Mini Reprohack

Let's reproduce papers in the wild!

By Paola Corrales and Elio Campitelli

February 19, 2022

One of the best ways of learning what makes a reproducible project is to try to reproduce real life projects instead of toy examples. You’ll quickly learn what works and what doesn’t and pick up tools and workflows from others.

Therefore we propose this optional homework in which you will do just that. You can do it at any moment during the workshop. Some paper require using particular packages or technologies that you might not be familiar at the start of the workshop. Most of them should have readmes with instructions, but if you’re stuck, you can always ask for help in the #reprohack Slack channel or leave it for later.

Reprohack is a project that organises meetups in which a bunch of people get together to reproduce results. In their website they host a database of papers submitted by their authors. Papers that have been reviewed at least one have a “Mean reproducibility score” which will tell you roughly how easy it is to reproduce it. To get the code of a paper, you need to go to the “Code URL” link that’s on its respective reprohack page.

Below there’s a curated list of some papers for you to chose with a short description of what you can expect. You are free to browse the list of papers tagged with “R” and select anyone that piques your interest.

Optional: Submit a review!

You can submit a review of each paper in its respective Reprohack page. This is a set of structure questions that are then sent to the authors. You are encouraged to submit a review if you can.

Package installation (especially Linux)

When reproducing papers you will most likely need to install a whole lot of new packages. This can take quite a while if you are a Linux user because packages that ship FORTRAN, C++ or other code needs to be compiled.

If you want to speed things up, you can use the RStudio Package Manager repository, which offers pre-compiled binaries for several linux distributions. Go to this page for setup instructions.

Curated list of papers

Analytic Reproducibility In Articles Receiving Open Data Badges At The Journal Psychological Science: An Observational Study

Mean reproducibility score: 9,5/10
Number of reviews: 2

This is a highly polished project that uses Docker to run the code in a container and render the result automatically. It’s also a study about reproducibility so the meta aspect is hard to resist.

No Effect Of Nature Representations On State Anxiety, Actual And Perceived Noise

Mean reproducibility score: 5,0/10
Number of reviews: 1

This paper has code and data available, but it doesn’t use RMarkdown to produce results, nor any way of defining a stable computational environment. On top of that, the code is not portable and it has some errors. On the other hand, since it doesn’t use any complicated technology like docker or renv, all the moving pieces can be understood by anyone with enough familiarity with R. Although all the code is there, it’s not straightforward to run it or reproduce the results.

The Role Of Conidia In The Dispersal Of Ascochyta Rabiei

Mean reproducibility score: NA
Number of reviews: 0

This paper uses Docker completely. That’s to say, it comes with a docker image which ships the computational environment, as well as all the code and data. Unlike Analytic Reproducibility…, the docker image does not create the paper automatically. From the description, the authors had submitted other papers to Reprohack before and used what they learnt from the reviews to improve the reproducibility of this one.

Mental Health and Social Contact During the COVID-19 Pandemic: An Ecological Momentary Assessment Study

Mean reproducibility score: 7,0/10
Number of reviews: 1

This paper doesn’t define a table computational environment, but the code is almost fully portable and seems to run without errors. If you manage to install all the packages, you should be able to run it.

Where Should New Parkrun Events Be Located? Modelling The Potential Impact Of 200 New Events On Socio-Economic Inequalities In Access And Participation

Mean reproducibility score: 7,0/10
Number of reviews: 3

This paper is bundled into an RStudio project and the code is portable. The code will install packages if needed. Some possible problems is that it uses packages related to spatial analysis, some of which might require some special system dependencies. It also warns that the analysis might not run in a lightweight computer.