Re: [R] Iterated Data Input/Output with Random Forests

From: jim holtman <jholtman_at_gmail.com>
Date: Mon 24 Jul 2006 - 03:33:08 EST

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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Received on Mon Jul 24 03:38:57 2006

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