run_and_get_deaths_recovered: run the simulation and get a vector of the number of deaths...
In jameshay218/vaxedemic: Optimal allocation of vaccination during a pandemic

for code testing purposes.

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.