veg<-read.table("VegR2.txt",header=TRUE,sep="\t")
vide<-read.table("VideR2.txt",header=TRUE,sep="\t")
vd<-vide[,3:8]

m<-metaMDS(veg)
m<-metaMDS(veg, previous = m)
ef<-envfit(m,vd)

dca<-decorana(veg,iweigh=1,iresc=4)
def<-envfit(dca,vd)

#NMDS un DCA salīdzinājums
plot(procrustes(m,dca))

lsk<-specnumber(veg,MARGIN=2)

#NMDS grafiks
plot(m,type="n",ann=FALSE,cex.axis=0.8,choices=c(1,2))
mtext("NMDS 1",side=1,cex=0.9,line=2)
mtext("NMDS 2",side=2,cex=0.9,line=2)
points(m,choices=c(1,2),display="species",col=gray(0.5),pch="+",cex=0.7,select=lsk<3)
points(m,choices=c(1,2),display="species",col="black",pch="+",cex=0.7,select=lsk>2)
#text(m,choices=c(1,2),col=gray(0.5),dis="sp",pos=4,cex=0.7,offset=0.2,select=lsk<3)
text(m,choices=c(1,2),col="black",dis="sp",pos=2,cex=0.7,offset=0.2,select=lsk>2)
abline(v=0,h=0,lty=3)
plot(ef,p.max=0.05,add=TRUE,col="Black",cex=0.8,font=2)
box()

#NMDS grafiks
plot(m,type="n",ann=FALSE,cex.axis=0.8,choices=c(1,2))
mtext("NMDS 1",side=1,cex=0.9,line=2)
mtext("NMDS 2",side=2,cex=0.9,line=2)
points(m,choices=c(1,2),display="species",col=gray(0.5),pch="+",cex=0.7,select=lsk<5)
points(m,choices=c(1,2),display="species",col="black",pch="+",cex=0.7,select=lsk>4)
#text(m,choices=c(1,2),col=gray(0.5),dis="sp",pos=4,cex=0.7,offset=0.2,select=lsk<5)
text(m,choices=c(1,2),col="black",dis="sp",pos=2,cex=0.7,offset=0.2,select=lsk>4)
abline(v=0,h=0,lty=3)
plot(ef,p.max=0.05,add=TRUE,col="Black",cex=0.8,font=2)
box()

plot(m,type="n",ann=FALSE,cex.axis=0.8,choices=c(1,2))
mtext("NMDS 1",side=1,cex=0.9,line=2)
mtext("NMDS 2",side=2,cex=0.9,line=2)
points(m,choices=c(1,2),display="sites",pch=21,cex=0.7,select=vide$Biotops=="Iepl",col="Black",bg="magenta")
points(m,choices=c(1,2),display="sites",pch=21,cex=0.7,select=vide$Biotops=="Pludm",col="Black",bg="blue")
points(m,choices=c(1,2),display="sites",pch=21,cex=0.7,select=vide$Biotops=="Embk",col="Black",bg="yellow")
points(m,choices=c(1,2),display="sites",pch=21,cex=0.7,select=vide$Biotops=="Prk",col="Black",bg="green")
points(m,choices=c(1,2),display="sites",pch=21,cex=0.7,select=vide$Biotops=="Pelk",col="Black",bg="gray")
abline(v=0,h=0,lty=3)
plot(ef,p.max=0.05,add=TRUE,col="Black",cex=0.8,font=2)
legend(x="topleft",legend=c("Ieplaka","Pludmale","Embr. kāpa","Priekškāpa","Pelēkā kāpa"),
	pch=21,pt.bg=c("magenta","blue","yellow","green","gray"))
box()


plot(dca,type="n",ann=FALSE,cex.axis=0.8,choices=c(1,2))
mtext("DCA 1",side=1,cex=0.9,line=2)
mtext("DCA 2",side=2,cex=0.9,line=2)
points(dca,choices=c(1,2),display="species",col=gray(0.5),pch="+",cex=0.7,select=lsk<5)
points(dca,choices=c(1,2),display="species",col="black",pch="+",cex=0.7,select=lsk>4)
#text(m,choices=c(1,2),col=gray(0.5),dis="sp",pos=4,cex=0.7,offset=0.2,select=lsk<5)
text(dca,choices=c(1,2),col="black",dis="sp",pos=4,cex=0.7,offset=0.2,select=lsk>4)
plot(def,p.max=0.05,add=TRUE,col="Black",cex=0.8,font=2)
box()

plot(dca,type="n",ann=FALSE,cex.axis=0.8,choices=c(1,2))
mtext("DCA 1",side=1,cex=0.9,line=2)
mtext("DCA 2",side=2,cex=0.9,line=2)
points(dca,choices=c(1,2),display="sites",pch=21,cex=0.7,select=vide$Biotops=="Iepl",col="Black",bg="magenta")
points(dca,choices=c(1,2),display="sites",pch=21,cex=0.7,select=vide$Biotops=="Pludm",col="Black",bg="blue")
points(dca,choices=c(1,2),display="sites",pch=21,cex=0.7,select=vide$Biotops=="Embk",col="Black",bg="yellow")
points(dca,choices=c(1,2),display="sites",pch=21,cex=0.7,select=vide$Biotops=="Prk",col="Black",bg="green")
points(dca,choices=c(1,2),display="sites",pch=21,cex=0.7,select=vide$Biotops=="Pelk",col="Black",bg="gray")
plot(def,p.max=0.05,add=TRUE,col="Black",cex=0.8,font=2)
legend(x="bottomright",legend=c("Ieplaka","Pludmale","Embr. kāpa","Priekškāpa","Pelēkā kāpa"),
	pch=21,pt.bg=c("magenta","blue","yellow","green","gray"))
box()