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
The code below works if I deploy it in an additional package, but not
when I patch the "stats" package, I get that kind of message:
C symbol name "as_matrix_dist" not in load table
Romain
as.matrix.dist <- function(x, ...) {
size <- as.integer(attr(x, "Size"))
if( !is.numeric(x) ){
storage.mode(x) <- "numeric"
}
df <- .External( "as_matrix_dist",
x = x, size = size, PACKAGE = "stats" )
labels <- attr(x, "Labels")
dimnames(df) <- if(is.null(labels)) list(1L:size,1L:size) else
list(labels,labels)
df
}
/**
* as.matrix.dist( d )
*/
SEXP as_matrix_dist(SEXP args){
args = CDR( args ) ; SEXP x = CAR( args );
args = CDR( args ) ; SEXP size = CAR( args );
int i,j,k;
int s = INTEGER(size)[0];
SEXP d ;
PROTECT( d = allocVector( REALSXP, s*s) );
double element;
for( i=0,k=0; i<s; i++){
REAL(d)[i+s*i] = 0.0 ;
for( j=i+1; j<s; j++,k++){
element = REAL(x)[k] ;
REAL( d )[ i + s*j ] = element ;
REAL( d )[ j + s*i ] = element ;
}
}
SEXP dims ;
PROTECT( dims = allocVector(INTSXP, 2 ) );
INTEGER(dims)[0] = s ;
INTEGER(dims)[1] = s ;
setAttrib( d, mkString("dim"), dims );
UNPROTECT(2); /* d, dims */
return( d ) ;
}
--
Romain Francois
Independent R Consultant
+33(0) 6 28 91 30 30
http://romainfrancois.blog.free.fr
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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