PyMARE 0.0.3rc2__tar.gz → 0.0.4__tar.gz

PyMARE-0.0.4/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2020- pymare developers
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

{PyMARE-0.0.3rc2 → PyMARE-0.0.4}/PKG-INFO

@@ -1,11 +1,11 @@
 Metadata-Version: 2.1
 Name: PyMARE
-Version: 0.0.3rc2
+Version: 0.0.4
 Summary: PyMARE: Python Meta-Analysis & Regression Engine
 Home-page: https://github.com/neurostuff/PyMARE
 Author: PyMARE developers
-Author-email: tyarkoni@gmail.com
-Maintainer: Tal Yarkoni
+Author-email: tsalo006@fiu.edu
+Maintainer: Taylor Salo
 Maintainer-email: tsalo006@fiu.edu
 License: MIT
 Description: 
@@ -28,12 +28,12 @@ Classifier: Environment :: Console
 Classifier: Intended Audience :: Science/Research
 Classifier: License :: OSI Approved :: MIT License
 Classifier: Operating System :: OS Independent
-Classifier: Programming Language :: Python :: 3.6
-Classifier: Programming Language :: Python :: 3.7
 Classifier: Programming Language :: Python :: 3.8
 Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
 Classifier: Topic :: Scientific/Engineering
-Requires-Python: >=3.6
+Requires-Python: >=3.8
 Description-Content-Type: text/x-rst
 Provides-Extra: doc
 Provides-Extra: tests

{PyMARE-0.0.3rc2 → PyMARE-0.0.4}/PyMARE.egg-info/PKG-INFO

@@ -1,11 +1,11 @@
 Metadata-Version: 2.1
 Name: PyMARE
-Version: 0.0.3rc2
+Version: 0.0.4
 Summary: PyMARE: Python Meta-Analysis & Regression Engine
 Home-page: https://github.com/neurostuff/PyMARE
 Author: PyMARE developers
-Author-email: tyarkoni@gmail.com
-Maintainer: Tal Yarkoni
+Author-email: tsalo006@fiu.edu
+Maintainer: Taylor Salo
 Maintainer-email: tsalo006@fiu.edu
 License: MIT
 Description: 
@@ -28,12 +28,12 @@ Classifier: Environment :: Console
 Classifier: Intended Audience :: Science/Research
 Classifier: License :: OSI Approved :: MIT License
 Classifier: Operating System :: OS Independent
-Classifier: Programming Language :: Python :: 3.6
-Classifier: Programming Language :: Python :: 3.7
 Classifier: Programming Language :: Python :: 3.8
 Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
 Classifier: Topic :: Scientific/Engineering
-Requires-Python: >=3.6
+Requires-Python: >=3.8
 Description-Content-Type: text/x-rst
 Provides-Extra: doc
 Provides-Extra: tests

{PyMARE-0.0.3rc2 → PyMARE-0.0.4}/PyMARE.egg-info/SOURCES.txt

@@ -1,3 +1,4 @@
+LICENSE
 MANIFEST.in
 README.md
 pyproject.toml
@@ -15,10 +16,15 @@ 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/estimators.py
+pymare/resources/datasets/michael2013.json
+pymare/resources/datasets/michael2013.tsv

{PyMARE-0.0.3rc2 → PyMARE-0.0.4}/PyMARE.egg-info/requires.txt

@@ -1,6 +1,6 @@
 numpy>=1.8.0
 pandas
-scipy
+scipy<1.13.0
 sympy
 wrapt
 
@@ -15,8 +15,9 @@ seaborn
 sphinx>=3.5
 sphinx-argparse
 sphinx-copybutton
-sphinx_gallery==0.10.1
+sphinx_gallery
 sphinx_rtd_theme
+sphinxcontrib-bibtex
 codecov
 coverage
 coveralls
@@ -26,6 +27,8 @@ flake8-docstrings
 flake8-isort
 pytest
 pytest-cov
+pystan
+arviz
 
 [doc]
 m2r
@@ -38,8 +41,9 @@ seaborn
 sphinx>=3.5
 sphinx-argparse
 sphinx-copybutton
-sphinx_gallery==0.10.1
+sphinx_gallery
 sphinx_rtd_theme
+sphinxcontrib-bibtex
 
