update docs

docs/api.rst

@@ -0,0 +1,7 @@
+Survivalstan API
+============
+
+.. toctree::
+   :maxdepth: 4
+
+   survivalstan

docs/conf.py

@@ -17,9 +17,9 @@
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 #
-# import os
-# import sys
-# sys.path.insert(0, os.path.abspath('.'))
+import os
+import sys
+sys.path.insert(0, os.path.abspath('../'))
 
 # -- General configuration ------------------------------------------------
 

docs/home.rst

@@ -0,0 +1,65 @@
+.. survivalstan documentation master file, created by
+   sphinx-quickstart on Fri Jan  6 06:25:53 2017.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+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 as `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: github.com/hammerlab/survivalstan/issues
+- Source Code: github.com/survivalstan/survivalstan
+
+Support
+-------
+
+If you are having issues or questions, please let us know.
+
+We can be reached by email (via github) or via https://gitter.im/survivalstan 
+
+License
+-------
+
+The project is licensed under the Apache 2.0 license.
+
+
+

docs/index.rst

@@ -3,76 +3,16 @@
    You can adapt this file completely to your liking, but it should at least
    contain the root `toctree` directive.
 
-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 as `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: github.com/hammerlab/survivalstan/issues
-- Source Code: github.com/survivalstan/survivalstan
-
-Support
--------
-
-If you are having issues or questions, please let us know.
-
-We can be reached by email (via github) or via https://gitter.im/survivalstan 
-
-License
--------
-
-The project is licensed under the Apache 2.0 license.
-
-
-Contents:
+.. include:: home.rst
 
 .. toctree::
-   :maxdepth: 2
+   :caption: Table of Contents
+   :name: mastertoc
+   :hidden:
 
+   home.rst
    Usage.ipynb
+   Examples.ipynb
+   api.rst
 
-Indices and tables
-==================
-
-* :ref:`genindex`
-* :ref:`modindex`
-* :ref:`search`