  Interest in the study of in-host microbial communities has increased in
recent years due to our improved understanding of the communities' significant
role in host health. As a result, the ability to model these communities using
differential equations, for example, and analyze the results has become
increasingly relevant. The size of the models and limitations in data
collection among many other considerations require that we develop new
parameter estimation methods to address the challenges that arise when using
traditional parameter estimation methods for models of these in-host microbial
communities. In this work, we present the challenges that appear when applying
traditional parameter estimation techniques to differential equation models of
microbial communities, and we provide an original, alternative method to those
techniques. We show the derivation of our method and how our method avoids the
limitations of traditional techniques while including additional benefits. We
also provide simulation studies to demonstrate our method's viability, the
application of our method to a model of intestinal microbial communities to
demonstrate the insights that can be gained from our method, and sample code to
give readers the opportunity to apply our method to their own research.
