/**
* Responds to an infection event by changing the herd's state from susceptible
* to infected.
*
* @param self the model.
* @param event an infection event.
* @param rng a random number generator.
*/
void
handle_infection_event (struct naadsm_model_t_ *self,
EVT_infection_event_t * event, RAN_gen_t * rng)
{
local_data_t *local_data;
HRD_herd_t *herd;
int latent_period, infectious_subclinical_period, infectious_clinical_period, immunity_period;
unsigned int day_in_disease_cycle;
#if DEBUG
g_log (G_LOG_DOMAIN, G_LOG_LEVEL_DEBUG, "----- ENTER handle_infection_event (%s)", MODEL_NAME);
#endif
local_data = (local_data_t *) (self->model_data);
herd = event->infected_herd;
if (local_data->production_type[herd->production_type] == FALSE)
{
#if DEBUG
g_debug ("unit is %s, sub-model does not apply", herd->production_type_name);
#endif
goto end;
}
day_in_disease_cycle = 0;
/* Latent period. */
latent_period = (int) round (PDF_random (local_data->latent_period, rng));
if (latent_period < 0)
{
#if DEBUG
g_log (G_LOG_DOMAIN, G_LOG_LEVEL_DEBUG,
"%s distribution returned %i for latent period, using 0 instead",
PDF_dist_type_name[local_data->latent_period->type], latent_period);
#endif
latent_period = 0;
}
if (event->override_initial_state == Latent)
{
if (event->override_days_in_state > 0 && event->override_days_left_in_state > 0)
{
/* Override both the days elapsed and the days left in the latent
* period. */
latent_period = event->override_days_in_state + event->override_days_left_in_state;
day_in_disease_cycle = event->override_days_in_state;
}
else if (event->override_days_in_state > 0)
{
/* Override just the days elapsed in the latent period. If the given
* value is greater than the sampled length of the latent period,
* extend the latent period. */
latent_period = MAX(latent_period, event->override_days_in_state);
day_in_disease_cycle = event->override_days_in_state;
}
else if (event->override_days_left_in_state > 0)
{
/* Override just the days left in the latent period. If the given
* value is greater than the sampled length of the latent period,
* extend the latent period. */
latent_period = MAX(latent_period, event->override_days_left_in_state);
day_in_disease_cycle = latent_period - event->override_days_left_in_state;
}
}
#if DEBUG
g_debug ("latent period will last %i days", latent_period);
#endif
/* Infectious subclinical period. */
infectious_subclinical_period =
(int) round (PDF_random (local_data->infectious_subclinical_period, rng));
if (infectious_subclinical_period < 0)
{
#if DEBUG
g_log (G_LOG_DOMAIN, G_LOG_LEVEL_DEBUG,
"%s distribution returned %i for infectious subclinical period, using 0 instead",
PDF_dist_type_name[local_data->infectious_subclinical_period->type],
infectious_subclinical_period);
#endif
infectious_subclinical_period = 0;
}
if (event->override_initial_state == InfectiousSubclinical)
{
day_in_disease_cycle = latent_period;
if (event->override_days_in_state > 0 && event->override_days_left_in_state > 0)
{
/* Override both the days elapsed and the days left in the infectious
* subclinical period. */
infectious_subclinical_period = event->override_days_in_state + event->override_days_left_in_state;
day_in_disease_cycle += event->override_days_in_state;
}
else if (event->override_days_in_state > 0)
{
/* Override just the days elapsed in the infectious subclinical
* period. If the given value is greater than the sampled length of
* the infectious subclinical period, extend the infectious
* subclinical period. */
infectious_subclinical_period = MAX(infectious_subclinical_period, event->override_days_in_state);
day_in_disease_cycle += event->override_days_in_state;
}
else if (event->override_days_left_in_state > 0)
{
/* Override just the days left in the infectious subclinical period.
* If the given value is greater than the sampled length of the
* infectious subclinical period, extend the infectious subclinical
* period. */
infectious_subclinical_period = MAX(infectious_subclinical_period, event->override_days_left_in_state);
day_in_disease_cycle += (infectious_subclinical_period - event->override_days_left_in_state);
}
}
#if DEBUG
g_debug ("infectiousness (with no visible signs) will last %i days", infectious_subclinical_period);
#endif
/* Infectious clinical period. */
infectious_clinical_period =
(int) round (PDF_random (local_data->infectious_clinical_period, rng));
if (infectious_clinical_period < 0)
{
#if DEBUG
g_log (G_LOG_DOMAIN, G_LOG_LEVEL_DEBUG,
"%s distribution returned %i for infectious clinical period, using 0 instead",
PDF_dist_type_name[local_data->infectious_clinical_period->type],
infectious_clinical_period);
#endif
infectious_clinical_period = 0;
}
if (event->override_initial_state == InfectiousClinical)
{
day_in_disease_cycle = latent_period + infectious_subclinical_period;
if (event->override_days_in_state > 0 && event->override_days_left_in_state > 0)
{
/* Override both the days elapsed and the days left in the infectious
* clinical period. */
infectious_clinical_period = event->override_days_in_state + event->override_days_left_in_state;
day_in_disease_cycle += event->override_days_in_state;
}
else if (event->override_days_in_state > 0)
{
/* Override just the days elapsed in the infectious clinical period.
