[R] Alternatives for explicit for() loops
stephen sefick
ssefick at gmail.com
Fri Nov 6 16:45:05 CET 2015
If you have multiple cores, you could try the foreach package. Jim's advice
still holds, but you would be farming the work out.
FWIW,
Stephen
On Fri, Nov 6, 2015 at 8:54 AM, jim holtman <jholtman at gmail.com> wrote:
> If you have code that is running for a long time, then take a small case
> that only runs for 5-10 minutes and turn on the RProfiler so that you can
> see where you are spending your time. In most cases, it is probably not
> the 'for' loops that are causing the problem, but some function/calculation
> you are doing within the loop that is consuming the time, and until you
> determine what section of code that is, is it hard to tell exactly what the
> problem is, much less the solution.
>
>
> Jim Holtman
> Data Munger Guru
>
> What is the problem that you are trying to solve?
> Tell me what you want to do, not how you want to do it.
>
> On Wed, Nov 4, 2015 at 9:09 AM, Maram SAlem <marammagdysalem at gmail.com>
> wrote:
>
> > Hi Jim,
> >
> > Thanks a lot for replying.
> >
> > In fact I'm trying to run a simulation study that enables me to calculate
> > the Bayes risk of a sampling plan selected from progressively type-II
> > censored Weibull model. One of the steps involves evaluating the expected
> > test time, which is a rather complicated formula that involves nested
> > multiple summations where the counters of the summation signs are
> > dependent, that's why I thought of I should create the incomb() function
> > inside the loop, or may be I didn't figure out how to relate its
> arguments
> > to the ones inside the loop had I created it outside it. I'm trying to
> > create a matrix of all the possible combinations involved in the
> summations
> > and then use the apply() function on each row of that matrix. The problem
> > is that the code I wrote works perfectly well for rather small values of
> > the sample size,n, and the censoring number, m (for example, n=8,m=4),but
> > when n and m are increased (say, n=25,m=15) the code keeps on running for
> > days with no output. That's why I thought I should try to avoid explicit
> > loops as much as possible, so I did my best in this regard but still the
> > code takes too long to execute,(more than three days), thus, i believe
> > there must be something wrong.
> >
> > Here's the full code:
> >
> > library(pbapply)
> > 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)
> > }
> > simpfun<- function (x,n,m,p,alpha,beta)
> > {
> > a<-factorial(n-m)/(prod((factorial(x)))*(factorial((n-m)- sum(x))))
> > b <- ((m-1):1)
> > c<- a*((p)^(sum(x)))*((1-p)^(((m-1)*(n-m))- sum(x%*%(as.matrix(b)))))
> > d <- n - cumsum(x) - (1:(m-1))
> > e<- n*(prod(d))*c
> > LD<-list()
> > for (i in 1:(m-1)) {
> > LD[[i]]<-seq(0,x[i],1)
> > }
> > LD[[m]]<-seq(0,(n-m-sum(x)),1)
> > LED<-expand.grid (LD)
> > LED<-as.matrix(LED)
> > store1<-numeric(nrow(LED))
> > for (j in 1:length(store1) )
> > {
> > incomb<-function(x,alpha,beta) {
> >
> > g<-((-1)^(sum(LED[j,])))*(gamma((1/beta)+1))*((alpha)^(-(1/beta)))
> > h <- choose(x, LED[j,-m])
> > ik<-prod(h)*choose((n-m-sum(x)),LED[j,m])
> > lm<-cumsum(LED[j,-m]) + (1:(m-1))
> > plm<-prod(lm)
> > gil<-g*ik/(plm)
> > hlm<-numeric(sum(LED[j,])+(m-1))
> > dsa<-length(hlm)
> > for (i in 1:dsa)
> > {
> > ppp<- sum(LED[j,])+(m-1)
> > hlm[i]<-
> > (choose(ppp,i))*((-1)^(i))*((i+1)^((-1)*((1/beta)+1)))
> > }
> > shl<-gil*(sum(hlm)+1)
> > return (shl)
> > }
> > store1[j]<-incomb(x,alpha=0.2,beta=2)
> > }
> > val1<- sum(store1)*e
> > return(val1)
> > }
> >
> > va<-pbapply(s,1,simpfun,n=6,m=4,p=0.3,alpha=0.2,beta=2)
> > EXP<-sum(va)
> >
> >
> >
> > Any help would be greatly appreciated.
