Mortality risk from United States coal electricity generation

Lucas Henneman 2023-08-11

This repository houses code for the manuscript entitled “Mortality risk from United States coal electricity generation”.

Directory contents

• code This directory stores all code used as part of the project.
  • 00_organize_data.R Code in this file reads in the outcome and exposure data into consistent formats.
  • 01_coal_pm_mortality_models.R Code in this file runs the stratified poisson models.
  • 02_CI_bootstrap.R Code in this file calculates the bootstrapped confidence intervals on the estimated hazard ratios
  • 03_deaths_contributed.R Code in this file combines coal power plant information with poisson model output to calculate deaths associated with each coal power plant’s SO₂ emissions.
  • 04_plots.R Code in this file creates many of the charts in figures in the manuscript and supplementary text.
  • 05_compare_geos_chem.R Code in this file compares the power plant deaths calculated in this study with comparable deaths calculated using GEOS-Chem adjoint sensitivities
  • 06_change_over_change.R Code in this file conducts the first-differences analysis described in the supplementary text
  • 07_plot_hyads_biggest_impactors.R Code in this file creates figures presented in the supplementary text showing facilities that contribute to coal PM_2.5 in metropolitan statistical areas
• data Sensitive health data is not included in this repository, but all other datasets are saved here.
  • cache_data This sub-directory houses various ZIP code level data for input into the models. Sensitive data and large files have not been pushed to Github.
  • adjoint_results This sub-directory houses deaths (total population) attributable to each coal unit from the GEOS-Chem adjoint sensitivities modeling.
  • coalpm25_to_obs_adjustment.csv This file contains regional and year-specific adjustment factors for HyADS-derived coal PM_2.5 to regional observed sulfate concentrations
• figures This directory contains figures from the manuscript
• results This directory contains two files related to the Risk Ratio estimations in the manuscript
  • poisson_model_coefs.csv Contains the central estimates of the relevant coefficients from the Poisson models used to estimate the RR
  • loglinear_coefs_boots.RData Contains the bootstrapped estimates of the relevant coefficients from the Poisson models used to estimate the RR confidence intervals