From maechler@stat.math.ethz.ch  Wed Jan 30 08:11:08 2002
From: maechler@stat.math.ethz.ch (maechler@stat.math.ethz.ch)
Date: Wed, 30 Jan 2002 09:11:08 +0100 (MET)
Subject: [Rd] cluster - clusplot.default (PR#1249)
Message-ID: <200201300811.JAA13573@pubhealth.ku.dk>

>>>>> "MM" == Martin Maechler <maechler@stat.math.ethz.ch> writes:

>>>>> "kjetil" == kjetil halvorsen <kjetilh@umsanet.edu.bo> writes:
    kjetil> The following code in clusplot.default (package
    kjetil> cluster) is in error:

    kjetil> x1 <- cmdscale(x, k = 2, eig = TRUE) var.dec <-
    kjetil> sum(x1$eig)/sum(diag(x1$x)) if (var.dec < 0) var.dec
    kjetil> <- 0 if (var.dec > 1) var.dec <- 1 x1 <- x1$points

    kjetil> x1 has components with names "points" and "eig", not
    kjetil> "x", so sum(diag(x1$x)) returns 0, the division
    kjetil> gives Inf which is later replaced by 1.  So in the
    kjetil> plot it is reported (always) that "These two
    kjetil> components explain 100% of the variability".

    MM> Thank you Kjetil.  Yes, there's definitely a problem
    MM> there.  However the solution is not as easy: Doing the
    MM> replacement you suggest is not enough, since var.dec
    MM> still is not scaled to [0,1].

    MM> Before the lines you cite above, there is

    MM>         ##x1 <- cmd(x, k = 2, eig = T, add = T)
    MM> ##if(x1$ac < 0) ## x1 <- cmd(x, k = 2, eig = T)

    MM> which was Rousseeuw et al's original code -- instead of
    MM> the x1 <- cmdscale(...) line above.  And cmd() was an
    MM> internal function calling directly into undocumented
    MM> S-plus internal Fortran code...  The original porter of
    MM> the cluster package had replaced the cmd() by cmdscale()
    MM> which seemed but was not ok.

    MM> I'll have a look.

This is fixed in the now current version of cluster, 1.4-0.

Note that cmdscale() will have an ``add ='' option from R 1.5.0 on.

Martin Maechler <maechler@stat.math.ethz.ch>	http://stat.ethz.ch/~maechler/
Seminar fuer Statistik, ETH-Zentrum  LEO C16	Leonhardstr. 27
ETH (Federal Inst. Technology)	8092 Zurich	SWITZERLAND
phone: x-41-1-632-3408		fax: ...-1228			<><

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[Rd] cluster - clusplot.default (PR#1249)
maechler@stat.math.ethz.ch