I am doing phylogenetic analysis of ecological community data set using
Picante package to find out PD, MPD, MNTD
I have run the following arguments
library(picante)
>tree4.phylotree<-read.tree("phylojune2016.edit.phy")
>tree4.phy<-read.csv("june2016.matrix.csv",sep=",",header = TRUE,row.names
= 1)
>tree4.out<-pd(tree4.phy,tree4.phylotree,include.root = FALSE)
>tree4.out[,3]<-mpd(tree4.phy,cophenetic(tree4.phylotree))
>tree4.out[,4]<-mntd(tree4.phy,cophenetic(tree4.phylotree))
>names(tree4.out)[3:4]<-c("MPD","MNTD")
When I randomize the matrix 999 times the following Error term appears
>tree4.mpd<-ses.mpd(tree4.phy,cophenetic(tree4.phylotree),runs = 999)
Error: C stack usage 15923904 is too close to the limit
How can I solve this error please? I will highly appreciate your help!
[[alternative HTML version deleted]]
______________________________________________
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
