DSAIDE (version 0.8.3)

simulate_evolution_stochastic: Stochastic simulation of a compartmental SIR-type model with wild-type and mutant strains and treatment

Description

Simulation of a stochastic 2-strain SIR model with the following compartments: Susceptibles (S), Infected with wild-type/sensitive and untreated (Iu), Infected with wild-type and treated (It), infected with resistant (Ir), Recovered and Immune (R). allows exploration of evolutionary dynamics

Usage

simulate_evolution_stochastic(
  S = 1000,
  Iu = 1,
  It = 1,
  Ir = 1,
  bu = 0.001,
  bt = 0.001,
  br = 0.001,
  cu = 0.001,
  ct = 0.01,
  f = 0,
  gu = 1,
  gt = 1,
  gr = 1,
  tmax = 100,
  rngseed = 100
)

Arguments

S

: initial number of susceptible hosts : numeric

Iu

: initial number of wild-type infected untreated hosts : numeric

It

: initial number of wild-type infected treated hosts : numeric

Ir

: initial number of resistant infected hosts : numeric

bu

: level/rate of infectiousness for hosts in the Iu compartment : numeric

bt

: level/rate of infectiousness for hosts in the It compartment : numeric

br

: level/rate of infectiousness for hosts in the Ir compartment : numeric

cu

: fraction of resistant mutant infections that an untreated host produces : numeric

ct

: fraction of resistant mutant infections that a treated host produces : numeric

f

: fraction of infected receiving treatment : numeric

gu

: rate at which a host leaves the Iu compartment : numeric

gt

: rate at which a person leaves the It compartment : numeric

gr

: rate at which a person leaves the Ir compartment : numeric

tmax

: maximum simulation time : numeric

rngseed

: seed for random number generator to allow reproducibility : numeric

Value

This function returns the simulation result as obtained from a call to the adaptivetau integrator in list form. The list element ts is a dataframe where the first column is "time," and the remaining columns are the variables

Warning

This function does not perform any error checking. So if you try to do something nonsensical (e.g. have negative values or fractions > 1), the code will likely abort with an error message

Details

A compartmental ID model with several states/compartments is simulated as a stochastic model using the adaptive tau algorithm as implemented by ssa.adaptivetau() in the adaptivetau package. See the manual of this package for more details.

References

See the manual for the adaptivetau package for details on the algorithm. The implemented model is loosely based on: Handel et al 2009 JTB "Antiviral resistance and the control of pandemic influenza: The roles of stochasticity, evolution and model details"

Examples

# NOT RUN {
# To run the simulation with default parameters just call the function:
result <- simulate_evolution_stochastic()
# To choose parameter values other than the standard one, specify them like such:
result <- simulate_evolution_stochastic(S = 2000,  tmax = 200, bt = 0.01)
# You should then use the simulation result returned from the function, like this:
plot(result$ts[ , "time"],result$ts[ , "S"],xlab='Time',ylab='Number Susceptible',type='l')
# }