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PyMC3 is a Python package for Bayesian statistical modeling and Probabilistic Machine Learning
focusing on advanced Markov chain Monte Carlo (MCMC) and variational inference (VI)
algorithms. Its flexibility and extensibility make it applicable to a
large suite of problems.

Check out the `getting started guide <http://docs.pymc.io/notebooks/getting_started>`__,  or
`interact with live examples <https://mybinder.org/v2/gh/pymc-devs/pymc3/master?filepath=%2Fdocs%2Fsource%2Fnotebooks>`__
using Binder!

Features
========

-  Intuitive model specification syntax, for example, ``x ~ N(0,1)``
   translates to ``x = Normal('x',0,1)``
-  **Powerful sampling algorithms**, such as the `No U-Turn
   Sampler <http://www.jmlr.org/papers/v15/hoffman14a.html>`__, allow complex models
   with thousands of parameters with little specialized knowledge of
   fitting algorithms.
-  **Variational inference**: `ADVI <http://www.jmlr.org/papers/v18/16-107.html>`__
   for fast approximate posterior estimation as well as mini-batch ADVI
   for large data sets.
-  Relies on `Theano <http://deeplearning.net/software/theano/>`__ which provides:
    *  Computation optimization and dynamic C compilation
    *  Numpy broadcasting and advanced indexing
    *  Linear algebra operators
    *  Simple extensibility
-  Transparent support for missing value imputation

Getting started
===============

If you already know about Bayesian statistics:
----------------------------------------------


-  `API quickstart guide <http://docs.pymc.io/notebooks/api_quickstart>`__
-  The `PyMC3 tutorial <http://docs.pymc.io/notebooks/getting_started>`__
-  `PyMC3 examples <http://docs.pymc.io/examples>`__ and the `API reference <http://docs.pymc.io/api>`__



Learn Bayesian statistics with a book together with PyMC3:
----------------------------------------------------------

-  `Probabilistic Programming and Bayesian Methods for Hackers <https://github.com/CamDavidsonPilon/Probabilistic-Programming-and-Bayesian-Methods-for-Hackers>`__: Fantastic book with many applied code examples.
-  `PyMC3 port of the book "Doing Bayesian Data Analysis" by John Kruschke <https://github.com/aloctavodia/Doing_bayesian_data_analysis>`__ as well as the `second edition <https://github.com/JWarmenhoven/DBDA-python>`__: Principled introduction to Bayesian data analysis.
-  `PyMC3 port of the book "Statistical Rethinking A Bayesian Course with Examples in R and Stan" by Richard McElreath <https://github.com/pymc-devs/resources/tree/master/Rethinking>`__
-  `PyMC3 port of the book "Bayesian Cognitive Modeling" by Michael Lee and EJ Wagenmakers <https://github.com/pymc-devs/resources/tree/master/BCM>`__: Focused on using Bayesian statistics in cognitive modeling.
-  `Bayesian Analysis with Python  <https://www.packtpub.com/big-data-and-business-intelligence/bayesian-analysis-python-second-edition>`__ (second edition) by Osvaldo Martin: Great introductory book. (`code <https://github.com/aloctavodia/BAP>`__ and errata).

PyMC3 talks
-----------

There are also several talks on PyMC3 which are gathered in this `YouTube playlist <https://www.youtube.com/playlist?list=PL1Ma_1DBbE82OVW8Fz_6Ts1oOeyOAiovy>`__

Installation
============

The latest release of PyMC3 can be installed from PyPI using ``pip``:

::

    pip install pymc3

**Note:** Running ``pip install pymc`` will install PyMC 2.3, not PyMC3,
from PyPI.

Or via conda-forge:

::

    conda install -c conda-forge pymc3

The current development branch of PyMC3 can be installed from GitHub, also using ``pip``:

::

    pip install git+https://github.com/pymc-devs/pymc3

To ensure the development branch of Theano is installed alongside PyMC3
(recommended), you can install PyMC3 using the ``requirements.txt``
file. This requires cloning the repository to your computer:

::

    git clone https://github.com/pymc-devs/pymc3
    cd pymc3
    pip install -r requirements.txt

However, if a recent version of Theano has already been installed on
your system, you can install PyMC3 directly from GitHub.

Another option is to clone the repository and install PyMC3 using
``python setup.py install`` or ``python setup.py develop``.


Dependencies
============

PyMC3 is tested on Python 2.7 and 3.6 and depends on Theano, NumPy,
SciPy, Pandas, and Matplotlib (see ``requirements.txt`` for version
information).

Optional
--------

In addtion to the above dependencies, the GLM submodule relies on
`Patsy <http://patsy.readthedocs.io/en/latest/>`__.


Citing PyMC3
============

Salvatier J., Wiecki T.V., Fonnesbeck C. (2016) Probabilistic programming
in Python using PyMC3. PeerJ Computer Science 2:e55
`DOI: 10.7717/peerj-cs.55 <https://doi.org/10.7717/peerj-cs.55>`__.

Contact
=======

We are using `discourse.pymc.io <https://discourse.pymc.io/>`__ as our main communication channel. You can also follow us on `Twitter @pymc_devs <https://twitter.com/pymc_devs>`__ for updates and other announcements.

To ask a question regarding modeling or usage of PyMC3 we encourage posting to our Discourse forum under the `“Questions” Category <https://discourse.pymc.io/c/questions>`__. You can also suggest feature in the `“Development” Category <https://discourse.pymc.io/c/development>`__.

To report an issue with PyMC3 please use the `issue tracker <https://github.com/pymc-devs/pymc3/issues>`__.

Finally, if you need to get in touch for non-technical information about the project, `send us an e-mail <pymc.devs@gmail.com>`__.

License
=======

`Apache License, Version
2.0 <https://github.com/pymc-devs/pymc3/blob/master/LICENSE>`__


Software using PyMC3
====================

- `Exoplanet <https://github.com/dfm/exoplanet>`__: a toolkit for modeling of transit and/or radial velocity observations of exoplanets and other astronomical time series.
- `Bambi <https://github.com/bambinos/bambi>`__: BAyesian Model-Building Interface (BAMBI) in Python.
- `pymc3_models <https://github.com/parsing-science/pymc3_models>`__: Custom PyMC3 models built on top of the scikit-learn API.
- `PMProphet <https://github.com/luke14free/pm-prophet>`__: PyMC3 port of Facebook's Prophet model for timeseries modeling
- `webmc3 <https://github.com/AustinRochford/webmc3>`__: A web interface for exploring PyMC3 traces
- `sampled <https://github.com/ColCarroll/sampled>`__: Decorator for PyMC3 models.
- `NiPyMC <https://github.com/PsychoinformaticsLab/nipymc>`__: Bayesian mixed-effects modeling of fMRI data in Python.
- `beat <https://github.com/hvasbath/beat>`__: Bayesian Earthquake Analysis Tool.
- `BayesFit <https://github.com/Slugocm/BayesFit>`__: Bayesian Psychometric Curve Fitting Tool.

Please contact us if your software is not listed here.

Papers citing PyMC3
===================

See `Google Scholar <https://scholar.google.de/scholar?oi=bibs&hl=en&authuser=1&cites=6936955228135731011>`__ for a continuously updated list.

Contributors
============

See the `GitHub contributor
page <https://github.com/pymc-devs/pymc3/graphs/contributors>`__

Support
=======

PyMC3 is a non-profit project under NumFOCUS umbrella. If you want to support PyMC3 financially, you can donate `here <https://www.flipcause.com/widget/widget_home/MTE4OTc=>`__.

Sponsors
========

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