model <- function(start, stop, stoc,
                       spec, dens,
                       b,
                       i_mat, i_dur,
                       ntype, ncov) {

# do stuff

}

simulate <- function(time_start, time_stop,
		       is_stochastic, mosquito_species,
                       mosquito_density,
                       mosquito_to_human_prob,
                       immunity_maternal, immunity_duration,
                       net_type, net_coverage) {

# do stuff

}

SimulationParameters <- setClass("SimulationParameters",
                                 slots=list(time_start="numeric",
                                            time_stop="numeric",
                                            is_stochastic="logical"))

# doesn't work
simulation_parameters <- SimulationParameters(
                             time_start=1990,
                             time_stop=2018,
                             is_stochastic=2)

# works
simulation_parameters <- SimulationParameters(
                             time_start=1990,
                             time_stop=2018,
                             is_stochastic=FALSE)

check <-function(object) {

  if(!object@net_type %in% c("net 1", "net 2"))
    return("A net must of type `net 1` or `net 2`.")

  coverage <- object@net_coverage
  if(coverage < 0 | coverage > 1)
    return("Net coverage must not be outside [0, 1].")
}

BednetParameters <- setClass("BednetParameters",
                             slots=list(net_type="character",
                                        net_coverage="numeric"),
                             validity = check)
                                   
# fails
bednet_parameters <- BednetParameters(net_type = "net 3",
                                      net_coverage = 0.3)

# fails
bednet_parameters <- BednetParameters(net_type = "net 2",
                                      net_coverage = 100)

Simulation <- setClass("Simulation",
                       slots=list(simulation_parameters="SimulationParameters",
                                  bednet_parameters="BednetParameters",
                                  immunity_parameters="ImmunityParameters",
                                  mosquito_parameters="MosquitoParameters"))

# ...don't show how to do but could create a "run" method
simulation <- Simulation(simulation_parameters=....)
result <- run(simulation)

# what parameters did I use to run my simulation?
simulation@simulation_parameters