/**
* Attaches the relevant prevalence chart to each herd structure.
*
* @param self the model.
* @param herds the herd list.
*/
void
attach_prevalence_charts (struct naadsm_model_t_ *self,
HRD_herd_list_t *herds)
{
local_data_t *local_data;
HRD_herd_t *herd;
unsigned int nherds;
unsigned int i;
#if DEBUG
g_log (G_LOG_DOMAIN, G_LOG_LEVEL_DEBUG,
"----- ENTER attach_prevalence_charts (%s)", MODEL_NAME);
#endif
local_data = (local_data_t *) (self->model_data);
nherds = HRD_herd_list_length (herds);
for (i = 0; i < nherds; i++)
{
herd = HRD_herd_list_get (herds, i);
if (local_data->production_type[herd->production_type] == TRUE)
herd->prevalence_curve = local_data->prevalence;
}
#if DEBUG
g_log (G_LOG_DOMAIN, G_LOG_LEVEL_DEBUG,
"----- EXIT attach_prevalence_charts (%s)", MODEL_NAME);
#endif
return;
}
/**
* Responds to a new day event by releasing any pending infections and
* stochastically generating infections.
*
* @param self the model.
* @param herds a list of herds.
* @param event a new day event.
* @param rng a random number generator.
* @param queue for any new events the model creates.
*/
void
handle_new_day_event (struct ergadm_model_t_ *self, HRD_herd_list_t * herds,
EVT_new_day_event_t * event, RAN_gen_t * rng, EVT_event_queue_t * queue)
{
local_data_t *local_data;
HRD_herd_t *herd1;
unsigned int nherds; /* number of herds */
unsigned int herd1_index, herd2_index;
gboolean herd1_can_be_source;
double distance;
GQueue *q;
EVT_event_t *pending_event;
struct Rect search_rect; /* for narrowing down radius searches using the
R-tree (spatial index) */
double mult; /* to account for latitude */
callback_t callback_data;
#if DEBUG
GString *s;
#endif
#if DEBUG
g_log (G_LOG_DOMAIN, G_LOG_LEVEL_DEBUG, "----- ENTER handle_new_day_event (%s)", MODEL_NAME);
#endif
local_data = (local_data_t *) (self->model_data);
/* Release any pending (due to airborne transport delays) events. */
local_data->rotating_index =
(local_data->rotating_index + 1) % local_data->pending_infections->len;
q = (GQueue *) g_ptr_array_index (local_data->pending_infections, local_data->rotating_index);
while (!g_queue_is_empty (q))
{
/* Remove the event from this model's internal queue and place it in the
* simulation's event queue. */
pending_event = (EVT_event_t *) g_queue_pop_head (q);
EVT_event_enqueue (queue, pending_event);
local_data->npending_infections--;
}
if (
#if defined(USE_RTREE) && USE_RTREE == 1
/* For debugging purposes, you can #define USE_RTREE to 0 to never use
* the spatial index, or 1 to always use it. */
TRUE ||
#endif
local_data->use_rtree_index)
{
/* Initialize a data structure used by the callback function. */
callback_data.self = self;
callback_data.herds = herds;
callback_data.event = event;
callback_data.rng = rng;
callback_data.queue = queue;
}
nherds = HRD_herd_list_length (herds);
for (herd1_index = 0; herd1_index < nherds; herd1_index++)
{
herd1 = HRD_herd_list_get (herds, herd1_index);
/* Can this herd be the source of an exposure? */
#if DEBUG
s = g_string_new (NULL);
g_string_sprintf (s, "unit \"%s\" is %s, state is %s: ",
herd1->official_id, herd1->production_type_name,
HRD_status_name[herd1->status]);
#endif
herd1_can_be_source =
local_data->param_block[herd1->production_type] != NULL
&& (herd1->status == InfectiousSubclinical || herd1->status == InfectiousClinical);
#if DEBUG
g_string_sprintfa (s, "%s be source", herd1_can_be_source ? "can" : "cannot");
g_log (G_LOG_DOMAIN, G_LOG_LEVEL_DEBUG, "%s", s->str);
g_string_free (s, TRUE);
#endif
if (!herd1_can_be_source)
continue;
if (local_data->use_rtree_index[herd1->production_type])
{
distance = local_data->max_spread[herd1->production_type] / GIS_DEGREE_DISTANCE;
mult = 1.0 / MIN (cos (DEG2RAD * (herd1->lat + distance)), cos(DEG2RAD * (herd1->lat - distance)));
