using R to copy files

Question

As part of a larger task performed in R run under windows, I would like to copy selected files between directories. Is it possible to give within R a command like cp patha/filea*.csv pathb (notice the wildcard, for extra spice)?

Facilitation

Answer 1

I don't think there is a direct way (shy of shelling-out), but something like the following usually works for me.

flist <- list.files("patha", "^filea.+[.]csv$", full.names = TRUE)
file.copy(flist, "pathb")

Notes:

• I purposely decomposed in two steps, they can be combined.
• See the regular expression: R uses true regex, and also separates the file pattern from the path, in two separate arguments.
• note the ^ and $ (beg/end of string) in the regex -- this is a common gotcha, as these are implicit to wildcard-type patterns, but required with regexes (lest some file names which match the wildcard pattern but also start and/or end with additional text be selected as well).
• In the Windows world, people will typically add the ignore.case = TRUE argument to list.files, in order to emulate the fact that directory searches are case insensitive with this OS.
• R's glob2rx() function provides a convenient way to convert wildcard patterns to regular expressions. For example fpattern = glob2rx('filea*.csv') returns a different but equivalent regex.

Axletree

I think the pattern should be "^filea.+[.]csv". – Bari

@Marek: right you are! Also, in particular in the Windows world, peopole will typically want to add the argument ignore.case = TRUE. I edited accordingly, thanks. – Axletree

you can use ?glob2rx to convert from wildcards to regexes. – Mohammadmohammed

@Edurardo Leoni: yes, you can. The nice, if only occasionally unsettling, thing about R is that you keep discovering ways of doing things. It's the first I heard about glob2rx in R; I typically write my regexes longhand (which btw for the globbing patterns isn't that hard), but yeah, glob2rx() works. I'll add this to the notes in the answer. – Axletree

If you are using this with intention to copy and replace files, then please do not forget to add overwrite = TRUE inside file.copy()! Lost an hour debugging this. – Taxiway

Answer 2

You can

• use system() to fire off a command as if it was on shell, incl globbing
• use list.files() aka dir() to do the globbing / reg.exp matching yourself and the copy the files individually
• use file.copy on individual files as shown in mjv's answer

Denaturalize

never heard of dir. It's exactly identical to list.files... strange to have both – Oleary

'dir' is older, but less intutive. – Burnette

Answer 3

For fellow script kiddies:

mainDir<-getwd() #so it creates the file wherever your working directory is
  subDir<-"name_of_my_new_sub-directory"
  dir.create(file.path(mainDir, subDir), showWarnings = FALSE)
  setwd(file.path(mainDir, subDir))

Burnette