[R] rcorr.cens Goodman-Kruskal gamma
Kim Vanselow
Vanselow at gmx.de
Tue Mar 10 11:22:06 CET 2009
Thanks to David and Frank for the suggestions. With a 2-dimensional input rcorr.cens and John Baron's implementation works good. But I am not able to calculate gamma for a multivariate matrix
example: columns=species; rows=releves; the numbers are BB-values (ordinal scale; 1<3 but 3-1 is not necessarily 2)
K. ceratoides S. caucasica A. tibeticum
A1 3 1 1
A2 0 3 2
A3 1 1 0
A4 2 2 0
A5 0 3 2
B1 1 1 1
B2 4 3 1
I want to calculate a distance matrix with scale unit "Goodman-Kruskals gamma" (instead of classical euclidean, bray curtis, manhattan etc.) which I can use for hierachical cluster analysis (e.g. amap, vegan, cluster) in order to compare the different releves.
Further suggestions would be greatly appreciated,
Thank you very much,
Kim
-------- Original-Nachricht --------
> Datum: Mon, 09 Mar 2009 13:27:29 -0500
> Von: Frank E Harrell Jr <f.harrell at vanderbilt.edu>
> An: David Winsemius <dwinsemius at comcast.net>
> CC: Kim Vanselow <Vanselow at gmx.de>, r-help at r-project.org
> Betreff: Re: [R] rcorr.cens Goodman-Kruskal gamma
> David Winsemius wrote:
> > I looked at the help page for rcorr.cens and was surprised that
> > function, designed for censored data and taking input as a Surv object,
> > was being considered for that purpose. This posting to r-help may be of
> > interest. John Baron offers a simple implementation that takes its input
> > as (x,y):
> >
> > http://finzi.psych.upenn.edu/R/Rhelp02/archive/19749.html
> >
> > goodman <- function(x,y){
> > Rx <- outer(x,x,function(u,v) sign(u-v))
> > Ry <- outer(y,y,function(u,v) sign(u-v))
> > S1 <- Rx*Ry
> > return(sum(S1)/sum(abs(S1)))}
> >
> > I then read Frank's response to John and it's clear that my impression
> > regarding potential uses of rcorr.cens was too limited. Appears that you
> > could supply a "y" vector to the "S" argument and get more efficient
> > execution.
>
> Yes rcorr.cens was designed to handle censored data but works fine with
> uncensored Y. You may need so specify Surv(Y) but first try just Y. It
> would be worth testing the execution speed of the two approaches.
>
> Frank
>
> --
> Frank E Harrell Jr Professor and Chair School of Medicine
> Department of Biostatistics Vanderbilt University
Dear r-helpers!
I want to classify my vegetation data with hierachical cluster analysis.
My Dataset consist of Abundance-Values (Braun-Blanquet ordinal scale; ranked) for each plant species and relevé.
I found a lot of r-packages dealing with cluster analysis, but none of them is able to calculate a distance measure for ranked data.
Podani recommends the use of Goodman and Kruskals' Gamma for the distance. I found the function rcorr.cens (outx=true) of the Hmisc package which should do it.
What I don't understand is how to define the input vectors x, y with my vegetation dataset. The other thing how I can use the output of rcorr.cens for a distance measure in the cluster analysis (e.g. in vegan or amap).
Any help would be greatly appreciated,
Thank you very much,
Kim
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