[R] Distance function

[Gavin Simpson]

On Thu, 2007-06-21 at 19:56 +0200, Birgit Lemcke wrote:
> Hello you all from the R Help mailing list!
> 
> I am working on a PowerBook with Mac Os X and use R 2.5.0.
> I used the distance function from the analogue package to perform a  
> similarity analysis using the Gowers Index and weighted Variables.
> My variables are bivariate data and measurements as well as interval  
> data transformed into minimum and maximum variables.
> I used this Code:
> 
> Dist.Gowa<-distance(Table1a ,Table0a ,method ="mixed", weights
                                                         ^^^^^^^^
>  
> (weighting),R = NULL )
   ^^^^^^^^^^^
Something is not right there (^^^^) is this exactly what you typed?

You should not send questions about contributed packages to the list ---
as detailed in the posting guide. Without seeing Table1a and Table0a, it
is hard to say why this is failing - I suspect something about the
structure of the two data frames is throwing the function off.

If you can, send me that data ***off-list*** and I will take a look for
you, but as I'm teaching all day tomorrow, it won't happen till after
the weekend now.

HTH

G

> 
> 
> weighting is a vector created by this code:
> 
>   (weighting<- c 
> (1/3,1/3,1/3,1/2,1/2,1/2,1/2,1/2,1/2,1/4,1/4,1/4,1/4,1/7,1/7,1/7,1/7,1/7 
> , 
> 1/7,1/7,1/3,1/3,1/3,1/5,1/5,1/5,1/5,1/5,1/9,1/9,1/9,1/9,1/9,1/9,1/9,1/9, 
> 1/9,1/5,1/5,1/5,1/5,1/5,1/7,1/7,1/7,1/7,1/7,1/7,1/7,1/7,1/7,1/7,1/7,1/7, 
> 1/7,1/7,1/5,1/5,1/5,1/5,1/5,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1, 
> 1,1))
> It contains the weightings for the variables of the two data tables.
> 
> My data tables look like this:
> 
> 
> Anth_cap1        8.0  NA   NA  4.0  5.0  1  1  3.0  5.0  2.4  4.5  5   
> 5  2  2  2  3  1  1  1  1
> Anth_crin1       5.0  NA   NA  3.5 11.0  1  1  3.0 10.0  2.0  4.5  3   
> 4  2  2  3  3  1  1  2  3
> Anth_eck1        7.0  NA   NA  6.0 12.0  1  1  6.0 11.0  2.0  3.0  3   
> 5  2  2  3  3  1  1  1  2
> 
> At the end of the analysis I get always this message:
> 
> 1: $ operator is deprecated for atomic vectors, returning NULL in:  
> object$na.action
> 2: $ operator is deprecated for atomic vectors, returning NULL in:  
> object$weights
> 
> Can anybody explain me what this means?
> 
> Does anybody know if I have to standardize my measurements. As I  
> understood this is included in Gowers Index. If not is there a  
> function with different options of standardization more than rescaler  
> from the reshape package provides?
> 
> Thanks for your help in advance.
> 
> Greetings
> 
> Birgit
> 
> Birgit Lemcke
> Institut fr Systematische Botanik
> Zollikerstrasse 107
> CH-8008 Zrich
> Switzerland
> Ph: +41 (0)44 634 8351
> birgit.lemcke at systbot.uzh.ch
> 
> 
> 
> 
> 
> 
> 	[[alternative HTML version deleted]]
> 
> ______________________________________________
> R-help at stat.math.ethz.ch 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.
-- 
%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%
 Gavin Simpson                 [t] +44 (0)20 7679 0522
 ECRC, UCL Geography,          [f] +44 (0)20 7679 0565
 Pearson Building,             [e] gavin.simpsonATNOSPAMucl.ac.uk
 Gower Street, London          [w] http://www.ucl.ac.uk/~ucfagls/
 UK. WC1E 6BT.                 [w] http://www.freshwaters.org.uk
%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%