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.