R help - Sep 2011 - help with hclust

Hello,

how can I get the similarity value (i.e., the inner cluster similarity) that was
used to cut a hierarchical tree at a specific height?

I would appreciate your help!

Best regards,
Madeleine

Hello,

I have two questions regarding hclust:

1) First I would like to cut a hclust tree at a specific height and receive the
cluster similarity at this height.
2) Next, I would like to receive all clusterings up to a given tree height that
fulfill a minimal required similarity (i.e., the inner cluster similarity of all
clusters needs to fulfill a given similarity value). How can I achieve that?

I would appreciate your help!

Best regards,
Madeleine

>From: Madeleine Seeland <madeleine.seeland <at> in.tum.de>
 >Subject: help with hclust
 >Date: 2011-09-14 08:14:48 GMT
 >Hello,
 >
 >I have two questions regarding hclust:
 >
 >1) First I would like to cut a hclust tree at a specific height and 
receive the cluster (di) similarity at this
 >height.


With an example:

hc <- hclust(dist(USArrests), "ave")
plot(hc, hang = -1)
hc.cf <- cophenetic(hc) #cophenetic distance

# cut cluster at height=50
rect.hclust(hc, h = 50)
hc.50 <- cutree(hc, h=50)


hc.simi <- NULL
for(i in unique(hc.50)) hc.simi <- c(hc.simi, 
max(as.matrix(hc.cf)[names(hc.50[hc.50==i]),names(hc.50[hc.50==i])]))
hc.simi
[1] 44.28392 44.83793 20.59851 38.52791 41.09477



 >2) Next, I would like to receive all clusterings up to a given tree 
height that fulfill a minimal required
 >similarity (i.e., the inner cluster similarity of all clusters 
needs to fulfill a given similarity
 >value). How can I achieve that?

For example, all clusterings with a (di)similarity at least 40

# which clusters have a maximum dissimilarity < 40

hc.le.40 <-unique(hc.50)[hc.simi<40]

# clusterings up to a height of 40

  hc.50[hc.50==hc.le.40[1]|hc.50==hc.le.40[2]]

    Connecticut        Florida          Idaho        Indiana         Kansas
              3              4              3              3              3
       Kentucky        Montana       Nebraska North Carolina           Ohio
              3              3              3              4              3
   Pennsylvania           Utah
              3              3





HTH,

MArcelino

 >
 >I would appreciate your help!
 >
 >Best regards,
 >Madeleine
 >



____________________________________

Marcelino de la Cruz Rot
Depto. Biologia Vegetal
EUIT Agricola
Universidad Politecnica de Madrid

tel: 34 + 913365435
____________________________________  
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