run_simulation: function to set up simulation from inputs, then run

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

Description

function to set up simulation from inputs, then run

Usage

run_simulation(simulation_flags, life_history_params, vax_params,
  seasonality_params, time_params, vax_alloc_period, processed_inputs,
  n_runs = 1, calculate_summaries_func = "return_all_res", other_info)

Arguments

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 element "efficacy"
seasonality_params	list of seasonality parameters. contains the elements tdelay (0 <= tdelay <= 364): shifts the seasonality function - changing this effectively changes the seed time. tdelay = 0 is seed at t = 0 in sinusoidal curve, roughly start of autumn in Northern hemisphere days_per_block: average seasonality over blocks of this many days amp: amplitude of seasonality
time_params	list of parameters to do with time steps in simulation.
vax_alloc_period	allocate vaccines once every this many timesteps
processed_inputs	list. output of setup_inputs function
n_runs	number of repeats to run
calculate_summaries_func	string specifying what function to use to calculate summaries.
other_info	list which provides information needed to calculate the summaries

Value

a list of lists containing results of main simulation loop (see main_simulation). The length of this list is equal to n_runs

jameshay218/vaxedemic documentation built on Jan. 30, 2020, 2:58 a.m.