Epipy Python tools for epidemiology

Epipy is a Python package for epidemiology. It contains tools for analyzing and visualizing epidemiology data.

To check out the code, report a bug, or contribute features, visit github, or visit me on twitter.

Installation

Install using pip:

pip install epipy

or clone the github repository and install using setup.py:

git clone https://github.com/cmrivers/epipy.git
python setup.py install

Note that I use the package seaborn to produce the nice plot aesthetics you see in my examples. Using seaborn is optional, but I highly recommend it.

Documentation

Basic epidemiology

• Summary statistics
• 2x2 table
  • Odds ratio
  • Relative risk
  • Attributable risk
  • Chi square
  • Diagnostic accuracy
• Cluster + case tree analysis

Plotting

• Case tree plot
• Checkerboard plot
• Epicurves
• Odds ratio plot
• Rolling proportion plot
• Steppe plot