main_simulation: main simulation loop

In jameshay218/vaxedemic: Optimal allocation of vaccination during a pandemic

Description

main simulation loop

Usage

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

Arguments

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

Value

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 July 29, 2018, 12:43 p.m.