def main():
global options
D1 = options.disease1
D2 = options.disease2
# Import EMR data into database
database = EMRDatabase()
database.import_data(options.emr_data_file,
options.diseases_file,
options.code2disease_file)
# Instantiate the OptimizeLogLikelihood class
opt_log_likelihood = OptimizeLogLikelihood(options.verbose)
opt_log_likelihood.set_opt_method(options.opt_method)
opt_log_likelihood.set_use_random_seed(options.use_random_seed)
opt_log_likelihood.setup_log_likelihood_func(database,
D1, D2,
options.tau1,
options.tau2,
options.overlap_type,
options.threshold_type,
options.prevalence_file,
options.norm_prval_method)
# Get optimized parameters
_, optimized_param, _ = opt_log_likelihood.run()
# Compute optimization paths
optimization_paths = []
for n in range(options.num_paths):
_, _, path = opt_log_likelihood.run(save_path=True)
optimization_paths.append(path)
log_likelihood_func = opt_log_likelihood.get_log_likelihood_func()
plot = __plot_contour(log_likelihood_func,
optimized_param,
optimization_paths,
options.tau1,
options.tau2,
options.overlap_type,
options.threshold_type,
options.norm_prval_method,
options.verbose)
plt.show()
def main():
global options
D1 = options.disease1
D2 = options.disease2
# Import EMR data into database
database = EMRDatabase()
database.import_data(options.emr_data_file, options.diseases_file,
options.code2disease_file)
# Instantiate the OptimizeLogLikelihood class
opt_log_likelihood = OptimizeLogLikelihood(options.verbose)
opt_log_likelihood.set_opt_method(options.opt_method)
opt_log_likelihood.set_use_random_seed(options.use_random_seed)
opt_log_likelihood.setup_log_likelihood_func(database, D1, D2,
options.tau1, options.tau2,
options.overlap_type,
options.threshold_type,
options.prevalence_file,
options.norm_prval_method)
# Get optimized parameters
_, optimized_param, _ = opt_log_likelihood.run()
# Compute optimization paths
optimization_paths = []
for n in range(options.num_paths):
_, _, path = opt_log_likelihood.run(save_path=True)
optimization_paths.append(path)
log_likelihood_func = opt_log_likelihood.get_log_likelihood_func()
plot = __plot_contour(log_likelihood_func, optimized_param,
optimization_paths, options.tau1, options.tau2,
options.overlap_type, options.threshold_type,
options.norm_prval_method, options.verbose)
plt.show()
