Everything with a script
The most basic aspect of reproducible research is that everything you do (convert data files, clean data, analyze data) should be accomplished via code. Pointing and clicking, and copy-paste, are not reproducible.
Ideally, get the data in the most-raw form possible. And get any/all data and meta data possible. And keep track of the provenance of all data files. (You don’t want to be asking, “Where did these microarray annotations come from?”)
If you need to download external data, such as from the web, it’s best to do so via a script, for example with wget or curl. (Consider the R package httr.) If that’s not feasible, at least document the source of the data (and perhaps the date/time it was acquired).
If you need to convert a data file from one form to another, use a script. For example, to convert an Excel file to a CSV file, I use xls2csv.py or xlsx2csv.py. Rather than opening the file in excel and saving each sheet by hand, do this with code.
Don’t hand-edit data files. If you need to delete some initial rows, or if you want to change some column names, don’t open up the file and edit it by hand. Write a script that does so. I like to write ruby scripts for this sort of thing; you might use python or perl, or even R.
All aspects of data cleaning should be in scripts. If you decide that you need to omit a couple of subjects, don’t go into the data file and delete those rows, but rather write a script that will delete those subjects and create a separate, revised data file. If you find some errors in the data, don’t go into the file and change it by hand, but rather make those changes via a script (or have the changes made to the primary database, in a documented and versioned way).
Each aspect of the analysis should be in scripts. Make these straight-forward to run. It shouldn’t be “run this set of lines to do this and those lines to do that,” or even worse, “change this variable and then re-run it to do that.” (I’ve written lots of scripts like that in the past; they’re neither pretty nor reproducible.) Ideally, break things up into functions, to make the code easier to follow and to avoid repeated code. More on this later.
Save your seeds for random number generation. While in many cases it is useful to re-run a simulation with independent replicates, if you want your simulations to be fully reproducible, use a defined seed and save it in your script. In R, I’ll typically use
runif(1, 0, 10^8)in an interactive session, and then copy that number into a line at the top of my script, like
set.seed(91820205). If I’m running multiple batches of simulations in parallel, I’ll typically use something like
set.seed(91820205 + i)for batch
Initially, it may seem like a hassle to do many of these things via code rather than by hand. But if the primary data should change (and it often does), repeating all of that by-hand extraction and editing is a huge hassle, while re-running the scripts should be super easy (particularly if automated, more on that later).
Now go to the page about automating the process.