[R] Help transfrom R to C

[Thomas Lumley]

On Mon, 5 Apr 2010, pinusan wrote:

>
> Dear R users,
>
> I would like to transform the following "for loop" from R-code to C-code
> because it takes really long time to have inc.freqy table.
> Unfortunately, I do not have experience to write C code.
> Plese, give me some example or advise to transfrom the R to C code.

I think you can just use

rowSums( test, unit.dist, "<=")

instead of your for() loop.

    -thomas



> I have attached the code and some result that I made in R.
>
> Have a nice day.
>
> Hong Su
>
> # Data import
> ct10_pt1_neartree<-read.table("~/Desktop/hongsu/clustered_pattern/ct10/ct10/ct10_58ft_pt1_neartree",
>       header=TRUE, sep=",", na.strings="NA", dec=".", strip.white=TRUE)
> test<-round(ct10_pt1_neartree, digits=1)
>
> # randomly select 2 data set for test
> test<-as.matrix(test[sample(2,replace=T),])
> test
>
> # Selected Data
>> test
>       Rpt1 Rpt2 Rpt3 Rpt4 Rpt5 Rpt6 Rpt7 Rpt8 Rpt9 Rpt10 Rpt11 Rpt12 Rpt13
> Trial1 19.3  9.1 20.7  3.0 21.4 14.5  8.2 10.5  7.4  11.0   6.9   9.5  15.4
> Trial2 24.5 22.2  4.9  7.8 20.9 12.5 18.3  6.5  7.6   2.2   8.9  19.6  21.1
>       Rpt14 Rpt15 Rpt16 Rpt17 Rpt18 Rpt19 Rpt20 Rpt21 Rpt22 Rpt23 Rpt24
> Rpt25
> Trial1  49.2  39.9  18.3  14.8  29.9  27.3  20.2  14.6   9.5  14.2   7.5
> 16.0
> Trial2  38.6  12.8   1.5  12.5   4.6  10.6  14.5  12.5   5.8  14.0  55.9
> 4.8
>       Rpt26 Rpt27 Rpt28 Rpt29 Rpt30 Rpt31 Rpt32
> Trial1  19.7  12.9   5.3   3.1  11.7  19.0  21.2
> Trial2   0.8  11.3   4.7  12.5   5.5   5.9   5.2
>
> # N of columns in test
> n.center.point<-ncol(test)
>
> # Maximum number in test
> max.dist<-max(test)
>
> # make distance
> unit.dist <- seq(0, round(max.dist, digit=1),0.1) # change file
>
>
> # for loop (need to change C)
> inc.freqy<-matrix(0,nrow(test), length(unit.dist))
>
> for(i in 1:nrow(test)){
>  for (j in 1:length(unit.dist)){
>    inc.freqy[i,j]<-length(test[i,][test[i,]<=unit.dist[j]])
>    }
>   }
>
> inc.freqy[,1:30]
>
> # partial result for inc.freqy
>> inc.freqy[,1:30]
>     [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13]
> [,14]
> [1,]    0    0    0    0    0    0    0    0    0     0     0     0     0
> 0
> [2,]    0    0    0    0    0    0    0    0    1     1     1     1     1
> 1
>     [,15] [,16] [,17] [,18] [,19] [,20] [,21] [,22] [,23] [,24] [,25] [,26]
> [1,]     0     0     0     0     0     0     0     0     0     0     0     0
> [2,]     1     2     2     2     2     2     2     2     3     3     3     3
>     [,27] [,28] [,29] [,30]
> [1,]     0     0     0     0
> [2,]     3     3     3     3
>
> -- 
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>
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>

Thomas Lumley			Assoc. Professor, Biostatistics
tlumley at u.washington.edu	University of Washington, Seattle