kernelmix 0.3.0__tar.gz

kernelmix-0.3.0/CHANGELOG.md

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+# Changelog
+
+## Unreleased
+
+- Add reproducible fitted-posterior comparisons with R and independent extension checks.
+- Add searchable documentation with grouped API pages and common questions.
+
+- Clarify model support, priors and notation; connect the guides and reference manual around analysis tasks.
+- Add a reproducible public-data ozone example, saved results and residual plots.
+- Document original-study gaps and platform verification limits.
+
+## 0.3.0
+
+- Matérn 3/2 and rational-quadratic kernels; predictive-process and random-Fourier GP bases.
+- Random slopes with full covariance; Gaussian AR1, exponential and fixed residual correlations.
+- Gaussian log-linear residual variance and variance prediction.
+- Delayed entry, competing causes, piecewise-constant predictor histories and left/interval-censored survival.
+- Cause-specific contrasts, cumulative incidence, path prediction and portable structured results.
+
+## 0.2.0
+
+- Poisson and NB2 count models with log observation-exposure offsets.
+- Right-censored proportional hazards with a piecewise-exponential baseline.
+- Gaussian random intercepts, known/new-cluster prediction and intercept summaries.
+- Survival/hazard predictions and plots; independent likelihood and posterior checks.
+
+## 0.1.0
+
+- Gaussian and probit BKMR with component or grouped exposure selection.
+- Joint predictions, exposure contrasts, diagnostics and non-pickle persistence.
+- Response, surface, inclusion and trace plots.
+- Fixed-state R comparisons and small independently integrated posterior checks.

kernelmix-0.3.0/CITATION.cff

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+cff-version: 1.2.0
+message: "Please cite KernelMix and the method papers listed in the README."
+title: "KernelMix: Bayesian kernel machine regression for exposure mixtures"
+type: software
+version: 0.3.0
+authors:
+  - family-names: Chapagain
+    given-names: Nilson
+repository-code: "https://github.com/nilson01/kernelmix"
+license: GPL-2.0-only

kernelmix-0.3.0/CONTRIBUTING.md

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+# Contributing
+
+Report bugs with a small example, package/dependency versions, the full error and
+the expected behavior. Remove confidential data before sharing an example.
+
+For a source checkout:
+
+```sh
+python -m pip install -e ".[dev]"
+python -m pytest
+python -m ruff check src tests tools
+```
+
+Include a regression test for a corrected defect. Method changes need an independent mathematical or numerical check and updated documentation. Software comparisons must state input transformations, priors and effect scales. Record example-data sources and licenses; exclude confidential data, fitted archives, credentials and local build files.
+
+## Build documentation
+
+The maintained sources are the README and Markdown guides in `docs`.
+
+Install the optional documentation tools:
+
+```sh
+python -m pip install ".[docs]"
+python -m mkdocs build --strict
+```
+
+The static website is written to `site/`. This command builds files locally; it does not deploy them. The site groups the maintained API chapter by task, adds search and renders equations with MathJax. Browser equation rendering requires access to the pinned MathJax CDN resource.
+
+To rebuild `docs/manual.pdf`, install a local `pdflatex` distribution, then run:
+
+```sh
+python tools/build_manual.py
+```
+
+Pandoc and LaTeX build the PDF; intermediate TeX is temporary. Inspect the resulting website and PDF after content changes, including links, equations, figures and page layout. Keep numerical evidence synchronized with the checks that actually ran.
+
+
+## Refresh the source example data
+
+The ozone source CSV was exported from R 4.5.0. To export another copy for a documented comparison:
+
+```sh
+Rscript tools/export_airquality.R destination.csv
+```
+
+Keep the source version, license, hash, units and row exclusions with any replacement. When source data change, regenerate affected results and record the new version.

kernelmix-0.3.0/LICENSE

@@ -0,0 +1,339 @@
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kernelmix-0.3.0/MANIFEST.in

@@ -0,0 +1,5 @@
+include LICENSE NOTICE README.md CONTRIBUTING.md CHANGELOG.md CITATION.cff mkdocs.yml
+recursive-include docs *.md *.pdf *.png *.csv *.json *.py *.js *.css
+recursive-include tests *.py *.json
+recursive-include tools *.py *.R
+prune .github

