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

Description Usage Arguments Value

View source: R/simulation.R

Description

function to set up simulation from inputs, then run

Usage

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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 elements "efficacy" and "propn_vax0" (initial proportion of vaccinated individuals; assumed constant across location, age and risk groups)

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 Dec. 10, 2018, 8:11 p.m.