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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 numbersInstallation
------------
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 installEpiPy 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 ./epipyAdd 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 startFor install the tools for TDD use:
pip install -r requirements.txt
pip install -r requirements-tdd.txtTo run the test suit use:
cd ./epipy
py.test testThen, 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 --continueAfter 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)