[R] Sampling the Distance Matrix
David L Carlson
dcarlson at tamu.edu
Wed Sep 23 23:23:04 CEST 2015
I think the OP wanted rows where all values were greater than .9.
If so, this works:
> set.seed(42)
> dst <- dist(cbind(rnorm(20), rnorm(20)))
> dst2 <- as.matrix(dst)
> diag(dst2) <- NA
> idx <- which(apply(dst2, 1, function(x) all(na.omit(x)>.9)))
> idx
13 18 19
13 18 19
> dst2[idx, idx]
13 18 19
13 NA 2.272407 3.606054
18 2.272407 NA 1.578150
19 3.606054 1.578150 NA
-------------------------------------
David L Carlson
Department of Anthropology
Texas A&M University
College Station, TX 77840-4352
-----Original Message-----
From: R-help [mailto:r-help-bounces at r-project.org] On Behalf Of William Dunlap
Sent: Wednesday, September 23, 2015 3:23 PM
To: Lorenzo Isella
Cc: r-help at r-project.org
Subject: Re: [R] Sampling the Distance Matrix
> mm <- cbind(1/(1:5), sqrt(1:5))
> d <- dist(mm)
> d
1 2 3 4
2 0.6492864
3 0.9901226 0.3588848
4 1.2500000 0.6369033 0.2806086
5 1.4723668 0.8748970 0.5213550 0.2413050
> which(as.matrix(d)>0.9, arr.ind=TRUE)
row col
3 3 1
4 4 1
5 5 1
1 1 3
1 1 4
1 1 5
I.e., the distances between mm's rows 3 & 1, 4 & 1, and 5,1 are more than 0.9
The as.matrix(d) is needed because dist returns the lower triangle of
the distance
matrix and an object of class "dist" and as.matrix.dist converts that
into a matrix.
Bill Dunlap
TIBCO Software
wdunlap tibco.com
On Wed, Sep 23, 2015 at 12:15 PM, Lorenzo Isella
<lorenzo.isella at gmail.com> wrote:
> Dear All,
> Suppose you have a distance matrix stored like a dist object, for
> instance
>
> x<-rnorm(20)
> y<-rnorm(20)
>
> mm<-as.matrix(cbind(x,y))
>
> dst<-(dist(mm))
>
> Now, my problem is the following: I would like to get the rows of mm
> corresponding to points whose distance is always larger of, let's say,
> 0.9.
> In other words, if I were to compute the distance matrix on those
> selected rows of mm, apart from the diagonal, I would get all entries
> larger than 0.9.
> Any idea about how I can efficiently code that?
> Regards
>
> Lorenzo
>
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