How to organize large R programs?

The standard answer is to use packages -- see the Writing R Extensions manual as well as different tutorials on the web.

It gives you

• a quasi-automatic way to organize your code by topic
• strongly encourages you to write a help file, making you think about the interface
• a lot of sanity checks via R CMD check
• a chance to add regression tests
• as well as a means for namespaces.

Just running source() over code works for really short snippets. Everything else should be in a package -- even if you do not plan to publish it as you can write internal packages for internal repositories.

As for the 'how to edit' part, the R Internals manual has excellent R coding standards in Section 6. Otherwise, I tend to use defaults in Emacs' ESS mode.

Update 2008-Aug-13: David Smith just blogged about the Google R Style Guide.

I like putting different functionality in their own files.

But I don't like R's package system. It's rather hard to use.

I prefer a lightweight alternative, to place a file's functions inside an environment (what every other language calls a "namespace") and attach it. For example, I made a 'util' group of functions like so:

util = new.env()

util$bgrep = function [...]

util$timeit = function [...]

while("util" %in% search())
  detach("util")
attach(util)

This is all in a file util.R. When you source it, you get the environment 'util' so you can call util$bgrep() and such; but furthermore, the attach() call makes it so just bgrep() and such work directly. If you didn't put all those functions in their own environment, they'd pollute the interpreter's top-level namespace (the one that ls() shows).

I was trying to simulate Python's system, where every file is a module. That would be better to have, but this seems OK.