CODEWITHSUNDEEP
filerfor-loopfilenames
Martin H
Martin H

Reputation: 749

How to iterate over file names in a R script?

A very simple R script adds a ascending row index to a textfile "0.txt" and also adds a header "time" to it. After that the data is written to a file "0-edit.txt"

data<-read.table("0.txt", header=TRUE,sep=",",row.names= NULL);
colnames(data)[1] = "time"
write.table(data,quote=FALSE,sep=", ","0-edit.txt");

Assume i have 4 files called 0.txt, 1.txt, 2.txt, ...in the same folder, how can I use a counter (or something else) to iterate over those file names in my script?

Upvotes: 12

Views: 39571

Answers (4)

Mason D
Mason D

Reputation: 71

Try this:

files <- list.files(path="", pattern=".txt", all.files=T, full.names=T)
for (file in files) {
## do stuff
}

You can use regular expressions for the pattern matching, so if you have lots of text files but only want the ones with numeric names, use "[0-9].txt" or "[0-3].txt".

Upvotes: 7

Matti Pastell
Matti Pastell

Reputation: 9303

Here is a solution without a loop using lapply:

infiles <- dir(pattern='\\.txt$')

change.files <- function(file){
  data <- read.table(file, header=TRUE, sep=",", row.names=NULL)
  colnames(data)[1] = "time"
  write.table(data, quote=FALSE, sep=", ", sub("\\.txt$","-edit.txt", file))
}

lapply(infiles , change.files)

For me the real advantage of this approach is that you can easily run it in parallel using mclapply (from multicore package) instead of lapply. Or parLapply from snow. Also to me it looks nicer.

Upvotes: 15

alaiacano
alaiacano

Reputation: 733

More generally, you can use dir() to get the files in a given directory, and use select to limit it to .txt files.

file.dir <- "/path/to/files"
for(infile in dir(file.dir, pattern="\\.txt$")) {
  outfile <- gsub("\\.txt$","-edit\\.txt", infile)

  data <- read.table(infile,header=TRUE,sep=",",row.names=NULL)
  colnames(data)[1] = "time"
  write.table(data,quote=FALSE,sep=", ",outfile)
}

Upvotes: 3

Joshua Ulrich
Joshua Ulrich

Reputation: 176728

for(i in 0:3) {
  infile <- paste(i,".txt",sep="")
  outfile <- paste(i,"-edit.txt",sep="")

  data <- read.table(infile,header=TRUE,sep=",",row.names=NULL)
  colnames(data)[1] = "time"
  write.table(data,quote=FALSE,sep=", ",outfile)
}

Upvotes: 15

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