R/initialize_events_nimue.R

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

# --------------------------------------------------
#   initialize event scheduling (nimue vaccine model)
#   Sean L. Wu (slwood89@gmail.com)
#   May 2021
#   1. setup_events
# --------------------------------------------------


#' @title Schedule events for individuals at initialisation (nimue vaccine model)
#' @param parameters model parameters from [get_parameters_nimue]
#' @param events model events
#' @param variables model variables
#' @param dt size of time step
#' @export
setup_events_nimue <- function(
    parameters,
    events,
    variables,
    dt
) {

    # E individuals
    bset_E <- variables$states$get_index_of("E")
    if (bset_E$size() > 0) {
        init_fn <- create_exposure_scheduler_listener_nimue(
            events = events,
            variables = variables,
            parameters = parameters,
            dt = dt
        )
        init_fn(timestep = 1, target =bset_E)
    }

    # IMild
    bset_IMild <- variables$states$get_index_of("IMild")
    if (bset_IMild$size() > 0) {
        init_fn <- create_event_scheduler_listener(
            event = events$recovery,
            duration = parameters$dur_IMild,
            func = make_rexp,
            shift = 1L,
            dt = dt
        )
        init_fn(timestep = 1, target =bset_IMild)
    }

    # IAsymp
    bset_IAsymp <- variables$states$get_index_of("IAsymp")
    if (bset_IAsymp$size() > 0) {
        init_fn <- create_event_scheduler_listener(
            event = events$recovery,
            duration = parameters$dur_IAsymp,
            func = make_rexp,
            shift = 1L,
            dt = dt
        )
        init_fn(timestep = 1, target =bset_IAsymp)
    }

    # ICase
    bset_ICase <- variables$states$get_index_of("ICase")
    if (bset_ICase$size() > 0) {
        init_fn <- create_event_scheduler_listener(
            event = events$hospitilisation,
            duration = parameters$dur_ICase,
            func = make_rerlang,
            shift = 1L,
            dt = dt
        )
        init_fn(timestep = 1, target =bset_ICase)
    }

    # IMVGetLive
    bset_IMVGetLive <- variables$states$get_index_of("IMVGetLive")
    if (bset_IMVGetLive$size() > 0) {
        init_fn <- create_event_scheduler_listener(
            event = events$stepdown,
            duration = parameters$dur_get_mv_survive,
            func = make_rerlang,
            shift = 1L,
            dt = dt
        )
        init_fn(timestep = 1, target =bset_IMVGetLive)
    }

    # IMVGetDie
    bset_IMVGetDie <- variables$states$get_index_of("IMVGetDie")
    if (bset_IMVGetDie$size() > 0) {
        init_fn <- create_event_scheduler_listener(
            event = events$death,
            duration = parameters$dur_get_mv_die,
            func = make_rerlang,
            shift = 1L,
            dt = dt
        )
        init_fn(timestep = 1, target =bset_IMVGetDie)
    }

    # IMVNotGetLive
    bset_IMVNotGetLive <- variables$states$get_index_of("IMVNotGetLive")
    if (bset_IMVNotGetLive$size() > 0) {
        init_fn <- create_event_scheduler_listener(
            event = events$recovery,
            duration = parameters$dur_not_get_mv_survive,
            func = make_rerlang,
            shift = 1L,
            dt = dt
        )
        init_fn(timestep = 1, target =bset_IMVNotGetLive)
    }

    # IMVNotGetDie
    bset_IMVNotGetDie <- variables$states$get_index_of("IMVNotGetDie")
    if (bset_IMVNotGetDie$size() > 0) {
        init_fn <- create_event_scheduler_listener(
            event = events$death,
            duration = parameters$dur_not_get_mv_die,
            func = make_rerlang,
            shift = 1L,
            dt = dt
        )
        init_fn(timestep = 1, target =bset_IMVNotGetDie)
    }

    # IOxGetLive
    bset_IOxGetLive <- variables$states$get_index_of("IOxGetLive")
    if (bset_IOxGetLive$size() > 0) {
        init_fn <- create_event_scheduler_listener(
            event = events$recovery,
            duration = parameters$dur_get_ox_survive,
            func = make_rerlang,
            shift = 1L,
            dt = dt
        )
        init_fn(timestep = 1, target =bset_IOxGetLive)
    }

    # IOxGetDie
    bset_IOxGetDie <- variables$states$get_index_of("IOxGetDie")
    if (bset_IOxGetDie$size() > 0) {
        init_fn <- create_event_scheduler_listener(
            event = events$death,
            duration = parameters$dur_get_ox_die,
            func = make_rerlang,
            shift = 1L,
            dt = dt
        )
        init_fn(timestep = 1, target =bset_IOxGetDie)
    }

    # IOxNotGetLive
    bset_IOxNotGetLive <- variables$states$get_index_of("IOxNotGetLive")
    if (bset_IOxNotGetLive$size() > 0) {
        init_fn <- create_event_scheduler_listener(
            event = events$recovery,
            duration = parameters$dur_not_get_ox_survive,
            func = make_rerlang,
            shift = 1L,
            dt = dt
        )
        init_fn(timestep = 1, target =bset_IOxNotGetLive)
    }

    # IOxNotGetDie
    bset_IOxNotGetDie <- variables$states$get_index_of("IOxNotGetDie")
    if (bset_IOxNotGetDie$size() > 0) {
        init_fn <- create_event_scheduler_listener(
            event = events$death,
            duration = parameters$dur_not_get_ox_die,
            func = make_rerlang,
            shift = 1L,
            dt = dt
        )
        init_fn(timestep = 1, target =bset_IOxNotGetDie)
    }

    # R
    if (is.finite(parameters$dur_R)) {
        bset_R <- variables$states$get_index_of("R")
        if (bset_R$size() > 0){
            init_fn <- create_event_scheduler_listener(
                event = events$immunity_loss,
                duration = parameters$dur_R,
                func = make_rerlang,
                shift = 1L,
                dt = dt
            )
            init_fn(timestep = 1, target =bset_R)
        }
    }

    # IRec
    bset_IRec <- variables$states$get_index_of("IRec")
    if (bset_IRec$size() > 0) {
        init_fn <- create_event_scheduler_listener(
            event = events$recovery,
            duration = parameters$dur_rec,
            func = make_rerlang,
            shift = 1L,
            dt = dt
        )
        init_fn(timestep = 1, target =bset_IRec)
    }

    # vaccination

    # vaxx no protect
    bset_v1v2 <- variables$vaccine_states$get_index_of(set = 2)
    if (bset_v1v2$size() > 0) {
        init_fn <- create_v0_to_v1v2_listener_nimue(
            variables = variables,
            events = events,
            parameters = parameters,
            func = make_rerlang,
            shift = 1L,
            dt = dt
        )
    }

    # vaxx w/protection
    bset_v3v4 <- variables$vaccine_states$get_index_of(set = 3)
    if (bset_v3v4$size() > 0) {
        init_fn <- create_v1v2_to_v3v4_listener_nimue(
            variables = variables,
            events = events,
            parameters = parameters,
            func = make_rerlang,
            shift = 1L,
            dt = dt
        )
    }

}