https://github.com/jarnorfb/epysurv

Epidemiological surveillance in Python
https://github.com/jarnorfb/epysurv

epidemiology outbreak-detection surveillance

Last synced: about 2 months ago
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Epidemiological surveillance in Python

• Host: GitHub
• URL: https://github.com/jarnorfb/epysurv
• Owner: JarnoRFB
• License: mit
• Created: 2019-03-20T16:39:46.000Z (almost 6 years ago)
• Default Branch: master
• Last Pushed: 2024-03-20T16:17:32.000Z (10 months ago)
• Last Synced: 2024-09-16T18:36:26.931Z (4 months ago)
• Topics: epidemiology, outbreak-detection, surveillance
• Language: Python
• Homepage:
• Size: 406 KB
• Stars: 10
• Watchers: 3
• Forks: 4
• Open Issues: 6
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
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# epysurv

`epysurv` is a Pythonic wrapper around the [R surveillance package](https://cran.r-project.org/web/packages/surveillance/index.html) 

that strives to implement a `scikit-learn` like API for epidemiological surveillance in Python. 

## In a nutshell

```python

from epysurv import data as epidata

from epysurv.models.timepoint import FarringtonFlexible

train, test = epidata.salmonella()

train.head()

#             n_cases  n_outbreak_cases  outbreak

# 2004-01-05        0                 0     False

# 2004-01-12        0                 0     False

# 2004-01-19        2                 0     False

# 2004-01-26        2                 0     False

# 2004-02-02        1                 0     False    

model = FarringtonFlexible()

model.fit(train)

model.predict(test)

#             n_cases  n_outbreak_cases  outbreak  alarm

# 2011-01-03        1                 0     False    0.0

# 2011-01-10        0                 0     False    0.0

# 2011-01-17        3                 0     False    0.0

# 2011-01-24        3                 0     False    0.0

# 2011-01-31        3                 0     False    0.0

```

## Installation

As `epysurv` requires both Python and R it can only be conveniently installed through [`conda`](https://docs.conda.io/en/latest/):

    conda install -c conda-forge epysurv 

## Documentation

You can read the [documentation](https://epysurv.readthedocs.io/en/latest/?badge=latest) or try 

an interactive demo on [binder](https://mybinder.org/v2/gh/JarnoRFB/epysurv/master?filepath=demo.ipynb).

## Development

To set up a local development environment, run

    conda env create -f env.yml

    conda activate epysurv-dev

    pip install -r requirements-dev.txt

    pre-commit install 

To run all tests, simply run 

    pytest

in the project's root directory.

If you want to contribute to the documentation, run

    pip install -r requirements-doc.txt

to install the necessary packages for building the sphinx documentation.

Pull requests are highly welcome!

## Related Projects

* https://github.com/lvphj/epydemiology

* https://github.com/cmrivers/epipy