[R] manipulating (extracting) data from distance matrices

[Michael Rennie]

Not really,

I'd actually want

f[4:6,4:6]

to get comparisons of observations 4 to 6 only. And I'm still left
with the upper triangular matrix. This is a problem since I want to
sum the distances over the blocks that I am extracting.

Then again, I could just divide the sum by two and get the answer....

And, if I want to sum blocks comparing distances among two groups, say

f[7:10,4:6]

then I'm in the triangluar matrix and not crossing the diagonal
anymore, so I should be okay.

I think I may have my answer, but any other tips are more than welcome.

Cheers,

Mike

On Tue, Jul 15, 2008 at 9:35 AM, stephen sefick <ssefick at gmail.com> wrote:
> how about this
> f <- as.matrix(dmat)
> f[,4:6]
> #you get repeats but I think this is what you want
>
> On Tue, Jul 15, 2008 at 9:07 AM, Michael Rennie <mdrennie at gmail.com> wrote:
>>
>> Hi all,
>>
>> Does anyone have any tips for extracting chunks of data from a distance
>> matrix?
>>
>> For instance, if one was interested in only a subset of distance
>> comparisons (i.e., that of rows 4 thru 6, and no others), is there a
>> simple way to pull that data out?
>>
>> >From some playing around with an example (below), I've been able to
>> figure out that a distance matrix in R is stored as a single vector,
>> running top to bottom and left to right, so if you know the size of
>> your distance matrix, you can figure out which elements to query and
>> stick them together using c().
>>
>> However, all this stuff is still indexed by the "labels" attribute.
>> Does anyone know of a way to use that to pull out subsets from the
>> distance matrix in a simpler manner than my example code below?
>>
>> ##############
>> # ex_dist.R
>> # example for
>> # manipulating
>> # distance matrices
>> ####################
>>
>> set.seed<-12345
>>
>> a<-sample(20:40, 10)
>> b<-sample(80:100, 10)
>> c<-sample(0:40, 10)
>>
>> dat<-data.frame(a,b,c)
>> dat
>>
>> dmat<-dist(dat, method="euclidean")
>> dmat
>>
>> dmat[1:6] #vector that stores the distance matrix runs descending down
>> columns, left to right
>>
>> #in a 10-element distance matrix, column lengths are 9,8,7,6....1
>>
>> #get comparisons of rows 1:4 (from dat) ONLY
>> #top-left matrix will consist of top 3 of first column, top 2 of
>> second col, top 1 or third col.
>>
>> topleft<-c(dmat[1:3],dmat[10:11],dmat[18])
>> topleft
>>
>> #get comparisons of rows 9:10 (from dat) ONLY
>> #bottom right 4
>>
>> bottomright<-c(dmat[8:9],dmat[16:17])
>> bottomright
>>
>> #######end#####
>>
>> I'm sure there's a simpler way to do this using the labels of the
>> distance matrix, but I can't see it. I've thought of converting it
>> using as.matrix(), which would allow me to pull out particular rows,
>> but I'm only interested in the triangluar matrix. Now, if there was a
>> way to as.matrix(dmat) such that I got the bottom triangular matrix
>> and zeros elsewhere, then I'd be in buisness. Any suggestions on how
>> to pull that off would be helpful.
>>
>> I'm certainly interested in any tips or tricks anyone might have for
>> working with distance matrices, or any material that people can point
>> me towards.
>>
>> Cheers,
>>
>> Mike
>>
>> --
>> Michael D. Rennie
>> Ph.D. Candidate
>> University of Toronto at Mississauga
>> 3359 Missisagua Rd. N.
>> Mississauga, ON L5L 1C6
>> Ph: 905-828-5452 Fax: 905-828-3792
>> www.utm.utoronto.ca/~w3rennie
>>
>> ______________________________________________
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>> PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>
>
>
> --
> Let's not spend our time and resources thinking about things that are so
> little or so large that all they really do for us is puff us up and make us
> feel like gods. We are mammals, and have not exhausted the annoying little
> problems of being mammals.
>
> -K. Mullis



-- 
--
Michael D. Rennie
Ph.D. Candidate
University of Toronto at Mississauga
3359 Missisagua Rd. N.
Mississauga, ON L5L 1C6
Ph: 905-828-5452 Fax: 905-828-3792
www.utm.utoronto.ca/~w3rennie