Overview

This file produces a report of the wastewater concentration of SARS-CoV-2 in different counties in NC. Data for this report was downloaded from the CDC website on 2024-07-22.

Download and clean data

Two data sources were pulled and merged for this analysis. One is a dataset of SARS-CoV-2 wastewater concentration at different sampling sites, which can be accessed here. The second, accessible here, contains summary information about SARS-CoV-2 wastewater concentration at different sites, with additional information about site location including county and state.

First we downloaded and cleaned the data from the CDC website.

if(params$download_raw_data){
  source(here("source", "01_data_download.R")) 
}else if(!file.exists(here::here("data", "raw.Rdata"))){
  source(here("source", "01_data_download.R")) 
}

source(here("source", "02_data_cleaning.R")) 

Analysis

Next we did a simple analysis of the concentrations across different counties in NC. Specifically, we calculated the median and interquartile range within each county, which are given in the table below:

source(here("source", "03_data_analysis.R"))
covid_table %>%
  knitr::kable()
county median q25 q75 population_served
Wilson 2.036000e-04 8.630000e-05 4.718000e-04 50000
Forsyth 2.311000e-04 9.640000e-05 6.339000e-04 92000
Lenoir 1.098700e-03 3.051000e-04 4.790900e-03 25000
Jackson 7.408257e+05 5.913577e+05 1.643449e+06 13296
Henderson 2.005935e+06 1.404020e+06 4.778317e+06 43633
Scotland 2.125908e+06 9.199582e+05 4.504154e+06 15527
Mcdowell 2.959382e+06 1.917805e+06 4.215519e+06 8459
Cumberland 5.552356e+06 3.810667e+06 1.144244e+07 151589
Swain,Jackson 7.489665e+06 4.181544e+06 1.267128e+07 10000
Onslow 8.689769e+06 2.881140e+06 1.650361e+07 41819
Forsyth,Guilford,Randolph,Davidson 1.008012e+07 7.140224e+06 1.321885e+07 116390
Guilford 1.090030e+07 8.839001e+06 3.490667e+07 135821
Buncombe,Henderson 1.175001e+07 7.649537e+06 1.747378e+07 173000
Pitt 1.396276e+07 8.261893e+06 3.036220e+07 89616
New Hanover 1.444451e+07 9.629462e+06 2.947398e+07 63052
Durham 1.490688e+07 1.042496e+07 2.663281e+07 142000
Rowan 1.588414e+07 7.733118e+06 3.273038e+07 26500
Carteret 1.616966e+07 8.822835e+06 4.519737e+07 3500
Durham,Orange 1.626229e+07 1.283364e+07 2.917262e+07 78141
Pender,Duplin 1.686007e+07 7.268376e+06 3.781589e+07 10000
Northampton,Halifax 1.941076e+07 9.920344e+06 2.499575e+07 14320
Watauga 2.029090e+07 1.050958e+07 4.154989e+07 26000
Mecklenburg 2.306376e+07 1.692153e+07 5.009678e+07 120000
Wake 2.873827e+07 1.667740e+07 4.945437e+07 75886

Visualization

Finally, we visualize the concentration across counties.

source(here("source", "04_data_visualization.R"))

First we look at boxplots of the log(concentration) of SARS-CoV-2 across counties in NC. The counties have been shorted from lowest to highest SARS-CoV-2 concentration.

plot1

Next, we visualize trends in SARS-CoV-2 concentration over time.

plot2