Re: [R] Dissimilarity 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 ï¿½cause there is an option to weight columns   differently what I havenï¿½t found in other functions. But now I donï¿½t 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. 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  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) >> Zusï¿½tzlich: 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 fï¿½r Systematische Botanik Zollikerstrasse 107 CH-8008 Zï¿½rich Switzerland Ph: +41 (0)44 634 8351 birgit.lemcke@systbot.uzh.ch 	[[alternative HTML version deleted]]