* If the given value is greater than the sampled length of the
* infectious clinical period, extend the infectious clinical period. */
infectious_clinical_period = MAX(infectious_clinical_period, event->override_days_in_state);
day_in_disease_cycle += event->override_days_in_state;
}
else if (event->override_days_left_in_state > 0)
{
/* Override just the days left in the infectious clinical period. If
* the given value is greater than the sampled length of the
* infectious clinical period, extend the infectious clinical period. */
infectious_clinical_period = MAX(infectious_clinical_period, event->override_days_left_in_state);
day_in_disease_cycle += (infectious_clinical_period - event->override_days_left_in_state);
}
}
#if DEBUG
g_debug ("infectiousness (with visible signs) will last %i days", infectious_clinical_period);
#endif
/* Natural immunity period. */
immunity_period = (int) round (PDF_random (local_data->immunity_period, rng));
if (immunity_period < 0)
{
#if DEBUG
g_log (G_LOG_DOMAIN, G_LOG_LEVEL_DEBUG,
"%s distribution returned %i for immunity period, using 0 instead",
PDF_dist_type_name[local_data->immunity_period->type], immunity_period);
#endif
immunity_period = 0;
}
if (event->override_initial_state == NaturallyImmune)
{
day_in_disease_cycle = latent_period + infectious_subclinical_period + infectious_clinical_period;
if (event->override_days_in_state > 0 && event->override_days_left_in_state > 0)
{
/* Override both the days elapsed and the days left in the immunity
* period. */
immunity_period = event->override_days_in_state + event->override_days_left_in_state;
day_in_disease_cycle += event->override_days_in_state;
}
else if (event->override_days_in_state > 0)
{
/* Override just the days elapsed in the immunity period. If the
* given value is greater than the sampled length of the immunity
* period, extend the immunity period. */
immunity_period = MAX(immunity_period, event->override_days_in_state);
day_in_disease_cycle += event->override_days_in_state;
}
else if (event->override_days_left_in_state > 0)
{
/* Override just the days left in the immunity period. If the given
* value is greater than the sampled length of the immunity period,
* extend the immunity period. */
immunity_period = MAX(immunity_period, event->override_days_left_in_state);
day_in_disease_cycle += (immunity_period - event->override_days_left_in_state);
}
}
#if DEBUG
g_debug ("natural immunity will last %i days", immunity_period);
#endif
HRD_infect (event->infected_herd, latent_period, infectious_subclinical_period,
infectious_clinical_period, immunity_period, day_in_disease_cycle);
end:
#if DEBUG
g_log (G_LOG_DOMAIN, G_LOG_LEVEL_DEBUG, "----- EXIT handle_infection_event (%s)", MODEL_NAME);
#endif
return;
}
/**
* Check whether herd 1 can infect herd 2 and if so, attempt to infect herd 2.
* This function is used by both the naive search and the R-tree (spatial
* index) search.
