From 624fba0b04d5bcd46d6141d6fdf639bd376f3a17 Mon Sep 17 00:00:00 2001
From: JulioAPeraza <jpera054@fiu.edu>
Date: Tue, 2 Apr 2024 11:39:32 -0400
Subject: [PATCH 01/11] Add correction term for multiple contrasts in
 Stouffer's combination test

---
 pymare/estimators/combination.py       | 74 +++++++++++++++++++++++---
 pymare/tests/test_combination_tests.py | 38 +++++++++++++
 2 files changed, 106 insertions(+), 6 deletions(-)

diff --git a/pymare/estimators/combination.py b/pymare/estimators/combination.py
index f2ffabc..3d198e7 100644
--- a/pymare/estimators/combination.py
+++ b/pymare/estimators/combination.py
@@ -1,4 +1,5 @@
 """Estimators for combination (p/z) tests."""
+
 import warnings
 from abc import abstractmethod
 
@@ -110,17 +111,78 @@ class StoufferCombinationTest(CombinationTest):
     """
 
     # Maps Dataset attributes onto fit() args; see BaseEstimator for details.
-    _dataset_attr_map = {"z": "y", "w": "v"}
-
-    def fit(self, z, w=None):
+    _dataset_attr_map = {"z": "y", "w": "n", "g": "v"}
+
+    def _inflation_term(self, z, w, g):
+        """Calculate the variance inflation term for each group.
+
+        This term is used to adjust the variance of the combined z-scorem when
+        multiple sample from the same group are present.
+
+        Parameters
+        ----------
+        z : array-like
+            Array of z-values.
+        w : array-like
+            Array of weights.
+        g : array-like
+            Array of group labels.
+
+        Returns
+        -------
+        sigma : float
+            The variance inflation term.
+        """
+        # Centering
+        all_samples_same = np.all(np.equal(z, z[0]), axis=0).all()
+        if not all_samples_same:
+            # Only center if the samples are not all the same, to prevent division by zero
+            # when calculating the correlation matrix.
+            mean_sample = z.mean(0)
+            z = z - mean_sample  # This centering is problematic for N=2
+
+        # Use the value for one voxel, as all voxels have the same group and weight
+        groups = g[:, 0]
+        weights = w[:, 0]
+
+        # Loop over groups
+        unique_groups = np.unique(groups)
+
+        sigma = 0
+        for group in unique_groups:
+            group_indices = np.where(groups == group)[0]
+            group_z = z[group_indices]
+
+            # For groups with only one sample the contribution to the summand is 0
+            n_samples = len(group_indices)
+            if n_samples < 2:
+                continue
+
+            # Calculate the within group correlation matrix and select the non-diagonal elements
+            corr = np.corrcoef(group_z, rowvar=True)
+            upper_indices = np.triu_indices(n_samples, k=1)
+            non_diag_corr = 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):
         """Fit the estimator to z-values, optionally with weights."""
-        return super().fit(z, w=w)
+        return super().fit(z, w=w, g=g)
 
-    def p_value(self, z, w=None):
+    def p_value(self, z, w=None, g=None):
         """Calculate p-values."""
         if w is None:
             w = np.ones_like(z)
-        cz = (z * w).sum(0) / np.sqrt((w**2).sum(0))
+
+        # Calculate the variance inflation term
+        sigma = self._inflation_term(z, w, g) if g is not None else 0
+
+        variance = (w**2).sum(0) + sigma
+
+        cz = (z * w).sum(0) / np.sqrt(variance)
         return ss.norm.sf(cz)
 
 
diff --git a/pymare/tests/test_combination_tests.py b/pymare/tests/test_combination_tests.py
index feacbc9..1b123ff 100644
--- a/pymare/tests/test_combination_tests.py
+++ b/pymare/tests/test_combination_tests.py
@@ -1,4 +1,5 @@
 """Tests for pymare.estimators.combination."""
+
 import numpy as np
 import pytest
 import scipy.stats as ss
@@ -33,6 +34,43 @@ def test_combination_test(Cls, data, mode, expected):
     assert np.allclose(z, expected, atol=1e-5)
 
