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Interest in the study of in-host microbial communities has increased inrecent years due to our improved understanding of the communities' significantrole in host health. As a result, the ability to model these communities usingdifferential equations, for example, and analyze the results has becomeincreasingly relevant. The size of the models and limitations in datacollection among many other considerations require that we develop newparameter estimation methods to address the challenges that arise when usingtraditional parameter estimation methods for models of these in-host microbialcommunities. In this work, we present the challenges that appear when applyingtraditional parameter estimation techniques to differential equation models ofmicrobial communities, and we provide an original, alternative method to thosetechniques. We show the derivation of our method and how our method avoids thelimitations of traditional techniques while including additional benefits. Wealso provide simulation studies to demonstrate our method's viability, theapplication of our method to a model of intestinal microbial communities todemonstrate the insights that can be gained from our method, and sample code togive readers the opportunity to apply our method to their own research.

Robust Parameter Estimation for Biological Systems: A Study on the Dynamics of Microbial Communities