Redundancies in the R package

[spoonerf]

Just making note of this while it is still current rather than expecting anyone to do anything about it!

Some redundancies in the R disease model:

• This has no real use: ` if(set_seed == TRUE) {

  seed <- rep
  set.seed(seed)
  } else {
  seed <- NULL
  }`

• The rep, risk_cap, rank_assign and set_seed parameters in the run_status() function are no longer used

Areas that could be improved:

• Currently all of the functions in the run_status() function are run every day. This is unnecessary for some functions, for example the mortality_risk() and sympt_risk functions could just be run once for each model run.