Description Usage Arguments Value
for code testing purposes.
1 2 3 4 | run_and_get_deaths_recovered(simulation_flags, life_history_params,
vax_params, sim_params, case_fatality_ratio_vec, X, labels, C3, K,
latitudes, cum_vax_pool_func, vax_allocation_func, tmax, tdiv,
vax_alloc_period)
|
simulation_flags |
named vector (or list) with the logical elements "normaliseTravel" and "seasonal" |
life_history_params |
named vector (or list) with the numeric elements "R0", "TR" (time to recovery) and "LP" (latent period) |
vax_params |
named vector (or list) with the numeric elements "efficacy" and "propn_vax0" (initial proportion of vaccinated individuals; assumed constant across location, age and risk groups) |
sim_params |
list with the numeric elements n_countries, n_ages, n_riskgroups and seed_vec. The last of these is a vector specifying the initial number of exposed individuals in each location, age and risk group |
case_fatality_ratio_vec |
vector of case fatality ratio in each location, age, risk group: length n_countries * n_ages * n_riskgroups |
X |
vector of population size in each location, age, risk group: length n_countries * n_ages * n_riskgroups |
latitudes |
a matrix with 1 column and n_countries rows, giving the latitude of each country in degrees. |
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 |
tmax |
the number of days for which to run the simulation |
tdiv |
the number of timesteps per day |
vax_alloc_period |
allocate vaccines once every this many timesteps |
contactMatrix |
either a square matrix with side length n_ages * n_riskgroups, or a list of such matrices, of length n_countries. If a single matrix, the contact matrix is assumed to be constant across countries. contactMatrix[i,j] denotes the amount of influence an individual of type i has on an individual of type j, where type includes age and risk groups. |
travelMatrix |
a square matrix with side length n_countries. travelMatrix[i,j] denotes the proportion of time an individual in country i spends in country j. If simulation_flags[["normaliseTravel"]] == TRUE, the code will row normalise travelMatrix for you. |
list containing the number of deaths and recovereds in each country/age/risk group
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