Support precomputed correlation matrix for calculating variance inflation term in Stouffers (#121)

* Support precomputed correlation matrix for calculating variance inflation term in Stouffers

* Update test_results.py

* Switch to macos-12 per actions/setup-python#850

* Update test_results.py

Author: JulioAPeraza

.github/workflows/testing.yml

@@ -38,7 +38,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: ["ubuntu-latest", "macos-latest"]
+        os: ["ubuntu-latest", "macos-12"]
         python-version: ["3.8", "3.9", "3.10", "3.11"]
 
     name: ${{ matrix.os }} with Python ${{ matrix.python-version }}

pymare/estimators/combination.py

@@ -113,7 +113,7 @@ class StoufferCombinationTest(CombinationTest):
     # Maps Dataset attributes onto fit() args; see BaseEstimator for details.
     _dataset_attr_map = {"z": "y", "w": "n", "g": "v"}
 
-    def _inflation_term(self, z, w, g):
+    def _inflation_term(self, z, w, g, corr=None):
         """Calculate the variance inflation term for each group.
 
         This term is used to adjust the variance of the combined z-score when
@@ -127,6 +127,8 @@ def _inflation_term(self, z, w, g):
             Array of weights.
         g : :obj:`numpy.ndarray` of shape (n, d)
             Array of group labels.
+        corr : :obj:`numpy.ndarray` of shape (n, n), optional
+            The correlation matrix of the z-values. If None, it will be calculated.
 
         Returns
         -------
@@ -157,26 +159,38 @@ def _inflation_term(self, z, w, g):
                 continue
 
             # Calculate the within group correlation matrix and sum the non-diagonal elements
-            corr = np.corrcoef(group_z, rowvar=True)
+            if corr is None:
+                if z.shape[1] < 2:
+                    raise ValueError("The number of features must be greater than 1.")
+                group_corr = np.corrcoef(group_z, rowvar=True)
+            else:
+                group_corr = corr[group_indices][:, group_indices]
+
             upper_indices = np.triu_indices(n_samples, k=1)
-            non_diag_corr = corr[upper_indices]
+            non_diag_corr = group_corr[upper_indices]
             w_i, w_j = weights[upper_indices[0]], weights[upper_indices[1]]
 
             sigma += (2 * w_i * w_j * non_diag_corr).sum()
 
         return sigma
 
-    def fit(self, z, w=None, g=None):
+    def fit(self, z, w=None, g=None, corr=None):
         """Fit the estimator to z-values, optionally with weights and groups."""
-        return super().fit(z, w=w, g=g)
+        return super().fit(z, w=w, g=g, corr=corr)
 
-    def p_value(self, z, w=None, g=None):
+    def p_value(self, z, w=None, g=None, corr=None):
         """Calculate p-values."""
         if w is None:
             w = np.ones_like(z)
 
+        if g is None and corr is not None:
+            warnings.warn("Correlation matrix provided without groups. Ignoring.")
+
+        if g is not None and corr is not None and g.shape[0] != corr.shape[0]:
+            raise ValueError("Group labels must have the same length as the correlation matrix.")
+
         # Calculate the variance inflation term, sum of non-diagonal elements of sigma.
-        sigma = self._inflation_term(z, w, g) if g is not None else 0
+        sigma = self._inflation_term(z, w, g, corr=corr) if g is not None else 0
 
         # The sum of diagonal elements of sigma is given by (w**2).sum(0).
         variance = (w**2).sum(0) + sigma

pymare/tests/test_combination_tests.py

@@ -79,3 +79,28 @@ def test_stouffer_adjusted():
     sigma_l1 = n_maps_l1 * (n_maps_l1 - 1)  # Expected inflation term
     z_expected_l1 = n_maps_l1 * common_sample / np.sqrt(n_maps_l1 + sigma_l1)
     assert np.allclose(z_l1, z_expected_l1, atol=1e-5)
+
+    # Test with correlation matrix and groups.
+    data_corr = data - data.mean(0)
+    corr = np.corrcoef(data_corr, rowvar=True)
+    results_corr = (
+        StoufferCombinationTest("directed").fit(z=data, w=weights, g=groups, corr=corr).params_
+    )
+    z_corr = ss.norm.isf(results_corr["p"])
+
+    z_corr_expected = np.array([5.00088912, 3.70356943, 4.05465924, 5.4633001, 5.18927878])
+    assert np.allclose(z_corr, z_corr_expected, atol=1e-5)
+
+    # Test with no correlation matrix and groups, but only one feature.
+    with pytest.raises(ValueError):
+        StoufferCombinationTest("directed").fit(z=data[:, :1], w=weights[:, :1], g=groups)
+
+    # Test with correlation matrix and groups of different shapes.
+    with pytest.raises(ValueError):
+        StoufferCombinationTest("directed").fit(z=data, w=weights, g=groups, corr=corr[:-2, :-2])
+
+    # Test with correlation matrix and no groups.
+    results1 = StoufferCombinationTest("directed").fit(z=_z1, corr=corr).params_
+    z1 = ss.norm.isf(results1["p"])
+
+    assert np.allclose(z1, [4.69574], atol=1e-5)

pymare/tests/test_results.py

@@ -87,8 +87,9 @@ def test_combination_test_results_from_arrays(dataset):
 
     # fit overwrites dataset_ attribute with None
     assert fitted_estimator.dataset_ is None
+
     # fit_dataset overwrites it with the Dataset
-    fitted_estimator.fit_dataset(dataset)
+    fitted_estimator.fit_dataset(Dataset(dataset.y))
     assert isinstance(fitted_estimator.dataset_, Dataset)
     # fit sets it back to None
     fitted_estimator.fit(z=dataset.y)