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https://github.com/sempwn/overdose-model-intro
Introduction to Bayesian hierarchical model of overdoses
https://github.com/sempwn/overdose-model-intro
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Introduction to Bayesian hierarchical model of overdoses
- Host: GitHub
- URL: https://github.com/sempwn/overdose-model-intro
- Owner: sempwn
- License: mit
- Created: 2019-01-21T18:44:00.000Z (almost 6 years ago)
- Default Branch: master
- Last Pushed: 2019-01-24T14:03:08.000Z (almost 6 years ago)
- Last Synced: 2024-10-12T01:22:34.369Z (3 months ago)
- Language: Jupyter Notebook
- Size: 2.97 MB
- Stars: 1
- Watchers: 2
- Forks: 1
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# overdose-model-intro
Introduction to Bayesian hierarchical model of opioid-related overdoses
## Background
This repo provides a notebook in order to learn and develop a mathematical model describing a population at risk of an opioid overdose and intervention through the use of *take-home naloxone* (THN) kits.
For description of model see supplementary materials in [Irvine, Michael A., et al. *Distribution of take-home opioid antagonist kits during a synthetic opioid epidemic in British Columbia, Canada: a modelling study.* The Lancet Public Health 3.5 (2018): e218-e225.](https://doi.org/10.1016/S2468-2667%2818%2930044-6)
## Getting started
These instructions will get you a copy of the notebook up and running on your local machine.
### Prerequisites
The easiest way to get up and running is to install [Anaconda](https://www.anaconda.com/download/_), which provides `python`, numerous scientific libraries as well as `jupyter`. Once [Anaconda](https://www.anaconda.com/download/) is installed, navigate to directory for this repository and run `jupyter` via the command line (using the example directory `/Projects/Tutorial/`):
```bash
cd /Projects/Tutorial/
jupyter notebook
```
You can also launch `jupyter` through the [Anaconda Navigator](https://www.anaconda.com/distribution/#feature-desktop-gui).
### Installing
The repository requires the library [pymc3](https://pymc3.readthedocs.io/en/latest/_) to run. To install open a terminal (can be done in a notebook session) and run the following command:
```bash
conda install -c conda-forge pymc3
```
For plotting install the package [seaborn](https://seaborn.pydata.org) using the following command
```bash
conda install -c anaconda seaborn
```
### Opening notebook
Once the jupyter session is running navigate to the notebook [model_introduction.ipynb](model_introduction.ipynb)
## License
This project is licensed under the MIT License - see the [LICENSE.md](LICENSE.md) file for details