An implementation framework to improve the transparency and reproducibility of computational models of infectious diseases
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).