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Create survival curves using kaplanmeier, the log-rank test and making plots.

Project description

kaplanmeier

PyPI Version License

  • kaplanmeier is Python package to compute the kaplan meier curves, log-rank test, and make the plot instantly. This work is build on the lifelines package.

Contents

Installation

  • Install kaplanmeier from PyPI (recommended). kaplanmeier is compatible with Python 3.6+ and runs on Linux, MacOS X and Windows.
  • Distributed under the MIT license.

Requirements

  • It is advisable to create a new environment. Pgmpy requires an older version of networkx and matplotlib.
conda create -n env_KM python=3.6
conda activate env_KM
pip install matplotlib numpy pandas seaborn lifelines

Quick Start

pip install kaplanmeier
  • Alternatively, install kaplanmeier from the GitHub source:
git clone https://github.com/erdogant/kaplanmeier.git
cd kaplanmeier
python setup.py install

Import kaplanmeier package

import kaplanmeier as km

Example:

df = km.example_data()
time_event=df['time']
censoring=df['Died'] 
labx=df['group']

# Compute survival
out=km.fit(time_event, censoring, labx)

Make figure with cii_alpha=0.05 (default)

km.plot(out)

km.plot(out, cmap='Set1', cii_lines=None, cii_alpha=0.05)

km.plot(out, cmap='Set1', cii_lines='line', cii_alpha=0.05)

km.plot(out, cmap=[(1, 0, 1),(0, 1, 1)])

km.plot(out, cmap='Set2')

km.plot(out, cmap='Set2', methodtype='custom')

  • df looks like this:
     time  Died  group
0     485     0      1
1     526     1      2
2     588     1      2
3     997     0      1
4     426     1      1
..    ...   ...    ...
175   183     0      1
176  3196     0      1
177   457     1      2
178  2100     1      1
179   376     0      1

[180 rows x 3 columns]

Citation

Please cite kaplanmeier in your publications if this is useful for your research. Here is an example BibTeX entry:

@misc{erdogant2019kaplanmeier,
  title={kaplanmeier},
  author={Erdogan Taskesen},
  year={2019},
  howpublished={\url{https://github.com/erdogant/kaplanmeier}},
}

References

Maintainers

Contribute

  • All kinds of contributions are welcome!

© Copyright

See LICENSE for details.

Project details


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This version

0.1.1

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