Chapter 9 Assessing computational reproducibility

The basic workflow is simple:

• obtain the (pre-publication) manuscript and any materials
• analyze the README, and possibly appendixes and data sections, to identify all data sources, and all processing instructions
• obtain all code
• obtain all data
• execute all code
• compare the output with the manuscript tables, figures, and in-text

In practice, this quickly becomes more complicated, and requires a multitude of if-then instructions. At the LDI Lab, we have implemented the generic workflow within a system called Jira, which replicators use to go through the steps above.

A complete workflow for reproducibility checks

At each step, additional information is requested, mostly through in-app fields and questionnaires, but also via some external tools if the Jira app did not provide the functionality. At the end, a report is created by the replicator, identifying all steps taken, which steps succeeded, and the final outcome.

We will first describe the prototypical report and its elements, and then walk through the detailed steps of the replicator’s journey through the system. In our live training, replicators will also work on examples to “get the hang of it.”