PyMARE 0.0.10__tar.gz → 0.0.11__tar.gz

{PyMARE-0.0.10 → pymare-0.0.11}/MANIFEST.in

@@ -1,2 +1,3 @@
 include versioneer.py
 include pymare/_version.py
+recursive-include pymare *.stan

pymare-0.0.11/PKG-INFO

@@ -0,0 +1,99 @@
+Metadata-Version: 2.4
+Name: PyMARE
+Version: 0.0.11
+Summary: PyMARE: Python Meta-Analysis & Regression Engine
+Home-page: https://github.com/neurostuff/PyMARE
+Author: PyMARE developers
+Author-email: tsalo006@fiu.edu
+Maintainer: Taylor Salo
+Maintainer-email: tsalo006@fiu.edu
+License: MIT
+Classifier: Development Status :: 3 - Alpha
+Classifier: Environment :: Console
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Topic :: Scientific/Engineering
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy>=1.8.0
+Requires-Dist: pandas
+Requires-Dist: scipy
+Requires-Dist: sympy
+Provides-Extra: doc
+Requires-Dist: m2r2; extra == "doc"
+Requires-Dist: matplotlib; extra == "doc"
+Requires-Dist: mistune; extra == "doc"
+Requires-Dist: numpydoc; extra == "doc"
+Requires-Dist: pillow; extra == "doc"
+Requires-Dist: recommonmark; extra == "doc"
+Requires-Dist: seaborn; extra == "doc"
+Requires-Dist: sphinx>=3.5; extra == "doc"
+Requires-Dist: sphinx-argparse; extra == "doc"
+Requires-Dist: sphinx-copybutton; extra == "doc"
+Requires-Dist: sphinx_gallery; extra == "doc"
+Requires-Dist: sphinx_rtd_theme; extra == "doc"
+Requires-Dist: sphinxcontrib-bibtex; extra == "doc"
+Requires-Dist: sphinxcontrib-mermaid; extra == "doc"
+Requires-Dist: docutils<0.21,>=0.18.1; extra == "doc"
+Provides-Extra: tests
+Requires-Dist: coverage; extra == "tests"
+Requires-Dist: flake8; extra == "tests"
+Requires-Dist: flake8-black; extra == "tests"
+Requires-Dist: flake8-docstrings; extra == "tests"
+Requires-Dist: flake8-isort; extra == "tests"
+Requires-Dist: pytest; extra == "tests"
+Requires-Dist: pytest-cov; extra == "tests"
+Provides-Extra: stan
+Requires-Dist: cmdstanpy<2,>=1.2; extra == "stan"
+Requires-Dist: arviz>=0.17; extra == "stan"
+Requires-Dist: scipy<1.13; python_version < "3.10" and extra == "stan"
+Provides-Extra: all
+Requires-Dist: m2r2; extra == "all"
+Requires-Dist: matplotlib; extra == "all"
+Requires-Dist: mistune; extra == "all"
+Requires-Dist: numpydoc; extra == "all"
+Requires-Dist: pillow; extra == "all"
+Requires-Dist: recommonmark; extra == "all"
+Requires-Dist: seaborn; extra == "all"
+Requires-Dist: sphinx>=3.5; extra == "all"
+Requires-Dist: sphinx-argparse; extra == "all"
+Requires-Dist: sphinx-copybutton; extra == "all"
+Requires-Dist: sphinx_gallery; extra == "all"
+Requires-Dist: sphinx_rtd_theme; extra == "all"
+Requires-Dist: sphinxcontrib-bibtex; extra == "all"
+Requires-Dist: sphinxcontrib-mermaid; extra == "all"
+Requires-Dist: docutils<0.21,>=0.18.1; extra == "all"
+Requires-Dist: coverage; extra == "all"
+Requires-Dist: flake8; extra == "all"
+Requires-Dist: flake8-black; extra == "all"
+Requires-Dist: flake8-docstrings; extra == "all"
+Requires-Dist: flake8-isort; extra == "all"
+Requires-Dist: pytest; extra == "all"
+Requires-Dist: pytest-cov; extra == "all"
+Requires-Dist: cmdstanpy<2,>=1.2; extra == "all"
+Requires-Dist: arviz>=0.17; extra == "all"
+Requires-Dist: scipy<1.13; python_version < "3.10" and extra == "all"
+Dynamic: license-file
+
+# PyMARE: Python Meta-Analysis & Regression Engine
+
+A Python library for mixed-effects meta-regression (including
+meta-analysis).
+
+# License
+
+PYMARE is licensed under the terms of the MIT license. See
+the file \'LICENSE\' for information on the history of this software,
+terms & conditions for usage, and a DISCLAIMER OF ALL WARRANTIES.
+
+All trademarks referenced herein are property of their respective
+holders.
+
+Copyright (c) 2019\--, PyMARE developers

