PyMetaAnalysis 0.1.0__py3-none-any.whl

pymetaanalysis-0.1.0.dist-info/METADATA

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+Metadata-Version: 2.4
+Name: PyMetaAnalysis
+Version: 0.1.0
+Summary: A pandas-first, auditable meta-analysis library for Python
+Project-URL: Documentation, https://zhaoboding.github.io/PyMetaAnalysis/
+Project-URL: Source, https://github.com/ZhaoboDing/PyMetaAnalysis
+Project-URL: Issues, https://github.com/ZhaoboDing/PyMetaAnalysis/issues
+Project-URL: Changelog, https://github.com/ZhaoboDing/PyMetaAnalysis/blob/main/CHANGELOG.md
+Author: PyMetaAnalysis contributors
+Maintainer-email: Zhaobo Ding <ding.zb@yahoo.com>
+License-Expression: MIT
+License-File: LICENSE
+Keywords: evidence-based medicine,meta-analysis,statistics,systematic review
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: Programming Language :: Python :: 3
+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 :: Medical Science Apps.
+Requires-Python: >=3.10
+Requires-Dist: numpy>=1.24
+Requires-Dist: pandas>=2.0
+Requires-Dist: scipy>=1.10
+Provides-Extra: dev
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+Requires-Dist: build>=1.2; extra == 'dev'
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+Requires-Dist: pandas-stubs>=2.0; extra == 'dev'
+Requires-Dist: ruff>=0.6; extra == 'dev'
+Requires-Dist: scipy-stubs>=1.10; extra == 'dev'
+Provides-Extra: docs
+Requires-Dist: mkdocs>=1.6; extra == 'docs'
+Provides-Extra: notebook
+Requires-Dist: ipykernel>=6.29; extra == 'notebook'
+Requires-Dist: jupyterlab>=4.0; extra == 'notebook'
+Requires-Dist: matplotlib>=3.7; extra == 'notebook'
+Requires-Dist: nbclient>=0.10; extra == 'notebook'
+Requires-Dist: nbformat>=5.10; extra == 'notebook'
+Provides-Extra: plot
+Requires-Dist: matplotlib>=3.7; extra == 'plot'
+Provides-Extra: test
+Requires-Dist: hypothesis>=6.100; extra == 'test'
+Requires-Dist: matplotlib>=3.7; extra == 'test'
+Requires-Dist: pytest-cov>=5.0; extra == 'test'
+Requires-Dist: pytest>=8.0; extra == 'test'
+Description-Content-Type: text/markdown
+
+# PyMetaAnalysis
+
+[![CI](https://github.com/ZhaoboDing/PyMetaAnalysis/actions/workflows/ci.yml/badge.svg)](https://github.com/ZhaoboDing/PyMetaAnalysis/actions/workflows/ci.yml)
+[![Documentation](https://github.com/ZhaoboDing/PyMetaAnalysis/actions/workflows/pages.yml/badge.svg)](https://zhaoboding.github.io/PyMetaAnalysis/)
+[![License: MIT](https://img.shields.io/badge/License-MIT-blue.svg)](LICENSE)
+
+PyMetaAnalysis is an early-stage, pandas-first Python library for conventional
+study-level meta-analysis. It accepts DataFrames, NumPy arrays, and ordinary
+Python sequences, then returns immutable, auditable result objects containing
+study effects, exclusions, weights, method choices, diagnostics, provenance,
+and structured reports.
+
+> **Early-stage:** the API may change during the 0.x series. Consequential
+> results should be reviewed against the analysis protocol and independently
+> checked.
+
+## Install
+
+```console
+python -m pip install PyMetaAnalysis
+```
+
+Install optional Matplotlib plotting support with:
+
+```console
+python -m pip install "PyMetaAnalysis[plot]"
+```
+
+The distribution name is `PyMetaAnalysis`; the import name is
+`meta_analyze`.
+
+## Quick start
+
+```python
+import meta_analyze as ma
+
+result = ma.meta_analysis(
+    effect=[0.12, 0.35, -0.08, 0.21],
+    variance=[0.04, 0.06, 0.03, 0.05],
+    study=["Trial A", "Trial B", "Trial C", "Trial D"],
+    model="random",
+    tau2_method="REML",
+)
+
+print(result.summary())
+print(result.study_results)
+```
+
+DataFrame column names work directly:
+
+```python
+result = ma.meta_analysis(
+    studies,
+    effect="effect",
+    variance="variance",
+    study="citation",
+    subgroup="region",
+)
+```
+
+Omit `study=` to use the DataFrame index. Supplying `subgroup=` returns a
+dedicated result containing group fits, the overall fit, and a formal test for
+subgroup differences.
+
+## Supported analyses
+
+| Input | Effects | Pooling/models |
+| --- | --- | --- |
+| Effect + sampling variance | Generic | Common/random inverse variance |