 
+def test_stouffer_adjusted():
+    """Test StoufferCombinationTest with weights and groups."""
+    # Test with weights and groups
+    data = np.array(
+        [
+            [2.1, 0.7, -0.2, 4.1, 3.8],
+            [1.1, 0.2, 0.4, 1.3, 1.5],
+            [-0.6, -1.6, -2.3, -0.8, -4.0],
+            [2.5, 1.7, 2.1, 2.3, 2.5],
+            [3.1, 2.7, 3.1, 3.3, 3.5],
+            [3.6, 3.2, 3.6, 3.8, 4.0],
+        ]
+    )
+    weights = np.tile(np.array([4, 3, 4, 10, 15, 10]), (data.shape[1], 1)).T
+    groups = np.tile(np.array([0, 0, 1, 2, 2, 2]), (data.shape[1], 1)).T
+
+    results = StoufferCombinationTest("directed").fit(z=data, w=weights, g=groups).params_
+    z = ss.norm.isf(results["p"])
+
+    z_expected = np.array([5.00088912, 3.70356943, 4.05465924, 5.4633001, 5.18927878])
+    assert np.allclose(z, z_expected, atol=1e-5)
+
+    # Test with weights and no groups. Limiting cases.
+    # Limiting case 1: all correlations are one.
+    n_maps_l1 = 5
+    common_sample = np.array([2.1, 0.7, -0.2])
+    data_l1 = np.tile(common_sample, (n_maps_l1, 1))
+    groups_l1 = np.tile(np.array([0, 0, 0, 0, 0]), (data_l1.shape[1], 1)).T
+
+    results_l1 = StoufferCombinationTest("directed").fit(z=data_l1, g=groups_l1).params_
+    z_l1 = ss.norm.isf(results_l1["p"])
+
+    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)
+
+
 @pytest.mark.parametrize("Cls,data,mode,expected", _params)
 def test_combination_test_from_dataset(Cls, data, mode, expected):
     """Test CombinationTest Estimators with PyMARE Datasets."""

From aa389e77eed611787159543a45ab60fc15469cfd Mon Sep 17 00:00:00 2001
From: JulioAPeraza <jpera054@fiu.edu>
Date: Tue, 2 Apr 2024 12:19:24 -0400
Subject: [PATCH 02/11] Update RTD yml

---
 .readthedocs.yml                       |  5 +++++
 pymare/estimators/combination.py       |  4 ++--
 pymare/tests/test_combination_tests.py | 20 ++++++++++----------
 3 files changed, 17 insertions(+), 12 deletions(-)

diff --git a/.readthedocs.yml b/.readthedocs.yml
index f994a7e..4e696ba 100644
--- a/.readthedocs.yml
+++ b/.readthedocs.yml
@@ -5,6 +5,11 @@
 # Required
 version: 2
 
+build:
+  os: "ubuntu-22.04"
+  tools:
+    python: "3.9"
+
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
   configuration: docs/conf.py
diff --git a/pymare/estimators/combination.py b/pymare/estimators/combination.py
index 3d198e7..61f18e9 100644
--- a/pymare/estimators/combination.py
+++ b/pymare/estimators/combination.py
@@ -116,8 +116,8 @@ class StoufferCombinationTest(CombinationTest):
     def _inflation_term(self, z, w, g):
         """Calculate the variance inflation term for each group.
 
-        This term is used to adjust the variance of the combined z-scorem when
-        multiple sample from the same group are present.
+        This term is used to adjust the variance of the combined z-score when
+        multiple sample come from the same group are present.
 
