How to organize large R programs?

When I undertake an R project of any complexity, my scripts quickly get long and confusing.

What are some practices I can adopt so that my code will always be a pleasure to work with? I'm thinking about things like

• Placement of functions in source files
• When to break something out to another source file
• What should be in the master file
• Using functions as organizational units (whether this is worthwhile given that R makes it hard to access global state)
• Indentation / line break practices.
  • Treat ( like {?
  • Put things like )} on 1 or 2 lines?

Basically, what are your rules of thumb for organizing large R scripts?

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.