brmspy 0.1.7__tar.gz

brmspy-0.1.7/LICENSE

@@ -0,0 +1,201 @@
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brmspy-0.1.7/PKG-INFO

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+Metadata-Version: 2.4
+Name: brmspy
+Version: 0.1.7
+Summary: Python-first access to R's brms with proper parameter names, ArviZ support, and cmdstanr performance
+Author-email: Remi Sebastian Kits <remi.sebastian.kits@gmail.com>, Adam Haber <adamhaber@gmail.com>
+Maintainer-email: Remi Sebastian Kits <remi.sebastian.kits@gmail.com>
+License: Apache-2.0
+Project-URL: Homepage, https://github.com/kaitumisuuringute-keskus/brmspy
+Project-URL: Repository, https://github.com/kaitumisuuringute-keskus/brmspy
+Project-URL: Documentation, https://kaitumisuuringute-keskus.github.io/brmspy/
+Project-URL: Bug Tracker, https://github.com/kaitumisuuringute-keskus/brmspy/issues
+Project-URL: Changelog, https://github.com/kaitumisuuringute-keskus/brmspy/blob/master/CHANGELOG.md
+Keywords: bayesian,regression,brms,stan,cmdstan,rpy2,multilevel-models,statistical-modeling
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Science/Research
+Classifier: Intended Audience :: Education
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Natural Language :: English
+Classifier: Operating System :: OS Independent
+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: Programming Language :: Python :: 3.14
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: R
+Classifier: Topic :: Scientific/Engineering
+Classifier: Topic :: Scientific/Engineering :: Mathematics
+Classifier: Topic :: Scientific/Engineering :: Information Analysis
+Classifier: Typing :: Typed
+Requires-Python: <3.15,>=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: cmdstanpy>=1.2.0
+Requires-Dist: numpy>1.24.4
+Requires-Dist: pandas>=1.3.0
+Requires-Dist: rpy2>=3.5.0
+Requires-Dist: arviz>=0.15.0
+Provides-Extra: dev
+Requires-Dist: pytest>=7.0.0; extra == "dev"
+Requires-Dist: pytest-cov>=4.0.0; extra == "dev"
+Requires-Dist: black>=23.0.0; extra == "dev"
+Requires-Dist: ruff>=0.1.0; extra == "dev"
+Requires-Dist: mypy>=1.0.0; extra == "dev"
+Requires-Dist: isort>=5.12.0; extra == "dev"
+Requires-Dist: pre-commit>=3.0.0; extra == "dev"
+Provides-Extra: viz
+Requires-Dist: matplotlib>=3.5.0; extra == "viz"
+Requires-Dist: seaborn>=0.12.0; extra == "viz"
+Provides-Extra: test
+Requires-Dist: pytest>=7.0.0; extra == "test"
+Requires-Dist: pytest-cov>=4.0.0; extra == "test"
+Requires-Dist: tqdm; extra == "test"
+Requires-Dist: pytest-xdist>=3.0.0; extra == "test"
+Provides-Extra: all
+Requires-Dist: brmspy[dev,test,viz]; extra == "all"
+Dynamic: license-file
+
+# brmspy
+
+Python-first access to R's [brms](https://paul-buerkner.github.io/brms/)  with proper parameter names, ArviZ support, and cmdstanr performance. The easiest way to run brms models from Python.
+
+This is an early development version of the library, use with caution.
