https://github.com/cmrivers/epipy

Python tools for epidemiology
https://github.com/cmrivers/epipy

Last synced: 3 months ago
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Python tools for epidemiology

• Host: GitHub
• URL: https://github.com/cmrivers/epipy
• Owner: cmrivers
• Created: 2013-08-28T13:58:57.000Z (about 11 years ago)
• Default Branch: master
• Last Pushed: 2023-07-06T21:03:57.000Z (over 1 year ago)
• Last Synced: 2024-07-14T22:50:42.484Z (4 months ago)
• Language: Python
• Homepage:
• Size: 8.99 MB
• Stars: 133
• Watchers: 22
• Forks: 39
• Open Issues: 10
• Metadata Files:
  • Readme: README.md

Awesome Lists containing this project

• awesome-healthmetrics - epipy: python tools for epidemiology

README

        
EpiPy

========

A Python package for epidemiology. Epipy is a Python package for epidemiology.

It contains tools for analyzing and visualizing epidemiology data.

Epipy can currently produce:

* stratified summary statistics

* case tree and checkerboard plots

* epicurves

* analysis of case attribute (e.g. sex) by generation

* 2x2 tables with odds ratio and relative risk

* summary of cluster basic reproduction numbers

Installation

------------

The github version of epipy is substantially further along that the pip version. I suggest installing from this repo when possible.

Install using pip:

    pip install epipy

    

Or clone the repository and install using setup.py:

    git clone https://github.com/cmrivers/epipy.git

    cd ./epipy

    pip install -r requirements.txt

    python setup.py install

EpiPy is in development. Please feel free to contribute.

Contact me at [email protected] or [@cmyeaton](http://twitter.com/cmyeaton) with any questions.

Learning Python

------------

New to Python? I teach a self-paced course on Python for epidemiologists over at [episkills.teachable.com](http://episkills.teachable.com).

Contributing/Development

------------

If you want to contribute in this great project. First fork this repo in github.

Clone your forked repo in your terminal using the appropriate command:

    git clone https://github.com/your-git-user-name/epipy.git

    cd ./epipy

Add this repo as upstream remote:

    git remote add upstream [email protected]:cmrivers/epipy.git

We use [gitflow](https://github.com/nvie/gitflow). Follow this [instructions](https://github.com/nvie/gitflow/wiki/Installation) to install.

    git branch master origin/master

    git flow init -d

    git flow feature start 

For install the tools for TDD use:

    

    pip install -r requirements.txt

    pip install -r requirements-tdd.txt

To run the test suit use:

    cd ./epipy

    py.test test

Then, do work and commit your changes. After finish your feature with coverage of test, please pull any change that ocurred from the upstream repo. You can use:

    git pull upstream master

If git fast-forward error is issue then use:

    git rebase upstream/master

Resolve the merge conflicts that couid exist using:

    git mergetool

    git rebase --continue

After everything is ok then:

    git flow feature publish 

When done, open a pull request to your feature branch.

Documentation

------------

The docs live at: [cmrivers.github.io/epipy](https://cmrivers.github.io/epipy)