R help - Dec 2008 - Globbing Files in R

Dear all,

For example I want to process set of files.

Typically  Perl's idiom would be:

__BEGIN__
@files = glob("/mydir/*.txt");

foreach my $file (@files) {
  # process the file
}
__END__

What's the R's way to do that?

- Gundala Viswanath
Jakarta - Indonesia

On Sun, Dec 21, 2008 at 9:35 AM, Gundala Viswanath <gundalav at gmail.com>
wrote:
> Dear all,
>
> For example I want to process set of files.
>
> Typically  Perl's idiom would be:
>
> __BEGIN__
> @files = glob("/mydir/*.txt");
>
> foreach my $file (@files) {
>  # process the file
> }
> __END__
>
> What's the R's way to do that?
The tools to do this are the functions list.files, grep (or variants
on grep) and perhaps glob2rx.  See the help files for each.

One approach is
> files <- list.files("~/Desktop")
> txtfiles <- files[grep(glob2rx("*.txt"), files)]
> txtfiles
[1] "notes312.txt" "stat324.txt"

Note that grep returns a vector of indices into the character vector,
not the character vectors themselves.

Try this:

file.names <- dir(pattern = glob2rx("/mydir/*.txt"))
for(fn in file.names) {
  DF <- read.table(fn, ...)
  ...
}

Another possibility is:

file.names <- .. as above ...
out <- lapply(file.names, function(fn) {
   DF <- read.table(fn, ...)
   ...
})

out will have one component per file formed from the result of the
each function application.


On Sun, Dec 21, 2008 at 10:35 AM, Gundala Viswanath <gundalav at
gmail.com> wrote:
> Dear all,
>
> For example I want to process set of files.
>
> Typically  Perl's idiom would be:
>
> __BEGIN__
> @files = glob("/mydir/*.txt");
>
> foreach my $file (@files) {
>  # process the file
> }
> __END__
>
> What's the R's way to do that?
>
> - Gundala Viswanath
> Jakarta - Indonesia
>
> ______________________________________________
> R-help at r-project.org 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.
>

Gundala Viswanath wrote:
> Typically  Perl's idiom would be:
> 
> __BEGIN__
> @files = glob("/mydir/*.txt");
> 
> foreach my $file (@files) {
>   # process the file
> }
> __END__
Something like this has been suggested in R-help before:

files <- dir()
results <- lapply(files, yourprocessing())

The dir function has path and pattern arguments to select the set of 
files you want.

This works fine when there are no problems, but often I'll use a for 
loop so problem files can be dealt with differently when necessary.

Perhaps something like this:

ProcessList <- dir(pattern="InPerson*")

for (i in 1:length(ProcessList))
{
   filename <- ProcessList[i]
   . . .
}


efg

Earl F Glynn
Overland Park, KS