+
+[![Python 3.10+](https://img.shields.io/badge/python-3.10+-blue.svg)](https://www.python.org/downloads/)
+[![License: Apache 2.0](https://img.shields.io/badge/License-Apache%202.0-blue.svg)](https://opensource.org/licenses/Apache-2.0)
+[![Documentation](https://img.shields.io/badge/docs-mkdocs-blue.svg)](https://kaitumisuuringute-keskus.github.io/brmspy/)
+[![Coverage](https://kaitumisuuringute-keskus.github.io/brmspy/badges/coverage.svg)](https://github.com/kaitumisuuringute-keskus/brmspy/actions)
+[![Tests](https://github.com/kaitumisuuringute-keskus/brmspy/workflows/Python%20Test%20Matrix/badge.svg)](https://github.com/kaitumisuuringute-keskus/brmspy/actions)
+
+## Installation
+
+```bash
+pip install brmspy
+```
+
+First-time setup (installs brms, cmdstanr, and CmdStan in R):
+
+```python
+from brmspy import brms
+brms.install_brms() # requires R to be installed already
+```
+
+## Quick Start
+
+```python
+from brmspy import brms, prior
+import arviz as az
+
+# Load data
+epilepsy = brms.get_brms_data("epilepsy")
+
+# Fit model
+model = brms.fit(
+    formula="count ~ zAge + zBase * Trt + (1|patient)",
+    data=epilepsy,
+    family="poisson",
+    priors=[
+        prior("normal(0, 1)", "b"),
+        prior("exponential(1)", "sd", group="patient"),
+        prior("student_t(3, 0, 2.5)", "Intercept")
+    ],
+    chains=4,
+    iter=2000
+)
+
+# Analyze
+az.summary(model.idata)
+az.plot_posterior(model.idata)
+```
+
+## Key Features
+
+- **Proper parameter names**: Returns `b_Intercept`, `b_zAge`, `sd_patient__Intercept` instead of generic names like `b_dim_0`
+- **arviz integration**: Returns `arviz.InferenceData` by default for Python workflow
+- **brms formula syntax**: Full support for brms formula interface including random effects
+- **Dual access**: Results include both `.idata` (arviz) and `.r` (brmsfit) attributes
+- **No reimplementation**: Delegates all modeling logic to real brms. No Python-side reimplementation, no divergence from native behavior. Opinionated wrappers that rebuild formulas or stancode in Python inevitably drift from brms and accumulate their own bugs.
+
+## API Reference
+
+[Documentation](https://kaitumisuuringute-keskus.github.io/brmspy/)
+
+### Setup Functions
+- `brms.install_brms()` - Install brms, cmdstanr, and CmdStan
+- `brms.get_brms_version()` - Get installed brms version
+
+### Data Functions
+- `brms.get_brms_data()` - Load example datasets from brms
+
+### Model Functions
+- `brms.formula()` - Define formula with kwargs
+- `brms.fit()` - Fit Bayesian regression model
+- `brms.summary()` - Generate summary statistics as DataFrame
+- `brms.make_stancode()` - Generate Stan code for model
+
+### Prediction Functions
+- `brms.posterior_epred()` - Expected value predictions (without noise)
+- `brms.posterior_predict()` - Posterior predictive samples (with noise)
+- `brms.posterior_linpred()` - Linear predictor values
+- `brms.log_lik()` - Log-likelihood values
+
+
+## Usage
+
+### Basic Model
+
+```python
+from brmspy import brms
+
+kidney = brms.get_brms_data("kidney")
+
+model = brms.fit(
+    formula="time ~ age + disease",
+    data=kidney,
+    family="gaussian",
+    chains=4,
+    iter=2000
+)
+```
+
+### With Priors
+
+```python
+from brmspy import prior
+
+model = brms.fit(
+    formula="count ~ zAge + (1|patient)",
+    data=epilepsy,
+    family="poisson",
+    priors=[
+        prior("normal(0, 0.5)", "b"),
+        prior("cauchy(0, 1)", "sd")
+    ],
+    chains=4
+)
+```
+
+### Model Summary
+
+```python
+from brmspy import summary
+
+# Get summary statistics as DataFrame
+summary_df = summary(model)
+print(summary_df)
+```
+
+### Predictions
+
+```python
+# Expected value (without noise)
+epred = brms.posterior_epred(model, newdata=new_data)
+
+# Posterior predictive (with noise)
+ypred = brms.posterior_predict(model, newdata=new_data)
+
+# Linear predictor
+linpred = brms.posterior_linpred(model, newdata=new_data)
+
+# Log likelihood
+loglik = brms.log_lik(model, newdata=new_data)
+```
+
+### Access Both Python and R Objects
+
+```python
+model = brms.fit(formula="y ~ x", data=data, chains=4)
+
+# Python workflow with arviz
+az.summary(model.idata)
+az.plot_trace(model.idata)
+
+# R workflow (if needed)
+import rpy2.robjects as ro
+ro.r('summary')(model.r)
+```
+
+## Sampling Parameters
+
+```python
+model = brms.fit(
+    formula="y ~ x + (1|group)",
+    data=data,
+    iter=2000,      # Total iterations per chain
+    warmup=1000,    # Warmup iterations
+    chains=4,       # Number of chains
+    cores=4,        # Parallel cores
+    thin=1,         # Thinning
+    seed=123        # Random seed
+)
+```
+
+## Requirements
+
+**Python**: 3.10-3.14
+
+**R packages** (auto-installed via `brms.install_brms()`):
+- brms >= 2.20.0
+- cmdstanr
+- posterior
+
+**Python dependencies**:
+- rpy2 >= 3.5.0
+- pandas >= 1.3.0
+- numpy >= 1.20.0
+- arviz (optional, for InferenceData)
+
+## Development
+
+```bash
+git clone https://github.com/kaitumisuuringute-keskus/brmspy.git
+cd brmspy
+./init-venv.sh
+pytest tests/ -v
+```
+
+## Architecture
+
+brmspy uses:
+- **brms::brm()** with cmdstanr backend for fitting (ensures proper parameter naming)
+- **posterior** R package for conversion to draws format
+- **arviz** for Python-native analysis and visualization
+- **rpy2** for Python-R communication
+
+Previous versions used CmdStanPy directly, which resulted in generic parameter names. Current version calls brms directly to preserve brms' parameter renaming logic.
