readme.Rmd

---
title: "Preparation of Data and Statistical Analysis"
author: "Ben Sabath"
date: "`r format(Sys.Date(), '%B %d, %Y')`"
output: github_document
---

This directory contains code covering the creation of the data set used for analysis by Xiao Wu
in the paper "Evaluating the Impact of Long-term Exposure to Fine Particulate Matter on Mortality Among the Elderly.".

The directory `Confounders` contains the process by which the zip code level demographic data, smoking and BMI data, and weather data are acquired and prepared for use. `Exposures` describes the preparation of the PM2.5 data. Please note that we are unable to provide the code and workflow, as our exposure data is provided by our collaborators. However, the PM2.5 exposure data we used is available for download [here](https://beta.sedac.ciesin.columbia.edu/data/set/aqdh-pm2-5-concentrations-contiguous-us-1-km-2000-2016). `HealthOutcomes` contains the code used to select data from the Medicare Beneficiary Summary Files. Finally, `MergedData` contains the process by which all these data sources are combined and cleaned in order to be analyzed by the code in `StatisticalAnalysis`.

We have included as much data as we are allowed to share and can feasibly include in a github repo (some files are too large to share). Where we are unable to share data, we have provided instructions on how to acquire the source data and prepare it for use with the data pipelines.

## Table of Contents

The directories can be read in any order; however, reading in the following order reflects how data flows 
in the pipeline. 

 - [Confounders](Confounders/readme.md) Overview of non health, non pm2.5 data used.
   - [Census Data](Confounders/census/readme.md) (All data needed provided)
   - [Smoking and BMI](Confounders/brfss/readme.md) (Some external data Downloads needed)
   - [Temperature and Humidity](Confounders/earth_engine/readme.md) (Some external data downloads needed)
- [PM2.5 Data](Exposures/readme.md) (Not fully reproducible)
- [Medicare Mortality Data](HealthOutcomes/readme.md) (Additional Data Acquisition Needed)
- [Merging Process](MergedData/readme.md)
- [Statistical Analysis](StatisticalAnalysis/README.md)