R/compartmental.R

In pahanc/malariasimulation_Ace_params: An individual based model for malaria

ODE_INDICES <- c(E = 1, L = 2, P = 3)
ADULT_ODE_INDICES <- c(Sm = 4, Pm = 5, Im = 6)

parameterise_mosquito_models <- function(parameters) {
  lapply(
    seq_along(parameters$species),
    function(i) {
      p <- parameters$species_proportions[[i]]
      m <- p * parameters$total_M
      growth_model <- create_aquatic_mosquito_model(
        parameters$beta,
        parameters$del,
        parameters$me,
        calculate_carrying_capacity(parameters, m, i),
        parameters$gamma,
        parameters$dl,
        parameters$ml,
        parameters$dpl,
        parameters$mup,
	parameters$use_Ace_mosq,
        m,
        parameters$model_seasonality,
        parameters$g0,
        parameters$g,
        parameters$h,
        calculate_R_bar(parameters),
        parameters$mum[[i]],
        parameters$blood_meal_rates[[i]],
        parameters$rainfall_floor
      )

      if (!parameters$individual_mosquitoes) {
        susceptible <- initial_mosquito_counts(
          parameters,
          i,
          parameters$init_foim,
          m
        )[ADULT_ODE_INDICES['Sm']]
        return(
          create_adult_mosquito_model(
            growth_model,
            parameters$mum[[i]],

            parameters$dem,
	    parameters$mosq_suppression[[i]],
	    parameters$mosq_seasonality[[i]],
	    parameters$use_Ace_mosq,
            susceptible * parameters$init_foim,
            parameters$init_foim
          )
        )
      }
      growth_model
    }
  )
}

parameterise_solvers <- function(models, parameters) {
  lapply(
    seq_along(models),
    function(i) {
      m <- parameters$species_proportions[[i]] * parameters$total_M
      init <- initial_mosquito_counts(parameters, i, parameters$init_foim, m)
      if (!parameters$individual_mosquitoes) {
        return(
          create_adult_solver(
            models[[i]],
            init,
            parameters$r_tol,
            parameters$a_tol,
            parameters$ode_max_steps
          )
        )
      }
      create_aquatic_solver(
        models[[i]],
        init[ODE_INDICES],
        parameters$r_tol,
        parameters$a_tol,
        parameters$ode_max_steps
      )
    }
  )
}

create_compartmental_rendering_process <- function(renderer, solvers, parameters) {
  if (parameters$individual_mosquitoes) {
    indices <- ODE_INDICES
  } else {
    indices <- c(ODE_INDICES, ADULT_ODE_INDICES)
  }

  function(timestep) {
    counts <- rep(0, length(indices))
    for (s_i in seq_along(solvers)) {
      if (parameters$species_proportions[[s_i]] > 0) {
        row <- solver_get_states(solvers[[s_i]])
      } else {
        row <- rep(0, length(indices))
      }
      for (i in seq_along(indices)) {
        renderer$render(
          paste0(names(indices)[[i]], '_', parameters$species[[s_i]], '_count'),
          row[[i]],
          timestep
        )
      }
      counts <- counts + row
    }
  }
}

#' @title Step mosquito solver
#' @description calculates total_M per species and updates the vector ode
#'
#' @param solvers for each species
#' @noRd
create_solver_stepping_process <- function(solvers, parameters) {
  function(timestep) {
    for (i in seq_along(solvers)) {
      if (parameters$species_proportions[[i]] > 0) {
        solver_step(solvers[[i]])
      }
    }
  }
}