[R-sig-phylo] Issue with SIMMAP on 500 sampled Trees

[Kimberly Lynn Foster]

Hello, I am looking at a family of fish and habitat transitions using SIMMAP in phytools.

I keep running into the error below when using a subsample of 500 trees. I used compare.tree and check.names to make sure all my tips match my data and visa versa. Any help would be greatly appreciated.

simtrees<-list(500)
YY<-list(500)
for (i in 1:500){

+ simtrees[[i]]<-make.simmap(CrenuchidTreesLadderized[[i]], habitattrait, model="ER", nsim=1000)
+ YY[[i]]<- describe.simmap(simtree[[i]], plot=F)
+ }
Error in MatrixExp(Y) : "mat" must be a square matrix



Kim

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[Liam J. Revell]

Hi Kimberly.

What version of phytools are you using? Neither make.simmap nor
describe.simmap call MatrixExp.

All the best, Liam

Liam J. Revell
Associate Professor, University of Massachusetts Boston
Profesor Asistente, Universidad Católica de la Ssma Concepción
web: http://faculty.umb.edu/liam.revell/, http://www.phytools.org

Post by Kimberly Lynn Foster
Hello, I am looking at a family of fish and habitat transitions using SIMMAP in phytools.
I keep running into the error below when using a subsample of 500 trees. I used compare.tree and check.names to make sure all my tips match my data and visa versa. Any help would be greatly appreciated.

simtrees<-list(500)
YY<-list(500)
for (i in 1:500){

+ simtrees[[i]]<-make.simmap(CrenuchidTreesLadderized[[i]], habitattrait, model="ER", nsim=1000)
+ YY[[i]]<- describe.simmap(simtree[[i]], plot=F)
+ }
Error in MatrixExp(Y) : "mat" must be a square matrix
Kim
[[alternative HTML version deleted]]
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https://stat.ethz.ch/mailman/listinfo/r-sig-phylo

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https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Searchable archive at http://www.mail-archive.com/r-sig-***@r-project.org/