Asis,
On 30 December 2013 at 19:01, Asis Hallab wrote:
| I need to select all unique un-ordered pairs from a two column table.
| Here each row represents a pair and
| two rows, un-ordered pairs p and q are identical if
| either first and second elements of p and q are identical, respectively,
| or if first element of p is identical to second element of q and vice versa.
|
| Hence:
| ( "A", "B" )
| ( "B", "A" )
| ( "A", "B" )
| are all identical pairs.
|
| Currently I have this generation of a mathematical set of unordered
| pairs implemented as follows - basically using a custom comparator for
| a standard set of standard vectors:
| "
| struct Comparator {
| bool operator()(const std::vector<std::string> & a, const
| std::vector<std::string> & b) {
| const bool swapA = a[0] < a[1];
| const std::string & al = swapA ? a[0] : a[1];
| const std::string & ar = swapA ? a[1] : a[0];
| const bool swapB = b[0] < b[1];
| const std::string & bl = swapB ? b[0] : b[1];
| const std::string & br = swapB ? b[1] : b[0];
| return al < bl || (al == bl && ar < br);
| }
| };
|
| SEXP extractProteinPairs( SEXP proteinAccessionMatrix, SEXP
| pairFirstMemberColIndex, SEXP pairSecondMemberColIndex ) {
| BEGIN_RCPP
|
| StringMatrix tbl( proteinAccessionMatrix );
| int colA( NumericVector( pairFirstMemberColIndex )( 0 ) );
| int colB( NumericVector( pairSecondMemberColIndex )( 0 ) );
| std::set<std::vector<std::string>, Comparator> prs;
|
| for ( int i=0; i<tbl.nrow(); ++i ) {
| CharacterVector r( tbl( i, _ ) );
| std::vector< std::string > p;
| p.push_back( std::string( r( colA ) ) );
| p.push_back( std::string( r( colB ) ) );
| prs.insert( p );
| }
|
| return( wrap( prs ) );
|
| END_RCPP
| }
| "
|
| I am wondering if this could not be sped up using the following
| algorithm sketched in "pseudo R":
|
| # input:
| pairsTable
| # a matrix with two columns and n rows, each representing an un-ordered pair
|
| # output:
| m <- matrix( ncol=2 )
| # a matrix with two columns, subset of input and initialized as given
|
| for_each row p in argument pairsTable {
| indices <- find all rows of m where EITHER column is identical with
| either p[[1]] or p[[2]]
| identityCandidates <- m[ indices, ]
| if( ! any( candidate in identiyCandidates identical with p ) ) {
| append p to m
| }
| }
|
| Would the above algorithm be faster than my implementation, because it
| does just two "find_all" for each column in the result matrix and a
| subsequent identity comparison with the current pair p?
Not sure.
| And if the algorithm is faster how would I best implement this in Rcpp?
Not sure either.
You have something that works. Maybe just profile it to see if there are any
bottlenecks.
| - The currently used Rcpp implementation given above takes
| approximately 29 secs on an input table with 3,018,671 rows, returning
| a subset with 2,597,797 unique un-ordered pairs (rows).
|
| - If I managed to explain my problem properly and did not confuse you too
much:
| Any comments and help will be much appreciated!
With that many objects it starts to matter how you store and access the
data. Maybe std::vector<std::string> is not the best -- I don't know.
But as you have something reasonably fast now -- is it worth spending days on
getting 29 secs down to 19 secs ?
Dirk
|
| A happy new year to everyone!
| Cheers!
| _______________________________________________
| Rcpp-devel mailing list
| Rcpp-devel@lists.r-forge.r-project.org
| https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel
--
Dirk Eddelbuettel | e...@debian.org | http://dirk.eddelbuettel.com
_______________________________________________
Rcpp-devel mailing list
Rcpp-devel@lists.r-forge.r-project.org
https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel
