data550-finalproject

Final project for DATA 550

Using CDC data on RSV (https://data.cdc.gov/Public-Health-Surveillance/Rates-of-Laboratory-Confirmed-RSV-COVID-19-and-Flu/kvib-3txy/about_data) and Flu (https://gis.cdc.gov/grasp/fluview/fluhosprates.html) compare weekly rates of RSV and Influenza, by race and age.

Code Description

code/01_data_cleaning.R

creates cleaned data from files found in data/raw/
saves data as CSV files found in data/ folder
run make data to run this script

code/02_regression_analysis.R

runs regression analysis of race on cumulative rate from cleaned data files in data/ folder
outputs regression summary tables to .rds files in output/ folder
run make regression to run this script

code/03_render_report.R

renders FluRSV_Report.Rmd
run make FluRSV_Report.html to run this script

FluRSV_Report.Rmd

reads in cleaned data files found in data/raw/
creates summary tables by race and age as well as epi curves for RSV and Flu
prints regression summary table for race on cumulative rate.
called by code/03_render_report.R

How to synchronize packages:

Run Rscript renv/activate.R.
Run make install to restore package versions.

How to build Docker image:

Run make resp_image

How to create FluRSV_Report.html report:

Run make docker-resp-report