> > Thanks a lot for your time.
> >
> > Best Regards,
> > Maram Salem
> >
> >
> > On 2 November 2015 at 00:27, jim holtman <jholtman at gmail.com> wrote:
> >
> >> Why are you recreating the incomb function within the loop instead of
> >> defining it outside the loop? Also you are referencing several
> variables
> >> that are global (e.g., m & j); you should be passing these in as
> parameters
> >> to the function.
> >>
> >>
> >> Jim Holtman
> >> Data Munger Guru
> >>
> >> What is the problem that you are trying to solve?
> >> Tell me what you want to do, not how you want to do it.
> >>
> >> On Sun, Nov 1, 2015 at 7:31 AM, Maram SAlem <marammagdysalem at gmail.com>
> >> wrote:
> >>
> >>> Hi All,
> >>>
> >>> I'm writing a long code that takes long time to execute. So I used the
> >>> Rprof() function and found out that the function that takes about 80%
> of
> >>> the time is the incomb () fucntion (below), and this is most probably
> >>> because of the many explicit for() loops I'm using.
> >>>
> >>> n=18;m=4;p=0.3;alpha=0.2;beta=2
> >>> x=c(3,0,0)
> >>> LD<-list()
> >>> for (i in 1:(m-1)) {
> >>> LD[[i]]<-seq(0,x[i],1)
> >>> }
> >>> LD[[m]]<-seq(0,(n-m-sum(x)),1)
> >>> LED<-expand.grid (LD)
> >>> LED<-as.matrix(LED)
> >>> store1<-numeric(nrow(LED))
> >>> h<- numeric(m-1)
> >>> lm<- numeric(m-1)
> >>> for (j in 1:length(store1) )
> >>> {
> >>> incomb<-function(x,alpha,beta) {
> >>>
> >>> g<-((-1)^(sum(LED[j,])))*(gamma((1/beta)+1))*((alpha)^(-(1/beta)))
> >>> for (i in 1:(m-1)) {
> >>> h[i]<- choose(x[i],LED[j,i])
> >>> }
> >>> ik<-prod(h)*choose((n-m-sum(x)),LED[j,m])
> >>> for (i in 1:(m-1)) {
> >>> lm[i]<-(sum(LED[j,1:i])) + i
> >>> }
> >>> plm<-prod(lm)
> >>> gil<-g*ik/(plm)
> >>> hlm<-numeric(sum(LED[j,])+(m-1))
> >>> dsa<-length(hlm)
> >>> for (i in 1:dsa)
> >>> {
> >>> ppp<- sum(LED[j,])+(m-1)
> >>> hlm[i]<-
> >>> (choose(ppp,i))*((-1)^(i))*((i+1)^((-1)*((1/beta)+1)))
> >>> }
> >>> shl<-gil*(sum(hlm)+1)
> >>> return (shl)
> >>> }
> >>> store1[j]<-incomb(x,alpha=0.2,beta=2)
> >>> }
> >>>
> >>>
> >>> I'm trying to use alternatives (for ex. to vectorize things) to the
> >>> explicit for() loops, but things don't work out.
> >>>
> >>> Any suggestions that can help me to speed up the execution of the
> >>> incomb()
> >>> function are much appreciated.
> >>>
> >>> Thanks a lot in advance.
> >>>
> >>> Maram Salem
> >>>
> >>> [[alternative HTML version deleted]]
> >>>
> >>> ______________________________________________
> >>> R-help at 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 at 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.
>
--
Stephen Sefick
**************************************************
Auburn University
Biological Sciences
331 Funchess Hall
Auburn, Alabama
36849
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sas0025 at auburn.edu
http://www.auburn.edu/~sas0025
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