I would argue that the most important tool for reproducible research is not Sweave or knitr but GNU make.

Consider, for example, all of the files associated with a manuscript. In the simplest case, I would have an R script for each figure plus a LaTeX file for the main text. And then a BibTeX file for the references.

Compiling the final PDF is a bit of work:

  • Run each R script through R to produce the relevant figure.
  • Run latex and then bibtex and then latex a couple of more times.

And the R scripts need to be run before latex is, and only if they’ve changed.

A simple example

GNU make makes this easy. In your directory for the manuscript, you create a text file called Makefile that looks something like the following (here using pdflatex).

mypaper.pdf: mypaper.bib mypaper.tex Figs/fig1.pdf Figs/fig2.pdf
	pdflatex mypaper
	bibtex mypaper
	pdflatex mypaper
	pdflatex mypaper

Figs/fig1.pdf: R/fig1.R
	cd R;R CMD BATCH fig1.R

Figs/fig2.pdf: R/fig2.R
	cd R;R CMD BATCH fig2.R

Each batch of lines indicates a file to be created (the target), the files it depends on (the prerequisites), and then a set of commands needed to construct the target from the dependent files. Note that the lines with the commands must start with a tab character (not spaces).

Another great feature: in the example above, you’d only build fig1.pdf when fig1.R changed. And note that the dependencies propagate. If you change fig1.R, then fig1.pdf will change, and so mypaper.pdf will be re-built.

One oddity: if you need to change directories to run a command, do the cd on the same line as the related command. The following would not work:

### this doesn't work ###
Figs/fig1.pdf: R/fig1.R
	cd R
	R CMD BATCH fig1.R

You can, however, use \ for a continuation line, line so:

### this works ###
Figs/fig1.pdf: R/fig1.R
	cd R;\
	R CMD BATCH fig1.R

Note that you still need to use the semicolon (;).

Using GNU make

You probably already have GNU make installed on your computer. Type make --version in a terminal/shell to see. (On Windows, go here to download make.)

To use make:

  • Go into the the directory for your project.
  • Create the Makefile file.
  • Every time you want to build the project, type make.
  • In the example above, if you want to build fig1.pdf without building mypaper.pdf, just type make fig1.pdf.

Frills

You can go along way with just simple make files as above, specifying the target files, their dependencies, and the commands to create them. But there are a lot of frills you can add, to save some typing.

I’ll give a very brief introduction to some of the options that I use. See the make documentation for further details.

Variables

If you’ll be repeating the same piece of code multiple times, you might want to define a variable.

For example, you might want to run R with the flag --vanilla. You could then define a variable R_OPTS:

R_OPTS=--vanilla

You refer to this variable as ${R_OPTS}, so in the R commands you would use something like

cd R;R CMD BATCH ${R_OPTS} fig1.R

An advantage of this is that you just need to type out the options you want once; if you change your mind about the R options you want to use, you just have to change them in the one place.

For example, I actually like to use the following:

R_OPTS=--no-save --no-restore --no-init-file --no-site-file

This is like --vanilla but without --no-environ (which I need because I use the .Renviron file to define R_LIBS, to say that I have R packages defined in an alternative directory).

Automatic variables

There are a bunch of automatic variables that you can use to save yourself a lot of typing. Here are the ones that I use most:

  • $@    the file name of the target
  • $<    the name of the first prerequisite (i.e., dependency)
  • $^    the names of all prerequisites (i.e., dependencies)
  • $(@D)    the directory part of the target
  • $(@F)    the file part of the target
  • $(<D)    the directory part of the first prerequisite (i.e., dependency)
  • $(<F)    the file part of the first prerequisite (i.e., dependency)

For example, in our simple example, we could simplify the lines

Figs/fig1.pdf: R/fig1.R
	cd R;R CMD BATCH fig1.R

We could instead write

Figs/fig1.pdf: R/fig1.R
	cd $(<D);R CMD BATCH $(<F)

The automatic variable $(<D) will take the value of the directory of the first prerequisite, R in this case. $(<F) will take value of the file part of the first prerequisite, fig1.R in this case.

Okay, that’s not really a simplification. There doesn’t seem to be much advantage to this, unless perhaps the directory were an obnoxiously long string and we wanted to avoid having to type it twice. The main advantage comes in the next section.

Pattern rules

If a number of files are to be built in the same way, you may want to use a pattern rule. The key idea is that you can use the symbol % as a wildcard, to be expanded to any string of text.

For example, our two figures are being built in basically the same way. We could simplify the example by including one set of lines covering both fig1.pdf and fig2.pdf:

Figs/%.pdf: R/%.R
	cd $(<D);R CMD BATCH $(<F)

This saves typing and makes the file easier to maintain and extend. If you want to add a third figure, you just add it as another dependency (i.e., prerequisite) for mypaper.pdf.

Our example, with the frills

Adding all of this together, here’s what our example Makefile will look like.

R_OPTS=--vanilla

mypaper.pdf: mypaper.bib mypaper.tex Figs/fig1.pdf Figs/fig2.pdf
	pdflatex mypaper
	bibtex mypaper
	pdflatex mypaper
	pdflatex mypaper

Figs/%.pdf: R/%.R
	cd $(<D);R CMD BATCH $(R_OPTS) $(<F)

The advantage of the added frills: less typing, and it’s easier to extend to include additional figures. The disadvantage: it’s harder for others who are less familiar with GNU Make to understand what it’s doing.

More complicated examples

There are complicated Makefiles all over the place. Poke around github and study them.

Here are some of my own examples:

And here are some examples from Mike Bostock:

Also look at the Makefile for Yihui Xie’s knitr package for R.

Resources


The source for this minimal tutorial is on github.

Also see my git/github guide, knitr in a knutshell tutorial, R package primer, and simple site tutorial.