library(permute)
library(lattice)
library(vegan)
library(MASS)
sem <- read.csv("F:/Desktop/case/Pei/New_vocs.csv", header = TRUE)
sem=na.omit(sem)
fix(sem)
attach(sem)
sem.x<-sem[,2:78]
sem.mds<-metaMDS(sem.x, "bray",autotransform = TRUE)
plt<-plot(sem.mds, display="sites", type= "n",main=paste("Stress=", round(sem.mds$stress,3)))
points (plt$sites[1:7,], pch=15, cex=2,bg=sem$color, col="red")
points (plt$sites[8:13,], pch=16, cex=2,bg=sem$color,col="blue")

with(sem, ordispider(sem.mds, Tree, col = "gray5"))
with(sem, ordihull(sem.mds, Tree, col = "gray5",lty = 2))


legend(0,0.82, c("F. auriculata", "F. hainanensis"),pch = c(15,16),col ="black", cex=1.5, text.font = 3,
       x.intersp = 0.25,y.intersp = 0.45,
       text.col = "black",  box.col = 0)