tests/testthat/examples/seir_odin.R

In richfitz/odin: ODE Generation and Integration

initial(S) <- N - I0
initial(E) <- 0
initial(I) <- I0
initial(R) <- 0

I0 <- 1

Births <- b * N
b <- 1 / 10
N <- 1e7
beta <- 10
sigma <- 1 / 3
delta <- 1 / 21
lat_hum <- 14

## people developing latent infection
new_inf <- beta * S * I / N
## i.e. proportion of humans surviving the latent period
surv <- exp(-b * lat_hum)
## people that become latent 'lath_um' days ago, less those that died
## during that time
lag_inf <- delay(new_inf  *  surv, lat_hum)

deriv(S) <- Births - b * S - new_inf + delta * R
deriv(E) <- new_inf - lag_inf - b * E
deriv(I) <- lag_inf  - (b + sigma) * I
deriv(R) <- sigma * I - b * R - delta * R