├── .coveragerc ├── .gitignore ├── .nojekyll ├── .travis.yml ├── LICENSE ├── MANIFEST.in ├── README.md ├── docs ├── Examples.ipynb ├── Makefile ├── Usage.ipynb ├── api.rst ├── conf.py ├── examples.rst ├── home.rst ├── index.rst ├── modules.rst ├── requirements.txt └── survivalstan.rst ├── example-notebooks ├── Test new_gamma_survival_model with simulated data.ipynb ├── Test pem_survival_model with simulated data.ipynb ├── Test pem_survival_model_randomwalk with simulated data.ipynb ├── Test pem_survival_model_timevarying with simulated data.ipynb ├── Try plotly for better looking plots.ipynb └── plotly_example_data.csv ├── lint.sh ├── pylintrc ├── requirements.txt ├── setup.cfg ├── setup.py ├── survivalstan ├── __init__.py ├── _version.py ├── formulas.py ├── models.py ├── sim.py ├── stan │ ├── exp_survival_model.stan │ ├── pem_survival_model.stan │ ├── pem_survival_model_gamma.stan │ ├── pem_survival_model_randomwalk.stan │ ├── pem_survival_model_tvc.stan │ ├── pem_survival_model_unstructured.stan │ ├── pem_survival_model_unstructured_varcoef.stan │ ├── pem_survival_model_varying_coefs.stan │ ├── pem_survival_model_varying_coefs2.stan │ ├── pem_survival_model_varying_coefs3.stan │ ├── pem_survival_model_varying_coefs4.stan │ ├── weibull_survival_model.stan │ └── weibull_survival_model_varying_coefs.stan ├── survivalstan.py └── utils.py ├── test ├── __init__.py ├── test_SurvivalStanData.py ├── test_byo-gamma_survival_model.py ├── test_byo-gamma_survival_model_sim.py ├── test_datasets.py ├── test_exp_survival_model.py ├── test_exp_survival_model_sim.py ├── test_formulas.py ├── test_jointmodel_datasets.py ├── test_pem_survival_model.py ├── test_pem_survival_model_sim.py ├── test_pem_survival_model_timevarying.py ├── test_pem_survival_model_timevarying_sim.py ├── test_pem_survival_model_varcoefs.py ├── test_pem_survival_model_varcoefs_sim.py ├── test_weibull_survival_model.py └── test_weibull_survival_model_sim.py ├── test_requirements.txt ├── 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