         Parameters
         ----------
diff --git a/pymare/tests/test_combination_tests.py b/pymare/tests/test_combination_tests.py
index 1b123ff..9f5f7e1 100644
--- a/pymare/tests/test_combination_tests.py
+++ b/pymare/tests/test_combination_tests.py
@@ -34,6 +34,16 @@ def test_combination_test(Cls, data, mode, expected):
     assert np.allclose(z, expected, atol=1e-5)
 
 
+@pytest.mark.parametrize("Cls,data,mode,expected", _params)
+def test_combination_test_from_dataset(Cls, data, mode, expected):
+    """Test CombinationTest Estimators with PyMARE Datasets."""
+    dset = Dataset(y=data)
+    est = Cls(mode).fit_dataset(dset)
+    results = est.summary()
+    z = ss.norm.isf(results.p)
+    assert np.allclose(z, expected, atol=1e-5)
+
+
 def test_stouffer_adjusted():
     """Test StoufferCombinationTest with weights and groups."""
     # Test with weights and groups
@@ -69,13 +79,3 @@ 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)
-
-
-@pytest.mark.parametrize("Cls,data,mode,expected", _params)
-def test_combination_test_from_dataset(Cls, data, mode, expected):
-    """Test CombinationTest Estimators with PyMARE Datasets."""
-    dset = Dataset(y=data)
-    est = Cls(mode).fit_dataset(dset)
-    results = est.summary()
-    z = ss.norm.isf(results.p)
-    assert np.allclose(z, expected, atol=1e-5)

From 3c8e58aa397645f220f48798a68443045261f939 Mon Sep 17 00:00:00 2001
From: JulioAPeraza <jpera054@fiu.edu>
Date: Tue, 2 Apr 2024 12:22:42 -0400
Subject: [PATCH 03/11] Update .readthedocs.yml

---
 .readthedocs.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.readthedocs.yml b/.readthedocs.yml
index 4e696ba..616b148 100644
--- a/.readthedocs.yml
+++ b/.readthedocs.yml
@@ -15,7 +15,6 @@ sphinx:
   configuration: docs/conf.py
 
 python:
-  version: 3.7
   install:
     - method: pip
       path: .

From 1973650dfaf91b77887a8d5ecc29051d22f47215 Mon Sep 17 00:00:00 2001
From: JulioAPeraza <jpera054@fiu.edu>
Date: Tue, 2 Apr 2024 12:22:44 -0400
Subject: [PATCH 04/11] Update combination.py

---
 pymare/estimators/combination.py | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/pymare/estimators/combination.py b/pymare/estimators/combination.py
index 61f18e9..8bcaf5b 100644
--- a/pymare/estimators/combination.py
+++ b/pymare/estimators/combination.py
@@ -134,12 +134,11 @@ def _inflation_term(self, z, w, g):
             The variance inflation term.
         """
         # Centering
+        # Only center if the samples are not all the same, to prevent division by zero
+        # when calculating the correlation matrix.
+        # This centering is problematic for N=2
         all_samples_same = np.all(np.equal(z, z[0]), axis=0).all()
-        if not all_samples_same:
-            # Only center if the samples are not all the same, to prevent division by zero
-            # when calculating the correlation matrix.
-            mean_sample = z.mean(0)
-            z = z - mean_sample  # This centering is problematic for N=2
+        z = z if all_samples_same else z - z.mean(0)
 
         # Use the value for one voxel, as all voxels have the same group and weight
         groups = g[:, 0]

From 919068490c582549bda4ad2e0a3d5d0c70a9ba33 Mon Sep 17 00:00:00 2001
From: JulioAPeraza <jpera054@fiu.edu>
Date: Tue, 2 Apr 2024 12:23:53 -0400
Subject: [PATCH 05/11] Update .readthedocs.yml

---
 .readthedocs.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.readthedocs.yml b/.readthedocs.yml
index 616b148..1d35214 100644
--- a/.readthedocs.yml
+++ b/.readthedocs.yml
@@ -20,4 +20,3 @@ python:
       path: .
       extra_requirements:
         - doc
-  system_packages: true

From c76a18878ab3465497a8d4a55beb5221ca4fe579 Mon Sep 17 00:00:00 2001
From: JulioAPeraza <jpera054@fiu.edu>
Date: Tue, 2 Apr 2024 12:30:45 -0400
Subject: [PATCH 06/11] Update setup.cfg