pymare-0.0.11/PyMARE.egg-info/PKG-INFO

@@ -0,0 +1,99 @@
+Metadata-Version: 2.4
+Name: PyMARE
+Version: 0.0.11
+Summary: PyMARE: Python Meta-Analysis & Regression Engine
+Home-page: https://github.com/neurostuff/PyMARE
+Author: PyMARE developers
+Author-email: tsalo006@fiu.edu
+Maintainer: Taylor Salo
+Maintainer-email: tsalo006@fiu.edu
+License: MIT
+Classifier: Development Status :: 3 - Alpha
+Classifier: Environment :: Console
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Topic :: Scientific/Engineering
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy>=1.8.0
+Requires-Dist: pandas
+Requires-Dist: scipy
+Requires-Dist: sympy
+Provides-Extra: doc
+Requires-Dist: m2r2; extra == "doc"
+Requires-Dist: matplotlib; extra == "doc"
+Requires-Dist: mistune; extra == "doc"
+Requires-Dist: numpydoc; extra == "doc"
+Requires-Dist: pillow; extra == "doc"
+Requires-Dist: recommonmark; extra == "doc"
+Requires-Dist: seaborn; extra == "doc"
+Requires-Dist: sphinx>=3.5; extra == "doc"
+Requires-Dist: sphinx-argparse; extra == "doc"
+Requires-Dist: sphinx-copybutton; extra == "doc"
+Requires-Dist: sphinx_gallery; extra == "doc"
+Requires-Dist: sphinx_rtd_theme; extra == "doc"
+Requires-Dist: sphinxcontrib-bibtex; extra == "doc"
+Requires-Dist: sphinxcontrib-mermaid; extra == "doc"
+Requires-Dist: docutils<0.21,>=0.18.1; extra == "doc"
+Provides-Extra: tests
+Requires-Dist: coverage; extra == "tests"
+Requires-Dist: flake8; extra == "tests"
+Requires-Dist: flake8-black; extra == "tests"
+Requires-Dist: flake8-docstrings; extra == "tests"
+Requires-Dist: flake8-isort; extra == "tests"
+Requires-Dist: pytest; extra == "tests"
+Requires-Dist: pytest-cov; extra == "tests"
+Provides-Extra: stan
+Requires-Dist: cmdstanpy<2,>=1.2; extra == "stan"
+Requires-Dist: arviz>=0.17; extra == "stan"
+Requires-Dist: scipy<1.13; python_version < "3.10" and extra == "stan"
+Provides-Extra: all
+Requires-Dist: m2r2; extra == "all"
+Requires-Dist: matplotlib; extra == "all"
+Requires-Dist: mistune; extra == "all"
+Requires-Dist: numpydoc; extra == "all"
+Requires-Dist: pillow; extra == "all"
+Requires-Dist: recommonmark; extra == "all"
+Requires-Dist: seaborn; extra == "all"
+Requires-Dist: sphinx>=3.5; extra == "all"
+Requires-Dist: sphinx-argparse; extra == "all"
+Requires-Dist: sphinx-copybutton; extra == "all"
+Requires-Dist: sphinx_gallery; extra == "all"
+Requires-Dist: sphinx_rtd_theme; extra == "all"
+Requires-Dist: sphinxcontrib-bibtex; extra == "all"
+Requires-Dist: sphinxcontrib-mermaid; extra == "all"
+Requires-Dist: docutils<0.21,>=0.18.1; extra == "all"
+Requires-Dist: coverage; extra == "all"
+Requires-Dist: flake8; extra == "all"
+Requires-Dist: flake8-black; extra == "all"
+Requires-Dist: flake8-docstrings; extra == "all"
+Requires-Dist: flake8-isort; extra == "all"
+Requires-Dist: pytest; extra == "all"
+Requires-Dist: pytest-cov; extra == "all"
+Requires-Dist: cmdstanpy<2,>=1.2; extra == "all"
+Requires-Dist: arviz>=0.17; extra == "all"
+Requires-Dist: scipy<1.13; python_version < "3.10" and extra == "all"
+Dynamic: license-file
+
+# PyMARE: Python Meta-Analysis & Regression Engine
+
+A Python library for mixed-effects meta-regression (including
+meta-analysis).
+
+# License
+
+PYMARE is licensed under the terms of the MIT license. See
+the file \'LICENSE\' for information on the history of this software,
+terms & conditions for usage, and a DISCLAIMER OF ALL WARRANTIES.
+
+All trademarks referenced herein are property of their respective
+holders.
+
+Copyright (c) 2019\--, PyMARE developers

