Survival analysis in Python, including Kaplan Meier, Nelson Aalen and regression
Project description
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()
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()
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:
More examples
There are some IPython notebook files in the repo, and you can view them online here.
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:
The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
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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