Skip to content

Update example_vaccine.py #322

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
merged 1 commit into from
May 6, 2025
Merged

Update example_vaccine.py #322

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
8 changes: 3 additions & 5 deletions examples/covasim_/vaccinating_elderly/example_vaccine.py
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,4 +1,3 @@
# -*- coding: utf-8 -*-
import os
import logging
import pandas as pd
Expand Down Expand Up @@ -70,23 +69,22 @@ def setup_test_case(verbose: bool = False):
for outcome_variable, expected_effect in expected_outcome_effects.items():
base_test_case = BaseTestCase(treatment_variable=vaccine, outcome_variable=outcome_variable)
causal_test_case = CausalTestCase(
base_test_case=base_test_case, expected_causal_effect=expected_effect, control_value=0, treatment_value=1
base_test_case=base_test_case, expected_causal_effect=expected_effect,
)
# 7. Obtain the minimal adjustment set for the causal test case from the causal DAG
minimal_adjustment_set = causal_dag.identification(base_test_case)

# 8. Build statistical model using the Linear Regression estimator
linear_regression_estimator = LinearRegressionEstimator(
treatment=vaccine.name,
base_test_case=base_test_case,
treatment_value=1,
control_value=0,
adjustment_set=minimal_adjustment_set,
outcome=outcome_variable.name,
df=obs_df,
)

# 9. Execute test and save results in dict
causal_test_result = causal_test_case.execute_test(linear_regression_estimator, obs_df)
causal_test_result = causal_test_case.execute_test(linear_regression_estimator)

if verbose:
logging.info("Causation:\n%s", causal_test_result)
Expand Down