PyStan: The Python Interface to Stan

PyStan provides a Python interface to Stan, a package for Bayesian inference using the No-U-Turn sampler, a variant of Hamiltonian Monte Carlo.

For more information on Stan and its modeling language, see the Stan User’s Guide and Reference Manual at http://mc-stan.org/.

Important links

HTML documentation: https://pystan.readthedocs.org
Issue tracker: https://github.com/stan-dev/pystan/issues
Source code repository: https://github.com/stan-dev/pystan
Stan: http://mc-stan.org/
Stan User’s Guide and Reference Manual (pdf) available at http://mc-stan.org

Similar projects

PyMC: http://pymc-devs.github.io/pymc/

Detailed Installation Instructions

Detailed installation instructions can be found in the doc/installation_beginner.md file.

Quick Installation

NumPy and Cython (version 0.22 or greater) are required. matplotlib is optional.

PyStan and the required packages may be installed from the Python Package Index using pip.

pip install pystan

Alternatively, if Cython (version 0.22 or greater) and NumPy are already available, PyStan may be installed from source with the following commands

git clone --recursive https://github.com/stan-dev/pystan.git
cd pystan
python setup.py install

If you encounter an ImportError after compiling from source, try changing out of the source directory before attempting import pystan. On Linux and OS X cd /tmp will work.

Example

import pystan
import numpy as np
import matplotlib.pyplot as plt

schools_code = """
data {
    int<lower=0> J; // number of schools
    real y[J]; // estimated treatment effects
    real<lower=0> sigma[J]; // s.e. of effect estimates
}
parameters {
    real mu;
    real<lower=0> tau;
    real eta[J];
}
transformed parameters {
    real theta[J];
    for (j in 1:J)
        theta[j] = mu + tau * eta[j];
}
model {
    eta ~ normal(0, 1);
    y ~ normal(theta, sigma);
}
"""

schools_dat = {'J': 8,
               'y': [28,  8, -3,  7, -1,  1, 18, 12],
               'sigma': [15, 10, 16, 11,  9, 11, 10, 18]}

sm = pystan.StanModel(model_code=schools_code)
fit = sm.sampling(data=schools_dat, iter=1000, chains=4)

print(fit)

eta = fit.extract(permuted=True)['eta']
np.mean(eta, axis=0)

# if matplotlib is installed (optional, not required), a visual summary and
# traceplot are available
fit.plot()
plt.show()

Metadata

Release files for pystan 2.17.1.0

For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.

Source distribution (sdist)

Source distribution for pystan 2.17.1.0
File	Size	Uploaded
pystan-2.17.1.0.tar.gz	13.9 MB	Jan 18, 2018	Details

Built distributions (wheels)

Table of built distributions (wheels) for pystan 2.17.1.0
File	Interpreter	ABI	Platform	Reset
pystan-2.17.1.0-cp36-cp36m-win_amd64.whl 45.5 MB Jan 18, 2018	CPython 3.6	CPython 3.6 pymalloc	Windows x86-64	Details
pystan-2.17.1.0-cp36-cp36m-win32.whl 45.3 MB Jan 18, 2018	CPython 3.6	CPython 3.6 pymalloc	Windows x86-32	Details
pystan-2.17.1.0-cp36-cp36m-manylinux1_x86_64.whl 68.1 MB Jan 18, 2018	CPython 3.6	CPython 3.6 pymalloc	Linux glibc 2.5+ x86-64	Details
pystan-2.17.1.0-cp36-cp36m-manylinux1_i686.whl 67.2 MB Jan 18, 2018	CPython 3.6	CPython 3.6 pymalloc	Linux glibc 2.5+ x86-32	Details
pystan-2.17.1.0-cp36-cp36m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl 48.0 MB Jan 20, 2018	CPython 3.6	CPython 3.6 pymalloc	macOS 10.10+ x86-64, macOS 10.6+ Intel (x86-64, i386), macOS 10.10+ Intel (x86-64, i386), macOS 10.9+ x86-64, macOS 10.9+ Intel (x86-64, i386)	Details
pystan-2.17.1.0-cp35-cp35m-win_amd64.whl 45.5 MB Jan 18, 2018	CPython 3.5	CPython 3.5 pymalloc	Windows x86-64	Details
pystan-2.17.1.0-cp35-cp35m-win32.whl 45.3 MB Jan 18, 2018	CPython 3.5	CPython 3.5 pymalloc	Windows x86-32	Details
pystan-2.17.1.0-cp35-cp35m-manylinux1_x86_64.whl 68.1 MB Jan 18, 2018	CPython 3.5	CPython 3.5 pymalloc	Linux glibc 2.5+ x86-64	Details
pystan-2.17.1.0-cp35-cp35m-manylinux1_i686.whl 67.2 MB Jan 18, 2018	CPython 3.5	CPython 3.5 pymalloc	Linux glibc 2.5+ x86-32	Details
pystan-2.17.1.0-cp35-cp35m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl 48.0 MB Jan 20, 2018	CPython 3.5	CPython 3.5 pymalloc	macOS 10.10+ x86-64, macOS 10.6+ Intel (x86-64, i386), macOS 10.9+ x86-64, macOS 10.10+ Intel (x86-64, i386), macOS 10.9+ Intel (x86-64, i386)	Details
pystan-2.17.1.0-cp34-cp34m-manylinux1_x86_64.whl 68.1 MB Jan 18, 2018	CPython 3.4	CPython 3.4 pymalloc	Linux glibc 2.5+ x86-64	Details
pystan-2.17.1.0-cp34-cp34m-manylinux1_i686.whl 67.2 MB Jan 18, 2018	CPython 3.4	CPython 3.4 pymalloc	Linux glibc 2.5+ x86-32	Details
pystan-2.17.1.0-cp27-cp27mu-manylinux1_x86_64.whl 68.1 MB Jan 18, 2018	CPython 2.7	CPython 2.7 pymalloc wide-unicode	Linux glibc 2.5+ x86-64	Details
pystan-2.17.1.0-cp27-cp27mu-manylinux1_i686.whl 67.2 MB Jan 18, 2018	CPython 2.7	CPython 2.7 pymalloc wide-unicode	Linux glibc 2.5+ x86-32	Details
pystan-2.17.1.0-cp27-cp27m-manylinux1_x86_64.whl 68.1 MB Jan 18, 2018	CPython 2.7	CPython 2.7 pymalloc	Linux glibc 2.5+ x86-64	Details
pystan-2.17.1.0-cp27-cp27m-manylinux1_i686.whl 67.2 MB Jan 18, 2018	CPython 2.7	CPython 2.7 pymalloc	Linux glibc 2.5+ x86-32	Details
pystan-2.17.1.0-cp27-cp27m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl 48.0 MB Jan 20, 2018	CPython 2.7	CPython 2.7 pymalloc	macOS 10.10+ Intel (x86-64, i386), macOS 10.6+ Intel (x86-64, i386), macOS 10.9+ x86-64, macOS 10.9+ Intel (x86-64, i386), macOS 10.10+ x86-64	Details