---
 setup.cfg | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.cfg b/setup.cfg
index 17959f6..a74a38a 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -57,7 +57,7 @@ doc =
     sphinx>=3.5
     sphinx-argparse
     sphinx-copybutton
-    sphinx_gallery==0.10.1
+    sphinx_gallery
     sphinx_rtd_theme
     sphinxcontrib-bibtex
 tests =

From 23b1e2e758714baf8906f41511d0227391319360 Mon Sep 17 00:00:00 2001
From: JulioAPeraza <jpera054@fiu.edu>
Date: Tue, 2 Apr 2024 12:49:38 -0400
Subject: [PATCH 07/11] Update testing.yml

---
 .github/workflows/testing.yml | 45 ++++++++++++++++-------------------
 1 file changed, 21 insertions(+), 24 deletions(-)

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index 050df84..db78a6c 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -6,10 +6,7 @@ on:
       - "master"
   pull_request:
     branches:
-      - '*'
-  schedule:
-    # Run tests every Sunday at 12am
-    - cron: '0 0 * * 0'
+      - "*"
 
 concurrency:
   group: environment-${{ github.ref }}
@@ -28,46 +25,46 @@ jobs:
       - id: result_step
         uses: mstachniuk/ci-skip@master
         with:
-          commit-filter: '[skip ci];[ci skip];[skip github]'
-          commit-filter-separator: ';'
+          commit-filter: "[skip ci];[ci skip];[skip github]"
+          commit-filter-separator: ";"
 
   run_tests:
     needs: check_skip
     if: ${{ needs.check_skip.outputs.skip == 'false' }}
     runs-on: ${{ matrix.os }}
     strategy:
-        fail-fast: false
-        matrix:
-            os: ["ubuntu-latest", "macos-latest"]
-            python-version: ["3.6", "3.7", "3.8", "3.9"]
-            include:
-              # ubuntu-20.04 is used only to test python 3.6
-              - os: "ubuntu-20.04"
-                python-version: "3.6"
-            exclude:
-              # ubuntu-latest does not support python 3.6
-              - os: "ubuntu-latest"
-                python-version: "3.6"
+      fail-fast: false
+      matrix:
+        os: ["ubuntu-latest", "macos-latest"]
+        python-version: ["3.6", "3.7", "3.8", "3.9"]
+        include:
+          # ubuntu-20.04 is used only to test python 3.6
+          - os: "ubuntu-20.04"
+            python-version: "3.6"
+        exclude:
+          # ubuntu-latest does not support python 3.6
+          - os: "ubuntu-latest"
+            python-version: "3.6"
     name: ${{ matrix.os }} with Python ${{ matrix.python-version }}
     defaults:
       run:
         shell: bash
     steps:
       - uses: actions/checkout@v2
-      - name: 'Set up python'
+      - name: "Set up python"
         uses: actions/setup-python@v2
         with:
-            python-version: ${{ matrix.python-version }}
-      - name: 'Display Python version'
+          python-version: ${{ matrix.python-version }}
+      - name: "Display Python version"
         shell: bash {0}
         run: python -c "import sys; print(sys.version)"
-      - name: 'Install PyMARE'
+      - name: "Install PyMARE"
         shell: bash {0}
         run: pip install -e .[tests,stan]
-      - name: 'Run tests'
+      - name: "Run tests"
         shell: bash {0}
         run: python -m pytest --pyargs pymare --cov=pymare
-      - name: 'Upload coverage to CodeCov'
+      - name: "Upload coverage to CodeCov"
         uses: codecov/codecov-action@v1
         if: success()
 

From cd291f1b2d8564c5979621babbf9851845e4f480 Mon Sep 17 00:00:00 2001
From: JulioAPeraza <jpera054@fiu.edu>
Date: Tue, 2 Apr 2024 12:52:21 -0400
Subject: [PATCH 08/11] Update testing.yml

