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lifelines 0.3.1.5

Survival analysis in Python, including Kaplan Meier, Nelson Aalen and regression

What is survival analysis and why should I learn it? Survival analysis was originally developed and applied heavily by the actuarial and medical community. Its purpose was to answer why do events occur now versus later under uncertainity (where events might refer to deaths, disease remission, etc.). This is great for researchers who are interested in measuring lifetimes: they can answer questions like what factors might influence deaths?

But outside of medicine and actuarial science, there are many other interesting and exciting applications of this lesser-known technique, for example: - SaaS providers are interested in measuring customer lifetimes, or time to first behaviours. - sociologists are interested in measure political parties lifetimes, or relationships, or marriages - Businesses are interested in what variables affect lifetime value

lifelines is a pure Python implementation of the best parts of survival analysis. We'd love to hear if you are using lifelines, please ping me at [@cmrn_dp](https://twitter.com/Cmrn_DP) and let me know your thoughts on the library.

Installation:

Dependencies:

The usual Python data stack: Numpy, Scipy, Pandas (a modern version please), Matplotlib

Installing

You can install lifelines using

pip install lifelines

Or getting the bleeding edge version with:

pip install git+https://github.com/CamDavidsonPilon/lifelines.git

or upgrade with

pip install --upgrade git+https://github.com/CamDavidsonPilon/lifelines.git

from the command line.

Intro to lifelines and survival analysis

Situation: 500 random individuals are born at time 0, currently it is time 12, so we have possibly not observed all death events yet.

# Create lifetimes, but censor all lifetimes after time 12
censor_after = 12
actual_lifetimes = np.random.exponential(10, size=500)
observed_lifetimes = np.minimum( actual_lifetimes, censor_after*np.ones(500) )
C = (actual_lifetimes < censor_after) #boolean array

Non-parametrically fit the survival curve:

from lifelines import KaplanMeierFitter

kmf = KaplanMeierFitter()
kmf.fit(observed_lifetimes, event_observed=C)

# fitter methods have an internal plotting method.
# plot the curve with the confidence intervals
kmf.plot()
kmf

It looks like 50% of all individuals are dead before time 7.

print kmf.survival_function_.head()

time            KM-estimate
0.000000        1.000
0.038912        0.998
0.120667        0.996
0.125719        0.994
0.133778        0.992

Non-parametrically fit the cumulative hazard curve:

from lifelines import NelsonAalenFitter

naf = NelsonAalenFitter()
naf.fit(observed_lifetimes, event_observed=C)

#plot the curve with the confidence intervals
naf.plot()
naf
print naf.cumulative_hazard_.head()

time       NA-estimate
0.000000     0.000000
0.038912     0.002000
0.120667     0.004004
0.125719     0.006012
0.133778     0.008024

Compare two populations using the logrank test:

from lifelines.statistics import logrank_test
other_lifetimes = np.random.exponential(3, size=500)

summary, p_value, results = logrank_test(observed_lifetimes, other_lifetimes, alpha=0.95)
print summary


Results
   df: 1
   alpha: 0.95
   t 0: -1
   test: logrank
   null distribution: chi squared

   __ p-value ___|__ test statistic __|__ test results __
         0.00000 |              268.465 |     True

(Less Quick) Intro to lifelines and survival analysis

If you are new to survival analysis, wondering why it is useful, or are interested in lifelines examples and syntax, please check out the Documentation and Tutorials page

Alternatively, you can use the IPython notebooks tutorials, located in the main directory of the repo:

  1. Introduction to survival analysis
  2. Using lifelines on real data

More examples

There are some IPython notebook files in the repo, and you can view them online here.

lifelines

License

The Feedback MIT License (FMIT)

Copyright (c) 2013, Cameron Davidson-Pilon

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

  1. The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
  2. Person obtaining a copy must return feedback to the authors.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

lifelines logo designed by Pulse designed by TNS from the Noun Project

 
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