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Library of Stan Models for Survival Analysis

Project description

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Survivalstan
============

Survivalstan is a library of Survival Models written in `Stan <http://mc-stan.org>`_

It also contains a number of utility functions helpful when doing survival analysis.

Typical usage:

::

import survivalstan
# .. prep your data
fit1 = survivalstan.fit_stan_survival_model(...)
survivalstan.utils.plot_stan_summary([fit1], metric=’Rhat’)
survivalstan.utils.plot_coefs([fit1])

Features
--------

- Variety of standard survival models
- Weibull, Exponential, and Gamma parameterization
- A variety of semi-parametric and non-parametric baseline hazards
- Supports time-varying-coefficients
- Estimate time-varying effects
- Varying-effects by group
- Extensible framework - bring your own Stan code, or edit the models provided
- Uses `pandas <https://pandas.pydata.org>`_ data frames & `patsy <https://pypi.python.org/pypi/patsy>`_ formulas
- Graphical posterior predictive checking
- Plot posterior estimates of key parameters using `seaborn <https://pypi.python.org/pypi/seaborn>`_
- Annotated posterior draws of parameter estimates, as `pandas <http://pandas.pydata.org>`_ dataframes
- Supports caching via `stancache <http://github.com/jburos/stancache>`_ or `pystan-cache <https://github.com/paulkernfeld/pystan-cache>`_

Installation
------------

Install survivalstan via pip:

::

pip install survivalstan

Contribute
----------

- Issue Tracker: http://github.com/hammerlab/survivalstan/issues
- Source Code: http://github.com/survivalstan/survivalstan

Support
-------

If you are having issues or questions, please let us know.

Please submit an issue `github <http://github.com/hammerlab/survivalstan/issues>`_ or via `gitter <https://gitter.im/survivalstan>`_

License
-------

The project is licensed under the Apache 2.0 license.


Documentation
-------------

`Documentation http://jburos.github.io/survivalstan`_ is available online.

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