---
 .github/workflows/testing.yml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index db78a6c..53e6630 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -7,6 +7,9 @@ on:
   pull_request:
     branches:
       - "*"
+  schedule:
+    # Run tests every Sunday at 12am
+    - cron: "0 0 * * 0"
 
 concurrency:
   group: environment-${{ github.ref }}

From 91880ee179d7c465e6f16d4246c4d123dec7770e Mon Sep 17 00:00:00 2001
From: JulioAPeraza <jpera054@fiu.edu>
Date: Tue, 2 Apr 2024 12:56:38 -0400
Subject: [PATCH 09/11] Run black

---
 pymare/__init__.py                          | 1 +
 pymare/datasets/__init__.py                 | 1 +
 pymare/datasets/metadat.py                  | 1 +
 pymare/effectsize/__init__.py               | 1 +
 pymare/effectsize/expressions.py            | 1 +
 pymare/estimators/__init__.py               | 1 +
 pymare/results.py                           | 1 +
 pymare/tests/conftest.py                    | 1 +
 pymare/tests/test_core.py                   | 1 +
 pymare/tests/test_datasets.py               | 1 +
 pymare/tests/test_effectsize_base.py        | 1 +
 pymare/tests/test_effectsize_expressions.py | 1 +
 pymare/tests/test_estimators.py             | 1 +
 pymare/tests/test_results.py                | 1 +
 pymare/tests/test_stan_estimators.py        | 1 +
 pymare/tests/test_stats.py                  | 1 +
 pymare/tests/test_utils.py                  | 1 +
 pymare/utils.py                             | 1 +
 18 files changed, 18 insertions(+)

diff --git a/pymare/__init__.py b/pymare/__init__.py
index 6f112e9..8127a73 100644
--- a/pymare/__init__.py
+++ b/pymare/__init__.py
@@ -1,4 +1,5 @@
 """PyMARE: Python Meta-Analysis & Regression Engine."""
+
 import sys
 import warnings
 
diff --git a/pymare/datasets/__init__.py b/pymare/datasets/__init__.py
index d4c0a6e..01d3f4d 100644
--- a/pymare/datasets/__init__.py
+++ b/pymare/datasets/__init__.py
@@ -1,4 +1,5 @@
 """Open meta-analytic datasets."""
+
 from .metadat import michael2013
 
 __all__ = [
diff --git a/pymare/datasets/metadat.py b/pymare/datasets/metadat.py
index f3fcfd5..4592520 100644
--- a/pymare/datasets/metadat.py
+++ b/pymare/datasets/metadat.py
@@ -1,4 +1,5 @@
 """Datasets from metadat."""
+
 import json
 import os.path as op
 
diff --git a/pymare/effectsize/__init__.py b/pymare/effectsize/__init__.py
index d0a5424..7dbfd8e 100644
--- a/pymare/effectsize/__init__.py
+++ b/pymare/effectsize/__init__.py
@@ -1,4 +1,5 @@
 """Tools for converting between effect-size measures."""
+
 from .base import (
     OneSampleEffectSizeConverter,
     TwoSampleEffectSizeConverter,
diff --git a/pymare/effectsize/expressions.py b/pymare/effectsize/expressions.py
index 2a56a61..6cc1eeb 100644
--- a/pymare/effectsize/expressions.py
+++ b/pymare/effectsize/expressions.py
@@ -1,4 +1,5 @@
 """Statistical expressions."""
+
 import json
 from collections import defaultdict
 from itertools import chain
diff --git a/pymare/estimators/__init__.py b/pymare/estimators/__init__.py
index c964654..5b48193 100644
--- a/pymare/estimators/__init__.py
+++ b/pymare/estimators/__init__.py
@@ -1,4 +1,5 @@
 """Estimators for meta-analyses and meta-regressions."""
+
 from .combination import FisherCombinationTest, StoufferCombinationTest
 from .estimators import (
     DerSimonianLaird,
diff --git a/pymare/results.py b/pymare/results.py
index b84b1f6..31c7d3e 100644
--- a/pymare/results.py
+++ b/pymare/results.py
@@ -1,4 +1,5 @@
 """Tools for representing and manipulating meta-regression results."""
+
 import itertools
 from functools import lru_cache
 from inspect import getfullargspec
diff --git a/pymare/tests/conftest.py b/pymare/tests/conftest.py
index 6a3e988..cce93c8 100644
--- a/pymare/tests/conftest.py
+++ b/pymare/tests/conftest.py
@@ -1,4 +1,5 @@
 """Data for tests."""
+
 import numpy as np
 import pytest
 
