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.