Organizing a data analysis is hard

Organizing data analysis is hard. Here's a couple reasons it gets tricky:

You have thousands of files
You can work with a single CSV file by hand. Maybe you could do a dozen, but you're not going to be able to keep track of thousands of files. You can't even count them without some sort of tool.
Data collection is ongoing
Not only do you have a bunch of files, but you keep getting more. Somehow you need to keep everything up-to-date with the latest data dump.
You want to be reproducible
You'd like anybody to be able to download your analysis and run it on their machine. Unfortunately, running it on your machine is often an ordeal.

Fortunately, there's a solution for all of these problems. You should use a tool called rake.

What is Rake?

Rake is a build utility; build utilities were originally designed to automate the process of compiling code from source. You can generalize the process to simply updating files based upon dependencies.

Let's look at how rake address the problems with organizing data analysis

You have thousands of files
No problem, you can handle everything programmatically. Rake will handle the tedious stuff.
Data collection is ongoing
Once your workflow is defined, processing new data doesn't require anything more than typing a single rake command into your shell. If you want to get really fancy, you don't even have to type it, you can automate the process using a chron job.
You want to be reproducible
Rake doesn't work well if you're not explicit about your workflow. The benefit of this is that, if it runs, it's probably reproducible (assuming you dealt with stuff like seeding your PRNG).

I use rake for all of my projects. Perhaps the most useful is my work on neuroscience data. I need to manage a bunch of brain recordings, preprocess them, and then run some analysis. The lab manages this process by hand and it takes up a lot of their time. My system is automated, so whenever I update my methods or get new data it's a simple matter of typing one command and then coming back a couple minutes (or hours depending) later to look at the results.

An example

To see how rake works, it's best to look at an example. Let's work with baby name data from the SSA. The SSA, by virtue of issuing social security cards, has a list of baby names for each year. What we want to do is look at the number of babies with a particular name plotted over time. Are certain names getting more or less popular? How many kids are named Elvis?

Rake requires that you have a specific file in your project directory named "Rakefile". This is where you specify your workflow. So let's walk through an example Rakefile.

Step 1

Our first step is downloading the data from the SSA's website. We can achieve this with the following entry in our Rakefile.

file "data/raw/" => [] do |t|
  mkdir_p "data/raw"
  sh "wget -O data/raw/"

The file at the start indicates that I'm denoting a file task (we'll get to the other types). "" is the file that I'm creating, the "=> []" syntax is used to express dependencies (more on that later). The code included within the do-end block is the action I take to create my file, namely make the directory and download the file from the SSA website. You can use any ruby command within the block; here I use the built-in system tools to make the "data/raw" directory and then run my shell command.

To execute this I simply run "rake data/raw/" in the same directory as my Rakefile. Note that once the file has been created, nothing happens when I repeat the command. The only time that rake executes a task is when the target doesn't exist or one of its dependencies is newer than the existing target file. You'll never repeat unnecessary work.

Step 2

The zip file that I've downloaded contains a bunch of text files of the form /yob****.txt" which contain the names data for a certain year. To extract these I can make a task

directory "data/processed"

yob_files = FileList[(1880..2014).map{|year| "data/processed/yob#{year}.txt"}]

yob_files.each do |yob_file|
  file yob_file => ["data/raw/", "data/processed"] do |t|
    sh "unzip -DD data/raw/ -d data/processed"

The first thing that I do is define a directory task.

We then make a list of all of the text files we want to extract. Here we make this list by taking each year between 1880 and 2014 and mapping it to the relevent file name. We then store it as a FileList, a structure which is simply a list of filenames which have some nice methods defined on it for ease of use.

We then iterate through this list of filenames and make file tasks for each one. The body is the same for each, running unzip on the zip file.

When we run rake, the zip file will only be unzipped once since rake checks to see if a task is necessary before running. Remember, a task only runs if the target doesn't exist or one of its dependencies is newer than the existing target file. Note that we need to make sure the timestamps work out by using the "-DD" flag, otherwise the timestamps for our unzipped files will be behind the timestamp of the zipped file.

Step 3

Working with all of the txt files is going to be painful. So our next step is consolidate them into a single csv file.

file "data/single-file.csv" => [*yob_files, "code/make-single-file.R"] do |t|
  sh "Rscript code/make-single-file.R --outfile #{} --yob_files #{yob_files}"

Now that we've gotten used to the syntax, this step is fairly self-explanatory.

Passing arguments to R is a little different though. You definitely want to make use of the argparse package. Otherwise, parsing the command line options in the above script is difficult since the number of txt files is variable.

Step 4

Now for the final product. We want to make some graphs.

def make_plot(name, sex, outfile)
  dir = directory outfile.pathmap("%d")
  file outfile => ["code/plot-name-by-year.R", "data/single-file.csv", dir] do |t|
    sh "Rscript code/plot-name-by-year.R --name #{name} --sex #{sex} --infile data/single-file.csv --outfile #{outfile}"
  multitask :make_plots => outfile

make_plot("Amelia", "F", "figs/amelia.pdf")
make_plot("Elvis", "M", "figs/elvis.pdf")
make_plot("John", "M", "figs/john.pdf")

We have full use of the ruby language, so we can define functions. This saves us a lot of copy-and-pasting.

We also can run our tasks in parallel. The multitask token indicates a task which can be done in parallel. This speeds things up considerably.

End Result

Anybody can replicate our figures just by downloading our source code and running the following command.

rake make_plots

Then rake will download the file, do the pre-processing, and make the figures (in parallel) automatically. It's great.

A word of caution

If you've read this far down, you're probably interested in using rake in your own work. Let me warn you about something.

This is very much a tool for managing your computational flow. There's the definite potential for things to spiral out of control when you start collaborating with others. Here's a short list of potential problems and solutions.

  • Your collaborator doesn't know ruby

    This is fairly common; ruby is not a standard stats/math language. For people who don't find learning languages fun, there's little reason to have heard of ruby, let alone have learned how to use it.

    Fortunately it's not too hard to teach them the basic syntax required to make simple tasks (it's just as easy as Make). You should take the lead on anything complex.

  • You have incompatable systems / packages

    This happened to me when a munging script that worked perfectly fine on my machine started spewing errors on my collaborators machine. It took me longer than I'd like to publicly admit to realize that the problem was that on my machine the command python refers to python3 while on his machine it refers to python2.

    This is easy fixed by making sure you have the same packages on all machines. Or if some machines can't run certain programs (ahem, matlab) then just work around it as much as you can.

  • Your collaborator doesn't use the command line

    View this as an opportunity; you can initiate them into the mysteries of the command line.

  • Your collaborator doesn't use Linux

    This is the worst case scenario. My understanding is that you should be mostly ok with OS X. Windows seems like it would be a nightmare (but maybe it'll work now that bash is coming to Windows). I haven't really dealt with this, but the solution is obvious: "borrow" their machine and install linux. Eventually they'll come around and thank you.