Earth Lab's environmental health team project to estimate daily air pollution exposures across the western U.S. (at the county, ZIP-code, and census tract levels) from 2008-2018.
To ensure that our work is reproducible, all code is written in open-source languages. Some scripts are in R and others are in Python, both due to specific functionalities in these languages and the different coding backgrounds of our research team members. Python scripts need Python 3; R versions beyond 3.5.2 should suffice.
This repository contains the following files and directories:
- General_Project_Functions: Scripts to obtain the prediction set locations as well as tools that are generally useful during the data processing, such as making buffers around points and reprojecting point coordinates.
- Get_PM25_Observations: Scripts to process PM2.5 observations from across the western U.S. These observations are used to train our machine learning models.
- Get_Earth_Observations: Scripts to download and process observations from data sets that are used both as inputs for our machine learning models during training and as inputs for our models in the prediction stage. The file Overall_steps provides all necessary directions. Individual README files (in each folder) provide more details, if there are any.
- Merge_Data: Scripts to merge all the data together and derive some spatio-temporal variables.
- Machine_Learning: Scripts to run and evaluate our machine learning models.
- Estimate_PM25: Scripts to use our machine learning models to make final predictions and to explore the prediction data sets over time and space.
If you are interested in using our code to download and process any of these datasets, we recommend using one of the docker containers that we have created for this purpose.
To pull and run a docker container with Python, execute:
docker pull earthlab/estimate-pm25
docker run -d earthlab/estimate-pm25
docker ps (to get the container name)
docker exec -it <container name> /bin/bash
To pull and run a docker container with R, execute:
docker pull earthlab/r-reidgroup
docker run -e PASSWORD=yourpassword -d -p 8787:8787 earthlab/r-reidgroup
Please contact Ellen Considine ([email protected]) with any questions.