SEIRdelay_MNRM_C: SEIR model with fixed delay via Modified Next Reaction Method...

In dd-harp/delay:

Description

Using the Modified Next Reaction Method (MNRM) for delays, simulate a SEIR model where the time spent in the E compartment is a deterministic period of length tau.

Usage

SEIRdelay_MNRM_C(tmax, S0, I0, beta, nu, tau, verbose = T, maxsize = 1e+06)

Arguments

tmax	maximum time of simulation
S0	initial number of susceptibles
I0	initial number of infectives
beta	effective contact rate
nu	duration of infectiousness
tau	duration of latent period fixed delay
verbose	print diagnostic information
maxsize	maximum size of output matrix; simulation will return early if this is exceeded

Details

The MNRM is described in: Anderson, D. F. (2007). A modified next reaction method for simulating chemical systems with time dependent propensities and delays. Journal of Chemical Physics, 127(21). https://doi.org/10.1063/1.2799998

Examples

 ## Not run: 
   out <- SEIRdelay_MNRM_C(tmax = 1e3,S0 = 1000,I0 = 5,beta = 0.001,nu = 1/5,tau = 10,verbose = TRUE)
   outd <- discretize(out)
   matplot(outd[,-1],type="l",col=c("blue","orange","red","purple"),lwd=1.5,lty=1,ylab="Count",xlab="Days")
   legend(x = "topleft",pch=rep(16,4),col=c("blue","orange","red","purple"),legend=c("S","E","I","R"))

## End(Not run)

dd-harp/delay documentation built on April 1, 2020, 2:33 a.m.