!head /Users/epi/pg_site1.csv

%load_ext rmagic

%%R
library(vegan)

%%R
mat<-read.csv("http://epi.whoi.edu/ipython/results/mdistefano/pg_site1.csv",header=T)

%%R             
dd <- mat[!is.na(mat$idcode) &
              !is.na(mat$temp) &
              !is.na(mat$sal) &
              !is.na(mat$count) &
              !is.na(mat$count) &
              !is.na(mat$subs),]

%%R
distmat<-vegdist(dd)

%%R
clusa<-hclust(distmat,"average")

%%R
print(clusa)

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

%%R
plot(dend1)

%%R
dend2 <- cut(dend1, h=0.07)
plot(dend2$upper)
plot(dend2$lower[[1]])



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