Assessing parameter identifiability in compartmental dynamic models using a computational approach: application to infectious disease transmission models

BACKGROUND: Mathematical modeling is now frequently used in outbreak investigations to understand underlying mechanisms of infectious disease dynamics, assess patterns in epidemiological data, and forecast the trajectory of epidemics. However, the successful application of mathematical models to guide public health interventions lies in the ability to reliably estimate model parameters and their corresponding uncertainty. Here, we present and illustrate a simple computational method for assessing parameter identifiability in compartmental epidemic models. METHODS: We describe a parametric bootstrap approach to generate simulated data from dynamical systems to quantify parameter uncertainty and identifiability. We calculate confidence intervals and mean squared error of estimated parameter distributions to assess parameter identifiability. To demonstrate this approach, we begin with a low-complexity SEIR model and work through examples of increasingly more complex compartmental models that correspond with applications to pandemic influenza, Ebola, and Zika. RESULTS: Overall, parameter identifiability issues are more likely to arise with more complex models (based on number of equations/states and parameters). As the number of parameters being jointly estimated increases, the uncertainty surrounding estimated parameters tends to increase, on average, as well. We found that, in most cases, R(0) is often robust to parameter identifiability issues affecting individual parameters in the model. Despite large confidence intervals and higher mean squared error of other individual model parameters, R(0) can still be estimated with precision and accuracy. CONCLUSIONS: Because public health policies can be influenced by results of mathematical modeling studies, it is important to conduct parameter identifiability analyses prior to fitting the models to available data and to report parameter estimates with quantified uncertainty. The method described is helpful in these regards and enhances the essential toolkit for conducting model-based inferences using compartmental dynamic models. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12976-018-0097-6) contains supplementary material, which is available to authorized users.