*/
void
check_and_infect (struct ergadm_model_t_ *self, HRD_herd_list_t * herds,
HRD_herd_t * herd1, HRD_herd_t * herd2,
EVT_new_day_event_t * event, RAN_gen_t * rng, EVT_event_queue_t * queue)
{
local_data_t *local_data;
gboolean herd2_can_be_target;
param_block_t *param_block;
double max_spread, distance, heading;
double distance_factor, herd1_size_factor, herd2_size_factor;
EVT_event_t *attempt_to_infect;
double r, P;
int delay;
int delay_index;
GQueue *q;
HRD_expose_t exposure_update;
#if DEBUG
GString *s;
#endif
#if DEBUG
g_log (G_LOG_DOMAIN, G_LOG_LEVEL_DEBUG, "----- ENTER check_and_infect (%s)", MODEL_NAME);
#endif
/* Are herd 1 and herd 2 the same? */
if (herd1 == herd2)
goto end;
local_data = (local_data_t *) (self->model_data);
/* Can herd 2 be the target of an exposure? */
#if DEBUG
s = g_string_new (NULL);
g_string_sprintf (s, "unit \"%s\" is %s, state is %s: ",
herd2->official_id, herd2->production_type_name,
HRD_status_name[herd2->status]);
#endif
param_block = local_data->param_block[herd1->production_type][herd2->production_type];
herd2_can_be_target = (param_block != NULL && herd2->status != Destroyed);
#if DEBUG
g_string_sprintfa (s, "%s be target", herd2_can_be_target ? "can" : "cannot");
g_log (G_LOG_DOMAIN, G_LOG_LEVEL_DEBUG, "%s", s->str);
g_string_free (s, TRUE);
#endif
if (!herd2_can_be_target)
goto end;
/* Is herd 2 close enough to herd 1? */
distance = GIS_local_distance (herd1->lat, herd1->lon, herd2->lat, herd2->lon);
max_spread = param_block->max_spread;
if (distance - max_spread > EPSILON)
{
#if DEBUG
g_log (G_LOG_DOMAIN, G_LOG_LEVEL_DEBUG, " unit \"%s\" too far (%g > %g)",
herd2->official_id, distance, max_spread);
#endif
goto end;
}
#if DEBUG
g_log (G_LOG_DOMAIN, G_LOG_LEVEL_DEBUG, " unit \"%s\" within range (%g <= %g)",
herd2->official_id, distance, max_spread);
#endif
/* Is herd 2 within the wind direction range? */
heading = GIS_local_heading (herd1->lat, herd1->lon, herd2->lat, herd2->lon);
if (param_block->wind_range_crosses_0
? (param_block->wind_dir_start - heading > EPSILON
&& heading - param_block->wind_dir_end >=
EPSILON) : (param_block->wind_dir_start - heading > EPSILON
|| heading - param_block->wind_dir_end >= EPSILON))
{
#if DEBUG
g_log (G_LOG_DOMAIN, G_LOG_LEVEL_DEBUG,
" unit \"%s\" outside wind angles (%g)", herd2->official_id, heading);
#endif
goto end;
}
#if DEBUG
g_log (G_LOG_DOMAIN, G_LOG_LEVEL_DEBUG,
" unit \"%s\" within wind angles (%g)", herd2->official_id, heading);
#endif
distance_factor = (max_spread - distance) / (max_spread - 1);
herd1_size_factor = local_data->herd_size_factor[herd1->index];
herd2_size_factor = local_data->herd_size_factor[herd2->index];
#if DEBUG
g_log (G_LOG_DOMAIN, G_LOG_LEVEL_DEBUG, " P = %g * %g * %g * %g * %g",
herd1_size_factor, herd1->prevalence, distance_factor, param_block->prob_spread_1km,
herd2_size_factor);
#endif
P =
herd1_size_factor * herd1->prevalence * distance_factor * param_block->prob_spread_1km *
herd2_size_factor;
r = RAN_num (rng);
if (r < P && herd2->status == Susceptible)
{
if (NULL != guilib_record_exposure)
{
exposure_update.dest_index = herd2->index;
exposure_update.dest_status = herd2->status;
exposure_update.src_index = herd1->index;
exposure_update.src_status = herd1->status;
exposure_update.exposure_method = "A";
exposure_update.success = -1;
guilib_record_exposure (exposure_update);
}
attempt_to_infect =
EVT_new_attempt_to_infect_event (herd1, herd2, event->day, "airborne spread");
delay = (int) round (PDF_random (param_block->delay, rng));
if (delay <= 0)
{
EVT_event_enqueue (queue, attempt_to_infect);
#if DEBUG
g_log (G_LOG_DOMAIN, G_LOG_LEVEL_DEBUG, " r (%g) < P (%g), target herd infected", r, P);
#endif
}
else
{
attempt_to_infect->u.attempt_to_infect.day = event->day + delay;
if (delay > local_data->pending_infections->len)
ergadm_extend_rotating_array (local_data->pending_infections, delay,
local_data->rotating_index);
delay_index = (local_data->rotating_index + delay) % local_data->pending_infections->len;
q = (GQueue *) g_ptr_array_index (local_data->pending_infections, delay_index);
g_queue_push_tail (q, attempt_to_infect);
local_data->npending_infections++;
#if DEBUG
g_log (G_LOG_DOMAIN, G_LOG_LEVEL_DEBUG,
" r (%g) < P (%g), target unit will be infected on day %i",
r, P, event->day + delay);
#endif
}
}
else
{
if (NULL != guilib_record_exposure)
{
exposure_update.dest_index = herd2->index;
exposure_update.dest_status = herd2->status;
exposure_update.src_index = herd1->index;
exposure_update.src_status = herd1->status;
exposure_update.exposure_method = "A";
exposure_update.success = 0;
guilib_record_exposure (exposure_update);
}
#if DEBUG
g_log (G_LOG_DOMAIN, G_LOG_LEVEL_DEBUG, " r (%g) >= P (%g), target unit not infected", r, P);
#endif
;
}
end:
#if DEBUG
g_log (G_LOG_DOMAIN, G_LOG_LEVEL_DEBUG, "----- EXIT check_and_infect (%s)", MODEL_NAME);
#endif
return;
}