4  SEIR

library(SimInf)

n <- 1000
u0 <- data.frame(S = rep(99, n), E = rep(0, n), I = rep(5, n), R = rep(0, n))

seir_t <- SEIR(u0 = u0, tspan = 1:150, beta = 0.003 * 99, epsilon = 0.033, gamma = 0.077)
res_t <- run(seir_t)
plot(res_t)

transitions <- c("S -> beta * S * I -> E",
                 "E -> epsilon * E -> I",
                 "I -> gamma * I -> R")
compartments <- c("S", "E", "I", "R")

mod <- mparse(transitions = transitions,
              compartments = compartments,
              gdata = c(beta = 0.003, epsilon = 0.033, gamma = 0.077),
              u0 = u0,
              tspan = 1:150)
res <- run(mod)
plot(res)

4.1 Vaccination

transitions <- c("S -> beta * S * I -> E",
                 "E -> epsilon * E -> I",
                 "I -> gamma * I -> R")
compartments <- c("S", "E", "I", "R")