kernelmix-0.3.0/NOTICE

@@ -0,0 +1,23 @@
+KernelMix
+Copyright (C) 2026 Nilson Chapagain
+
+KernelMix implements selected Bayesian kernel machine regression methods described
+by Bobb et al. (2015), DOI 10.1093/biostatistics/kxu058, and Bobb et al. (2018),
+DOI 10.1186/s12940-018-0413-y.
+
+The R package bkmr 0.2.2, by Jennifer F. Bobb and contributors, is a reference for
+prior conventions, likelihoods and posterior summaries. Its GPL-2 source informed
+this implementation. The installed package is used in optional reference checks.
+KernelMix uses distinct Python code and sampling proposals. Count/survival
+fitting uses elliptical slice sampling (Murray, Adams and MacKay, 2010,
+https://proceedings.mlr.press/v9/murray10a.html). Standard count and survival
+likelihood references and selected priors are identified in docs/methods.md.
+The original authors have not endorsed this package. Source papers and their
+figures are not bundled.
+
+KernelMix code and documentation are distributed under GNU GPL version 2 only,
+without warranty. See LICENSE. NumPy, SciPy and Matplotlib retain their own licenses.
+
+Additional kernel definitions follow Rasmussen and Williams (2006), Gaussian Processes for Machine Learning, chapter 4. Random Fourier features follow Rahimi and Recht (2007). Predictive processes follow Banerjee et al. (2008), DOI 10.1111/j.1467-9868.2008.00663.x. Residual variance/correlation and survival data conventions are separately cited in the structured-model guide. These are model ingredients, not claims of new estimators or complete upstream interfaces.
+
+The bundled airquality CSV is exported from R 4.5.0 datasets::airquality. The original measurements are credited to the New York State Department of Conservation and the National Weather Service; see Chambers et al. (1983), Graphical Methods for Data Analysis, and the R datasets documentation. This export and its test fixture are distributed under GPL-2.0 as part of this package.

kernelmix-0.3.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: kernelmix
+Version: 0.3.0
+Summary: Bayesian kernel machine regression for exposure mixtures
+Author: Nilson Chapagain
+License-Expression: GPL-2.0-only
+Project-URL: Repository, https://github.com/nilson01/kernelmix
+Project-URL: Issues, https://github.com/nilson01/kernelmix/issues
+Project-URL: Documentation, https://nilson01.github.io/kernelmix/
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+License-File: NOTICE
+Requires-Dist: numpy>=1.24
+Requires-Dist: scipy>=1.10
+Provides-Extra: docs
+Requires-Dist: pypandoc_binary>=1.15; extra == "docs"
+Requires-Dist: mkdocs<2,>=1.6; extra == "docs"
+Requires-Dist: pymdown-extensions<11,>=10; extra == "docs"
+Provides-Extra: plots
+Requires-Dist: matplotlib>=3.7; extra == "plots"
+Provides-Extra: dev
+Requires-Dist: pytest>=7.4; extra == "dev"
+Requires-Dist: ruff>=0.9; extra == "dev"
+Requires-Dist: build>=1.2; extra == "dev"
+Requires-Dist: twine>=5; extra == "dev"
+Requires-Dist: matplotlib>=3.7; extra == "dev"
+Dynamic: license-file
+
+# KernelMix
+
+KernelMix fits Bayesian kernel machine regression (BKMR) for exposure mixtures in Python.
+It models how an outcome varies with several exposures together, allowing curved associations and interactions between exposures. Other measured variables enter as linear adjustment terms.
+
+To handle different outcome types, the package combines this exposure function with continuous, binary, count or survival models. NumPy and SciPy handle fitting and prediction; R is not required.
+
+| Task | Start here |
+| --- | --- |
+| Choose an outcome model and priors | [Models and assumptions](docs/methods.md) |
+| Fit, inspect, predict and compare exposures | [Analysis tutorial](docs/tutorial.md) |
+| Model clusters, kernels or detailed survival records | [Structured models](docs/structured.md) |
+| Find arguments and result fields | [API reference](docs/api.md) |
+| Check numerical evidence and limitations | [Evidence](docs/reproduction.md) |
+
+## Install
+
+Install directly from GitHub:
+
+```sh
+python -m pip install "kernelmix[plots] @ git+https://github.com/nilson01/kernelmix.git@main"
+```
+
+Or, from a downloaded source folder:
+
+```sh
+python -m pip install ".[plots]"
+```
+
+Python 3.10 or later is required. Omit `[plots]` if plots are not needed.
+
+## Example
+
+```python
+import numpy as np
+from kernelmix import fit, univariate_response, plot_response
+
+rng = np.random.default_rng(17)
+Z = rng.normal(size=(24, 2))
+y = np.sin(Z[:, 0]) + 0.3 * Z[:, 1] + rng.normal(0, 0.5, 24)
+result = fit(y, Z, draws=200, warmup=200, chains=2, seed=17)
+print(result.summary())
+curve = univariate_response(result, variable=0, points=25, seed=17)
+ax = plot_response(curve)
+```
+
+Example output (first rows):
+
+```text
+BKMRFit(family='gaussian', n=24, exposures=2, chains=2, draws=200)
+95% pointwise credible intervals
+Parameter             Mean         SD      Lower      Upper
+lambda               16.93      9.047      4.145      38.61
+sigma2              0.2159    0.08346     0.1142     0.4188
+```
+
+These short chains illustrate the output and trigger mixing warnings. For an analysis, use longer runs and inspect agreement between chains and effective sample sizes, which account for dependence between draws.
+
+![Exposure response curve with pointwise 95% credible intervals](docs/figures/response.png)
+
+The curve varies the first exposure with the second at its median, relative to the all-median exposure profile. It describes a fitted association; a causal interpretation requires additional assumptions.
+
+## Documentation
+
+Browse the [searchable documentation](https://nilson01.github.io/kernelmix/).
+
+The [common questions](docs/faq.md) explain prediction scales, missing values, selection and diagnostics. The [observed ozone example](docs/airquality.md) includes source data and saved results. Download the [reference manual](docs/manual.pdf) for offline reading. Contributors can find [development checks](docs/development.md) separately.
+
+## References and license
+
+[Bobb et al. (2015)](https://doi.org/10.1093/biostatistics/kxu058) introduced BKMR for exposure-mixture analysis. [Bobb et al. (2018)](https://doi.org/10.1186/s12940-018-0413-y) described the R software and its binary-outcome extension. KernelMix implements these methods separately in Python and adds count and survival likelihoods, defined in the [model guide](docs/methods.md).
+
+We compare selected Gaussian and probit posterior summaries and conditional calculations, including random intercepts, with installed R [`bkmr`](https://cran.r-project.org/package=bkmr) 0.2.2. The [evidence summary](docs/reproduction.md) records results and limits. See [NOTICE](NOTICE) for attribution and [LICENSE](LICENSE) for GPL-2.0-only terms.