pymare-0.0.11/PyMARE.egg-info/SOURCES.txt

@@ -0,0 +1,52 @@
+LICENSE
+MANIFEST.in
+README.md
+pypi_description.md
+pyproject.toml
+setup.cfg
+setup.py
+versioneer.py
+PyMARE.egg-info/PKG-INFO
+PyMARE.egg-info/SOURCES.txt
+PyMARE.egg-info/dependency_links.txt
+PyMARE.egg-info/not-zip-safe
+PyMARE.egg-info/requires.txt
+PyMARE.egg-info/top_level.txt
+pymare/__init__.py
+pymare/_version.py
+pymare/core.py
+pymare/results.py
+pymare/stats.py
+pymare/utils.py
+pymare/datasets/__init__.py
+pymare/datasets/metadat.py
+pymare/effectsize/__init__.py
+pymare/effectsize/base.py
+pymare/effectsize/expressions.json
+pymare/effectsize/expressions.py
+pymare/estimators/__init__.py
+pymare/estimators/combination.py
+pymare/estimators/estimators.py
+pymare/estimators/stan/meta_regression.stan
+pymare/resources/datasets/michael2013.json
+pymare/resources/datasets/michael2013.tsv
+pymare/tests/__init__.py
+pymare/tests/conftest.py
+pymare/tests/test_combination_tests.py
+pymare/tests/test_core.py
+pymare/tests/test_datasets.py
+pymare/tests/test_effectsize_base.py
+pymare/tests/test_effectsize_expressions.py
+pymare/tests/test_estimators.py
+pymare/tests/test_metafor_alignment.py
+pymare/tests/test_results.py
+pymare/tests/test_robumeta_alignment.py
+pymare/tests/test_stan_estimators.py
+pymare/tests/test_stats.py
+pymare/tests/test_utils.py
+pymare/tests/utils.py
+pymare/tests/data/metafor_reference.json
+pymare/tests/data/metafor_small_sample.csv
+pymare/tests/data/robumeta_correlated_effects.csv
+pymare/tests/data/robumeta_reference.json
+pymare/tests/data/stan_validation.json

{PyMARE-0.0.10 → pymare-0.0.11}/PyMARE.egg-info/requires.txt

@@ -1,14 +1,7 @@
-pandas
-sympy
-wrapt
-
-[:python_version != "3.9" or extra != "stan"]
 numpy>=1.8.0
+pandas
 scipy
-
-[:python_version == "3.9" and extra == "stan"]
-numpy<2.0,>=1.8.0
-scipy<1.13
+sympy
 
