Thanks a lot Jim and Boris for replying.
Sent from my iPhone
> On Nov 9, 2015, at 1:13 AM, jim holtman <jholt...@gmail.com> wrote:
>
> You need to take a close look at the function incomb that you are creating.
> I see what appears to be a constant value
> ("*(gamma((1/beta)+1))*((alpha)^(-(1/beta)))") being computed that you might
> only have to compute once before the function. You are also referencing many
> variables (m, LED, j, ...) that are not being passed in that are in the
> global environment; it is probably better to pass them in to the function. I
> am not sure what 'pbapply' is doing for you since I see this is new to the
> code that you first sent out.
>
> I would be good it you told us what the function is trying to do; you are
> showing us how you want to do it, not what you want to do. Are there other
> ways of doing it? If speed is your problem, then consider the "Rcpp" package
> and write the function is C++ which might be faster, but again, take a look
> at what you are doing to see if there are other ways. I don't have time to
> dig into the code, since there is a lack of comments, to understand why you
> are using, e.g., 'choose', 'prod', etc.). There are probably a lot of ways
> of speeding up the code, if could tell us what you want to accomplish.
>
>
> 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 8, 2015 at 4:48 AM, Maram SAlem <marammagdysa...@gmail.com>
>> wrote:
>> Thanks all for replying.
>>
>> In fact I've used the the Rprof() function and found out that the incomb()
>> function (in my code above) takes about 80% of the time, but I didn't
>> figure out which part of the function is causing the delay. So I thought
>> that this may be due to the for() loops.
>> I MUST run this code for rather large values of n and m, so is there any way
>> that can help me do that without having to wait for more than three days to
>> reach an output. N.B. I'll have to repeat these runs for may be 70 or 80
>> times , and this means HUGE time
>>
>> I'd appreciate any sort of help.
>> Thanks in advance.
>>
>> Maram Salem
>>
>>> On 6 November 2015 at 16:54, jim holtman <jholt...@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 <marammagdysa...@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 thoug!
ht 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 <jholt...@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 <marammagdysa...@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]]
>>>>>>
>>>>>> ______________________________________________
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>>>>>> 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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