[R] Speeding nested loops up

[stephen sefick]

foreach and allied packages have helped me speed up some code
significantly.  I have four cores in my machine and this allows me to
get away with this...
HTH

Stephen

On Wed, Aug 17, 2011 at 9:59 PM, Jim Holtman <jholtman at gmail.com> wrote:
> anytime my code starts to take more than a couple of minutes to run what might look like a simple set of commands, I use Rprof to see where the time goes.  Run this on your script and you might get some insight into the problem area.  If it ran for an hour, I would defintely take a deep dive into it.
>
> Sent from my iPad
>
> On Aug 17, 2011, at 20:14, mark_horo <markknightnz at yahoo.co.nz> wrote:
>
>> Hi I'm trying to speed my loop up. Any Suggestions?? At the moment it takes a
>> few days to run.
>>
>> THE CODE
>> ---------------------------------------------------------------------------------------------------
>>    for(i in 1:11) {
>>        for (j in 3:12) {
>>            for (k in 1:273107) {
>>                        y[k,1] <- x[i,j,k]
>>                        print(y)
>>                                Rainfall_dataset <- read.table("1km_grid_nzmg.csv",
>>                                header=TRUE, sep=",", na.strings="NA", dec=".", strip.white=TRUE)
>>
>>                                t <- Rainfall_dataset
>>                                print(t)
>>
>>                                p<-cbind(t,y)
>>                                #y<-cbind(t,y)
>>                                #print(y)
>>            }
>>                        # This where you write out array y to a csv file
>>                        # Save output as a csv file
>>                        site <- paste("site",i,"-",j)
>>
>>                            csvfile <- paste(site,sep=".","csv"); print(csvfile)
>>                            path<- paste("c:/Data/",csvfile)
>>                            print(path)
>>                            write.csv(p,file=path, row.names = TRUE)
>>        }
>>    }
>>
>> --
>> View this message in context: http://r.789695.n4.nabble.com/Speeding-nested-loops-up-tp3751485p3751485.html
>> Sent from the R help mailing list archive at Nabble.com.
>>
>> ______________________________________________
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>> and provide commented, minimal, self-contained, reproducible code.
>
> ______________________________________________
> 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.
>



-- 
Stephen Sefick
____________________________________
| Auburn University                                         |
| Biological Sciences                                      |
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| Auburn, Alabama                                         |
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| sas0025 at auburn.edu                                  |
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