Abstract
This primer describes the statistical uncertainty in mechanistic models and provides R code to quantify it. We begin with an overview of mechanistic models for infectious disease, and then describe the sources of statistical uncertainty in the context of a case study on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We describe the statistical uncertainty as belonging to 3 categories: data uncertainty, stochastic uncertainty, and structural uncertainty. We demonstrate how to account for each of these via statistical uncertainty measures and sensitivity analyses broadly, as well as in a specific case study on estimating the basic reproductive number, ${R}_0$, for SARS-CoV-2.