#1,2
bk.veg<-read.csv2("veg.csv", row.names = 1)
bk.coord<-read.csv("geo.coord.csv", row.names = 1)
rownames(bk.veg)==rownames(bk.coord)
summary(bk.coord)
summary(bk.veg)

#3
hist(bk.veg$Bromus.erectus)
hist(log(bk.veg$Bromus.erectus+1))

library(vegan)
hist(
decostand(bk.veg$Bromus.erectus, method="standardize")
)

#4
hell<-vegdist(decostand(bk.veg, method="hellinger"),
              method="euclidean")
eucli<-vegdist(log(bk.veg+1),
              method="euclidean")
chord<-vegdist(decostand(log(bk.veg+1), method="standardize", 
                         MARGIN=1),
              method="euclidean")
chi<-vegdist(decostand(log(bk.veg+1), method="chi.square"),
              method="euclidean")
bray<-vegdist(log(bk.veg+1),
              method="bray")

#5
jacc<-vegdist(decostand(bk.veg, method="pa"),
              method="jacc")
sor<-vegdist(decostand(bk.veg, method="pa"),
              method="bray")

#6
mantel(eucli, chi)
mantel(eucli, hell)
mantel(eucli, bray)
mantel(sor, bray)

#7
plot(Longdeg~Latdeg, bk.coord)
distances<-vegdist(bk.coord, method="euclidean")

#8
mantel(distances, bray)
mantel(distances, eucli)