 [stan]
 pystan

PyMARE-0.0.4/pymare/__init__.py

@@ -0,0 +1,50 @@
+"""PyMARE: Python Meta-Analysis & Regression Engine."""
+
+import sys
+import warnings
+
+from .core import Dataset, meta_regression
+from .effectsize import OneSampleEffectSizeConverter, TwoSampleEffectSizeConverter
+
+__all__ = [
+    "Dataset",
+    "meta_regression",
+    "OneSampleEffectSizeConverter",
+    "TwoSampleEffectSizeConverter",
+]
+
+from . import _version
+
+__version__ = _version.get_versions()["version"]
+del _version
+
+
+def _py367_deprecation_warning():
+    """Deprecation warnings message.
+
+    Notes
+    -----
+    Adapted from NiMARE.
+    """
+    py36_warning = (
+        "Python 3.6 and 3.7 support is deprecated and will be removed in release 0.0.5 of PyMARE. "
+        "Consider switching to Python 3.8, 3.9."
+    )
+    warnings.filterwarnings("once", message=py36_warning)
+    warnings.warn(message=py36_warning, category=FutureWarning, stacklevel=3)
+
+
+def _python_deprecation_warnings():
+    """Raise deprecation warnings.
+
+    Notes
+    -----
+    Adapted from NiMARE.
+    """
+    if sys.version_info.major == 3 and (
+        sys.version_info.minor == 6 or sys.version_info.minor == 7
+    ):
+        _py367_deprecation_warning()
+
+
+_python_deprecation_warnings()

{PyMARE-0.0.3rc2 → PyMARE-0.0.4}/pymare/_version.py

@@ -8,11 +8,11 @@ import json
 
 version_json = '''
 {
- "date": "2022-03-07T16:12:42-0500",
+ "date": "2024-04-17T13:45:32-0500",
  "dirty": false,
  "error": null,
- "full-revisionid": "573a22616617245598c7fc8440650ed75e82941c",
- "version": "0.0.3rc2"
+ "full-revisionid": "624968ecc3acf081014853004b3c3804b788e562",
+ "version": "0.0.4"
 }
 '''  # END VERSION_JSON
 

{PyMARE-0.0.3rc2 → PyMARE-0.0.4}/pymare/core.py

@@ -5,6 +5,8 @@ from functools import partial
 import numpy as np
 import pandas as pd
 
+from pymare.utils import _check_inputs_shape, _listify
+
 from .estimators import (
     DerSimonianLaird,
     Hedges,
@@ -24,40 +26,39 @@ class Dataset:
     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
         containing the y values.
-        Default is None.
+        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
         containing v values.
-        Default is None.
+        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),
         or a list of strings giving the names of the columns in data containing the X values.
-        Default is None.
+        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``.
-        Default is None.
+        Default = None.
     data : None or :obj:`pandas.DataFrame`, optional
         A pandas DataFrame containing y, v, X, and/or n 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.
-        Default is None.
+        Default = None.
     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).
-        Default is None.
+        Default = None.
     add_intercept : :obj:`bool`, optional
         If True, an intercept column is automatically added to the predictor matrix.
         If False, the predictors matrix is passed as-is to estimators.
-        Default is True.
+        Default = True.
     """
 
     def __init__(
         self, y=None, v=None, X=None, n=None, data=None, X_names=None, add_intercept=True
     ):
-
         if y is None and data is None:
             raise ValueError(
                 "If no y values are provided, a pandas DataFrame "
@@ -65,12 +66,25 @@ class Dataset:
                 "data argument."
             )
 
+        if (X is None) and (not add_intercept):
+            raise ValueError("If no X matrix is provided, add_intercept must be True!")
+
         # Extract columns from DataFrame
         if data is not None:
             y = data.loc[:, y or "y"].values
-            v = data.loc[:, v or "v"].values
-            X_names = X or "X"
-            X = data.loc[:, X_names].values
+
+            # v is optional
+            if (v is not None) or ("v" in data.columns):
+                v = data.loc[:, v or "v"].values
+
+            # X is optional
+            if (X is not None) or ("X" in data.columns):
+                X_names = X or "X"
+                X = data.loc[:, X_names].values
+
+            # n is optional
+            if (n is not None) or ("n" in data.columns):
+                n = data.loc[:, n or "n"].values
 
