R/events_base.R

In mrc-ide/safir2: Individual-Based Model of COVID Transmission

# base set of events for safir2 models

#' @title Create disease progression events
#' @description Create named list of [individual::TargetedEvent] objects which
#' simulate disease progression. The list of events is as follows:
#'
#'  * `exposure`: scheduled when an individual is infected
#'  * `mild_infection`: scheduled from `exposure`
#'  * `asymp_infection`: scheduled from `exposure`
#'  * `severe_infection`: scheduled from `exposure`
#'  * `hospitilisation`: scheduled from `severe_infection`
#'  * `ICU_get_live`: scheduled from `hospitilisation`
#'  * `ICU_get_die`: scheduled from `hospitilisation`
#'  * `hosp_get_live`: scheduled from `hospitilisation`
#'  * `hosp_get_die`: scheduled from `hospitilisation`
#'  * `ICU_not_get_live`: scheduled from `hospitilisation`
#'  * `ICU_not_get_die`: scheduled from `hospitilisation`
#'  * `hosp_not_get_live`: scheduled from `hospitilisation`
#'  * `hosp_not_get_die`: scheduled from `hospitilisation`
#'  * `stepdown`: scheduled from `ICU_get_live`
#'  * `recovery`: scheduled from `mild_infection`, `asymp_infection`, `ICU_not_get_live`, `hosp_get_live`, `hosp_not_get_live`
#'  * `immunity_loss`: scheduled from `recovery`
#'  * `death`: scheduled from `ICU_get_die`, `ICU_not_get_die`, `hosp_get_die`, `hosp_not_get_die`
#'
#' @param parameters model parameters
#' @importFrom individual TargetedEvent
#' @export
create_events <- function(parameters) {

  stopifnot(is.numeric(parameters$population))

  # pop size
  N <- sum(parameters$population)

  list(
    # Human infection events
    exposure = TargetedEvent$new(N), # S->E, scheduled by infection_process_zzz
    mild_infection = TargetedEvent$new(N), # E->IMild, scheduled by create_exposure_update_listener
    asymp_infection = TargetedEvent$new(N),
    severe_infection = TargetedEvent$new(N),
    hospitilisation = TargetedEvent$new(N),
    ICU_get_live = TargetedEvent$new(N), # need ICU, gets bed, lives
    ICU_get_die = TargetedEvent$new(N), # need ICU, gets bed, dies
    hosp_get_live = TargetedEvent$new(N), # need hosp, gets bed, lives
    hosp_get_die = TargetedEvent$new(N), # need hosp, gets bed, dies
    ICU_not_get_live = TargetedEvent$new(N), # need ICU, doesn't get bed, lives
    ICU_not_get_die = TargetedEvent$new(N), # need ICU, doesn't get bed, dies
    hosp_not_get_live = TargetedEvent$new(N), # need hosp, doesn't get bed, lives
    hosp_not_get_die = TargetedEvent$new(N), # need hosp, doesn't get bed, dies
    stepdown = TargetedEvent$new(N),
    recovery = TargetedEvent$new(N),
    immunity_loss = TargetedEvent$new(N),
    death = TargetedEvent$new(N)
  )
}



#' @title Attach listeners to events
#' @description defines processes for events that can be scheduled in the future
#'
#' @param variables list of variables in the model
#' @param events a list of events in the model
#' @param parameters the model parameters
#' @param shift schedule future events after minimum number of time step delay
#' @param shift_exposure schedule exposure event after minimum number of time step delay
#' @export
attach_event_listeners <- function(
  variables,
  events,
  parameters,
  shift = 1L,
  shift_exposure = 1L
) {

  dt <- parameters$dt

  # Exposure ----------
  add_named_listener(
    event = events$exposure,
    name = "state_update",
    listener = create_state_update_listener(
      states = variables$states,
      destination = "E"
    )
  )

  add_named_listener(
    event = events$exposure,
    name = "scheduler",
    listener = create_exposure_scheduler_listener(
      events = events,
      variables = variables,
      parameters = parameters,
      shift = shift_exposure
    )
  )

