covid-alberta.R

# COVID-19 cases in Alberta, Canada
# cases over time and some analyses
library(PVAClone)

dat <- data.frame(
  date=c("2020-03-05", "2020-03-06", "2020-03-07", "2020-03-08", "2020-03-09", "2020-03-10", "2020-03-11", 
         "2020-03-12", "2020-03-13", "2020-03-14", "2020-03-15", "2020-03-16"),
  cases=c(1, 2, 2, 4, 7, 14, 19, 
          23, 29, 39, 56, 74))

m <- pva(dat$cases, ricker("none"), 10)

K <- -coef(m)["a"]/coef(m)["b"]

prx <- 0:(nrow(dat)*3)
pr <- numeric(length(prx))
pr[1] <- log(dat$cases[1])
for (i in 2:length(pr))
    pr[i] <- pr[i-1] + coef(m)["a"] + coef(m)["b"]*exp(pr[i-1])
pr <- exp(pr)

plot(prx, pr, type="l", ylab="# of cases", xlab=paste("Days since", dat$date[1]))
lines(seq_len(nrow(dat))-1, dat$cases, col=2, type="b", lwd=2, pch=19)
abline(h=K, col=4, lty=3)