From romain.francois at dbmail.com  Fri Apr 24 14:14:37 2009
From: romain.francois at dbmail.com (Romain Francois)
Date: Fri, 24 Apr 2009 14:14:37 +0200
Subject: [Rd] speedup for as.matrix.dist
In-Reply-To: <49E9D72D.9030409@dbmail.com>
References: <49E9D72D.9030409@dbmail.com>
Message-ID: <49F1AD2D.8070400@dbmail.com>

Hi,

I found the init.c file I did not see before.

 > m <- expand.grid( x = 1:20, y = 1:20, z = 1:20 )
 > d <- dist( m )
 > system.time( out <- as.matrix( d ) )
   user  system elapsed
  3.006   1.252   4.429
 > old.as.matrix.dist <- function(x, ...)
+ {
+     size <- attr(x, "Size")
+     df <- matrix(0, size, size)
+     df[row(df) > col(df)] <- x
+     df <- df + t(df)
+     labels <- attr(x, "Labels")
+     dimnames(df) <-
+ if(is.null(labels)) list(1L:size,1L:size) else list(labels,labels)
+     df
+ }
 > system.time( out <- old.as.matrix.dist( d ) )
   user  system elapsed
 17.471   2.964  21.304


Romain

Romain Francois wrote:
> Hello,
>
> I am trying to patch as.matrix.dist to achieve some speedup.
>
> > m <- expand.grid( x = 1:20, y = 1:20, z = 1:20 )
> > d <- dist( m )
> > system.time( out <- stats:::as.matrix.dist( d ) )
>   user  system elapsed
> 15.355   3.110  19.123
> > system.time( out <- as.matrix.dist( d ) )
>   user  system elapsed
>  3.153   0.480   3.782


-- 
Romain Francois
Independent R Consultant
+33(0) 6 28 91 30 30
http://romainfrancois.blog.free.fr


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[Rd] speedup for as.matrix.dist
Romain Francois