Survival Analysis

This repository is created for the applications from cancer team. The goal of the program is to infer the survival rate simply from mortality incidence ratio of the diease and the background mortality.

Install

The package require python=3.7 and preliminary packages, Numpy, Scipy, and Pytest. If want to run the examples, Pandas, Jupyter and Maplotlib are also required.

To install, simply clone the repository and install,

git clone https://github.com/ihmeuw-msca/Survival.git && cd Survival
python setup.py install

Example

After installation, to use the code, we need data for mir (mortality incidence ratio), other_mortality and optional disease_period, for more details, please check the docstring. And we could create object and do the computation.

from survival import MIRModel

model = MIRModel(mir, other_mortality, disease_period=5)
model.compute_excess_mortality()

survival_rate = model.get_survival_rate(num_years=5)

For the result, survival_rate is a dictionary with survival_rate['abs'] store the absolute survival rate and survival_rate['rel'] store the relative survival rate. And the argument num_years=5 indicates that we compute the 5 years survival rate.

For more detailed examples please check examples.