WIP

Signed-off-by: Adam Li <[email protected]>

Author: adam2392

doc/references.bib

@@ -70,6 +70,28 @@ @inproceedings{Park2021conditional
   organization = {PMLR}
 }
 
+@article{peters2016causal,
+  title={Causal inference by using invariant prediction: identification and confidence intervals},
+  author={Peters, Jonas and B{\"u}hlmann, Peter and Meinshausen, Nicolai},
+  journal={Journal of the Royal Statistical Society Series B: Statistical Methodology},
+  volume={78},
+  number={5},
+  pages={947--1012},
+  year={2016},
+  publisher={Oxford University Press}
+}
+
+@article{shah2018goodness,
+  title={Goodness-of-fit tests for high dimensional linear models},
+  author={Shah, Rajen D and B{\"u}hlmann, Peter},
+  journal={Journal of the Royal Statistical Society Series B: Statistical Methodology},
+  volume={80},
+  number={1},
+  pages={113--135},
+  year={2018},
+  publisher={Oxford University Press}
+}
+
 @inproceedings{Runge2018cmi,
   title     = {Conditional independence testing based on a nearest-neighbor estimator of conditional mutual information},
   author    = {Runge, Jakob},

pywhy_stats/residual.py

@@ -0,0 +1,114 @@
+"""KSample testing for equality of (conditional) distributions.
+
+If the distributions are marginal distributions being compared, then
+the test is a standard two-sample test, where the KS statistic, or
+Mann-Whitney U statistic, is used to test for equality of distributions.
+
+If the distributions are conditional distributions being compared, then
+the test is a conditional two-sample test, where the KS statistic, or
+Mann-Whitney U statistic, is used to test for equality of the
+residual distributions, where the residuals are computed by regressing
+the target variable, Y, on the conditioning variable, X.
+
+The test statistic is described fully in :footcite:`peters2016causal`
+and :footcite:`shah2018goodness`.
+"""
+
+import numpy as np
+from scipy.stats import kstest
+
+from .pvalue_result import PValueResult
+
+
+def ksample(Y, Z):
+    stat, pval = kstest(Y[Z == 1], Y[Z == 0])
+
+    return PValueResult(pvalue=pval, statistic=stat)
+
+
+def condksample(Y, Z, X, residual_test="ks", target_predictor=None, combine_pvalues=True):
+    r"""
+    Calulates the 2-sample test statistic.
+
+    Parameters
+    ----------
+    Y : ndarray, shape (n_samples,)
+        Target or outcome features
+    X : ndarray, shape (n_samples, n_features)
+        Features to condition on
+    Z : list or ndarray, shape (n_samples,)
+        List of zeros and ones indicating which samples belong to
+        which groups.
+    target_predictor : sklearn.BaseEstimator, default=None
+        Method to predict the target given the covariates. If None,
+        uses a spline regression with 4 knots and degree 3 as
+        described in :footcite:`peters2016causal`.
+    residual_test : {"whitney_levene", "ks"}, default="ks"
+        Test of the residuals between the groups
+    combine_pvalues: bool, default=True
+        If True, returns hte minimum of the corrected pvalues.
+
+    Returns
+    -------
+    pvalue : float
+        The computed *k*-sample p-value.
+    r2 : float
+        r2 score of the regression fit
+    model : object
+        Fitted regresion model, if return_model is True
+    """
+    from sklearn.metrics import r2_score
+
+    if target_predictor is None:
+        from sklearn.linear_model import LinearRegression
+        from sklearn.model_selection import GridSearchCV
+        from sklearn.pipeline import Pipeline
+        from sklearn.preprocessing import SplineTransformer
+
+        pipe = Pipeline(
+            steps=[
+                ("spline", SplineTransformer(n_knots=4, degree=3)),
+                ("linear", LinearRegression()),
+            ]
+        )
+        param_grid = {
+            "spline__n_knots": [3, 5, 7, 9],
+        }
+        target_predictor = GridSearchCV(
+            pipe, param_grid, n_jobs=-2, refit=True, scoring="neg_mean_squared_error"
+        )
+
+    target_predictor.fit(X, Y)
+    Y_pred = target_predictor.predict(X)
+    residuals = Y - Y_pred
+    r2 = r2_score(Y, Y_pred)
+
+    if residual_test == "whitney_levene":
+        from scipy.stats import levene, mannwhitneyu
+
+        _, mean_pval = mannwhitneyu(
+            residuals[np.asarray(Z, dtype=bool)],
+            residuals[np.asarray(1 - Z, dtype=bool)],
+        )
+        _, var_pval = levene(
+            residuals[np.asarray(Z, dtype=bool)],
+            residuals[np.asarray(1 - Z, dtype=bool)],
+        )
+        # Correct for multiple tests
+        if combine_pvalues:
+            pval = min(mean_pval * 2, var_pval * 2, 1)
+        else:
+            pval = (min(mean_pval * 2, 1), min(var_pval * 2, 1))
+    elif residual_test == "ks":
+        from scipy.stats import kstest
+
+        _, pval = kstest(
+            residuals[np.asarray(Z, dtype=bool)],
+            residuals[np.asarray(1 - Z, dtype=bool)],
+        )
+    else:
+        raise ValueError(f"Test {residual_test} not a valid option.")
+
+    return PValueResult(
+        statistic=r2, pvalue=pval, additional_info={"target_predictor": target_predictor}
+    )