R/mda_processes.R

In pahanc/malariasimulation_Ace_params: An individual based model for malaria

#' @title Create listeners for MDA events
#' @param variables the variables available in the model
#' @param administer_event the event schedule for drug administration
#' @param drug the drug to administer
#' @param timesteps timesteps for each round
#' @param coverages the coverage for each round
#' @param min_age minimum age for the target population
#' @param max_age maximum age for the target population
#' @param correlations correlation parameters
#' @param int_name the name of this intervention (either 'smc' or 'mda')
#' @param parameters the model parameters
#' @param renderer the model renderer object
#' @description will create a listener for administering each round of drugs
#' @noRd
create_mda_listeners <- function(
  variables,
  administer_event,
  drug,
  timesteps,
  coverages,
  min_age,
  max_age,
  correlations,
  int_name,
  parameters,
  renderer
  ) {
  function(timestep) {
    time_index = which(timesteps == timestep)
    coverage <- coverages[[time_index]]
    age <- get_age(variables$birth$get_values(), timestep)

    in_age <- which((age > min_age) & (age < max_age))
    target <- in_age[sample_intervention(in_age, int_name, coverage, correlations)]

    successful_treatments <- bernoulli(
      length(target),
      parameters$drug_efficacy[[drug]]
    )
    to_move <- individual::Bitset$new(parameters$human_population)
    to_move$insert(target[successful_treatments])

    renderer$render('n_mda_treated', to_move$size(), timestep)

    if (to_move$size() > 0) {
      # Move Diseased
      diseased <- variables$state$get_index_of(c('D', 'A'))$and(to_move)
      if (diseased$size() > 0) {
        variables$state$queue_update('Tr', diseased)
      }

      # Move everyone else
      other <- to_move$copy()$and(diseased$not(TRUE))
      if (other$size() > 0) {
        variables$state$queue_update('S', other)
      }

      # Update infectivity
      variables$infectivity$queue_update(
        variables$infectivity$get_values(
          to_move
        ) * parameters$drug_rel_c[[drug]],
        to_move
      )

      # Update drug
      variables$drug$queue_update(drug, to_move)
      variables$drug_time$queue_update(timestep, to_move)
    }

    # Schedule next round
    if (time_index < length(timesteps)) {
      administer_event$schedule(timesteps[[time_index + 1]] - timestep)
    }
  }
}