Thanks Mark,

but anyway I will try to read it in French first.

Birgit


Am 21.06.2007 um 10:14 schrieb Mark Difford:

>
> Hi Birgit,
>
> If French is a problem, then you will unfortunately (because you  
> miss out on
> Chessel's marvellous insights) have to do with the terser, more  
> formal stuff
> (publications), on the "Links" page of the ade4 site.  Most of this  
> is in
> English:
>
> http://pbil.univ-lyon1.fr/ADE-4/links.php?lang=eng
> ## Chessel's stuff
> http://pbil.univ-lyon1.fr/R/perso/pagechessel.html
>
> Hope that helps.
>
> PS: There is also a brief overview of the one-table methods  
> provided by the
> ade4 package in an R Newsletter:
> http://cran.r-project.org/doc/Rnews/Rnews_2004-1.pdf
>
>
> Birgit Lemcke wrote:
>>
>> Hello Mark,
>>
>> thank you for your additional advices.
>> I had already a short look at the vegan package but I think I have to
>> look closer and also at the ade4 package.
>>
>> Unfortunately I am basically from Germany and my French is perhaps
>> only a rudimental school french but anyway, I would like to have a
>> look at this lecture notes, but I can not open the link you wrote me.
>> Ah sorry now the link works.
>>
>> Greetings and thanks a lot.
>>
>> Birgit
>>
>> Hey Gavin,
>> I found it funny that your institute is in the Gower Street.
>>
>>
>>
>> Am 20.06.2007 um 21:49 schrieb Mark Difford:
>>
>>>
>>> Hi Birgit,
>>>
>>> Just to add to what Gavin has said.  There are two other very  
>>> powerful
>>> packages in R that handle this kind of thing: ade4 and vegan.   
>>> Have a
>>> thorough look at both of them.  You should be looking at Principal
>>> Coordinate Analysis (Classical Scaling) and Non Metric
>>> Multidimensional
>>> Scaling (NMDS)---with, as Gavin has said, your species as rows.  At
>>> least
>>> the first of these methods goes hand-in-glove with cluster analysis.
>>>
>>> Given that you are based in Switzerland, and perhaps are Swiss, you
>>> probably
>>> therefore read and speak French as a second/third language.  You may
>>> therefore find the ade4 package more useful, since its authors are
>>> French,
>>> and its principal authors, Prof. Daniel Chessel &c., have made
>>> publicly
>>> available some exceptionally useful documentation on these methods
>>> on their
>>> ade4 website.  These are mainly Prof. Chessel's lecture notes:
>>>
>>> http://pbil.univ-lyon1.fr/R/enseignement.html
>>>
>>> I hope that speeds you on your way.
>>>
>>> Regards,
>>> Mark.
>>>
>>> PS: Apropos of the Legendre & Legendre text: It's well worth buying
>>> if you
>>> work in this area; one of its authors, Pierre Legendre, now
>>> collaborates
>>> with Jari Oksanen on some functions of the vegan package.
>>>
>>>
>>> Gavin Simpson wrote:
>>>>
>>>> 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@systbot.uzh.ch
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> 	[[alternative HTML version deleted]]
>>>>>
>>>>> ______________________________________________
>>>>> R-help@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
>>>> %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% 
>>>> ~%~%
>>>>
>>>> ______________________________________________
>>>> R-help@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.
>>>>
>>>>
>>>
>>> -- 
>>> View this message in context: http://www.nabble.com/Re%3A-
>>> Dissimilarity-tf3952667.html#a11220912
>>> Sent from the R help mailing list archive at Nabble.com.
>>>
>>> ______________________________________________
>>> R-help@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.
>>
>> Birgit Lemcke
>> Institut für Systematische Botanik
>> Zollikerstrasse 107
>> CH-8008 Zürich
>> Switzerland
>> Ph: +41 (0)44 634 8351
>> birgit.lemcke@systbot.uzh.ch
>>
>>
>>
>>
>>
>>
>> 	[[alternative HTML version deleted]]
>>
>>
>> ______________________________________________
>> R-help@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.
>>
>>
>
> -- 
> View this message in context: http://www.nabble.com/Re%3A- 
> Dissimilarity-tf3952667.html#a11228522
> Sent from the R help mailing list archive at Nabble.com.
>
> ______________________________________________
> R-help@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.

Birgit Lemcke
Institut für Systematische Botanik
Zollikerstrasse 107
CH-8008 Zürich
Switzerland
Ph: +41 (0)44 634 8351
birgit.lemcke@systbot.uzh.ch






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