         self.y = ensure_2d(y)
         self.v = ensure_2d(v)
@@ -79,20 +93,71 @@ class Dataset:
         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)
+
     def _get_predictors(self, X, names, add_intercept):
         if X is None and not add_intercept:
             raise ValueError(
                 "No fixed predictors found. If no X matrix is "
                 "provided, add_intercept must be True!"
             )
+
         X = pd.DataFrame(X)
         if names is not None:
-            X.columns = names
+            X.columns = _listify(names)
+
         if add_intercept:
             intercept = pd.DataFrame({"intercept": np.ones(len(self.y))})
             X = pd.concat([intercept, X], axis=1)
+
         return X.values, X.columns.tolist()
 
+    def to_df(self):
+        """Convert the dataset to a pandas DataFrame.
+
+        Returns
+        -------
+        :obj:`pandas.DataFrame`
+            A DataFrame containing the y, v, X, and n values.
+        """
+        if self.y.shape[1] == 1:
+            df = pd.DataFrame({"y": self.y[:, 0]})
+
+            if self.v is not None:
+                df["v"] = self.v[:, 0]
+
+            if self.n is not None:
+                df["n"] = self.n[:, 0]
+
+            df[self.X_names] = self.X
+
+        else:
+            all_dfs = []
+            for i_set in range(self.y.shape[1]):
+                df = pd.DataFrame(
+                    {
+                        "set": np.full(self.y.shape[0], i_set),
+                        "y": self.y[:, i_set],
+                    }
+                )
+
+                if self.v is not None:
+                    df["v"] = self.v[:, i_set]
+
+                if self.n is not None:
+                    df["n"] = self.n[:, i_set]
+
+                # X is the same across sets
+                df[self.X_names] = self.X
+
+                all_dfs.append(df)
+
+            df = pd.concat(all_dfs, axis=0)
+
+        return df
+
 
 def meta_regression(
     y=None,
@@ -114,19 +179,19 @@ def meta_regression(
     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
         containing the y values.
-        Default is None.
+        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
         containing v values.
-        Default is None.
+        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),
         or a list of strings giving the names of the columns in data containing the X values.
-        Default is None.
+        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``.
-        Default is None.
+        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,
         and data is passed directly to the selected estimator.
@@ -138,13 +203,13 @@ def meta_regression(
     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).
-        Default is None.
+        Default = None.
     add_intercept : :obj:`bool`, optional
         If True, an intercept column is automatically added to the predictor matrix.
         If False, the predictors matrix is passed as-is to estimators.
-        Default is True.
+        Default = True.
     method : {"ML", "REML", "DL", "HE", "WLS", "FE", "Stan"}, optional
-        Name of estimation method. Default is 'ML'.
+        Name of estimation method. Default = 'ML'.
         Supported estimators include:
 
             - 'ML': Maximum-likelihood estimator
@@ -155,10 +220,10 @@ def meta_regression(
             - 'Stan': Full Bayesian MCMC estimation via Stan
     ci_method : {"QP"}, optional
         Estimation method to use when computing uncertainty estimates.
-        Currently only 'QP' is supported. Default is 'QP'.
+        Currently only 'QP' is supported. Default = 'QP'.
         Ignored if ``method == 'Stan'``.
     alpha : :obj:`float`, optional
-        Desired alpha level (CIs will have 1 - alpha coverage). Default is 0.05.
+        Desired alpha level (CIs will have 1 - alpha coverage). Default = 0.05.
     **kwargs
         Optional keyword arguments to pass onto the chosen estimator.
 

PyMARE-0.0.4/pymare/datasets/__init__.py

@@ -0,0 +1,7 @@
+"""Open meta-analytic datasets."""
+
+from .metadat import michael2013
+
+__all__ = [
+    "michael2013",
+]

