Final Project: Opioid Overdose Mortality Data for Georgia (2020)

The data set contains information on the number of opioid overdose deaths and the population of each county in Georgia in 2020. The goal of this study is to examine the relationship between county-level measures of social vulnerability, access to health care, and observed overdose mortality rates. The key variables of interest include: poverty rate, vacancy rate, unemployment rate, percentage of Black population, distance to interstates, and distance to treatment centers.

Contents of the Repository

raw_data/

• includes the raw_data to generate output and report

data/

• includes the data after preprocessing

code/

• includes the code files to preprocess the raw data and create a table1 and plots

output/

• includes the output files (table1 and plots)

report/

• includes the compiled report

Code Description

code/01_data_preprocessing.R

• preprocess the data
• save the data as a .rds object in data/ folder

code/02_data_structure_table1.R

• create a table1 that describes the data
• save the table as a .rds object in output/ folder

code/03_make_plots.R

• create a bar plot that describes the distribution of urban-rural continuum code.
• create a histogram that describes the distribution of unemployment rate.
• save the plots as .png objects in output/ folder

code/04_render_report.R

• renders GA_Opioid_Report.Rmd

report.Rmd

• imports data generated by code/01_data_preprocessing.R
• reads table1 generated by code/02_data_structure_table1.R
• reads plots generated by code/03_make_plots.R

Contents of the Report

• The GA_Opioid_Report includes the data set structure, Table1 summarizing the characteristics of variables, maps of each variable, bar plot and histogram showing the distribution of some variables (urban-rural continuum code and unemployment rate), and the results of fitting a Poisson regression model.

• For the maps in the report, I just wrote the code in .rmd files because they required the tmap package and could not be saved as .png flies.

Building the Docker image

• Run make final_project to build the Docker image.
• This is a link to the image on DockerHub: https://hub.docker.com/repository/docker/hayoungjung/final_project/general

Generating the report

• Run make report/GA_Opioid_Report.html command in your terminal, and this will sequentially execute the R script files and generate the report.

Note

• The report can only be generated on a Mac or Linux OS.