diff --git a/pymare/tests/test_core.py b/pymare/tests/test_core.py
index 8ce58b1..12fd1b4 100644
--- a/pymare/tests/test_core.py
+++ b/pymare/tests/test_core.py
@@ -1,4 +1,5 @@
 """Tests for pymare.core."""
+
 import numpy as np
 import pandas as pd
 import pytest
diff --git a/pymare/tests/test_datasets.py b/pymare/tests/test_datasets.py
index fcf312f..26859e1 100644
--- a/pymare/tests/test_datasets.py
+++ b/pymare/tests/test_datasets.py
@@ -1,4 +1,5 @@
 """Tests for the pymare.datasets module."""
+
 import pandas as pd
 
 from pymare import datasets
diff --git a/pymare/tests/test_effectsize_base.py b/pymare/tests/test_effectsize_base.py
index 0616fa8..515b8cb 100644
--- a/pymare/tests/test_effectsize_base.py
+++ b/pymare/tests/test_effectsize_base.py
@@ -1,4 +1,5 @@
 """Tests for pymare.effectsize.base."""
+
 import numpy as np
 import pandas as pd
 import pytest
diff --git a/pymare/tests/test_effectsize_expressions.py b/pymare/tests/test_effectsize_expressions.py
index b28a675..9c33c9d 100644
--- a/pymare/tests/test_effectsize_expressions.py
+++ b/pymare/tests/test_effectsize_expressions.py
@@ -1,4 +1,5 @@
 """Tests for pymare.effectsize.expressions."""
+
 import pytest
 from sympy import Symbol
 from sympy.core.sympify import SympifyError
diff --git a/pymare/tests/test_estimators.py b/pymare/tests/test_estimators.py
index 339e163..8b6fece 100644
--- a/pymare/tests/test_estimators.py
+++ b/pymare/tests/test_estimators.py
@@ -1,4 +1,5 @@
 """Tests for pymare.estimators.estimators."""
+
 import numpy as np
 import pytest
 
diff --git a/pymare/tests/test_results.py b/pymare/tests/test_results.py
index 2baf3bd..5b00742 100644
--- a/pymare/tests/test_results.py
+++ b/pymare/tests/test_results.py
@@ -1,4 +1,5 @@
 """Tests for pymare.results."""
+
 import numpy as np
 import pytest
 
diff --git a/pymare/tests/test_stan_estimators.py b/pymare/tests/test_stan_estimators.py
index c685ecd..71efc28 100644
--- a/pymare/tests/test_stan_estimators.py
+++ b/pymare/tests/test_stan_estimators.py
@@ -1,4 +1,5 @@
 """Tests for estimators that use stan."""
+
 import pytest
 
 from pymare.estimators import StanMetaRegression
diff --git a/pymare/tests/test_stats.py b/pymare/tests/test_stats.py
index c350f3f..f01d434 100644
--- a/pymare/tests/test_stats.py
+++ b/pymare/tests/test_stats.py
@@ -1,4 +1,5 @@
 """Tests for pymare.stats."""
+
 from pymare import stats
 
 
diff --git a/pymare/tests/test_utils.py b/pymare/tests/test_utils.py
index 474b8f8..7ff794c 100644
--- a/pymare/tests/test_utils.py
+++ b/pymare/tests/test_utils.py
@@ -1,4 +1,5 @@
 """Tests for pymare.utils."""
+
 import os.path as op
 
 import numpy as np
diff --git a/pymare/utils.py b/pymare/utils.py
index b159a48..d03ea9a 100644
--- a/pymare/utils.py
+++ b/pymare/utils.py
@@ -1,4 +1,5 @@
 """Miscellaneous utility functions."""
+
 import os.path as op
 
 import numpy as np

From a718ac4c485fced7c67f414a2e394c7509edacc5 Mon Sep 17 00:00:00 2001
From: JulioAPeraza <jpera054@fiu.edu>
Date: Tue, 2 Apr 2024 15:03:34 -0400
Subject: [PATCH 10/11] Make sure solutions and symbols match

