#Community analysis for South China Sea corals

#Loading essential package
library(vegan)
library(matrixStats)

#Reading species distribution file
distribution<-t(read.csv(file="Distribution.csv",header=TRUE,row.names=1)[,-1])

#Performing NMDS
mdsSCS<-metaMDS(distribution,distance="jaccard",k=2,trymax=10000,autotransform=TRUE,trace=1)

#Plotting NMDS
plot(mdsSCS,display="sites",type="text",cex=0.8)

#Computing Jaccard distances
distSCS<-vegdist(distribution,method="jaccard")
distSCS<-as.matrix(distSCS)

#Plotting heatmap based on Jaccard distances
heatmap(distSCS,Rowv=NA,Colv=NA,symm=TRUE)

#Plotting barplot based on Jaccard distances
distdata<-matrix(0,nrow=20,ncol=19)
rownames(distdata)<-rownames(distSCS)
for(i in 1:20){
	distdata[i,]<-distSCS[(1:20)[-i],i]
	}
distplot<-barplot(height=rowMeans(distdata),las=2,ylim=c(0,0.85),ylab="Jaccard distance")
segments(distplot,rowMeans(distdata)-rowSds(distdata),distplot,rowMeans(distdata)+rowSds(distdata),lwd=1)
arrows(distplot,rowMeans(distdata)-rowSds(distdata),distplot,rowMeans(distdata)+rowSds(distdata),lwd=1,angle=90,code=3,length=0.05)