README.md

bayesian-envhealth-models

Project description

Bayesian models for environmental health. This code is used for the paper Name, Y., Parks, R.M. et al. (202X). Title with hyperlink. Journal Name.

Aims:

• Aim 1. File src/bayesian_envhealth_models/models.py.

Directory structure

.
├── .gitignore
├── .pre-commit-config.yaml
├── README.md
├── data
├── src/bayesian_envhealth_models
│   └── models.py
├── output
├── scripts
│   └── model_run.py
└── reports

Folder	File	Description
src/bayesian_envhealth_models	models.py	numpyro models
scripts	model_run.py	Script to run the numpyro model

Running the code

1. Create a fresh conda environment mamba create -n envhealth-env hatch and install the required packages pip install -e ."[dev]".
2. Edit the config file scripts/conf/model_config.yaml to specify the data and output directories.
3. python scripts/model_run.py

Data availability

Data used in the analysis are controlled by the XX who do not have permission to release data to third parties. Individual mortality data can be requested through XX (e.g. the US CDC). If you would like a file containing simulated data that allow you to test the code, please contact robbie.parks@columbia.edu.

Adapted from:

• https://num.pyro.ai/en/stable/examples/mortality.html
• https://github.com/theorashid/mortality-statsmodel/blob/master/mortality_statsmodel/car.py