calc_prop_vacc: Calculate the total proportion vaccinated by routine...

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

Description

This function calculates the proportion immune due to vaccination given the proportion vaccinated at each routine activity and the effectiveness of each dose. The function assumes that vaccination events are dependent by default, where individuals that have recieved the first dose are the most likely to recieve the second dose and those that have received both the first and second doses are the most likely to receive the third. The function uses either the two-dose or three-dose method based on the length of V.

Usage

calc_prop_vacc(V, effectiveness, independent = FALSE)

Arguments

V	a vector giving the proportion vaccinated for up to three routine immunization activities
effectiveness	scalar or vector giving the vaccine effectiveness for each number of doses
independent	logical indicating if receipt of routine vaccine dose is depends on the number of prior doses received (default = FALSE)

Value

A scalar giving the total proportion of the population immune due to vaccination

Author(s)

John Giles

See Also

Other prop_vacc: calc_doses_SIA(), calc_doses(), calc_prop_vacc_SIA()

Examples

# 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)

gilesjohnr/propvacc documentation built on Aug. 24, 2020, 3:20 a.m.