This repository holds the processed data, modeling code, and figures for my thesis on ecological modeling of endocrine therapy resistance in breast cancer. It applies the logistic and Lotka-Volterra competition models of population growth from classic ecological theory (see e.g. Gotelli's Primer of Ecology). The Stan code is deeply inspired by Bob Carpenter's case study on ODEs in Stan using Lotka-Volterra dynamics.
The code for the image processing pipeline described in the paper, guidance on
how to run the code, and documentation of the methods used are described in
the image_processing directory of this repository. These details are
provided both in a directory-specific readme as well as in the methods section
of the associated paper. If you have additional questions, please contact
Zachary Susswein.