main_simulation: main simulation loop
In jameshay218/vaxedemic: Optimal allocation of vaccination during a pandemic

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.