R/examples/calc_prop_vacc.R

In gilesjohnr/propvacc: Functions to model and simulate vaccine dose coverage

# Two dose measles vaccine: routine without SIA
calc_prop_vacc(V=c(0.9, 0.8),
               effectiveness=c(0.84, 0.941),
               independent=FALSE)

calc_prop_vacc(V=c(0.9, 0.8),
               effectiveness=c(0.84, 0.941),
               independent=TRUE)

# Three dose vaccine: routine without SIA
calc_prop_vacc(V=c(0.9, 0.8, 0.7),
               effectiveness=c(0.85, 0.9, 0.95))

# Estimate posterior distribution of proportion vaccinated given uncertainty around MCV1 and MCV2
n <- 1000
sims <- rep(NA, n)
for (i in 1:n) {

  sims[i] <- calc_prop_vacc(V=c(rbeta(1,40,1), rbeta(1,4,2)),
                      effectiveness=c(0.85, 0.94),
                      independent=FALSE)
}

q <- quantile(sims, c(0.025, 0.5, 0.975))

par(mfrow=c(1,1))
hist(sims, breaks=100, col='cyan', xlab='Proportion vaccinated')
abline(v=q[2], lwd=3)
abline(v=q[c(1,3)], lty=2, lwd=2)