simple_sirs is written to work alongside the deSolve::ode() function, and
it will return an object with the proportion of individuals found in each of
the SIR compartments at each of the specified time points.
Arguments
- time
vector of values for which to generate the projection (length in days).
- state
initial state for compartment populations. This should be a named vector for starting values of S_wild, I_wild, R_wild, S_captive, I_captive, R_captive.
- parameters
list of parameters to generate projection. The parameters should include transmission parameters, immunity and recovery rates, and proportion of infected humans.
Value
when used with the deSolve::ode() function, it will return a
dataframe with the proportion of individuals in each of the SIR
compartments at each time point.
Details
Use simple_sirs to calculate persistence
(via rootSolve::run_steady()), along with how compartment sizes change
through a projection. If cumulative infections are desired, use
simple_sir_with_cumulative instead. The parameter boost is included in
the ODE equations for captive deer to allow implementation of applying
vaccine boosters to captive deer herds as a potential management alternative
to influence outbreak dynamics. See the vignette
Management_Alternative_Systems.Rmd to see an example of its use. In all
other cases where boosters would not be applied, boost should be set to 0.
Examples
if (FALSE) {
# prepare the input parameters:
example_inits <- c(S_wild = 1, I_wild = 0,
R_wild = 0, S_captive = 1,
I_captive = 0, R_captive = 0)
# set the time to run
example_times <- seq(0, 500, by = 1)
# Set parameters of transmission, immunity, recovery
example_params <- c(alpha_immunity = 0.03,
beta_aero_ww = 0.01,
beta_aero_cw = 0.01,
beta_aero_cc = 0.02,
beta_aero_hw = 0.01,
beta_aero_hc = 0.2,
beta_dc_ww = 0.01,
beta_dc_cw = 0.01,
beta_dc_cc = 0.01,
gamma_recov = 0.01,
I_human = 0.05,
boost = 0)
# run the ode function:
deSolve::ode(y = example_inits, times = example_times,
parms = example_params, func = whitetailedSIRS::simple_sirs)
}