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)
for S in SETUP:
# Update config information according to the current setup
custom_settings = {
'simulation': {
'i_contact': I_CONTACT[S[0]],
'e_contact': E_CONTACT[S[0]],
'STRENGTH': S[0],
'area': S[1]
}
}
# 1. Initialize the experiment
exp = Experiment()
exp.load_config(
config_file='experiments/simulation/sim_exp1/config.json',
custom_settings=custom_settings)
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']):
from sbayes.experiment_setup import Experiment
from sbayes.simulation import Simulation
from sbayes.mcmc_setup import MCMC
if __name__ == '__main__':
# When performing the MCMC iterate over different setups (inheritance)
INHERITANCE = [False, True]
for IN in INHERITANCE:
# 1. Initialize the experiment
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']):
from sbayes.experiment_setup import Experiment
from sbayes.simulation import Simulation
from sbayes.mcmc_setup import MCMC
if __name__ == '__main__':
import os
# 1. Initialize the experiment
exp = Experiment()
exp.load_config(config_file='experiments/simulation/sim_exp3/config.json')
exp.log_experiment()
# 2. Simulate contact areas
sim = Simulation(experiment=exp)
sim.run_simulation()
sim.log_simulation()
# Iterate over different setups (different number of areas)
NUMBER_AREAS = range(1, 8)
for N in NUMBER_AREAS:
# Update config information according to the current setup
exp.config['model']['n_areas'] = N
# 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']):
from sbayes.experiment_setup import Experiment
from sbayes.load_data import Data
from sbayes.mcmc_setup import MCMC
if __name__ == '__main__':
# Initialize the experiment
exp = Experiment()
exp.load_config(config_file='experiments/south_america/config.json')
exp.log_experiment()
# Load Data
dat = Data(experiment=exp)
# Features
dat.load_features()
# Counts for priors
dat.load_universal_counts()
dat.load_inheritance_counts()
# Log
dat.log_loading()
NUMBER_AREAS = range(1, 8)
# Rerun experiment to check for consistency
for run in range(exp.config['mcmc']['N_RUNS']):
for N in NUMBER_AREAS:
# Update config information according to the current setup
exp.config['model']['N_AREAS'] = N
from sbayes.experiment_setup import Experiment
from sbayes.load_data import Data
from sbayes.mcmc_setup import MCMC
if __name__ == '__main__':
# Initialize the experiment
exp = Experiment()
exp.load_config(config_file='experiments/balkan/config.json')
exp.log_experiment()
# Load Data
dat = Data(experiment=exp)
# Features
dat.load_features()
# Counts for priors
dat.load_universal_counts()
dat.load_inheritance_counts()
# Log
dat.log_loading()
NUMBER_AREAS = range(1, 8)
# Rerun experiment to check for consistency
for run in range(exp.config['mcmc']['N_RUNS']):
for N in NUMBER_AREAS:
# Update config information according to the current setup
exp.config['model']['N_AREAS'] = N
from sbayes.experiment_setup import Experiment
from sbayes.simulation import Simulation
from sbayes.mcmc_setup import MCMC
if __name__ == '__main__':
# When performing the MCMC iterate over different setups (inheritance)
INHERITANCE = [False, True]
for IN in INHERITANCE:
# 1. Initialize the experiment
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']):
N_BACKGROUND = 20
N_AREA = 10
# Spatial distribution
BBOX = Rectangle(left=0, bottom=0, right=100, top=100)
AREA_MEAN = np.array([35, 60])
AREA_STD = 10
# Generate spatial locations
background_locations = generate_background_locations(N_BACKGROUND, BBOX)
area_locations = generate_area_locations(N_AREA, AREA_MEAN, AREA_STD)
plot_locations(background_locations, area_locations)
# 1. Initialize the experiment
exp = Experiment()
exp.load_config(config_file='../config.json')
exp.log_experiment()
# When simulating iterate over different setups (different areas and strengths of contact)
I_CONTACT = [1.5, 2, 2.5]
E_CONTACT = [1.25, 0.75, 0.25]
STRENGTH = range(len(E_CONTACT))
AREA = [4, 6, 3, 8]
SETUP = list(itertools.product(STRENGTH, AREA))
for S in SETUP:
# Update config information according to the current setup
exp.config['simulation']['I_CONTACT'] = I_CONTACT[S[0]]
exp.config['simulation']['E_CONTACT'] = E_CONTACT[S[0]]
exp.config['simulation']['STRENGTH'] = S[0]