`R/simulate_idsurveillance_ode.R`

`simulate_idsurveillance_ode.Rd`

This model allows for the exploration of the impact of ID surveillance on transmission dynamics

simulate_idsurveillance_ode( S = 1000, P = 1, tmax = 200, bP = 0, bA = 0, bI = 0.001, gP = 0.5, f = 0, d = 0, w = 0, m = 0, n = 0, rP = 0, rA = 0, rI = 0.5 )

S | : initial number of susceptible hosts : numeric |
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P | : initial number of infected pre-symptomatic hosts : numeric |

tmax | : maximum simulation time : numeric |

bP | : rate of transmission from presymptomatic to susceptible host : numeric |

bA | : rate of transmission from asymptomatic to susceptible host : numeric |

bI | : rate of transmission from symptomatic to susceptible host : numeric |

gP | : the rate at which presymptomatic hosts move to the next stage : numeric |

f | : fraction of asymptomatic hosts : numeric |

d | : rate at which infected hosts die : numeric |

w | : the rate at which host immunity wanes : numeric |

m | : the rate of births : numeric |

n | : the rate of natural deaths : numeric |

rP | : rate of pre-symptomatic host removal due to surveillance : numeric |

rA | : rate of asymptomatic host removal due to surveillance : numeric |

rI | : rate of symptomatic host removal due to surveillance : numeric |

This function returns the simulation result as obtained from a call to the deSolve ode solver.

A compartmental ID model with several states/compartments is simulated as a set of ordinary differential equations. The function returns the output from the odesolver as a matrix, with one column per compartment/variable. The first column is time.

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

The UI of the app 'Parasite Model', which is part of the DSAIDE package, contains more details.

# To run the simulation with default parameters just call the function: result <- simulate_idsurveillance_ode() # To choose parameter values other than the standard one, # specify the parameters you want to change, e.g. like such: result <- simulate_idsurveillance_ode(S = 2000, tmax = 100, f = 0.5) # 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')