the problem seems to be related to the size of the
phylogeny. My data set consists of ~1100 taxa with four discrete
character states data (though I encounter the same problem with binary
character analyses, as well). When I run ace, I receive this error:
"Error in eigen(Q * phy$edge.length[i], symmetric = FALSE) : infinite or
missing values in 'x'"
The error can be replicated on simulated binary character data, although
the above error is occasionally substituted by the following, instead:
"Warning message: In sqrt(diag(solve(h))) : NaNs produced"
but only when the number of simulated tips is drastically reduced (<500).
Over many simulated datasets I got both previously mentioned errors, the
one below, as well as a list of warnings (which usually seem to result
from flat likelihood surfaces):
"In nlminb(rep(ip, length.out = np), function(p) dev(p), ... :imaginary
parts discarded in coercion."
I am not entirely sure why these errors occur but it seems to be an
underflow issue with calculating likelihoods, because as the number of
tips in simulated data decrease, the error rate is reduced, although
simulations with fewer than 100 tips still occasionally fail, and my
dataset of 1100 species always fails. Incidentally, a strikingly similar
problem occurs in BayesTraits, which also cannot be used to analyze
large datasets.
I would greatly appreciate any help or advice that anybody can offer.
Thanks in advance,
Andy
Andy Raduski
Graduate Student, Igic Lab
University of Illinois at Chicago
840 W Taylor St., MC067
Chicago, IL 60607
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Emmanuel Paradis
IRD, Montpellier, France
ph: +33 (0)4 67 16 64 47
fax: +33 (0)4 67 16 64 40
http://ape.mpl.ird.fr/
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