Hi
Several options
Coding in C+ or other similar language (you seem to be more familiar with them)
Using debug and find out how your function behaves in steps
Using function with smaller m, n with Rprof to see where the time is spent.
I believe that coding in R like it was C+ is the way to hell. There is nothing
wrong with cycles however if you compute something which can be computed easily
by vectorised approach you loose efficiency.
e.g.
you compute this
m<-5
> for ( i in 1:m-1)
+ {
+ b[i]<- (m-i)
+ }
> b
[1] 4 3 2 1
but you can achieve it by
b <- ((m-1):1)
Time comparison:
> m<-1e5
> system.time(for ( i in 1:m-1) {b[i]<- (m-i)})
user system elapsed
11.61 0.00 12.11
> system.time(bb <- ((m-1):1))
user system elapsed
0 0 0
> all.equal(b,bb)
[1] TRUE
So the time gain is huge only in this small computation.
Cheers
Petr
> -----Original Message-----
> From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of Maram
> SAlem
> Sent: Tuesday, October 20, 2015 6:33 PM
> To: William Dunlap
> Cc: r-help@r-project.org
> Subject: Re: [R] Error in rep.int() invalid 'times' value
>
> Yes Indeed William. f1() works perfectly well and took only 30 secs to
> execute f1(25,15), but I wonder if there is anyway to speed up the
> execution of the rest of my code (almost seven hours now) ?
>
> Thanks for helping.
>
> Maram Salem
>
> On 20 October 2015 at 18:11, William Dunlap <wdun...@tibco.com> wrote:
>
> > f0 is essentially your original code put into a function, so expect
> it
> > to fail in the same way your original code did.
> > f1 should give the same answer as f0, but it should use less memory
> > and time.
> > Bill Dunlap
> > TIBCO Software
> > wdunlap tibco.com
> >
> >
> > On Tue, Oct 20, 2015 at 2:05 AM, Maram SAlem
> > <marammagdysa...@gmail.com>
> > wrote:
> > > Thanks William. I've tried the first code, ( with f0() ), but still
> > > for n=25, m=15 , I got this:
> > >
> > >> s<-f0(25,15)
> > > Error in rep.int(rep.int(seq_len(nx), rep.int(rep.fac, nx)), orep)
> :
> > > invalid 'times' value
> > > In addition: Warning message:
> > > In rep.int(rep.int(seq_len(nx), rep.int(rep.fac, nx)), orep) :
> > > NAs introduced by coercion to integer range
> > >
> > >
> > > I don't know if this is related to the memory limits of my laptop,
> > > or it doesn't have to do with the memory.
> > >
> > > Any help on how to fix this error will be greatly appreciated.
> > >
> > > Thanks All.
> > >
> > > Maram Salem
> > >
> > > On 15 October 2015 at 17:52, William Dunlap <wdun...@tibco.com>
> wrote:
> > >>
> > >> Doing enumerative combinatorics with rejection methods rarely
> works
> > >> well. Try mapping your problem to the problem of choosing
> > >> m-1 items from n-1. E.g., your code was
> > >>
> > >> f0 <- function(n, m) {
> > >> stopifnot(n > m)
> > >> D<-matrix(0,nrow=n-m+1,ncol=m-1)
> > >> for (i in 1:m-1){
> > >> D[,i]<-seq(0,n-m,1)
> > >> }
> > >> ED <- do.call(`expand.grid`,as.data.frame(D))
> > >> ED<-unname(as.matrix(ED))
> > >> lk<-which(rowSums(ED)<=(n-m))
> > >> ED[lk,]
> > >> }
> > >>
> > >> and I think the following does the same thing in much less space
> by
> > >> transforming the output of combn().
> > >>
> > >> f1 <- function(n, m) {
> > >> stopifnot(n > m)
> > >> r0 <- t(diff(combn(n-1, m-1)) - 1L)
> > >> r1 <- rep(seq(from=0, len=n-m+1), choose( seq(to=m-2, by=-1,
> > >> len=n-m+1), m-2))
> > >> cbind(r0[, ncol(r0):1, drop=FALSE], r1, deparse.level=0) }
> > >>
> > >> The code for adding the last column is a bit clumsy and could
> > >> probably
> > be
> > >> improved. Both f0 and f1 could also be cleaned up to work for
> m<=2.
> > >>
> > >> See Feller vol. 1 or Benjamin's "Proofs that (really) count" for
> > >> more on this sort of thing.
> > >>
> > >>
> > >>
> > >> Bill Dunlap
> > >> TIBCO Software
> > >> wdunlap tibco.com
> > >>
> > >> On Thu, Oct 15, 2015 at 7:45 AM, Maram SAlem
> > >> <marammagdysa...@gmail.com
> > >
> > >> wrote:
> > >>>
> > >>> Dear All,
> > >>>
> > >>> I'm trying to do a simple task (which is in fact a tiny part of a
> > larger
> > >>> code).
> > >>>
> > >>> I want to create a matrix, D, each of its columns is a sequence
> > >>> from 0
> > to
> > >>> (n-m), by 1. Then, using D, I want to create another matrix ED,
> > >>> whose rows represent all the possible combinations of the
> elements
> > >>> of the columns
> > of
> > >>> D. Then from ED, I'll select only the rows whose sum is less than
> > >>> or equal to (n-m), which will be called the matrix s. I used the
> > >>> following code:
> > >>>
> > >>> > n=5
> > >>> > m=3
> > >>> > D<-matrix(0,nrow=n-m+1,ncol=m-1) for (i in 1:m-1)
> > >>> + {
> > >>> + D[,i]<-seq(0,n-m,1)
> > >>> + }
> > >>> > ED <- do.call(`expand.grid`,as.data.frame(D))
> > >>> > ED<-as.matrix(ED)
> > >>>
> > >>> > lk<-which(rowSums(ED)<=(n-m))
> > >>>
> > >>> > s<-ED[lk,]
> > >>>
> > >>>
> > >>> This works perfectly well. But for rather larger values of n and
> m
> > (which
> > >>> are not so large actually), the number of all possible
> > >>> combinations of the columns of D gets extremely large giving me
> > >>> this error (for n=25,
> > m=15):
> > >>>
> > >>> > ED <- do.call(`expand.grid`,as.data.frame(D))
> > >>> Error in rep.int(rep.int(seq_len(nx), rep.int(rep.fac, nx)),
> orep) :
> > >>> invalid 'times' value
> > >>> In addition: Warning message:
> > >>> In rep.int(rep.int(seq_len(nx), rep.int(rep.fac, nx)), orep) :
> > >>> NAs introduced by coercion to integer range
> > >>>
> > >>>
> > >>> Any help or suggestions will be greatly appreciated.
> > >>>
> > >>> Thanks,
> > >>>
> > >>> Maram Salem
> > >>>
> > >>> [[alternative HTML version deleted]]
> > >>>
> > >>> ______________________________________________
> > >>> R-help@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.
> > >>
> > >>
> > >
> >
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help@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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