EpiDynamics (version 0.3.1)

SIRScaledAdditiveNoise: SIR model with Scaled additive noise (P 6.2).

Description

Solves a SIR model with scaled additive noise.

Usage

SIRScaledAdditiveNoise(pars = NULL, init = NULL, time = NULL, ...)

Arguments

pars

vector with 5 parameters: transmission rate, recovery rate, per capita death rate, the total population size and the number of steps that will change noise term. The names of these values must be "beta", "gamma", "mu", "N" and "step", respectively. All parameters must be positive and all rates are specified in days. The birth rate is assumed to be constant and equal to mu * N, therefore preventing extinction of the host population. Noise terms are generated as a function of the time step and its magnitude is a function of the rate of each process.

init

vector with 2 values: the initial population size that are susceptible and infectious. The names of these values must be "X" and "Y", respectively. All initial conditions must be positive.

time

time sequence for which output is wanted; the first value of times must be the initial time.

...

further arguments passed to ode function.

Value

list. The first element, *$model, is the model function. The second, third and fourth elements are the vectors (*$pars, *$init, *$time, containing the pars, init and time arguments of the function. The fifth element *$results is a data.frame with up to as many rows as elements in time. First column contains the time. The following columns contain the proportion of susceptibles, infectious and recovered.

Details

This is the R version of program 6.2 from page 197 of "Modeling Infectious Disease in humans and animals" by Keeling & Rohani.

References

Keeling, Matt J., and Pejman Rohani. Modeling infectious diseases in humans and animals. Princeton University Press, 2008.

See Also

ode.

Examples

# NOT RUN {
# Parameters and initial conditions.
parameters <- c(beta = 1, gamma = 1 / 10, mu = 1 / (50 * 365),
                N = 1e6, step = 1)
initials <- c(X = 1e5, Y = 500)

# Solve and plot.
sir.scaled.additive.noise <- 
SIRScaledAdditiveNoise(pars = parameters, 
                       init = initials, time = 5 * 365)
PlotMods(sir.scaled.additive.noise)

# }