+| Two-group events + totals | OR, RR, RD | Common MH OR/RR; common/random IV |
+| Two-group means + SDs + sizes | MD, Hedges' g | Common/random inverse variance |
+
+Random-effects inverse-variance models support REML (default), Paule-Mandel,
+and DerSimonian-Laird tau-squared estimators. Mean confidence intervals support
+the normal default plus unmodified and safeguarded Hartung-Knapp variants.
+Eligible random-effects fits include an HTS prediction interval.
+
+Sparse binary behavior is explicit: study-level and Mantel-Haenszel continuity
+corrections are separate, relative-effect double-zero/double-all rows remain
+visible as exclusions, and RD exposes
+`rd_zero_variance="correct" | "exclude"`.
+
+## Inspect and report
+
+```python
+result.estimate
+result.display_estimate
+result.ci
+result.tau2
+result.i2
+result.i2_method
+result.diagnostics
+result.provenance
+
+methods_text = result.method_details()
+report = result.report()
+payload = report.to_dict()
+json_text = report.to_json()
+markdown = report.to_markdown()
+```
+
+OR and RR remain on the log model scale in auditable numeric attributes;
+`display_estimate`, `display_ci`, and `display_prediction_interval` provide
+exponentiated ratios.
+
+Rows excluded by missing-value or sparse-data policies remain in
+`study_results` with a stable `row_id`, `included=False`, and an
+`exclusion_reason`.
+
+## Sensitivity and plots
+
+```python
+leave_one_out = result.leave_one_out().to_dataframe()
+cumulative = result.cumulative(order="publication_year").to_dataframe()
+
+ax = result.forest(show_prediction_interval=True)
+ax = result.funnel()
+```
+
+Plotting methods return Matplotlib axes and never call `show()`. Funnel plots
+are descriptive small-study-effect diagnostics, not proof of publication bias.
+
+## Documentation
+
+The complete documentation is published at
+[zhaoboding.github.io/PyMetaAnalysis](https://zhaoboding.github.io/PyMetaAnalysis/).
+
+- [Installation](docs/installation.md)
+- [Getting started](docs/getting-started.md)
+- [Input data and row decisions](docs/guides/input-data.md)
+- [Generic](docs/guides/generic-effects.md), [binary](docs/guides/binary-outcomes.md), and [continuous](docs/guides/continuous-outcomes.md) guides
+- [Choosing methods](docs/guides/method-selection.md) and [statistical formulas](docs/methods/statistical-methods.md)
+- [Sensitivity analysis](docs/guides/sensitivity-analysis.md) and [plotting](docs/guides/plotting.md)
+- [Public API](docs/reference/api.md), [result objects](docs/reference/results.md), and [report schema](docs/reference/report-schema.md)
+- [Validation strategy](docs/validation.md) and [scope/limitations](docs/limitations.md)
+- [Citation guidance](docs/citation.md)
+- [R `meta`/`metafor` mapping](docs/guides/r-interoperability.md)
+
+An executable [end-to-end notebook](examples/quickstart.ipynb) uses synthetic
+data to demonstrate analysis, provenance, reporting, sensitivity, and plotting.
+
+Build the complete site locally with:
+
+```console
+python -m pip install ".[docs]"
+python -m mkdocs serve
+```
+
+## Validation status
+
+The test suite combines hand calculations, statistical invariants, numerical
+edge cases, and committed R `metafor` reference fixtures. CI covers Python
+3.10–3.13, declared dependency lower bounds, strict typing/linting, docs, and
+distribution builds.
+
+This is independent cross-software validation, not a formal external
+statistical audit. See [validation](docs/validation.md) for exact coverage.
+
+## Contributing
+
+See [CONTRIBUTING.md](CONTRIBUTING.md) and the full
+[development guide](docs/development.md). Statistical changes require formula
+documentation, boundary tests, and an independent comparison where available.
+
+Security-sensitive reports should follow [SECURITY.md](SECURITY.md).
+
+## License
+
+[MIT](LICENSE)

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pymetaanalysis-0.1.0.dist-info/licenses/LICENSE

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+MIT License
+
+Copyright (c) 2026 PyMetaAnalysis contributors
+
+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.