[R] Dissimilarity

Gavin Simpson gavin.simpson at ucl.ac.uk
Wed Jun 20 17:46:17 CEST 2007


On Wed, 2007-06-20 at 16:13 +0200, Birgit Lemcke wrote:
> Hello Stephen,
> 
> I am happy that you help me. Thanks a million.
> 
> It is a good feeling that you confirm my assumption that dsvdis is  
> not able to deal with missing data, because it says me that I am not  
> completely incapable.
> Okay now I have the problem what to do.
> I used this function cause there is an option to weight columns  
> differently what I havent found in other functions.
> 
> But now I dont understand why I have to transpose the species as  
> columns? As I read in the help manual of dsvdis this function  
> calculates dissimilarities between rows.
> I have to calculate the dissimilarities between species that are in  
> rows by the use of morphological characters that are in columns.

If you really what to measure the associations between species then
leave them as you had them as the rows. But make sure you are choosing a
dissimilarity coefficient that works well for species associations.
There is a whole section in Legendre and Legendre 1998 Numerical Ecology
2nd English Edition Elsevier which may help here.

HTH

G

> 
> Am I completely wrong with my thoughts?
> 
> Birgit
> 
> Am 20.06.2007 um 15:52 schrieb Stephen B. Cox:
> 
> > Hi Birgit - looks like you have a few issues here.
> >
> > Birgit Lemcke <birgit.lemcke <at> systbot.uzh.ch> writes:
> >
> >>
> >> Hello you all!
> >>
> >> I am a completely new user of R and I have a problem to solve.
> >> I am using Mac OS X on a PowerBook.
> >>
> >> I have a table that looks like this:
> >>
> >>             species X1 X2 X3 X4 X5 X6 X7 X8 X9 X10 X11 X12 X13 X14
> >> X15 X16 X17 X18 X19 X20 X21
> >> 1        Anth_cap1  1  0  0  1  0  1  0  0  1   0   0   0   0   0
> >> 0   0   1   0   0   0   1
> >> 2       Anth_crin1  1  0  0  1  0  1  0  0  1   0   1   0   0   0
> >> 0   0   0   1   0   0   1
> >> 3        Anth_eck1  1  0  0  1  0  1  0  0  1   0   0   0   0   0
> >> 0   0   0   1   0   0   1
> >> 4       Anth_gram1  1  0  0  1  0  1  0  0  1  NA  NA  NA  NA   0
> >> 0   0   0   1   0   0   0
> >> 5       Anth_insi1  1  0  0  1  0  1  0  0  1   0   0   0   1   0
> >> 0   0   0   1   0   0   1
> >>
> >> All columns  are binary coded characters.
> >> The Import was done by this
> >>
> >> Test<-read.table("TestRFemMalBivariat1.csv",header = TRUE, sep = ";")
> >
> > First - you need to transpose the matrix to have species as  
> > columns.  You can do
> > this with:
> >
> > d2 = data.frame(t(Test[,-1]))
> > colnames(d2) = Test[,1]  #now use d2
> >
> >
> >
> >> Now I try to perform a similarity analysis with the dsvdis function
> >> of the labdsv package with the sorensen-Index.
> >>
> >> My first question is if all zeros in my table are seen as missing
> >> values and if it islike that how can I change without turning zero
> >> into other numbers?
> >
> > no - the zeros are valid observations.  the na's are missing data.
> >
> >
> >>   DisTest<-dsvdis(Test, index = "sorensen")
> >>
> >> But I always get back this error message:
> >>
> >> Warnung in symbol.For("dsvdis") :'symbol.For' is not needed: please
> >> remove it
> >> Fehler in dsvdis(Test, index = "sorensen") :
> >> 	NA/NaN/Inf in externem Funktionsaufruf (arg 1)
> >> Zustzlich: Warning message:
> >> NAs durch Umwandlung erzeugt
> >
> >
> >
> > Second - you have an issue with missing data.  It looks like dsvdis  
> > does not
> > like the NA's - so you must make a decision about what to do.   
> > Delete that
> > species, delete that site, or whatever...
> >
> > Finally - the warning over symbol.For is an issue with the labdsv  
> > library itself
> > - nothing you are doing wrong.  The results will still be valid -  
> > but the use of
> > symbol.For is something that will eventually need to be changed in  
> > the labdsv
> > library.
> >
> > hth,
> >
> > stephen
> 
> Birgit Lemcke
> Institut fr Systematische Botanik
> Zollikerstrasse 107
> CH-8008 Zrich
> Switzerland
> Ph: +41 (0)44 634 8351
> birgit.lemcke at systbot.uzh.ch
> 
> 
> 
> 
> 
> 
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> 
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