 [all]
 m2r2
@@ -26,17 +19,18 @@ sphinx_rtd_theme
 sphinxcontrib-bibtex
 sphinxcontrib-mermaid
 docutils<0.21,>=0.18.1
-codecov
 coverage
-coveralls
 flake8
 flake8-black
 flake8-docstrings
 flake8-isort
 pytest
 pytest-cov
-pystan
-arviz
+cmdstanpy<2,>=1.2
+arviz>=0.17
+
+[all:python_version < "3.10"]
+scipy<1.13
 
 [doc]
 m2r2
@@ -56,13 +50,14 @@ sphinxcontrib-mermaid
 docutils<0.21,>=0.18.1
 
 [stan]
-pystan
-arviz
+cmdstanpy<2,>=1.2
+arviz>=0.17
+
+[stan:python_version < "3.10"]
+scipy<1.13
 
 [tests]
-codecov
 coverage
-coveralls
 flake8
 flake8-black
 flake8-docstrings

{PyMARE-0.0.10 → pymare-0.0.11}/README.md

@@ -7,6 +7,8 @@ A Python library for mixed-effects meta-regression (including meta-analysis).
 [![DOI](https://zenodo.org/badge/228903736.svg)](https://zenodo.org/badge/latestdoi/228903736)
 [![Documentation Status](https://readthedocs.org/projects/pymare/badge/?version=latest)](http://pymare.readthedocs.io/en/latest/?badge=latest)
 ![GitHub CI](https://github.com/neurostuff/pymare/actions/workflows/testing.yml/badge.svg)
+![Lint](https://github.com/neurostuff/pymare/actions/workflows/linting.yml/badge.svg)
+![robumeta alignment](https://github.com/neurostuff/pymare/actions/workflows/robumeta-alignment.yml/badge.svg)
 [![Codecov](https://codecov.io/gh/neurostuff/PyMARE/branch/master/graph/badge.svg)](https://codecov.io/gh/neurostuff/pymare)
 
 **PyMARE is alpha software under heavy development; we reserve the right to make major changes to the API.**

{PyMARE-0.0.10 → pymare-0.0.11}/pymare/_version.py

@@ -8,11 +8,11 @@ import json
 
 version_json = '''
 {
- "date": "2025-04-28T12:37:45-0500",
+ "date": "2026-08-20T15:09:51-0500",
  "dirty": false,
  "error": null,
- "full-revisionid": "d79d3e37c84f969d75b0190d2110e8aea16ef852",
- "version": "0.0.10"
+ "full-revisionid": "d882dfbda4ecb4bfed59b62a9842067942575c80",
+ "version": "0.0.11"
 }
 '''  # END VERSION_JSON
 

{PyMARE-0.0.10 → pymare-0.0.11}/pymare/core.py

@@ -24,27 +24,34 @@ class Dataset:
     Parameters
     ----------
     y : None or :obj:`numpy.ndarray` of shape (K,) or :obj:`str`, optional
-        1d array of study-level estimates with length K, or the name of the column in data
+        1d array of observation-level estimates with length K, or the name of the column in data
         containing the y values.
         Default = None.
     v : None or :obj:`numpy.ndarray` of shape (K,) or :obj:`str`, optional
-        1d array of study-level variances with length K, or the name of the column in data
+        1d array of observation-level variances with length K, or the name of the column in data
         containing v values.
         Default = None.
     X : None or :obj:`numpy.ndarray` of shape (K,[P]) or :obj:`list` of :obj:`str`, optional
-        1d or 2d array containing study-level predictors (dimensions K x P),
+        1d or 2d array containing observation-level predictors (dimensions K x P),
         or a list of strings giving the names of the columns in data containing the X values.
         Default = None.
     n : None or :obj:`numpy.ndarray` of shape (K,) or :obj:`str`, optional
-        1d array of study-level sample sizes (length K), or the name of the corresponding column
-        in ``data``.
+        1d array of observation-level ``n`` values (length K), or the name of the
+        corresponding column in ``data``.
+        Default = None.
+    g : None or :obj:`numpy.ndarray` of shape (K,) or :obj:`str`, optional
+        1d array of group labels with length K, or the name of the
+        corresponding column in ``data``. Observations sharing a label are
+        treated as statistically dependent.
+        Estimators that support dependent estimates use this to widen their inference
+        accordingly; estimators that do not simply ignore it.
         Default = None.
     data : None or :obj:`pandas.DataFrame`, optional
-        A pandas DataFrame containing y, v, X, and/or n values.
+        A pandas DataFrame containing y, v, X, n, and/or g values.
         By default, columns are expected to have the same names as arguments
         (e.g., the y values will be expected in the 'y' column).
         This can be modified by passing strings giving column names to any of the ``y``, ``v``,
-        ``X``, or ``n`` arguments.
+        ``X``, ``n``, or ``g`` arguments.
         Default = None.
     X_names : None or :obj:`list` of :obj:`str`, optional
         List of length P containing the names of the predictors.
@@ -57,7 +64,15 @@ class Dataset:
     """
 
