[R] Distance function

From: Birgit Lemcke <birgit.lemcke_at_systbot.uzh.ch>
Date: Thu, 21 Jun 2007 19:56:54 +0200


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 )

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 für Systematische Botanik
Zollikerstrasse 107
CH-8008 Zürich
Switzerland
Ph: +41 (0)44 634 8351
birgit.lemcke_at_systbot.uzh.ch

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