Simulations python3 code:

• spike_in_plots13_ordered.py contains code for five models of spiking in risk factors, including correlation calculation
• spike_in_plot_3loci.py is an example of three risk factors
• spike_in_plots_thresholdforfive.py is an example of a multifactorial threshold model
• spike_in_plots14_hetcalc.py is a failed attempt to employ a formula for the relative risk of the heterogeneity model

Rheumatoid arthritis python3 code:

• calc_risk_square_modelrandomizations.py is code for generating odds ratios, including for two permutation controls
• fewsnps_obstoexp_distribution.ipynb is a Jupyter notebook for matching known risk SNPs to additive or multiplicative effect, based on the output from calc_risk_square_modelrandomizations.py
• eira_randomised_distibutions.ipynb plots all SNPs from the output of calc_risk_square_modelrandomizations.py
• SE.ipynb plots the output from GEISA

Other:

• dr_tools.py is support code (library) for the other ones
• Model_I-V_sim.py does not produce plots, but instead allows the user to play around with numbers to try out the five models of spike_in_plots13_ordered.py

All programs run in Python 3.7, and some have been tested in Python 3.6.