Hi Felipe.

I can't figure out your code or why tip labels might be being stripped. Can you post a fully reproducible example of this problem?


All the best,

Liam J. Revell, Associate Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http://blog.phytools.org

On 8/6/2017 11:23 PM, Felipe Rossetto wrote:
Hi Liam,
I was using the function simmap for stochastic mapping, but when I run
these following code, the character history is mapped along the phylogeny
branches, but the tip labels disappears:

# function to compute the states
foo<-function(char1){
  y<-sapply(char1$maps,function(char1) names(char1)[1])
  names(y)<-char1$edge[,1]
  y<-y[as.character(length(char1$tip)+1:char1$Nnode)]
  return(y)
}
XX<-sapply(mtrees,foo)
pies<-t(apply(XX,1,function(char1,levels,Nsim)
summary(factor(char1,levels))/Nsim,levels=c("0","1","2"),Nsim=100))

# done computing the states

*# code to plot the tree*
*mtrees<-rescaleSimmap(mtrees,1)*
*cols<-c("black","red", "yellow"); names(cols)<-c(0,1,2)*
*par(mar=rep(0.1,4))*
*plot.phylo(mtrees[[1]],plot=FALSE,no.margin=T)*
*plotSimmap(mtrees[[1]],cols,pts=FALSE,lwd=3,ftype="off", add=TRUE)*
*text(1,1:length(mtrees[[1]]$tip),mtrees[[1]]$tip.label, pos=4,font=3)*
*nodelabels(pie=pies,cex=0.6,piecol=cols)*

Is there a code for maintaining the tip labels in the phylogeny with
characters mapped?

Mnay thanks in advance

Felipe Rossetto
Herbário FUEL
Departamento de Biologia Animal e Vegetal
Universidade Estadual de Londrina
Rodovia Celso Garcia Cid, PR 445 Km 380, Campus Universitário
Caixa postal 10.011
CEP: 86057-970
Londrina, Paraná, Brasil
CV: http://buscatextual.cnpq.br/buscatextual/visualizacv.do?id=K4211230P7

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