---
 pymare/effectsize/base.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pymare/effectsize/base.py b/pymare/effectsize/base.py
index ac15b9a..68d8642 100644
--- a/pymare/effectsize/base.py
+++ b/pymare/effectsize/base.py
@@ -68,7 +68,7 @@ def solve_system(system, known_vars=None):
 
     # solver will return a dict if there's only one non-dummy expression
     if isinstance(solutions, dict):
-        solutions = [list(solutions.values())]
+        solutions = [[solutions[s] for s in symbols]]
 
     # Prepare the dummy list and data args in a fixed order
     dummy_list = list(dummies)

From 539974edea25fe4249b3584eef0b4a74c3bdd391 Mon Sep 17 00:00:00 2001
From: JulioAPeraza <jpera054@fiu.edu>
Date: Fri, 5 Apr 2024 11:59:45 -0400
Subject: [PATCH 11/11] Update combination.py

---
 pymare/estimators/combination.py | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/pymare/estimators/combination.py b/pymare/estimators/combination.py
index 8bcaf5b..6f9f41a 100644
--- a/pymare/estimators/combination.py
+++ b/pymare/estimators/combination.py
@@ -117,15 +117,15 @@ def _inflation_term(self, z, w, g):
         """Calculate the variance inflation term for each group.
 
         This term is used to adjust the variance of the combined z-score when
-        multiple sample come from the same group are present.
+        multiple sample come from the same study.
 
         Parameters
         ----------
-        z : array-like
+        z : :obj:`numpy.ndarray` of shape (n, d)
             Array of z-values.
-        w : array-like
+        w : :obj:`numpy.ndarray` of shape (n, d)
             Array of weights.
-        g : array-like
+        g : :obj:`numpy.ndarray` of shape (n, d)
             Array of group labels.
 
         Returns
@@ -133,14 +133,13 @@ def _inflation_term(self, z, w, g):
         sigma : float
             The variance inflation term.
         """
-        # Centering
         # Only center if the samples are not all the same, to prevent division by zero
         # when calculating the correlation matrix.
         # This centering is problematic for N=2
         all_samples_same = np.all(np.equal(z, z[0]), axis=0).all()
         z = z if all_samples_same else z - z.mean(0)
 
-        # Use the value for one voxel, as all voxels have the same group and weight
+        # Use the value from one feature, as all features have the same groups and weights
         groups = g[:, 0]
         weights = w[:, 0]
 
@@ -157,7 +156,7 @@ def _inflation_term(self, z, w, g):
             if n_samples < 2:
                 continue
 
-            # Calculate the within group correlation matrix and select the non-diagonal elements
+            # Calculate the within group correlation matrix and sum the non-diagonal elements
             corr = np.corrcoef(group_z, rowvar=True)
             upper_indices = np.triu_indices(n_samples, k=1)
             non_diag_corr = corr[upper_indices]
@@ -168,7 +167,7 @@ def _inflation_term(self, z, w, g):
         return sigma
 
     def fit(self, z, w=None, g=None):
-        """Fit the estimator to z-values, optionally with weights."""
+        """Fit the estimator to z-values, optionally with weights and groups."""
         return super().fit(z, w=w, g=g)
 
     def p_value(self, z, w=None, g=None):
@@ -176,9 +175,10 @@ def p_value(self, z, w=None, g=None):
         if w is None:
             w = np.ones_like(z)
 
-        # Calculate the variance inflation term
+        # 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
 
+        # The sum of diagonal elements of sigma is given by (w**2).sum(0).
         variance = (w**2).sum(0) + sigma
 
         cz = (z * w).sum(0) / np.sqrt(variance)