+
+## License
+
+Apache License 2.0
+
+## Credits
+
+- Original concept: [Adam Haber](https://github.com/adamhaber)
+- Current maintainer: [Remi Sebastian Kits](https://github.com/braffolk)
+- Built on [brms](https://paul-buerkner.github.io/brms/) by Paul-Christian Bürkner

brmspy-0.1.7/README.md

@@ -0,0 +1,218 @@
+# brmspy
+
+Python-first access to R's [brms](https://paul-buerkner.github.io/brms/)  with proper parameter names, ArviZ support, and cmdstanr performance. The easiest way to run brms models from Python.
+
+This is an early development version of the library, use with caution.
+
+[![Python 3.10+](https://img.shields.io/badge/python-3.10+-blue.svg)](https://www.python.org/downloads/)
+[![License: Apache 2.0](https://img.shields.io/badge/License-Apache%202.0-blue.svg)](https://opensource.org/licenses/Apache-2.0)
+[![Documentation](https://img.shields.io/badge/docs-mkdocs-blue.svg)](https://kaitumisuuringute-keskus.github.io/brmspy/)
+[![Coverage](https://kaitumisuuringute-keskus.github.io/brmspy/badges/coverage.svg)](https://github.com/kaitumisuuringute-keskus/brmspy/actions)
+[![Tests](https://github.com/kaitumisuuringute-keskus/brmspy/workflows/Python%20Test%20Matrix/badge.svg)](https://github.com/kaitumisuuringute-keskus/brmspy/actions)
+
+## Installation
+
+```bash
+pip install brmspy
+```
+
+First-time setup (installs brms, cmdstanr, and CmdStan in R):
+
+```python
+from brmspy import brms
+brms.install_brms() # requires R to be installed already
+```
+
+## Quick Start
+
+```python
+from brmspy import brms, prior
+import arviz as az
+
+# Load data
+epilepsy = brms.get_brms_data("epilepsy")
+
+# Fit model
+model = brms.fit(
+    formula="count ~ zAge + zBase * Trt + (1|patient)",
+    data=epilepsy,
+    family="poisson",
+    priors=[
+        prior("normal(0, 1)", "b"),
+        prior("exponential(1)", "sd", group="patient"),
+        prior("student_t(3, 0, 2.5)", "Intercept")
+    ],
+    chains=4,
+    iter=2000
+)
+
+# Analyze
+az.summary(model.idata)
+az.plot_posterior(model.idata)
+```
+
+## Key Features
+
+- **Proper parameter names**: Returns `b_Intercept`, `b_zAge`, `sd_patient__Intercept` instead of generic names like `b_dim_0`
+- **arviz integration**: Returns `arviz.InferenceData` by default for Python workflow
+- **brms formula syntax**: Full support for brms formula interface including random effects
+- **Dual access**: Results include both `.idata` (arviz) and `.r` (brmsfit) attributes
+- **No reimplementation**: Delegates all modeling logic to real brms. No Python-side reimplementation, no divergence from native behavior. Opinionated wrappers that rebuild formulas or stancode in Python inevitably drift from brms and accumulate their own bugs.