     def __init__(
-        self, y=None, v=None, X=None, n=None, data=None, X_names=None, add_intercept=True
+        self,
+        y=None,
+        v=None,
+        X=None,
+        n=None,
+        data=None,
+        X_names=None,
+        add_intercept=True,
+        g=None,
     ):
         if y is None and data is None:
             raise ValueError(
@@ -86,16 +101,36 @@ class Dataset:
             if (n is not None) or ("n" in data.columns):
                 n = data.loc[:, n or "n"].values
 
+            # g is optional. Compare against None explicitly: `g or "g"` calls
+            # bool() on the value, which raises for an array of labels passed
+            # alongside a DataFrame.
+            if (g is not None) or ("g" in data.columns):
+                g = data.loc[:, "g" if g is None else g].values if np.ndim(g) == 0 else g
+
         self.y = ensure_2d(y)
         self.v = ensure_2d(v)
         self.n = ensure_2d(n)
+        self.g = ensure_2d(g)
         X, names = self._get_predictors(X, X_names, add_intercept)
         self.X = X
         self.X_names = names
 
         _check_inputs_shape(self.y, self.X, "y", "X", row=True)
         _check_inputs_shape(self.y, self.v, "y", "v", row=True, column=True)
-        _check_inputs_shape(self.y, self.n, "y", "n", row=True, column=True)
+        _check_inputs_shape(self.y, self.n, "y", "n", row=True)
+        # A single column of n broadcasts across parallel datasets. The
+        # estimators already handle that, and per-observation quantities such
+        # as n or weights usually do not vary by parallel dataset.
+        if self.n is not None and self.n.shape[1] != 1:
+            _check_inputs_shape(self.y, self.n, "y", "n", column=True)
+        _check_inputs_shape(self.y, self.g, "y", "g", row=True)
+        if self.g is not None and self.g.shape[1] != 1:
+            # One label per observation. A (K, D) array would be silently
+            # reduced to its first column later, quietly discarding the rest.
+            raise ValueError(
+                "g must contain one group label per observation, with shape "
+                f"(K,) or (K, 1); got {self.g.shape}."
+            )
 
     def _get_predictors(self, X, names, add_intercept):
         if X is None and not add_intercept:
@@ -120,7 +155,7 @@ class Dataset:
         Returns
         -------
         :obj:`pandas.DataFrame`
-            A DataFrame containing the y, v, X, and n values.
+            A DataFrame containing the y, v, X, n, and g values.
         """
         if self.y.shape[1] == 1:
             df = pd.DataFrame({"y": self.y[:, 0]})
@@ -131,6 +166,9 @@ class Dataset:
             if self.n is not None:
                 df["n"] = self.n[:, 0]
 
