R help - Mar 2009 - [cluster package question] What is the "sum of the dissimilarities" in the pam command ?

Hello Martin Maechler and All,

A simple question (I hope):
How can I compute the "sum of the dissimilarities" that appears in the
pam
command (from the cluster package) ?

Is it the "manhattan" distance (such as the one implemented by
"dist") ?


I am asking since I am running clustering on a dataset. I found 7 medoids
with the pam command, and from it I have the medoid to which each
observation belongs to. But when I check it, I find only (about) 90% of
observations has the minimum manhattan distance to the medoids that pam
predicted.

If this is the manhattan distance that is used, I will create some toy data
to see if I can reproduce this.

Thanks,
Tal



-- 
----------------------------------------------


My contact information:
Tal Galili
Phone number: 972-50-3373767
FaceBook: Tal Galili
My Blogs:
http://www.r-statistics.com/
http://www.talgalili.com
http://www.biostatistics.co.il

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>>>>> "TG" == Tal Galili <tal.galili at
gmail.com>
>>>>>     on Sun, 29 Mar 2009 03:09:17 +0300 writes:
    TG> Hello Martin Maechler and All,
    TG> A simple question (I hope):
    TG> How can I compute the "sum of the dissimilarities" that
appears in the pam
    TG> command (from the cluster package) ?


    TG> Is it the "manhattan" distance (such as the one implemented
by "dist") ?


well, it first depends if  'x'  in  pam(x, k, dist, metric, ...)
is *itself* a dissimilarity object or not.
-->  help(daisy)  and  help(dist)

If it is *not*  --- which I assume from your question ---
then the answer depends on the 'metric' argument of pam().

As you did not mention that, I assume  you left 'metric' at its
default which is "euclidean", i.e.,
not "manhattan".



    TG> I am asking since I am running clustering on a dataset. I found 7
medoids
    TG> with the pam command, and from it I have the medoid to which each
    TG> observation belongs to. But when I check it, I find only (about) 90%
of
    TG> observations has the minimum manhattan distance to the medoids that
pam
    TG> predicted.

    TG> If this is the manhattan distance that is used, I will create some
toy data
    TG> to see if I can reproduce this.

Yes, specifying some reproducible toy data and specific R code
is almost always useful and typically more productive when
asking such questions by e-mail.

Regards,
Martin Maechler, ETH Zurich

    TG> Thanks,
    TG> Tal

    TG> ----------------------------------------------


    TG> My contact information:
    TG> Tal Galili
    TG> Phone number: 972-50-3373767
    TG> FaceBook: Tal Galili
    TG> My Blogs:
    TG> http://www.r-statistics.com/
    TG> http://www.talgalili.com
    TG> http://www.biostatistics.co.il