In rplzzz/vdhcovid: COVID-19 data by health district from Virginia Department of Health

library('dplyr')
library('ggplot2')

colors = c(AlbemarleCounty='red', Charlottesvillecity='orange', FluvannaCounty='cyan',
           GreeneCounty='green', LouisaCounty='blue', NelsonCounty='magenta')

vadjust <- function(x1, x2, sat) {
  x0 <- 0.5*(x1 + x2)
  k <- log(100*sat - 1) / (x0-x1)
  function(x) {
    v <- ifelse(x >= x1, sat / (1 + exp(-k*(x-x0))), 0)
    1 - v
  }
}

vaxest <- data.frame(date=seq(as.Date('2021-01-01'), as.Date('2021-07-01'), by='month'),
                     vaxfrac=1-vadjust(2, 9, 0.75)(seq(1,7)))

ggplot(filter(vaweeklyvax, district=='Thomas Jefferson'), aes(x=date, y=vaxfrac)) +
  geom_line(size=0.8, mapping=aes(x=date, y=vaxfrac, color=locality)) +
  geom_line(data=vaxest, size=1.25, linetype='A757') +
  ylab('Vaccinated fraction of total population') +
  scale_color_manual(values=colors) +
  theme_bw()

filter(vaweeklyvax, locality=='AlbemarleCounty', date < lubridate::now()) -> acvax
ggplot(acvax, aes(x=date, y=ndose)) + geom_line(size=1.2) + 
  ylab('Weekly final doses administered') +
  ggtitle('Albemarle county', 'Vaccination rate over time') +
  theme_bw()

rplzzz/vdhcovid documentation built on July 2, 2021, 7:43 a.m.