From c0eeb1ad58584f1d285e355be013cd941caf3671 Mon Sep 17 00:00:00 2001 From: Jacki Buros Date: Wed, 18 Jan 2017 23:02:28 +0000 Subject: [PATCH] update docs --- docs/api.rst | 7 +++++ docs/conf.py | 6 ++-- docs/home.rst | 65 ++++++++++++++++++++++++++++++++++++++++++++ docs/index.rst | 74 +++++--------------------------------------------- 4 files changed, 82 insertions(+), 70 deletions(-) create mode 100644 docs/api.rst create mode 100644 docs/home.rst diff --git a/docs/api.rst b/docs/api.rst new file mode 100644 index 0000000..fca1eda --- /dev/null +++ b/docs/api.rst @@ -0,0 +1,7 @@ +Survivalstan API +============ + +.. toctree:: + :maxdepth: 4 + + survivalstan diff --git a/docs/conf.py b/docs/conf.py index 06bd381..852ba10 100644 --- a/docs/conf.py +++ b/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 ------------------------------------------------ diff --git a/docs/home.rst b/docs/home.rst new file mode 100644 index 0000000..8f5b0fd --- /dev/null +++ b/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 `_ + +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 `_ data frames & `patsy `_ formulas +- Graphical posterior predictive checking +- Plot posterior estimates of key parameters using `seaborn `_ +- Annotated posterior draws of parameter estimates, as `pandas `_ dataframes +- Supports caching via as `stancache `_ or `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. + + + diff --git a/docs/index.rst b/docs/index.rst index 5ce996e..490e7a4 100644 --- a/docs/index.rst +++ b/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 `_ - -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 `_ data frames & `patsy `_ formulas -- Graphical posterior predictive checking -- Plot posterior estimates of key parameters using `seaborn `_ -- Annotated posterior draws of parameter estimates, as `pandas `_ dataframes -- Supports caching via as `stancache `_ or `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`