Continuous time HMM for Mycobacterium avium subsp. paratuberculosis infection progression.

This repository contains data and code associated with "Characterizing infectious disease progression through discrete states using Hidden Markov models"

Contents

Python scripts R scripts data plots

Python scripts

This direcory contains all scripts needed to run models, conduct the initialzation paramter sensitivity analysis (sensitivity_analysis.py), calculate bootstrap confidence intervals (bootstrap_CI.py), and run the diagnostic algorithm (test.sa and sim_hmm.py) to determine the utility of the hmm in predicting cow progression path.

R scripts

This directory contains the files necessary to process data, and produce plots.

Data

This directory contains all data necessary to run the models and produce all figures and tables. The data is organized by figure and table.