Pylint

Author: jmafoster1

causal_testing/estimation/abstract_regression_estimator.py

@@ -56,9 +56,14 @@ def __init__(
                 [base_test_case.treatment_variable.name] + sorted(list(adjustment_set)) + sorted(list(effect_modifiers))
             )
             self.formula = f"{base_test_case.outcome_variable.name} ~ {'+'.join(terms)}"
-        self.setup_formula()
+        self.setup_covariates()
 
-    def setup_formula(self):
+    def setup_covariates(self):
+        """
+        Parse the formula and set up the covariates from the design matrix so we can use them in the statsmodels array
+        API. This allows us to only parse the formula once, rather than using the formula API, which parses it every
+        time the regression model is fit, which can be a lot if using causal test adequacy.
+        """
         if self.df is not None:
             _, covariate_data = dmatrices(self.formula, self.df, return_type="dataframe")
             self.covariates = covariate_data.columns

causal_testing/estimation/linear_regression_estimator.py

@@ -92,7 +92,7 @@ def gp_formula(
         formula = gp.run_gp(ngen=ngen, pop_size=pop_size, num_offspring=num_offspring, seeds=seeds)
         formula = gp.simplify(formula)
         self.formula = f"{self.base_test_case.outcome_variable.name} ~ I({formula}) - 1"
-        self.setup_formula()
+        self.setup_covariates()
 
     def estimate_coefficient(self) -> EffectEstimate:
         """Estimate the unit average treatment effect of the treatment on the outcome. That is, the change in outcome

causal_testing/main.py

@@ -442,7 +442,6 @@ def save_results(self, results: List[CausalTestResult], output_path: str = None)
         result_index = 0
 
         for test_config in test_configs["tests"]:
-
             # Create a base output first of common entries
             base_output = {
                 "name": test_config["name"],

docs/source/tutorials/vaccinating_elderly/causal_test_results.json

@@ -7,8 +7,8 @@
     "expected_effect": {
       "cum_vaccinations": "NoEffect"
     },
-    "formula": "cum_vaccinations ~ max_doses",
     "alpha": 0.05,
+    "formula": "cum_vaccinations ~ max_doses",
     "skip": false,
     "passed": false,
     "result": {
@@ -35,8 +35,8 @@
     "expected_effect": {
       "cum_vaccinated": "NoEffect"
     },
-    "formula": "cum_vaccinated ~ max_doses",
     "alpha": 0.05,
+    "formula": "cum_vaccinated ~ max_doses",
     "skip": false,
     "passed": false,
     "result": {
@@ -63,8 +63,8 @@
     "expected_effect": {
       "cum_infections": "NoEffect"
     },
-    "formula": "cum_infections ~ max_doses",
     "alpha": 0.05,
+    "formula": "cum_infections ~ max_doses",
     "skip": false,
     "passed": false,
     "result": {
@@ -91,8 +91,8 @@
     "expected_effect": {
       "cum_vaccinations": "SomeEffect"
     },
-    "formula": "cum_vaccinations ~ vaccine",
     "alpha": 0.05,
+    "formula": "cum_vaccinations ~ vaccine",
     "skip": false,
     "passed": true,
     "result": {
@@ -119,8 +119,8 @@
     "expected_effect": {
       "cum_vaccinated": "SomeEffect"
     },
-    "formula": "cum_vaccinated ~ vaccine",
     "alpha": 0.05,
+    "formula": "cum_vaccinated ~ vaccine",
     "skip": false,
     "passed": true,
     "result": {
@@ -147,8 +147,8 @@
     "expected_effect": {
       "cum_infections": "SomeEffect"
     },
-    "formula": "cum_infections ~ vaccine",
     "alpha": 0.05,
+    "formula": "cum_infections ~ vaccine",
     "skip": false,
     "passed": true,
     "result": {
@@ -175,8 +175,8 @@
     "expected_effect": {
       "cum_vaccinated": "NoEffect"
     },
-    "formula": "cum_vaccinated ~ cum_vaccinations + vaccine",
     "alpha": 0.05,
+    "formula": "cum_vaccinated ~ cum_vaccinations + vaccine",
     "skip": false,
     "passed": false,
     "result": {
@@ -205,8 +205,8 @@
     "expected_effect": {
       "cum_infections": "NoEffect"
     },
-    "formula": "cum_infections ~ cum_vaccinations + vaccine",
     "alpha": 0.05,
+    "formula": "cum_infections ~ cum_vaccinations + vaccine",
     "skip": false,
     "passed": true,
     "result": {
@@ -235,8 +235,8 @@
     "expected_effect": {
       "cum_infections": "NoEffect"
     },
-    "formula": "cum_infections ~ cum_vaccinated + vaccine",
     "alpha": 0.05,
+    "formula": "cum_infections ~ cum_vaccinated + vaccine",
     "skip": false,
     "passed": true,
     "result": {