# [R] Proportion of equal entries in dist()?

Bert Gunter gunter.berton at gene.com
Tue Jan 20 19:57:16 CET 2015

```...

(just a comment)

and since this appears to be O(m^2 x n), where m,n are the number of
rows and columns (correction requested if I got this wrong), it would
appear that some basically C level functionality -- perhaps the one
Jean suggested? -- would be required for even moderately "large"
matrices.

Cheers,
Bert

Bert Gunter
Genentech Nonclinical Biostatistics
(650) 467-7374

"Data is not information. Information is not knowledge. And knowledge
is certainly not wisdom."
Clifford Stoll

On Tue, Jan 20, 2015 at 10:10 AM, Adams, Jean <jvadams at usgs.gov> wrote:
> Jorge,
>
> I have not used it myself, but you might find the dist() function in the
> proxy package to be useful.
>
> http://cran.r-project.org/web/packages/proxy/index.html
>
> Jean
>
> On Mon, Jan 19, 2015 at 7:38 AM, Jorge I Velez <jorgeivanvelez at gmail.com>
> wrote:
>
>> Dear all,
>>
>> Given vectors "x" and "y", I would like to compute the proportion of
>> entries that are equal, that is, mean(x == y).
>>
>> Now, suppose I have the following matrix:
>>
>> n <- 1e2
>> m <- 1e4
>> X <- matrix(sample(0:2, m*n, replace = TRUE), ncol = m)
>>
>> I am interested in calculating the above proportion for every pairwise
>> combination of rows.  I came up with the following:
>>
>> myd <- function(X, p = NROW(X)){
>> D <- matrix(NA, p, p)
>> for(i in 1:p) for(j in 1:p) if(i > j) D[i, j] <- mean(X[i, ] == X[j,])
>> D
>> }
>>
>> system.time(d <- myd(X))
>>
>> However, in my application n and m are much more larger than in this
>> example and the computational time might be an issue.  I would very much
>> appreciate any suggestions on how to speed the "myd" function.
>>
>> Note:  I have done some experiments with the dist() function and despite
>> being much, much, much faster than "myd", none of the default distances
>> fits my needs.  I would also appreciate any suggestions on how to include
>> "my own" distance function in dist().
>>
>> Thank you very much for your time.
>>
>> Best regards,
>> Jorge Velez.-
>>
>>         [[alternative HTML version deleted]]
>>
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>>
>
>         [[alternative HTML version deleted]]
>
> ______________________________________________
> 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.

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