%load_ext rmagic

%%R
library(vegan)

%%R
spmat<-read.csv("http://epi.whoi.edu/ipython/results/mdistefano/pg_site1_sp.csv",header=T)


%%R
print(head(spmat))

%%R             
dd <- na.omit(spmat)
dd1 <- dd[3:6]
print(head(dd1))

%%R
distmat1<-vegdist(dd1)

%%R
clusa1<-hclust(distmat1,"average")

%%R
print(clusa1)

%%R
print(dend1 <- as.dendrogram(clusa1))

%%R
plot(dend1)

%%R
dend12 <- cut(dend1, h=0.06)
plot(dend12$upper)
plot(dend12$lower[[1]])

lines = !jist -p hclust.ipynb
print lines[0].replace("https://gist.github.com", "http://nbviewer.ipython.org")