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.harr...@vanderbilt.edu> > An: David Winsemius <dwinsem...@comcast.net> > CC: Kim Vanselow <vanse...@gmx.de>, r-help@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 -- Computer Bild Tarifsieger! GMX FreeDSL - Telefonanschluss + DSL für nur 17,95 Euro/mtl.!* http://dsl.gmx.de/?ac=OM.AD.PD003K11308T4569a ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
