Hi All,
i've problem to understand how to work with R to generate a hierarchical
clustering
my data are in a csv and looks like :
idcode,count,temp,sal,depth_m,subs
16001,136,4.308,32.828,63.46,47
16001,109,4.31,32.829,63.09,49
16001,107,4.302,32.822,62.54,47
16001,87,4.318,32.834,62.54,48
16002,82,4.312,32.832,63.28,49
16002,77,4.325,32.828,65.65,46
16002,77,4.302,32.821,62.36,47
16002,71,4.299,32.832,65.84,37
16002,70,4.302,32.821,62.54,49
where idcode is a specie identification number
and the other fields are environmental parameters.
library(vegan)
mat<-read.csv("http://epi.whoi.edu/ipython/results/mdistefano/pg_site1.csv",header=T)
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),]
distmat<-vegdist(dd)
clusa<-hclust(distmat,"average")
print(clusa)
Call:
hclust(d = distmat, method = "average")
Cluster method : average
Distance : bray
Number of objects: 8036
print(dend1 <- as.dendrogram(clusa))
'dendrogram' with 2 branches and 8036 members total, at height
0.3194225
dend2 <- cut(dend1, h=0.07)
a complete run with plots is available here :
http://nbviewer.ipython.org/5492912
i'm trying try to group together the species (idcode's) that are sharing
similar environmental parameters
like (looking at the plots) i should be able to retrieve the list of idcode for
each branch at "cut-level" X
in the example :
X = 0.07
branches1 : [idcodeA, .. .. ,idcodeJ]
..
..
branche6 : [idcodeB, .. .. , idcodeK]
Many thanks for your precious help!!!
Massimo.
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