  # # IMild ----------
  #
  # events$mild_infection$add_listener(
  #   create_state_update_listener(
  #     variables$states,
  #     "IMild"
  #   )
  # )
  #
  # events$mild_infection$add_listener(
  #   create_event_scheduler_listener(
  #     event = events$recovery,
  #     duration = parameters$dur_IMild,
  #     func = make_rexp,
  #     shift = shift,
  #     dt = dt
  #   )
  # )
  #
  # # IAsymp ----------
  #
  # events$asymp_infection$add_listener(
  #   create_state_update_listener(
  #     variables$states,
  #     "IAsymp"
  #   )
  # )
  #
  # events$asymp_infection$add_listener(
  #   create_event_scheduler_listener(
  #     event = events$recovery,
  #     duration = parameters$dur_IAsymp,
  #     func = make_rexp,
  #     shift = shift,
  #     dt = dt
  #   )
  # )
  #
  # # ICase ----------
  #
  # events$severe_infection$add_listener(
  #   create_state_update_listener(
  #     variables$states,
  #     "ICase"
  #   )
  # )
  #
  # events$severe_infection$add_listener(
  #   create_event_scheduler_listener(
  #     event = events$hospitilisation,
  #     duration = parameters$dur_ICase,
  #     func = make_rerlang,
  #     shift = shift,
  #     dt = dt
  #   )
  # )
  #
  # # Hospitalisation (no state update, queues other events) ----------
  #
  # events$hospitilisation$add_listener(
  #   create_hospital_scheduler_listener(
  #     parameters = parameters,
  #     variables = variables,
  #     events = events
  #   )
  # )
  #
  # # ICU (hospitalised, mechanical ventilation) ----------
  #
  # events$ICU_get_live$add_listener(
  #   create_state_update_listener(
  #     variables$states,
  #     "ICUGetLive"
  #   )
  # )
  #
  # events$ICU_get_live$add_listener(
  #   create_event_scheduler_listener(
  #     event = events$stepdown,
  #     duration = parameters$dur_get_mv_survive,
  #     func = make_rerlang,
  #     shift = shift,
  #     dt = dt
  #   )
  # )
  #
  # events$ICU_get_die$add_listener(
  #   create_state_update_listener(
  #     variables$states,
  #     "ICUGetDie"
  #   )
  # )
  #
  # events$ICU_get_die$add_listener(
  #   create_event_scheduler_listener(
  #     event = events$death,
  #     duration = parameters$dur_get_mv_die,
  #     func = make_rerlang,
  #     shift = shift,
  #     dt = dt
  #   )
  # )
  #
  # events$ICU_not_get_live$add_listener(
  #   create_state_update_listener(
  #     variables$states,
  #     "ICUNotGetLive"
  #   )
  # )
  #
  # events$ICU_not_get_live$add_listener(
  #   create_event_scheduler_listener(
  #     event = events$recovery,
  #     duration = parameters$dur_not_get_mv_survive,
  #     func = make_rerlang,
  #     shift = shift,
  #     dt = dt
  #   )
  # )
  #
  # events$ICU_not_get_die$add_listener(
  #   create_state_update_listener(
  #     variables$states,
  #     "ICUNotGetDie"
  #   )
  # )
  #
  # events$ICU_not_get_die$add_listener(
  #   create_event_scheduler_listener(
  #     event = events$death,
  #     duration = parameters$dur_not_get_mv_die,
  #     func = make_rerlang,
  #     shift = shift,
  #     dt = dt
  #   )
  # )
  #
  # # hosp (hospitalised, oxygen) ----------
  #
  # events$hosp_get_live$add_listener(
  #   create_state_update_listener(
  #     variables$states,
  #     "hospGetLive"
  #   )
  # )
  #
  # events$hosp_get_live$add_listener(
  #   create_event_scheduler_listener(
  #     event = events$recovery,
  #     duration = parameters$dur_get_ox_survive,
  #     func = make_rerlang,
  #     shift = shift,
  #     dt = dt
  #   )
  # )
  #
  # events$hosp_get_die$add_listener(
  #   create_state_update_listener(
  #     variables$states,
  #     "hospGetDie"
  #   )
  # )
  #
  # events$hosp_get_die$add_listener(
  #   create_event_scheduler_listener(
  #     event = events$death,
  #     duration = parameters$dur_get_ox_die,
  #     func = make_rerlang,
  #     shift = shift,
  #     dt = dt
  #   )
  # )
  #
  # events$hosp_not_get_live$add_listener(
  #   create_state_update_listener(
  #     variables$states,
  #     "hospNotGetLive"
  #   )
  # )
  #
  # events$hosp_not_get_live$add_listener(
  #   create_event_scheduler_listener(
  #     event = events$recovery,
  #     duration = parameters$dur_not_get_ox_survive,
  #     func = make_rerlang,
  #     shift = shift,
  #     dt = dt
  #   )
  # )
  #
  # events$hosp_not_get_die$add_listener(
  #   create_state_update_listener(
  #     variables$states,
  #     "hospNotGetDie"
  #   )
  # )
  #
  # events$hosp_not_get_die$add_listener(
  #   create_event_scheduler_listener(
  #     event = events$death,
  #     duration = parameters$dur_not_get_ox_die,
  #     func = make_rerlang,
  #     shift = shift,
  #     dt = dt
  #   )
  # )
  #
  #
  # # Recovery events
  # events$recovery$add_listener(
  #   create_state_update_listener(
  #     variables$states,
  #     "R"
  #   )
  # )
  #
  # if (is.finite(parameters$dur_R)) {
  #   events$recovery$add_listener(
  #     create_event_scheduler_listener(
  #       event = events$immunity_loss,
  #       duration = parameters$dur_R,
  #       func = make_rerlang,
  #       shift = shift,
  #       dt = dt
  #     )
  #   )
  # }
  #
  # # Stepdown events
  # events$stepdown$add_listener(
  #   create_state_update_listener(
  #     variables$states,
  #     "IRec"
  #   )
  # )
  #
  # events$stepdown$add_listener(
  #   create_event_scheduler_listener(
  #     event = events$recovery,
  #     duration = parameters$dur_rec,
  #     func = make_rerlang,
  #     shift = shift,
  #     dt = dt
  #   )
  # )
  #
  # # Death events
  # events$death$add_listener(
  #   create_state_update_listener(
  #     variables$states,
  #     "D"
  #   )
  # )
  #
  # # Loss of immunity
  # events$immunity_loss$add_listener(
  #   create_state_update_listener(
  #     variables$states,
  #     "S"
  #   )
  # )

}