Hi all

I am playing around with synthetic cophylogenetic data. In one example, which represents a very extreme case of high agreement between the host and parasite phylogenies (the data was generated with 51 cospeciation, 2 sorting and 1 duplication events), I get a warning when using ace() to label the cophylogenetic nodes of the parasite tree:

fit.P<-ace(Pfreq[,2],obj$trees[[2]])
Warning message:
In sqrt(1/out$hessian) : NaNs produced

Where Pfreq[,2] is a vector of frequencies:

>  Pfreq[,2]
 [1] 100.00000 100.00000  69.70874 100.00000 100.00000 100.00000 100.00000 100.00000
 [9] 100.00000 100.00000 100.00000  37.86408  38.44660  62.13592  61.55340 100.00000
[17] 100.00000 100.00000 100.00000 100.00000 100.00000 100.00000 100.00000 100.00000
[25] 100.00000 100.00000 100.00000 100.00000  62.13592 100.00000 100.00000 100.00000
[33] 100.00000 100.00000 100.00000 100.00000 100.00000 100.00000 100.00000 100.00000
[41] 100.00000 100.00000  68.15534 100.00000 100.00000 100.00000 100.00000 100.00000
[49] 100.00000 100.00000 100.00000 100.00000 100.00000

The following works fine

nodelabels.cophylo(pie=fit.P$ace/100, piecol=c("green","red"),cex=0.5, which="right")

but I have noticed that there is a NA in fit.P$sigma2. It would be nice to know whether this warning is important or not.

Thank you very much for your attention.

Juan A. Balbuena


--

Dr. Juan A. Balbuena
Cavanilles Institute of Biodiversity and Evolutionary Biology
University of Valencia                                           
http://www.uv.es/~balbuena
P.O. Box 22085                                                   
http://www.uv.es/cophylpaco
46071 Valencia, Spain

e-mail:
j.a.balbu...@uv.es    tel. +34 963 543 658    fax +34 963 543 733
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