Total release size: 1.0 GB

Release files / pystan-2.17.1.0.tar.gz

Download URL	pystan-2.17.1.0.tar.gz
Size	13.9 MB
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Release files / pystan-2.17.1.0-cp36-cp36m-win_amd64.whl

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Size	45.5 MB
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Release files / pystan-2.17.1.0-cp36-cp36m-win32.whl

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Size	45.3 MB
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Release files / pystan-2.17.1.0-cp36-cp36m-manylinux1_x86_64.whl

Download URL	pystan-2.17.1.0-cp36-cp36m-manylinux1_x86_64.whl
Size	68.1 MB
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Release files / pystan-2.17.1.0-cp36-cp36m-manylinux1_i686.whl

Download URL	pystan-2.17.1.0-cp36-cp36m-manylinux1_i686.whl
Size	67.2 MB
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Release files / pystan-2.17.1.0-cp36-cp36m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl

Download URL	pystan-2.17.1.0-cp36-cp36m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl
Size	48.0 MB
Tags	CPython 3.6 CPython 3.6 pymalloc macOS 10.10+ Intel (x86-64, i386) macOS 10.10+ x86-64 macOS 10.6+ Intel (x86-64, i386) macOS 10.9+ Intel (x86-64, i386) macOS 10.9+ x86-64
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Release files / pystan-2.17.1.0-cp35-cp35m-win_amd64.whl

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Size	45.5 MB
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Release files / pystan-2.17.1.0-cp35-cp35m-manylinux1_x86_64.whl

Download URL	pystan-2.17.1.0-cp35-cp35m-manylinux1_x86_64.whl
Size	68.1 MB
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Release files / pystan-2.17.1.0-cp35-cp35m-manylinux1_i686.whl

Download URL	pystan-2.17.1.0-cp35-cp35m-manylinux1_i686.whl
Size	67.2 MB
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Release files / pystan-2.17.1.0-cp35-cp35m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl

Download URL	pystan-2.17.1.0-cp35-cp35m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl
Size	48.0 MB
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Release files / pystan-2.17.1.0-cp34-cp34m-manylinux1_x86_64.whl

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Size	68.1 MB
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Release files / pystan-2.17.1.0-cp34-cp34m-manylinux1_i686.whl

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Size	67.2 MB
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Release files / pystan-2.17.1.0-cp27-cp27mu-manylinux1_x86_64.whl

Download URL	pystan-2.17.1.0-cp27-cp27mu-manylinux1_x86_64.whl
Size	68.1 MB
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Release files / pystan-2.17.1.0-cp27-cp27mu-manylinux1_i686.whl

Download URL	pystan-2.17.1.0-cp27-cp27mu-manylinux1_i686.whl
Size	67.2 MB
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Release files / pystan-2.17.1.0-cp27-cp27m-manylinux1_x86_64.whl

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Size	68.1 MB
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Size	67.2 MB
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Release files / pystan-2.17.1.0-cp27-cp27m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl

Download URL	pystan-2.17.1.0-cp27-cp27m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl
Size	48.0 MB
Tags	CPython 2.7 CPython 2.7 pymalloc macOS 10.10+ Intel (x86-64, i386) macOS 10.10+ x86-64 macOS 10.6+ Intel (x86-64, i386) macOS 10.9+ Intel (x86-64, i386) macOS 10.9+ x86-64
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