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Distance function
3 messages · Birgit Lemcke, 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]]
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