PyMARE-0.0.4/pymare/datasets/metadat.py

@@ -0,0 +1,55 @@
+"""Datasets from metadat."""
+
+import json
+import os.path as op
+
+import pandas as pd
+
+from pymare.utils import get_resource_path
+
+
+def michael2013():
+    """Load a dataset of studies on the persuasive power of a brain image.
+
+    This dataset was published in :footcite:t:`michael2013non`,
+    and was curated in metadat :footcite:p:`white2022metadat`.
+
+    Returns
+    -------
+    df : :obj:`~pandas.DataFrame`
+        A dataframe with the following columns:
+
+        - ``"Study"``: the study name
+        - ``"No_brain_n"``: the sample size for no-brain-image condition
+        - ``"No_brain_m"``: mean agreement rating for no-brain-image condition
+        - ``"No_brain_s"``: standard deviation of agreement rating for no-brain-image condition
+        - ``"Brain_n"``: the sample size for brain-image condition
+        - ``"Brain_m"``: mean agreement rating for brain-image condition
+        - ``"Brain_s"``: standard deviation of agreement rating for brain-image condition
+        - ``"Included_Critique"``: whether a critique was included in the study or not
+        - ``"Medium"``: the medium of the study
+        - ``"Compensation"``: notes on the compensation of the study
+        - ``"Participant_Pool"``: notes on where participants were recruited
+        - ``"yi"``: Raw mean difference, calculated as Brain_m - No_brain_m
+        - ``"vi"``: Corresponding sampling variance
+
+    metadata : :obj:`dict`
+        A dictionary with metadata about the columns in the dataset.
+
+    Notes
+    -----
+    For more information about this dataset, see metadat's documentation:
+    https://wviechtb.github.io/metadat/reference/dat.michael2013.html
+
+    References
+    ----------
+    .. footbibliography::
+    """
+    dataset_dir = op.join(get_resource_path(), "datasets")
+    tsv_file = op.join(dataset_dir, "michael2013.tsv")
+    json_file = op.join(dataset_dir, "michael2013.json")
+    df = pd.read_table(tsv_file)
+    with open(json_file, "r") as fo:
+        metadata = json.load(fo)
+
+    return df, metadata

{PyMARE-0.0.3rc2 → PyMARE-0.0.4}/pymare/effectsize/__init__.py

@@ -1,4 +1,5 @@
 """Tools for converting between effect-size measures."""
+
 from .base import (
     OneSampleEffectSizeConverter,
     TwoSampleEffectSizeConverter,

{PyMARE-0.0.3rc2 → PyMARE-0.0.4}/pymare/effectsize/base.py

@@ -25,7 +25,7 @@ def solve_system(system, known_vars=None):
         A dictionary of known variables to use
         when evaluating the solution. Keys are the names of parameters
         (e.g., 'sem', 't'), values are numerical data types (including
-        numpy arrays). Default is None.
+        numpy arrays). Default = None.
 
     Returns
     -------
@@ -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)
@@ -90,7 +90,6 @@ class EffectSizeConverter(metaclass=ABCMeta):
     """Base class for effect size converters."""
 
     def __init__(self, data=None, **kwargs):
-
         kwargs = {k: v for k, v in kwargs.items() if v is not None}
 
         if data is not None:
@@ -134,7 +133,7 @@ class EffectSizeConverter(metaclass=ABCMeta):
         incremental : :obj:`bool`, optional
             If True, updates data incrementally (i.e., existing data will be preserved unless
             they're overwritten by incoming keys). If False, all existing data is dropped first.
-            Default is False.
+            Default = False.
         **kwargs
             Data values or arrays; keys are the names of the quantities.
             All inputs to ``__init__`` are valid.
@@ -231,7 +230,7 @@ class OneSampleEffectSizeConverter(EffectSizeConverter):
         Column names must match the controlled names listed below for
         kwargs. If additional kwargs are provided, they will take
         precedence over the values in the data frame.
-        Default is None.
+        Default = None.
     m : None or :obj:`numpy.ndarray`, optional
         Means or other continuous estimates
     sd : None or :obj:`numpy.ndarray`, optional
@@ -509,7 +508,6 @@ def compute_measure(
 
     # Select or infer converter class
     if comparison == "infer":
-
         one_samp_inputs = {"m", "sd", "n", "r"}
         two_samp_inputs = {"m1", "m2", "sd1", "sd2", "n1", "n2"}
 

{PyMARE-0.0.3rc2 → PyMARE-0.0.4}/pymare/estimators/__init__.py

@@ -1,4 +1,5 @@
 """Estimators for meta-analyses and meta-regressions."""
+
 from .combination import FisherCombinationTest, StoufferCombinationTest
 from .estimators import (
     DerSimonianLaird,