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Lifelines

lifelines is a implementation of survival analysis in Python. What benefits does lifelines offer over other survival analysis implementations?

• built on top of Pandas
• internal plotting methods
• simple and intuitive API (designed for humans)
• only does survival analysis (No unnecessary features or second-class implementations)

Contents:

• Quickstart
  • Installation
  • Kaplan-Meier and Nelson-Aalen
  • Getting Data in The Right Format
  • Survival Regression
• Introduction to Survival Analysis
  • Applications
  • Censorship
  • Survival function
  • Hazard curve
• Survival analysis with lifelines
  • Estimating the Survival function using Kaplan-Meier
  • Estimating hazard rates using Nelson-Aalen
  • Other types of censorship
• Survival Regression
  • Cox’s proportional hazard model
  • Aalen’s Additive model
  • Cox’s Time Varying Proportional Hazard model
  • Model Selection in Survival Regression
• Testing the Proportional Hazard Assumptions
  • Checking assumptions with check_assumptions
• Assesing Cox model fit using residuals (work in progress)
  • Martingale residuals
  • Deviance residuals
• More Examples and Recipes
  • Statistically compare two populations
  • Model selection using lifelines
  • Plotting multiple figures on a plot
  • Plotting options and styles
  • Transforming survival-table data into lifelines format
  • Transforming observational data into survival-table format
  • Set the index/timeline of a estimate
  • Example SQL query to get survival data from a table
  • Example SQL queries and transformations to get time varying data
  • Example cumulative sums over time-varying covariates
  • Sample size determination under a CoxPH model
  • Power determination under a CoxPH model
  • Problems with convergence in the Cox Proportional Hazard Model
  • Adding weights to observations in a Cox model
  • Correlations between subjects in a Cox model

Installation

Dependencies are from the typical Python data-stack: Numpy, Pandas, Scipy, and optionally Matplotlib. Install using:

pip install lifelines

Source code and Issue Tracker

Available on Github, CamDavidsonPilon/lifelines Please report bugs, issues and feature extensions there. We also have Gitter channel open to discuss lifelines:

Citing lifelines

The following link will bring you to a page where you can find the latest citation for lifelines:

Citation for lifelines

Indices and tables

• Index
• Module Index
• Search Page