R help - Sep 2015 - Sampling the Distance Matrix

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

> 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
>
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

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
>
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
______________________________________________
R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.