Hi Beatriz,
These are messages related to optimization, as you likely surmised. It
might be okay. What's the convergence flag in the output of
fitDiscrete? If it's zero (i.e. it successfully converged) then it's okay.
Others with more expertise will probably chime in...
HTH,
Dan.
Beatriz Guzm�n wrote:
> Hi all:
>
> I am using the geiger package to estimate the phylogenetic signal of
> one discrete trait. I would like to compare the negative log
> likelihood when there is no signal
> (using a tree transformed lambda=0)to that when lambda was estimated
> using the original tree topology using a likelihood ratio test.
> However, I have a problem when
> estimating lambda using the original tree topology.
>
> *What I am doing is this:*
>> mytree<-read.nexus("MCC.nex")
>> mydata<-read.csv("DataPhySig.csv")
>> col<-mydata$Colour
>> names(col)<-mydata$SP
>> col_lambda<- fitDiscrete(mytree, col, transform="lambda")
>
> *And this is the error I get:*
>
> DLSODA- Warning..Internal T (=R1) and H (=R2) are
> such that in the machine, T + H = T on the next step
> (H = step size). Solver will continue anyway.
> In above message, R1 = 0, R2 = 0
>
> DINTDY- T (=R1) illegal
> In above message, R1 = 7.42108e-219
>
> T not in interval TCUR - HU (= R1) to TCUR (=R2)
> In above message, R1 = 0, R2 = 0
>
> DINTDY- T (=R1) illegal
> In above message, R1 = 8.94663e-219 .....
>
> The analysis estimates a negative logLikelihood but I'm not sure
> whether I could trust the value.
>
> Has anyone experienced this problem before? I would be very pleased
> whether someone could help me to solve it.
>
> Thanks
>
> Teresa
>
> [[alternative HTML version deleted]]
>
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--
Daniel Fulop, Ph.D.
Postdoctoral Scholar
Dept. Plant Biology, UC Davis
Maloof Lab, Rm. 2220
Life Sciences Addition, One Shields Ave.
Davis, CA 95616
510-253-7462
dfu...@ucdavis.edu
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