This lesson is still being designed and assembled (Pre-Alpha version)

Reproducibility Assessment: Glossary

Key Points

Code Inspection
  • Code inspection is the first step in reproducibility assessment. The inspection provides important information about the analytical workflow, computational requirements, and input data.

  • A main file contains essential code that facilitates reproducibility when more than one code file is required to repeat the analysis. The main file acts as the starting point in fully-automated push-button reproduction by running all code files in the proper sequence.

  • By provding the author’s contact information, computing requirements, and licensing terms, code header metadata signals to users of the author’s transparency and willingness to assist with reuse.

  • Non-executable comments in the code serve as a roadmap of the analytical workflow by identifying code segments and their purpose.

Code Execution
  • Executing code tests the reusability of the research compendium, which is a fundamental criterion of reproducibility.

  • Prior to running the code, the computing enviroment will need to meet the same or comparable techinical requirements as described in compendium documentation.

  • Simple errors that prevent code from fully executing can be easily addressed.

Output Review
  • Every table, figure, and in-text number in the manuscript should be accounted for in code outputs.

  • The curating for reproducibilty workflow includes identifying specific commands in code files that produce outputs, and then verifying that reported results can be reproduced using that code.

  • Curators should document discrepanices found during the code output and manuscript review process and take steps to address them.

Glossary

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