R/pull_wastewater.R

In nctriadresearch/nccovid: Pull North Carolina Covid-19 Outbreak Information

#' Pull Wastewaster Treatment Data
#' 
#' A helper function to pull SARS-CoV-2 Copies Detected in Wastewater
#' @param county_in a string vector indicating the counties served
#'     with a default of \code{NULL} returning all counties
#' @examples 
#' raw_dat <- pull_wastewater(county_in = "Guilford")
#' raw_dat <- raw_dat[!is.na(sars_cov2_raw_copiesL)][,copies_log10 := log10(sars_cov2_normalized)]
#' 
#' par(mar = c(5, 4, 4, 4) + 0.3)
#' plot(copies_log10~date_new, data = raw_dat, type ="b", 
#'     xlab = "Date", ylab = "SARS-CoV-2 RNA Copies (Log10)")
#' par(new = TRUE)
#' plot(log10(cases_new_cens_per10k)~date_new, data = raw_dat,
#' 		 type = "l", axes = FALSE, bty = "n", xlab = "", ylab = "", col = "orange")
#' axis(side=4, at = pretty(range(log10(raw_dat$cases_new_cens_per10k))))
#' mtext("Log10(New Cases per 100k)", side=4, line=3)
#' title("Guilford SARS-CoV-2 Detected in Wastewater vs New Cases per 100k")
#' @export

pull_wastewater <- function(county_in = NULL){
	url <- "https://raw.githubusercontent.com/conedatascience/covid-data/master/data/timeseries/waste-water.csv"
	dat_raw <- data.table::fread(url)
	
	if(!is.null(county_in)){
		dat_raw <- dat_raw[county_names %in% county_in]
	}
	
	return(dat_raw)
	
}