1 Files

1.1 Names

File names should be meaningful and end in .R. Avoid using special characters in file names - stick with numbers, letters, -, and _.

# Good

# Bad
fit models.R

If files should be run in a particular order, prefix them with numbers. If it seems likely you’ll have more than 10 files, left pad with zero:


If you later realise that you’ve missed some steps, it’s tempting to use 02a, 02b, etc. However, I think it’s generally better to bite the bullet and rename all files.

Pay attention to capitalization, since you, or some of your collaborators, might be using an operating system with a case-insensitive file system (e.g., Microsoft Windows or OS X) which can lead to problems with (case-sensitive) revision control systems. Prefer file names that are all lower case, and never have names that differ only in their capitalization.

1.2 Organisation

It’s hard to describe exactly how you should organise your code across multiple files. I think the best rule of thumb is that if you can give a file a concise name that still evokes its contents, you’ve arrived at a good organisation. But getting to that point is hard.

1.3 Internal structure

Use commented lines of - and = to break up your file into easily readable chunks.

# Load data ---------------------------

# Plot data ---------------------------

If your script uses add-on packages, load them all at once at the very beginning of the file. This is more transparent than sprinkling library() calls throughout your code or having hidden dependencies that are loaded in a startup file, such as .Rprofile.