Fig 1.
Flow diagram depicting the 6 implementation framework reproducibility categories (left), their associated elements (center), and the scientific disciples from which references were identified (right).
Width of the lines are proportional to the number of references gathered from each scientific disciple to justify the inclusion of each category and element. Question 5.1, “Does the model in the publication use input data?” is omitted from the figure.
Fig 2.
The categories of the reproducibility framework are depicted for the example of a susceptible-infectious-recovered (SIR) model. The SIR model is described using equations in a model description (3) and implemented using a model implementation in the R language (“code”) (4). The code runs in an analytical software, in this case R (2), which runs in some computational environment with an operating system (1). The model implementation can import data (5) and operate on it. The model implementation produces results in the form of new data or visualizations that leave the analytical software (e.g., as PDF) and/or the computational environment (e.g., as printout). The experimental protocol describes the entire workflow and how the categories interact (6).
Table 1.
Implementation framework categories, elements, and relevant examples.