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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/

PyStan3 / Stan3

The development of PyStan3 with updated API can be found under stan-dev/pystan-next

Detailed Installation Instructions

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

Windows Installation Instructions

Detailed installation instructions for Windows can be found in docs under PyStan on Windows

Quick Installation (Linux and macOS)

NumPy and Cython (version 0.22 or greater) are required. matplotlib is optional. ArviZ is recommended for visualization and analysis.

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

To install latest development version user can also use pip

pip install git+https://github.com/stan-dev/pystan

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()

# updated traceplot can be plotted with
import arviz as az
az.plot_trace(fit)

Metadata

Release files for pystan 2.19.1.1

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Source distribution (sdist)

Source distribution for pystan 2.19.1.1
File	Size	Uploaded
pystan-2.19.1.1.tar.gz	16.2 MB	Oct 27, 2019	Details

Built distributions (wheels)

Table of built distributions (wheels) for pystan 2.19.1.1
File	Interpreter	ABI	Platform	Reset
pystan-2.19.1.1-cp38-cp38-win_amd64.whl 79.8 MB Aug 12, 2020	CPython 3.8	CPython 3.8	Windows x86-64	Details
pystan-2.19.1.1-cp38-cp38-win32.whl 55.7 MB Aug 12, 2020	CPython 3.8	CPython 3.8	Windows x86-32	Details
pystan-2.19.1.1-cp38-cp38-manylinux1_x86_64.whl 62.6 MB Aug 12, 2020	CPython 3.8	CPython 3.8	Linux glibc 2.5+ x86-64	Details
pystan-2.19.1.1-cp38-cp38-macosx_10_9_x86_64.whl 37.4 MB Aug 12, 2020	CPython 3.8	CPython 3.8	macOS 10.9+ x86-64	Details
pystan-2.19.1.1-cp37-cp37m-win_amd64.whl 79.8 MB Oct 27, 2019	CPython 3.7	CPython 3.7 pymalloc	Windows x86-64	Details
pystan-2.19.1.1-cp37-cp37m-win32.whl 55.7 MB Oct 27, 2019	CPython 3.7	CPython 3.7 pymalloc	Windows x86-32	Details
pystan-2.19.1.1-cp37-cp37m-manylinux1_x86_64.whl 67.3 MB Oct 27, 2019	CPython 3.7	CPython 3.7 pymalloc	Linux glibc 2.5+ x86-64	Details
pystan-2.19.1.1-cp37-cp37m-macosx_10_6_intel.whl 39.1 MB Oct 27, 2019	CPython 3.7	CPython 3.7 pymalloc	macOS 10.6+ Intel (x86-64, i386)	Details
pystan-2.19.1.1-cp36-cp36m-win_amd64.whl 79.8 MB Oct 27, 2019	CPython 3.6	CPython 3.6 pymalloc	Windows x86-64	Details
pystan-2.19.1.1-cp36-cp36m-win32.whl 55.7 MB Oct 27, 2019	CPython 3.6	CPython 3.6 pymalloc	Windows x86-32	Details
pystan-2.19.1.1-cp36-cp36m-manylinux1_x86_64.whl 67.3 MB Oct 27, 2019	CPython 3.6	CPython 3.6 pymalloc	Linux glibc 2.5+ x86-64	Details
pystan-2.19.1.1-cp36-cp36m-macosx_10_6_intel.whl 37.4 MB Oct 27, 2019	CPython 3.6	CPython 3.6 pymalloc	macOS 10.6+ Intel (x86-64, i386)	Details
pystan-2.19.1.1-cp35-cp35m-win_amd64.whl 79.8 MB Oct 27, 2019	CPython 3.5	CPython 3.5 pymalloc	Windows x86-64	Details
pystan-2.19.1.1-cp35-cp35m-win32.whl 55.7 MB Oct 27, 2019	CPython 3.5	CPython 3.5 pymalloc	Windows x86-32	Details
pystan-2.19.1.1-cp35-cp35m-manylinux1_x86_64.whl 67.2 MB Oct 27, 2019	CPython 3.5	CPython 3.5 pymalloc	Linux glibc 2.5+ x86-64	Details
pystan-2.19.1.1-cp35-cp35m-macosx_10_6_intel.whl 37.4 MB Oct 27, 2019	CPython 3.5	CPython 3.5 pymalloc	macOS 10.6+ Intel (x86-64, i386)	Details
pystan-2.19.1.1-cp27-cp27mu-manylinux1_x86_64.whl 67.2 MB Oct 27, 2019	CPython 2.7	CPython 2.7 pymalloc wide-unicode	Linux glibc 2.5+ x86-64	Details
pystan-2.19.1.1-cp27-cp27m-manylinux1_x86_64.whl 67.2 MB Oct 27, 2019	CPython 2.7	CPython 2.7 pymalloc	Linux glibc 2.5+ x86-64	Details
pystan-2.19.1.1-cp27-cp27m-macosx_10_6_intel.whl 37.4 MB Oct 27, 2019	CPython 2.7	CPython 2.7 pymalloc	macOS 10.6+ Intel (x86-64, i386)	Details

Total release size: 1.1 GB

Release files / pystan-2.19.1.1.tar.gz

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Size	16.2 MB
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Size	79.8 MB
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Size	55.7 MB
Tags	CPython 3.8 Windows x86-32
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Size	67.2 MB
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SHA-256 checksum How to use checksums	`2baa4106ddc7fb90712bd0e5ab8693ce130b001c6166839247511326edc6d0ba`
BLAKE2b-256 checksum How to use checksums	`cebd449fb3b6d5a04cc908c343d3546e425e00a829a13c185c9a627a9f0e8bd3`
Upload date	Oct 27, 2019
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/1.11.0 pkginfo/1.4.2 requests/2.21.0 setuptools/40.1.0 requests-toolbelt/0.8.0 tqdm/4.19.5 CPython/3.6.6`

Release files / pystan-2.19.1.1-cp27-cp27m-macosx_10_6_intel.whl

Download URL	pystan-2.19.1.1-cp27-cp27m-macosx_10_6_intel.whl
Size	37.4 MB
Tags	CPython 2.7 CPython 2.7 pymalloc macOS 10.6+ Intel (x86-64, i386)
SHA-256 checksum How to use checksums	`4a0820df5fcd13c7a4cae75d59809adee72d1135a604dc2b5f068d4ac8ca349e`
BLAKE2b-256 checksum How to use checksums	`58ef51902e2bbdb8ea2aa7f1d97c78bc08348b5e4b70dd9659ec8231c0500b6a`
Upload date	Oct 27, 2019
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/1.11.0 pkginfo/1.4.2 requests/2.21.0 setuptools/40.1.0 requests-toolbelt/0.8.0 tqdm/4.19.5 CPython/3.6.6`

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pystan 2.19.1.1

PyStan: The Python Interface to Stan

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PyStan3 / Stan3

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Release files / pystan-2.19.1.1-cp36-cp36m-win_amd64.whl

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Release files / pystan-2.19.1.1-cp35-cp35m-win_amd64.whl

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Release files / pystan-2.19.1.1-cp35-cp35m-macosx_10_6_intel.whl

Release files / pystan-2.19.1.1-cp27-cp27mu-manylinux1_x86_64.whl

Release files / pystan-2.19.1.1-cp27-cp27m-manylinux1_x86_64.whl

Release files / pystan-2.19.1.1-cp27-cp27m-macosx_10_6_intel.whl

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