[R] locating element in distance matrix

[David Winsemius]

On Jan 11, 2013, at 1:51 PM, David L Carlson wrote:

> If you have a dist object (created by dist()) or if you used lower.tri(x) to
> extract the lower triangle of the matrix, which() will not work since the
> matrix is now stored as a numeric vector with n(n-1)/2 elements where n is
> the number of rows/columns. In that case you must compute the original
> row/column values from the position along the vector:
> 
>> dwhich <- function(d, indx) {
> +     i <- round((1+sqrt(1+8*length(d)))/2, 0)
> +     rowd <- unlist(sapply(2:i, function(x) x:i))
> +     cold <- rep(1:(i-1), (i-1):1)
> +     return(data.frame(indx=indx, row=rowd[indx], col=cold[indx]))
> + }

Wouldn't it be easier to leave the distance matrix structure intact and just make the diagonal and upper.tri positions Inf?

> dwhich <- function(d) {
+      d[row(d) <= col(d)] <- Inf
+       which(d == min(d,na.rm=FALSE), arr.ind=TRUE) 
+  }
> dwhich(dm)
   row col
10  10   1

-- 

>> set.seed(42)
>> x <- matrix(rnorm(100), 10, 10)
>> d <- dist(x)
>> dm <- as.matrix(dist(x, diag=TRUE, upper=TRUE))
>> dm <- dm[lower.tri(dm)]
>> dwhich(d, which(d==min(d)))
>  indx row col
> 1    9  10   1
>> dwhich(dm, which(dm==min(dm)))
>  indx row col
> 1    9  10   1
> 
> 
>> -----Original Message-----
>> From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-
>> project.org] On Behalf Of David Winsemius
>> Sent: Friday, January 11, 2013 12:37 PM
>> To: eliza botto
>> Cc: r-help at r-project.org
>> Subject: Re: [R] locating element in distance matrix
>> 
>> 
>> On Jan 11, 2013, at 9:55 AM, eliza botto wrote:
>> 
>>> 
>>> Dear useRs,
>>> I have a very basic question. I have a distance matrix and i skipped
>>> the upper part of it deliberately.
>> 
>> I have no idea what htat means. Code is always helpful in resolving
>> ambiguities.
>> 
>>> The distance matrix is 1000*1000.  Then i used "min" command to
>>> extract the lowest value from that matrix. Now i want to know what
>>> is the location of that lowest element? More precisely, the row and
>>> column number of that lowest element.
>>> Thanks in advance
>> 
>> ?which
>> which( distmat == min(distmat), arr.ind=TRUE)
>> 
>> (It's possible to have more than one match and it would  be up to you
>> to decide how to break ties.)
>> 
>> --
>> 
>> David Winsemius, MD
>> Alameda, CA, USA
>> 
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> 

David Winsemius
Alameda, CA, USA