tests/testthat/test-seir.R

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)
    
})
shannong19/simCAM documentation built on May 30, 2019, 6:26 a.m.