+
+## API Reference
+
+[Documentation](https://kaitumisuuringute-keskus.github.io/brmspy/)
+
+### Setup Functions
+- `brms.install_brms()` - Install brms, cmdstanr, and CmdStan
+- `brms.get_brms_version()` - Get installed brms version
+
+### Data Functions
+- `brms.get_brms_data()` - Load example datasets from brms
+
+### Model Functions
+- `brms.formula()` - Define formula with kwargs
+- `brms.fit()` - Fit Bayesian regression model
+- `brms.summary()` - Generate summary statistics as DataFrame
+- `brms.make_stancode()` - Generate Stan code for model
+
+### Prediction Functions
+- `brms.posterior_epred()` - Expected value predictions (without noise)
+- `brms.posterior_predict()` - Posterior predictive samples (with noise)
+- `brms.posterior_linpred()` - Linear predictor values
+- `brms.log_lik()` - Log-likelihood values
+
+
+## Usage
+
+### Basic Model
+
+```python
+from brmspy import brms
+
+kidney = brms.get_brms_data("kidney")
+
+model = brms.fit(
+    formula="time ~ age + disease",
+    data=kidney,
+    family="gaussian",
+    chains=4,
+    iter=2000
+)
+```
+
+### With Priors
+
+```python
+from brmspy import prior
+
+model = brms.fit(
+    formula="count ~ zAge + (1|patient)",
+    data=epilepsy,
+    family="poisson",
+    priors=[
+        prior("normal(0, 0.5)", "b"),
+        prior("cauchy(0, 1)", "sd")
+    ],
+    chains=4
+)
+```
+
+### Model Summary
+
+```python
+from brmspy import summary
+
+# Get summary statistics as DataFrame
+summary_df = summary(model)
+print(summary_df)
+```
+
+### Predictions
+
+```python
+# Expected value (without noise)
+epred = brms.posterior_epred(model, newdata=new_data)
+
+# Posterior predictive (with noise)
+ypred = brms.posterior_predict(model, newdata=new_data)
+
+# Linear predictor
+linpred = brms.posterior_linpred(model, newdata=new_data)
+
+# Log likelihood
+loglik = brms.log_lik(model, newdata=new_data)
+```
+
+### Access Both Python and R Objects
+
+```python
+model = brms.fit(formula="y ~ x", data=data, chains=4)
+
+# Python workflow with arviz
+az.summary(model.idata)
+az.plot_trace(model.idata)
+
+# R workflow (if needed)
+import rpy2.robjects as ro
+ro.r('summary')(model.r)
+```
+
+## Sampling Parameters
+
+```python
+model = brms.fit(
+    formula="y ~ x + (1|group)",
+    data=data,
+    iter=2000,      # Total iterations per chain
+    warmup=1000,    # Warmup iterations
+    chains=4,       # Number of chains
+    cores=4,        # Parallel cores
+    thin=1,         # Thinning
+    seed=123        # Random seed
+)
+```
+
+## Requirements
+
+**Python**: 3.10-3.14
+
+**R packages** (auto-installed via `brms.install_brms()`):
+- brms >= 2.20.0
+- cmdstanr
+- posterior
+
+**Python dependencies**:
+- rpy2 >= 3.5.0
+- pandas >= 1.3.0
+- numpy >= 1.20.0
+- arviz (optional, for InferenceData)
+
+## Development
+
+```bash
+git clone https://github.com/kaitumisuuringute-keskus/brmspy.git
+cd brmspy
+./init-venv.sh
+pytest tests/ -v
+```
+
+## Architecture
+
+brmspy uses:
+- **brms::brm()** with cmdstanr backend for fitting (ensures proper parameter naming)
+- **posterior** R package for conversion to draws format
+- **arviz** for Python-native analysis and visualization
+- **rpy2** for Python-R communication
+
+Previous versions used CmdStanPy directly, which resulted in generic parameter names. Current version calls brms directly to preserve brms' parameter renaming logic.
+
+## License
+
+Apache License 2.0
+
+## Credits
+
+- Original concept: [Adam Haber](https://github.com/adamhaber)
+- Current maintainer: [Remi Sebastian Kits](https://github.com/braffolk)
+- Built on [brms](https://paul-buerkner.github.io/brms/) by Paul-Christian Bürkner