Alberta COVID19 Wastewater Chart in R

alberta_covid19_wastewater.R

library(data.table)
library(jsonlite)
library(ggplot2)
library(jsonlite)
library(glue)

tmpfile <- tempfile(fileext = ".json")
download.file("https://chi-covid-data.pages.dev/aplWasteWaterAbData.json",tmpfile)

json_data <- jsonlite::read_json(tmpfile)$data
unlink(tmpfile)
rm(tmpfile)

data <- rbindlist(lapply(names(json_data),function(x,data=json_data){
  cbind(rbindlist(data[[x]]),location=x)
}))

rm(json_data)

data[,date:=as.Date(date)]

p <- ggplot(data,aes(x=date))+
  geom_step(aes(y=avg),alpha=0.5)+
  geom_point(aes(y=avg))+
  stat_smooth(aes(y=avg))+
  facet_wrap(~location,scales = "free_y")+
  scale_y_continuous(name="Viral Copies per Person")+
  scale_x_date(name=NULL, 
               date_breaks="1 month",
               date_labels = "%b",
               date_minor_breaks = "1 week")+
  theme_bw()+
  labs(title="Alberta: COVID19 in Wastewater",
       subtitle=glue::glue("Latest Data as of: {max(data$date,na.rm=T)}"),
       caption=glue::glue("Data Source: Alberta Health, Alberta Precision Laboratories & Centre for Health Informatics\n{Sys.Date()}")
  )

ggsave(glue::glue("{Sys.Date()}_-_COVID19_Wastewater.png"),plot=p,units="in",width=6,height=4,dpi=150,scale = 1.2)