[R] for loop help

[Anthony Steven Dick]

Thanks Adai. You can tell by the clumsiness of my script that I am new 
to R and to programming. After wrestling with it this morning, I found 
that the following worked best:

pre.outliers<-subset(final.roi.df, gFDR4FWHM >= 1.96)
               detach(final.roi.df)
               attach(pre.outliers)
               outliers <- subset(pre.outliers, gtvalue4FWHM >= 0.00)
               if(length(outliers$gtvalue4FWHM)==0) {
               print("NA")
               next
               }
....


Thanks for the other suggestions. I have incorporated them.

Anthony


Adaikalavan Ramasamy wrote:
> Try changing
>
>    outliers <- subset(pre.outliers, gtvalue4FWHM >= 0.00)
>
> to
>
>    w <- which( gtvalue4FWHM >= 0.00 )
>    outliers( length(w) > 0, pre.outliers[ w, ],  NA )
>
>
> Other comments:
>
> 1. Make sure you detach(data_gcs) at the end of the loops
>
>
> 2. scale() works on columns by default, so try
>     current.roi.plus.z <- data.frame(current.roi,
>                                   scale(current.roi[, c(15,18,21,24)]) )
>
>
> 3. For simple statements, you can use ifelse() syntax. Also see all(). 
> Using these two functions, you can try
>
>  testextrem <- function(x) ifelse( all(abs(x[ 1:4 ]) < c(2.5)), 1, 0)
>
>
> 4. Try to minimise the use of attach() in loops.
>
> 5. You might be interested in learning more about apply(), tapply(), 
> split() etc.
>
>
> If this does not help, then please resend a simplified version of the 
> codes, preferably with a simple toy example to illustrate.
>
> Regards, Adai
>
>
>
> Anthony Steven Dick wrote:
>> Hello-
>>
>> I have a script which steps through a series of subjects, and for the 
>> subjects I remove outlying values. After removing these outliers, I 
>> specify a cutoff, keeping only values over a certain value (e.g., 
>> 1.96). I want to populate a matrix with a statistic of the values 
>> that make the cutoff (for example, the mean). However, in some 
>> subjects, after outliers and the cutoff are specified, there are no 
>> data that meet the criteria (I get <0 rows> (or 0-length row.names)). 
>> Here the script dies.
>>
>> The solution I think is to specify a break so that the matrix will be 
>> populated with a value (such as NA) and it will move on to the next 
>> subject in the loop. However, I haven't been able to figure this out. 
>> If anyone has any suggestions I would very much appreciate them. I 
>> have paster part of the script below up to the point where it dies.
>>
>> Thanks.
>>
>> for (ss in levels(ss.list)) {
>>         print(ss)
>>         ss.count = ss.count + 1          query.string <- 
>> paste("SELECT * FROM ",ss,";",sep="")
>>         #print(query.string)
>>         data_gcs <- dbGetQuery(con, query.string)
>>         attach(data_gcs)
>>         names(data_gcs)
>>         mat_row = 0
>>             for(i in levels(roi.list)){
>>             print (i)
>>             current.roi <- data_gcs[data_gcs$ROI==i,]
>>             current.roi.plus.z <- data.frame(current.roi, 
>> scale(current.roi[,15]), scale(current.roi[,18]), 
>> scale(current.roi[,21]), scale(current.roi[,24]))
>>             testextrem <- function(x) {if ((abs(x[1]) < 2.5) & 
>> (abs(x[2]) < 2.5) & (abs(x[3]) < 2.5) & (abs(x[4]) < 2.5)) return(1) 
>> else return(0)}
>>             filtervector <- apply(as.vector(current.roi.plus.z[,c(27, 
>> 28, 29, 30)]), 1, FUN=testextrem)
>>             current.roi.plus.z.filter <- 
>> data.frame(current.roi.plus.z, filtervector)
>>             final.roi.df <- 
>> current.roi.plus.z.filter[which(current.roi.plus.z.filter$filtervector==1),] 
>>
>>             #print (final.roi.df)
>>             kicked.out<-(length(filtervector) - 
>> sum(filtervector))/length(filtervector)
>>             print(kicked.out)
>>             matrix.col = matrix.col + 1
>>             attach(final.roi.df)
>>             names(final.roi.df)
>>             print(matrix.col)
>>             #set cutoff for FDR. per voxel p values (of Z dist) .05 = 
>> 1.96, .01 = 2.575, .001 = 3.277, .005 = 3.479 BE SURE TO CHANGE THE 
>> VARIABLE EACH TIME YOU CHANGE CONDITION
>>                pre.outliers<-subset(final.roi.df, gFDR4FWHM >= 1.96)
>>                detach(final.roi.df)
>>                attach(pre.outliers)
>>                outliers<-subset(pre.outliers, gtvalue4FWHM >= 0.00)
>> ...and the script dies here because there are no data in "outliers".
>>
>


-- 
Anthony Steven Dick, Ph.D.
Post-Doctoral Scholar
Human Neuroscience Laboratory
Biological Sciences Division
University of Chicago
5841 S. Maryland Ave. MC-2030
Chicago, IL 60637
Phone: (773)-834-7770
Email: adick at uchicago.edu
Alternate email: anthony at anthonymail.com

Please visit my homepage at http://home.uchicago.edu/~adick/