[R] How can we make a vector call a function element-wise efficiently?

[Eik Vettorazzi]

Hi,
you compute the same results for logx many times. So it is easier and
time saving tabulating all intermediate results.

smth. like
 n<-100000
 CT=6000	#assignment to CT
 NT=29535210	#assignment to NT
 i <- 0:(n-1)
 lookup<- lchoose(NT-n, CT-i) + lchoose(n, i)
 lgmax<-cummax(lookup)
 calsta2<-function(c) lgmax[c] + log(sum(exp(lookup[1:c] - lgmax[c])))

should help for a start, but I think, you are running into numerical
troubles, since you are dealing with very high and low (on log scale)
numbers and calsta constantly returns 57003.6 for c>38 (the summands in
sum(exp(logx - logmax)) will become 0 for c>38).

#check
sapply(1:50,calsta2)
sapply(1:50,calsta)

hth

Am 11.02.2011 06:12, schrieb zhaoxing731:
> Hello
> 	I have a time-comsuming program which need to simplify, I have tested the annotated program as follow:
> 
>> #define function which will be call
> 
>> calsta <- function(c, n=100000) 
> + { 
> +   i <- seq(from=0, length=c) 
> +   logx <- lchoose(NT-n, CT-i) + lchoose(n, i) 
> +   logmax <- max(logx) 
> +   logmax + log(sum(exp(logx - logmax))) 
> + } 
>> CT=6000	#assignment to CT
>> NT=29535210	#assignment to NT
>>
>> vec<-c(2331,524,918,218,1100,547,289,1167,450,1723)
>> vec
>  [1] 2331  524  918  218 1100  547  289 1167  450 1723
>> vec<-rep(vec,1000)#replicate the vec 1000 times
>> length(vec)
> [1] 10000 
> 
>> #then I'd like to make vector "vec" call function calsta element-wise
>> #and save the output to vector "result"
> 
>> system.time(result<-sapply(vec,calsta))
>    user  system elapsed 
>   26.45    0.03   26.70 
>>
>> system.time(for (i in 1:10000) result[i]=calsta(vec[i]))
>    user  system elapsed 
>   27.74    0.14   28.94 
> 
> I have about  300,000 such 26.70/ 28.94 seconds, so the approximate computation time is 100 days
> What a terrible thing to do!!!
> Any modification, nomatter how subtle, will be a big help for me
> 
> Thank you in advance
> 
> Yours sincerely
>  
> 
> 
> 
> ZhaoXing
> Department of Health Statistics
> West China School of Public Health
> Sichuan University
> No.17 Section 3, South Renmin Road
> Chengdu, Sichuan 610041
> P.R.China
> 
> __________________________________________________
> ¸Ï¿ì×¢²áÑÅ»¢³¬´óÈÝÁ¿Ãâ·ÑÓÊÏä?
> 
> 
> 
> 
> ______________________________________________
> R-help at r-project.org mailing list
> 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.


-- 
Eik Vettorazzi
Institut für Medizinische Biometrie und Epidemiologie
Universitätsklinikum Hamburg-Eppendorf

Martinistr. 52
20246 Hamburg

T ++49/40/7410-58243
F ++49/40/7410-57790