def run_experiment(path: Path, custom_settings: dict):
# 1. Initialize the experiment
exp = Experiment()
exp.load_config(config_file=path / 'config.json',
custom_settings=custom_settings)
if exp.config['model']['n_areas'] == "TBD":
exp.config['model']['n_areas'] = 2
# 2. Simulate contact areas
sim = Simulation(experiment=exp)
sim.run_simulation()
# 3. Define MCMC
mc = MCMC(data=sim, experiment=exp)
# 4. Warm-up sampler and sample from posterior
mc.warm_up()
mc.sample()
# 5. Evaluate ground truth
mc.eval_ground_truth()
# 6. Log sampling statistics and save samples to file
mc.save_samples(run=0)
exp = Experiment()
exp.load_config(
config_file='experiments/simulation/sim_exp2/config.json',
custom_settings={'model': {
'INHERITANCE': IN
}})
exp.log_experiment()
# 2. Simulate contact areas
sim = Simulation(experiment=exp)
sim.run_simulation()
sim.log_simulation()
# 3. Define MCMC
mc = MCMC(data=sim, experiment=exp)
mc.log_setup()
# Rerun experiment to check for consistency
for run in range(exp.config['mcmc']['N_RUNS']):
# 4. Sample from posterior
mc.warm_up()
mc.sample()
# 5. Evaluate ground truth
mc.eval_ground_truth()
# 6. Log sampling statistics and save samples to file
mc.log_statistics()
mc.save_samples(run=run)