[R] correlation as distance/dissimilarity

From: Martin Maechler <maechler_at_stat.math.ethz.ch>
Date: Thu 15 Sep 2005 - 01:49:10 EST

I've been asked (privately)

>>>>> "CarlosJ" == jaramilloc <jaramilloc@si.edu> >>>>> on Wed, 14 Sep 2005 09:40:22 -0400 writes:

     ..........

    CarlosJ> In Kaufman & Rousseeuw 2000 book on Cluster Analysis, it says that 
    CarlosJ> Daisy can compute Pearson correlation between variables and then 
    CarlosJ> transform these to dissimilarities.  

I don't think it does say this. But it does talk about doing it "your self", e.g., on pages 17--19.

    CarlosJ> Has this capability being 
    CarlosJ> implemented in the Cluster package for R?  It seems that is not 
    CarlosJ> there.  How could I do that using R?
    CarlosJ> I would appreciate your help.

It has never been explicitly in R, because in the past 'everyone' has thought this was obvious and trivial. The "past" here was when S was used by statisticians, mathematicians or engineers...

Anyway, here is an example on how to do this.

> dd <- as.dist((1 - cor(USJudgeRatings))/2)
> plot(hclust(dd))
> round(1000 * dd)

     CONT INTG DMNR DILG CFMG DECI PREP FAMI ORAL WRIT PHYS
INTG  567                                                  
DMNR  577   18                                             
DILG  494   64   82                                        
CFMG  432   93   93   21                                   
DECI  457   99   98   22    9                              
PREP  494   61   72   11   21   21                         
FAMI  513   66   79   21   32   29    5                    
ORAL  506   44   47   23   25   26    8    9               
WRIT  522   46   53   20   29   27    7    5    3          
PHYS  473  129  106   94   60   64   76   78   54   72     
RTEN 517 31 28 35 36 38 25 29 9 16 47 I'm going to add the example to the help page for 'dist' in R-2.2.0

Martin Maechler



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