+            if self.g is not None:
+                df["g"] = self.g[:, 0]
+
             df[self.X_names] = self.X
 
         else:
@@ -147,7 +185,12 @@ class Dataset:
                     df["v"] = self.v[:, i_set]
 
                 if self.n is not None:
-                    df["n"] = self.n[:, i_set]
+                    # A single column of n applies to every parallel dataset,
+                    # which the constructor allows and the estimators honour.
+                    df["n"] = self.n[:, i_set if self.n.shape[1] > 1 else 0]
+
+                if self.g is not None:
+                    df["g"] = self.g[:, 0]
 
                 # X is the same across sets
                 df[self.X_names] = self.X
@@ -170,6 +213,7 @@ def meta_regression(
     method="ML",
     ci_method="QP",
     alpha=0.05,
+    g=None,
     **kwargs,
 ):
     """Fit the standard meta-regression/meta-analysis model to provided data.
@@ -177,29 +221,29 @@ def meta_regression(
     Parameters
     ----------
     y : None or :obj:`numpy.ndarray` of shape (K,) or :obj:`str`, optional
-        1d array of study-level estimates with length K, or the name of the column in data
+        1d array of observation-level estimates with length K, or the name of the column in data
         containing the y values.
         Default = None.
     v : None or :obj:`numpy.ndarray` of shape (K,) or :obj:`str`, optional
-        1d array of study-level variances with length K, or the name of the column in data
+        1d array of observation-level variances with length K, or the name of the column in data
         containing v values.
         Default = None.
     X : None or :obj:`numpy.ndarray` of shape (K,[P]) or :obj:`list` of :obj:`str`, optional
-        1d or 2d array containing study-level predictors (dimensions K x P),
+        1d or 2d array containing observation-level predictors (dimensions K x P),
         or a list of strings giving the names of the columns in data containing the X values.
         Default = None.
     n : None or :obj:`numpy.ndarray` of shape (K,) or :obj:`str`, optional
-        1d array of study-level sample sizes (length K), or the name of the corresponding column
-        in ``data``.
+        1d array of observation-level ``n`` values (length K), or the name of the
+        corresponding column in ``data``.
         Default = None.
     data : None or :obj:`pandas.DataFrame` or :obj:`~pymare.core.Dataset`, optional
-        If a Dataset instance is passed, the y, v, X, n and associated arguments are ignored,
+        If a Dataset instance is passed, the y, v, X, n, g and associated arguments are ignored,
         and data is passed directly to the selected estimator.
-        If a pandas DataFrame, y, v, X and/or n values are taken from the DF columns.
+        If a pandas DataFrame, y, v, X, n and/or g values are taken from the DF columns.
         By default, columns are expected to have the same names as arguments
         (e.g., the y values will be expected in the 'y' column).
-        This can be modified by passing strings giving column names to any of the y, v, X, or n
-        arguments.
+        This can be modified by passing strings giving column names to any of the y, v, X, n, or
+        g arguments.
     X_names : None or :obj:`list` of :obj:`str`, optional
         List of length P containing the names of the predictors.
         Ignored if ``data`` is provided (use ``X`` to specify columns).
@@ -224,6 +268,11 @@ def meta_regression(
         Ignored if ``method == 'Stan'``.
     alpha : :obj:`float`, optional
         Desired alpha level (CIs will have 1 - alpha coverage). Default = 0.05.
+    g : None or :obj:`numpy.ndarray` of shape (K,) or :obj:`str`, optional
+        Group labels marking dependent estimates, or the name of the corresponding column in
+        ``data``. Estimates with the same label are treated as one group by estimators that
+        support cluster-robust inference.
+        Default = None.
     **kwargs
         Optional keyword arguments to pass onto the chosen estimator.
 
@@ -237,7 +286,7 @@ def meta_regression(
     """
     # if data is None or not isinstance(data, Dataset):
     if data is None or not data.__class__.__name__ == "Dataset":
-        data = Dataset(y, v, X, n, data, X_names, add_intercept)
+        data = Dataset(y, v, X, n, data, X_names, add_intercept, g=g)
 
     method = method.lower()