context("SEIR functions")
library(gridExtra)
test_that("SEIR from deSolve is correct", {
T <- 365
init_vals <- c(9500, 0, 500, 0) #SEIR
beta <- .06
gamma <- .03
alpha <- .02
N <- sum(init_vals)
step <- 1
## Plot the SIR
do_plot = TRUE
seir_data <- SEIR(T, init_vals, beta, gamma,
alpha, step, SEIR_inner, do_plot)
## Optimize function
inits <- c(beta, gamma, alpha)
params <- optim(par=inits, fn=SSE_SEIR, data=seir_data,
init_vals = init_vals, hessian = TRUE)
## Change SEIR data to SIR
sir_data <- data.frame(t = results$t,
S = results$S + results$E,
I = results$I,
R = results$R)
init_sir <- inits[-3]
init_vals_sir <- init_vals[-2]
params_sir <- optim(par=init_sir, fn=SSE_SIR, data=sir_data,
init_vals = init_vals_sir, hessian = TRUE)
r0_seir <- params$par[1] / params$par[2]
r0_sir <- params_sir$par[1] / params_sir$par[2]
c(r0_seir, r0_sir)
})
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