[R] as.dist with diagonal unequal zero

[Birgit Lemcke]

This are distances but between male and female plants of the same  
species.

species	 A  B  C  D E --> male
	     A
	     B
              C
              D
               |
             female


I would like to do a Manteltest.

Birgit


Am 10.10.2007 um 16:59 schrieb Gustaf Rydevik:

> On 10/10/07, Birgit Lemcke <birgit.lemcke at systbot.uzh.ch> wrote:
>> Hello and sorry that I still haven´t found a solution for my problem.
>>
>> I need to extract the lower and upper triangle from a square matrix
>> including the diagonal. This diagonal is not zero in that special  
>> case.
>> I tried with as.dist
>>
>> w<-as.dist(w, diag = TRUE)
>>> w
>>     1  2  3  4  5
>> 1  0
>> 2  2  0
>> 3  3  8  0
>> 4  4  9 14  0
>> 5  5 10 15 20  0
>>
>> but found no way to keep the diagonal that is in the matrix.
>>
>> I also tried this but as I expected it makes no difference:
>>
>> w<-matrix(1:25, ncol=5, nrow=5)
>>> upperTriangle(w)<-NA
>>> w
>>       [,1] [,2] [,3] [,4] [,5]
>> [1,]    1   NA   NA   NA   NA
>> [2,]    2    7   NA   NA   NA
>> [3,]    3    8   13   NA   NA
>> [4,]    4    9   14   19   NA
>> [5,]    5   10   15   20   25
>>> w<-as.dist(w, diag = TRUE)
>>> w
>>     1  2  3  4  5
>> 1  0
>> 2  2  0
>> 3  3  8  0
>> 4  4  9 14  0
>> 5  5 10 15 20  0
>>
>> Is there perhaps a possibility to give the diagonal as a vector
>> within as.dist?
>>
>> I would be glad if somebody could help me.
>>
>> 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
>>
>
> What do you want to do with the lower triangle matrix?
> A distance matrix must be zero on the diagonal, since dist(a,a)==0 for
> all a, so it cannot be distances that you measure.
>
> best,
> Gustaf
>
>
> -- 
> Gustaf Rydevik, M.Sci.
> tel: +46(0)703 051 451
> address:Essingetorget 40,112 66 Stockholm, SE
> skype:gustaf_rydevik

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