HMGPS2 - Analysis of Microbial Dynamics

MATLAB scripts are provided here for performing the GP-based analysis of microbial dynamics. Scripts are provided to perform the parameter estimation for Figure 4 in the main paper (hmp_4comp_paramest.m), as well as the component selection presented in Supplemental Table S6 (hmp_model_selection.m). Other scripts provide auxiliary functions used by these two main scripts, including MCMC chain generation, and estimation of Bayes Factors. More details can be found in readme.txt and in the scripts themselves. A demo (demo.m) is also included which constructs a mock dataset with known dynamics and performs model selection and parameter inference for it. MATLAB and GPstuff 4.6 are required.