Maybe
dmat<-dist(dat, method="euclidean",upper = TRUE,diag = TRUE)
can fix your problem with the triangular matrix?
Cheers
Jon
Michael Rennie wrote:
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 <[EMAIL PROTECTED]> 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 <[EMAIL PROTECTED]> 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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