[R] Error in dist.mat[com.names, com.names] : subscript out of bounds

[nuria]

Hi!

I want to estimate the phylogenetic diversity. I use the SDMTools package.
In the line 3 of the "sntd.a" function appears this error and I don't know
the reason. 

my.phylo<-read.tree("150_BootstrapConsensusTree_Cantabrian_ML.nwk")
my.sample <- read.delim("C:/Filogenia/my.sample.txt")
my.sample<-read.table("my.sample.txt",sep="\t", header=T, row.names=1)
library(SDMTools)
dist.mat<-cophenetic(my.phylo)
sntd.a.function <- function(x){
   com.names <- names(x[x > 0])
   my.com.dist <- dist.mat[com.names, com.names]       
   diag(my.com.dist) = NA                              
   wt.sd(apply(my.com.dist,1,min,na.rm=T), x[x>0])     
}

result<-apply(my.sample, MARGIN = 1, sntd.a.function)

Error in dist.mat[com.names, com.names] : subscript out of bounds
Called from: FUN(newX[, i], ...)
Browse[1]> 

150_BootstrapConsensusTree_Cantabrian_ML.nwk
<http://r.789695.n4.nabble.com/file/n4710412/150_BootstrapConsensusTree_Cantabrian_ML.nwk>  
my.txt <http://r.789695.n4.nabble.com/file/n4710412/my.txt>  


Thanks!!!!




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