Description Usage Arguments Value

main simulation loop

1 2 | ```
main_simulation(tmax, tdiv, vax_alloc_period, LD, S0, E0, I0, R0, SV0, EV0,
IV0, RV0, params, cum_vax_pool_func, vax_allocation_func)
``` |

`tmax` |
number of days for which to run simulation |

`tdiv` |
number of timesteps per day |

`vax_alloc_period` |
allocate vaccines every this number of timesteps |

`LD` |
force of infection matrix: multiply by the I vector to get force of infection. a square matrix of side length maxIndex = n_countries * n_ages * n_riskgroups |

`S0` |
numeric vector of length max_Index: initial number of unvaccinated susceptibles in each location, age, risk group |

`E0` |
numeric vector of length max_Index: initial number of unvaccinated exposed |

`I0` |
numeric vector of length max_Index: initial number of unvaccinated infectious |

`R0` |
numeric vector of length max_Index: initial number of unvaccinated removed |

`SV0` |
numeric vector of length max_Index: initial number of vaccinated susceptibles |

`EV0` |
numeric vector of length max_Index: initial number of vaccinated exposed |

`IV0` |
numeric vector of length max_Index: initial number of vaccinated infectious |

`RV0` |
numeric vector of length max_Index: initial number of vaccinated removed |

`params` |
list of model parameters |

`cum_vax_pool_func` |
a function of time which gives the numebr of vaccines ever produced at that time |

`vax_allocation_func` |
a function of the current state of the simulation which gives the number of vaccines to allocate to each location, age, risk group |

list containing the elements: beta: infectivity parameter S: matrix containing the number of unvaccinated susceptibles in each location, age, risk group at each timestep. nrow(S) = n_groups = n_countres * n_ages * n_riskgroups ncol(S) = tend = tmax * tdiv E: same as Smat but for unvaccinated exposed I: same as Smat but for unvaccinated infectious R: same as Smat but for unvaccinated removed SV: same as Smat but for vaccinated susceptible EV: same as Smat but for vaccinated exposed IV: same as Smat but for vaccinated infectious RV: same as Smat but for vaccinated removed vax_pool: numeric vector containing number of vaccines available at each timestep.

jameshay218/vaxedemic documentation built on Dec. 10, 2018, 8:11 p.m.

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