Thanks a lot Petr for ur reply and advice. Hope I 'd be able to minmize time as
much as possible.
Regards,
Maram Salem
Sent from my iPhone
> On Oct 21, 2015, at 9:28 AM, PIKAL Petr <petr.pi...@precheza.cz> wrote:
>
> 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]]
>>
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