/
events.R
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events.R
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# --------------------------------------------------
# create event functions
# May 2021
# 1. create_events
# 2. create_event_scheduler_listener
# 3. create_state_update_listener
# 4. attach_event_listeners
# --------------------------------------------------
#' @title Create events
#'
#' @param parameters model parameters
#' @importFrom individual TargetedEvent
#' @export
create_events <- function(parameters) {
# 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),
imv_get_live = TargetedEvent$new(N), # need ICU, gets bed, lives
imv_get_die = TargetedEvent$new(N), # need ICU, gets bed, dies
iox_get_live = TargetedEvent$new(N), # need hosp, gets bed, lives
iox_get_die = TargetedEvent$new(N), # need hosp, gets bed, dies
imv_not_get_live = TargetedEvent$new(N), # need ICU, doesn't get bed, lives
imv_not_get_die = TargetedEvent$new(N), # need ICU, doesn't get bed, dies
iox_not_get_live = TargetedEvent$new(N), # need hosp, doesn't get bed, lives
iox_not_get_die = TargetedEvent$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 A listener to schedule future events
#' @description a listener to be attached to a \code{\link[individual]{TargetedEvent}}
#' to schedule a future event when that event fires.
#' @param event the future event to be schedule
#' @param duration mean duration of waiting time to be scheduled
#' @param func either \code{\link{make_rerlang}} or \code{\link{make_rexp}}
#' @param shift add integer number of time steps to sampled value
#' @param dt size of time step
#' @export
create_event_scheduler_listener <- function(event, duration, func, shift, dt) {
dwell <- func(mu = duration, dt = dt, shift = shift)
function(timestep, target) {
event$schedule(target = target, delay = dwell(n = target$size()))
}
}
#' @title A listener to update state
#' @description a listener to be attached to a \code{\link[individual]{TargetedEvent}}
#' to update state when that event fires.
#' @param states a \code{\link[individual]{CategoricalVariable}} object
#' @param destination the destination state
#' @export
create_state_update_listener <- function(states, destination) {
function(timestep, target) {
states$queue_update(value = destination, index = target)
}
}
#' @title Attach listeners to events
#' @description defines processes for events that can be scheduled in the future
#'
#' @param variables list of variables in the model
#' @param events a list of events in the model
#' @param parameters the model parameters
#' @param dt size of time step
#' @param shift schedule future events after minimum number of time step delay
#' @param shift_exposure schedule exposure event after minimum number of time step delay
#' @export
attach_event_listeners <- function(
variables,
events,
parameters,
dt,
shift = 1L,
shift_exposure = 1L
) {
# Exposure ----------
events$exposure$add_listener(
create_state_update_listener(
variables$states,
"E"
)
)
events$exposure$add_listener(
create_exposure_scheduler_listener(
events,
variables,
parameters,
dt = dt,
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$add_listener(
create_hospital_scheduler_listener_cpp(
parameters = parameters,
variables = variables,
events = events
)
)
# IMV (hospitalised, mechanical ventilation) ----------
events$imv_get_live$add_listener(
create_state_update_listener(
variables$states,
"IMVGetLive"
)
)
events$imv_get_live$add_listener(
create_event_scheduler_listener(
event = events$stepdown,
duration = parameters$dur_get_mv_survive,
func = make_rerlang,
shift = shift,
dt = dt
)
)
events$imv_get_die$add_listener(
create_state_update_listener(
variables$states,
"IMVGetDie"
)
)
events$imv_get_die$add_listener(
create_event_scheduler_listener(
event = events$death,
duration = parameters$dur_get_mv_die,
func = make_rerlang,
shift = shift,
dt = dt
)
)
events$imv_not_get_live$add_listener(
create_state_update_listener(
variables$states,
"IMVNotGetLive"
)
)
events$imv_not_get_live$add_listener(
create_event_scheduler_listener(
event = events$recovery,
duration = parameters$dur_not_get_mv_survive,
func = make_rerlang,
shift = shift,
dt = dt
)
)
events$imv_not_get_die$add_listener(
create_state_update_listener(
variables$states,
"IMVNotGetDie"
)
)
events$imv_not_get_die$add_listener(
create_event_scheduler_listener(
event = events$death,
duration = parameters$dur_not_get_mv_die,
func = make_rerlang,
shift = shift,
dt = dt
)
)
# IOx (hospitalised, oxygen) ----------
events$iox_get_live$add_listener(
create_state_update_listener(
variables$states,
"IOxGetLive"
)
)
events$iox_get_live$add_listener(
create_event_scheduler_listener(
event = events$recovery,
duration = parameters$dur_get_ox_survive,
func = make_rerlang,
shift = shift,
dt = dt
)
)
events$iox_get_die$add_listener(
create_state_update_listener(
variables$states,
"IOxGetDie"
)
)
events$iox_get_die$add_listener(
create_event_scheduler_listener(
event = events$death,
duration = parameters$dur_get_ox_die,
func = make_rerlang,
shift = shift,
dt = dt
)
)
events$iox_not_get_live$add_listener(
create_state_update_listener(
variables$states,
"IOxNotGetLive"
)
)
events$iox_not_get_live$add_listener(
create_event_scheduler_listener(
event = events$recovery,
duration = parameters$dur_not_get_ox_survive,
func = make_rerlang,
shift = shift,
dt = dt
)
)
events$iox_not_get_die$add_listener(
create_state_update_listener(
variables$states,
"IOxNotGetDie"
)
)
events$iox_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"
)
)
}