suffolk covid-19 wastewater plot.sh

#!/usr/bin/env bash
set -eu -o pipefail

data_path="/home/timmc/warehouse/biobot-data.csv"
png_path_prefix="/home/timmc/warehouse/biobot-data.Suffolk"

case "$1" in
    fetch)
        curl -sS https://raw.githubusercontent.com/biobotanalytics/covid19-wastewater-data/master/wastewater_by_county.csv > "$data_path"
        ;;

    plot)
        Rscript - <<EOF
d = read.csv("$data_path", header=T, sep=',')
d.Suffolk=subset(d, d\$name=='Suffolk County, MA')
d.Suffolk\$timestamp=as.Date(d.Suffolk\$sampling_week)

xwindow = as.Date(c('2020-01-01', '2022-03-01'))

# Log y axis
png("${png_path_prefix}.log.png", height=800, width=1200, units='px')
plot(
  d.Suffolk\$timestamp, d.Suffolk\$effective_concentration_rolling_average,
  type='l',
  log='y',
  xlim=xwindow,
)
dev.off()

# Linear y axis
png("${png_path_prefix}.lin.png", height=800, width=1200, units='px')
plot(
  d.Suffolk\$timestamp, d.Suffolk\$effective_concentration_rolling_average,
  type='l',
  xlim=xwindow,
  ylim=c(0, max(d.Suffolk\$effective_concentration_rolling_average) * 1.1),
)
abline(h=0) # draw y=0 line since origin does not start at 0
dev.off()

EOF
        ;;
    *)
        >&2 echo "Usage: $0 <fetch|plot>"
        exit 1
        ;;
esac