kernelmix-0.3.0/README.md

@@ -0,0 +1,73 @@
+# KernelMix
+
+KernelMix fits Bayesian kernel machine regression (BKMR) for exposure mixtures in Python.
+It models how an outcome varies with several exposures together, allowing curved associations and interactions between exposures. Other measured variables enter as linear adjustment terms.
+
+To handle different outcome types, the package combines this exposure function with continuous, binary, count or survival models. NumPy and SciPy handle fitting and prediction; R is not required.
+
+| Task | Start here |
+| --- | --- |
+| Choose an outcome model and priors | [Models and assumptions](docs/methods.md) |
+| Fit, inspect, predict and compare exposures | [Analysis tutorial](docs/tutorial.md) |
+| Model clusters, kernels or detailed survival records | [Structured models](docs/structured.md) |
+| Find arguments and result fields | [API reference](docs/api.md) |
+| Check numerical evidence and limitations | [Evidence](docs/reproduction.md) |
+
+## Install
+
+Install directly from GitHub:
+
+```sh
+python -m pip install "kernelmix[plots] @ git+https://github.com/nilson01/kernelmix.git@main"
+```
+
+Or, from a downloaded source folder:
+
+```sh
+python -m pip install ".[plots]"
+```
+
+Python 3.10 or later is required. Omit `[plots]` if plots are not needed.
+
+## Example
+
+```python
+import numpy as np
+from kernelmix import fit, univariate_response, plot_response
+
+rng = np.random.default_rng(17)
+Z = rng.normal(size=(24, 2))
+y = np.sin(Z[:, 0]) + 0.3 * Z[:, 1] + rng.normal(0, 0.5, 24)
+result = fit(y, Z, draws=200, warmup=200, chains=2, seed=17)
+print(result.summary())
+curve = univariate_response(result, variable=0, points=25, seed=17)
+ax = plot_response(curve)
+```
+
+Example output (first rows):
+
+```text
+BKMRFit(family='gaussian', n=24, exposures=2, chains=2, draws=200)
+95% pointwise credible intervals
+Parameter             Mean         SD      Lower      Upper
+lambda               16.93      9.047      4.145      38.61
+sigma2              0.2159    0.08346     0.1142     0.4188
+```
+
+These short chains illustrate the output and trigger mixing warnings. For an analysis, use longer runs and inspect agreement between chains and effective sample sizes, which account for dependence between draws.
+
+![Exposure response curve with pointwise 95% credible intervals](docs/figures/response.png)
+
+The curve varies the first exposure with the second at its median, relative to the all-median exposure profile. It describes a fitted association; a causal interpretation requires additional assumptions.
+
+## Documentation
+
+Browse the [searchable documentation](https://nilson01.github.io/kernelmix/).
+
+The [common questions](docs/faq.md) explain prediction scales, missing values, selection and diagnostics. The [observed ozone example](docs/airquality.md) includes source data and saved results. Download the [reference manual](docs/manual.pdf) for offline reading. Contributors can find [development checks](docs/development.md) separately.
+
+## References and license
+
+[Bobb et al. (2015)](https://doi.org/10.1093/biostatistics/kxu058) introduced BKMR for exposure-mixture analysis. [Bobb et al. (2018)](https://doi.org/10.1186/s12940-018-0413-y) described the R software and its binary-outcome extension. KernelMix implements these methods separately in Python and adds count and survival likelihoods, defined in the [model guide](docs/methods.md).
+
+We compare selected Gaussian and probit posterior summaries and conditional calculations, including random intercepts, with installed R [`bkmr`](https://cran.r-project.org/package=bkmr) 0.2.2. The [evidence summary](docs/reproduction.md) records results and limits. See [NOTICE](NOTICE) for attribution and [LICENSE](LICENSE) for GPL-2.0-only terms.