Guest Post: Two simple things to make your research more reproducible, by Thomas Wallis

In this guest post, experimental psychologist Thomas Wallis (University of Tübingen) proposes two simple ideas how you can make your work more reproducible.

wallis_reproducibilityThis is a guest post by Thomas Wallis, who is a Humboldt Postdoctoral Fellow in vision science at the University of Tübingen. Based on his experience, I asked him to propose two ideas for political scientists to improve reproducibility.

Data are kept private

The push for improving the transparency and reproducibility of research is taking hold in many fields, and it’s great to see. I’m grateful for the opportunity to share my ideas with readers in political science. I am a postdoctoral fellow researching human visual perception, using a combination of behavioural experiments and mechanistic modelling of perceptual processes. In my field (as in many others) it is typical for data, analyses and the code used to conduct experiments to be kept private – only “available upon request to the authors”, which is a recipe for disaster. Thankfully, this culture is slowly changing.

In this post I will outline two simple things I think are useful to improve reproducibility. Since I don’t know the research culture in political science, maybe these are things that you already do as a field. If so, great! If not, maybe you find these suggestions useful.

One reason that people are resistant to making their materials publicly available is that it can seem like a lot of effort. I can sympathise with this: for some of my early papers it would be a lot of effort to present all the materials so that they could be understood by another human.

Can you reproduce your own work?

The thing is, I am effectively not the same human who layed out that spreadsheet all those years ago. If I needed to go back and reproduce something from an old paper, it would probably take a few very unpleasant days. When I realised this, I made a big effort to improve my workflow with the aim that I should be able to reproduce my work with ease, years after the fact. Making materials available publicly is a simple extension of this approach to one’s personal scientific workflow.

With this in mind, I started blogging about things I’ve found useful. For example, setting up a project directory in a principled and extensible way helps you and others understand what is where. Version control is a good thing but it can be overengineered and sometimes frustrating. Finally, integrating analyses into the manuscript using tools like knitr is great from the perspective of a reproducibility perfectionist, but I’ve found can make things difficult in practice when your collaborators aren’t using these tools.

For this post, I wanted to concentrate on two simple steps that would easily improve the reproducibility of political science.

Tip 1: Script all your analyses

In my opinion, the analyses in a scientific paper should be documented in a text file that can be executed to reproduce all the results (including figures and tables) in the paper. You can produce scripts in any good analysis environment, including R, Stata, SAS, SPSS and Python. If the analysis is complicated maybe this will include multiple files and functions. If that’s the case, always tie the analyses together in a master script that, when executed, regenerates the whole thing.

If you currently do your analyses in a spreadsheet: strongly consider changing your tools. It makes the analyses extremely hard to audit because you have to click through the cells to see the actual formulae. Furthermore, I would argue that spreadsheets are more prone to copy-paste and click-and-drag errors than code. Daniel Lemire has two posts on how spreadsheets have contributed to two controversial analyses in economics, and makes strong points there about why scientists shouldn’t be using them.

Tip 2. Give people the data as a text file

You have some data, and you’ve done your analysis and written up your paper. Now you want to make your data available to others. As Thomas Leeper has previously written on this blog, it’s a good idea to put your data in an archive.

The data file used for the analysis should obviously be provided, in whatever format you used it (an R data file, SPSS data file, Stata file, Matlab file, etc…). What I’m suggesting here is that you could also provide tabular data in a delimited text format (like .csv). This means that people can use your data in whatever analysis environment they like (well, except maybe Matlab). Any analysis environment, including spreadsheeting software, can export data files to delimited text formats.

Better yet, make the data in the .csv informative so that things are as human-readable as possible. Instead of

Gender, Age, Education
0, 28, 2
1, 27, 1
0, 32, 3

use something more like

Gender, Age, Education
'Female', 28, 'Bachelor'
'Male', 27, 'High School'
'Female', 32, 'Postgraduate'

Any analysis program worth its salt (see link above) should be able to import that, and realise that Age is a numeric variable whereas the other two are categorical.

Maybe using scripts and distributing plain text data is already standard practice in political science: if so, great! If not, I think these would be simple steps you could take to improve the reproducibility of your science.

About Thomas Wallis

tom_wallis_reproducibilityThomas Wallis is a Humboldt Postdoctoral Fellow, at the Bethge and Wichmann Laboratories at the University of Tuebingen. His own research focuses on the question: How do we visually experience the world around us in a coherent way, simply from the patterns of photons hitting our retinae? He blogs at Practical Vision Science.

Advertisements
Tagged , , ,

One thought on “Guest Post: Two simple things to make your research more reproducible, by Thomas Wallis

  1. […] was invited to write a guest post for the blog Political Science Replication. For those who have been reading my blog for a while there’s not much new there, but feel […]

    Like

Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out / Change )

Twitter picture

You are commenting using your Twitter account. Log Out / Change )

Facebook photo

You are commenting using your Facebook account. Log Out / Change )

Google+ photo

You are commenting using your Google+ account. Log Out / Change )

Connecting to %s

%d bloggers like this: