R help - Jul 2006 - Iterated Data Input/Output with Random Forests

Hi,

I am currently writing code to input a few thousand files, run them through the
Random Forests package, and then output corresponding results.

When I use the code below:

zz<-textConnection("ex.lm.out", "w")
sink(zz)
tempData<-read.delim(paste("allSnps",1,"Phenotype.phn",sep=""),header=TRUE,sep=",",quote="\"",dec=".")
tempData[[1]]<-factor(tempData[[1]])
tempData.rf<-randomForest(tempData[[1]]~.,data=tempData,importance=TRUE,proximity=TRUE,outscale=TRUE,replace=TRUE)
tempData.rf
zz<-file(paste("ex",1,".data",sep=""),
"w")
cat(ex.lm.out, sep="\n", file=zz)
sink()
close(zz)

I am able to successfully input and output for one file. However, if I try to
use a for loop or a while statement e.g.

for(i in 1:2)
{
zz<-textConnection("ex.lm.out", "w")
sink(zz)
tempData<-read.delim(paste("allSnps",i,"Phenotype.phn",sep=""),header=TRUE,sep=",",quote="\"",dec=".")
tempData[[1]]<-factor(tempData[[1]])
tempData.rf<-randomForest(tempData[[1]]~.,data=tempData,importance=TRUE,proximity=TRUE,outscale=TRUE,replace=TRUE)
tempData.rf
zz<-file(paste("ex",i,".data",sep=""),
"w")
cat(ex.lm.out, sep="\n", file=zz)
sink()
close(zz)
}

I get no error statements but the output is blank. Without the for statement,
setting i<-1 works fine.

One other related question is that right now I am trying to gett the loop to
work by using the paste() function with a variable (i). However, the paste
function returns a string.

If I wanted to make a loop of

tempData$pheno1
tempData$pheno2
tempData$pheno3
...

the paste() function will not work. Is there some other method to achieve the
desired effect? Thank you in advance! I have only been working with R for a few
days so please bear with my lack of knowledge!

John Zhou

For your last question of the 'paste', try

tempdata[paste('pheno', i, sep='')]



On 7/23/06, johnzhou@fas.harvard.edu <johnzhou@fas.harvard.edu>
wrote:
>
> Hi,
>
> I am currently writing code to input a few thousand files, run them
> through the
> Random Forests package, and then output corresponding results.
>
> When I use the code below:
>
> zz<-textConnection("ex.lm.out", "w")
> sink(zz)
> tempData<-read.delim(paste("allSnps",1,"Phenotype.phn
>
",sep=""),header=TRUE,sep=",",quote="\"",dec=".")
> tempData[[1]]<-factor(tempData[[1]])
> tempData.rf
>
<-randomForest(tempData[[1]]~.,data=tempData,importance=TRUE,proximity=TRUE,outscale=TRUE,replace=TRUE)
> tempData.rf
> zz<-file(paste("ex",1,".data",sep=""),
"w")
> cat(ex.lm.out, sep="\n", file=zz)
> sink()
> close(zz)
>
> I am able to successfully input and output for one file. However, if I try
> to
> use a for loop or a while statement e.g.
>
> for(i in 1:2)
> {
> zz<-textConnection("ex.lm.out", "w")
> sink(zz)
> tempData<-read.delim(paste("allSnps",i,"Phenotype.phn
>
",sep=""),header=TRUE,sep=",",quote="\"",dec=".")
> tempData[[1]]<-factor(tempData[[1]])
> tempData.rf
>
<-randomForest(tempData[[1]]~.,data=tempData,importance=TRUE,proximity=TRUE,outscale=TRUE,replace=TRUE)
> tempData.rf
> zz<-file(paste("ex",i,".data",sep=""),
"w")
> cat(ex.lm.out, sep="\n", file=zz)
> sink()
> close(zz)
> }
>
> I get no error statements but the output is blank. Without the for
> statement,
> setting i<-1 works fine.
>
> One other related question is that right now I am trying to gett the loop
> to
> work by using the paste() function with a variable (i). However, the paste
> function returns a string.
>
> If I wanted to make a loop of
>
> tempData$pheno1
> tempData$pheno2
> tempData$pheno3
> ...
>
> the paste() function will not work. Is there some other method to achieve
> the
> desired effect? Thank you in advance! I have only been working with R for
> a few
> days so please bear with my lack of knowledge!
>
> John Zhou
>
> ______________________________________________
> R-help@stat.math.ethz.ch 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.
>


-- 
Jim Holtman
Cincinnati, OH
+1 513 646 9390

What is the problem you are trying to solve?

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