search_rect.boundary[0] = herd1->lon - (distance * mult) - EPSILON;
search_rect.boundary[1] = herd1->lat - distance - EPSILON;
search_rect.boundary[2] = herd1->lon + (distance * mult) + EPSILON;
search_rect.boundary[3] = herd1->lat + distance + EPSILON;
callback_data.herd1 = herd1;
RTreeSearch (herds->spatial_index, &search_rect, callback, &callback_data);
}
else
for (herd2_index = 0; herd2_index < nherds; herd2_index++)
check_and_infect (self, herds, herd1,
HRD_herd_list_get (herds, herd2_index), event, rng, queue);
}
#if DEBUG
g_log (G_LOG_DOMAIN, G_LOG_LEVEL_DEBUG, "----- EXIT handle_new_day_event (%s)", MODEL_NAME);
#endif
return;
}
int
main (int argc, char *argv[])
{
int verbosity = 0;
const char *herd_file = NULL;
unsigned int nherds;
HRD_herd_t *herd;
int i; /* loop counter */
char *summary;
GError *option_error = NULL;
GOptionContext *context;
GOptionEntry options[] = {
{ "herd-file", 'h', 0, G_OPTION_ARG_FILENAME, &herd_file, "SpreadModel 3.0 herd file", NULL },
{ "verbosity", 'V', 0, G_OPTION_ARG_INT, &verbosity, "Message verbosity level (0 = simulation output only, 1 = all debugging output)", NULL },
{ NULL }
};
context = g_option_context_new ("");
g_option_context_add_main_entries (context, options, /* translation = */ NULL);
if (!g_option_context_parse (context, &argc, &argv, &option_error))
{
g_error ("option parsing failed: %s\n", option_error->message);
}
g_option_context_free (context);
/* Set the verbosity level. */
if (verbosity < 1)
{
g_log_set_handler (NULL, G_LOG_LEVEL_DEBUG, silent_log_handler, NULL);
g_log_set_handler ("herd", G_LOG_LEVEL_DEBUG, silent_log_handler, NULL);
}
/* Get the list of herds. */
herds = HRD_new_herd_list ();
if (herd_file)
yyin = fopen (herd_file, "r");
else if (yyin == NULL)
yyin = stdin;
while (!feof (yyin))
yyparse ();
if (yyin != stdin)
fclose (yyin);
nherds = HRD_herd_list_length (herds);
#if DEBUG
g_debug ("%i herds read", nherds);
summary = HRD_herd_list_to_string (herds);
g_log (G_LOG_DOMAIN, G_LOG_LEVEL_DEBUG, "\n%s", summary);
free (summary);
#endif
printf ("<herds>\n");
for (i = 0; i < nherds; i++)
{
herd = HRD_herd_list_get (herds, i);
printf (" <herd>\n");
printf (" <id>%s</id>\n", herd->official_id);
printf (" <production-type>%u</production-type>\n", herd->production_type);
printf (" <size>%u</size>\n", herd->size);
printf (" <location>\n");
printf (" <latitude>%g</latitude>\n", herd->y);
printf (" <longitude>%g</longitude>\n", herd->x);
printf (" </location>\n");
printf (" <status>%s</status>\n", HRD_status_name[herd->status]);
printf (" </herd>\n");
}
printf ("</herds>\n");
/* Clean up. */
HRD_free_herd_list (herds);
return EXIT_SUCCESS;
}
/**
* Computes the size factor for each herd.
*
* @param herds a list of herds.
* @return an array containing the size factor for each herd.
*/
double *
build_size_factor_list (HRD_herd_list_t * herds)
{
HRD_herd_t *herd;
unsigned int nherds; /* number of herds */
unsigned int max_size = 0; /* size of largest herd */
gsl_histogram *histogram;
PDF_dist_t *herd_size_dist;
double *size_factor;
unsigned int i; /* loop counter */
#if DEBUG
char *s;
#endif
#if DEBUG
g_log (G_LOG_DOMAIN, G_LOG_LEVEL_DEBUG, "----- ENTER build_size_factor_list");
#endif
nherds = HRD_herd_list_length (herds);
size_factor = g_new (double, nherds);
/* Find the largest herd. */
for (i = 0; i < nherds; i++)
{
herd = HRD_herd_list_get (herds, i);
if (herd->size > max_size)
max_size = herd->size;
}
#if DEBUG
g_log (G_LOG_DOMAIN, G_LOG_LEVEL_DEBUG, "largest herd = %u", max_size);
#endif
/* Build a histogram with one bin for each herd size. */
histogram = gsl_histogram_alloc (max_size);
g_assert (histogram != NULL);
gsl_histogram_set_ranges_uniform (histogram, 0.5, (double) max_size + 0.5);
for (i = 0; i < nherds; i++)
{
herd = HRD_herd_list_get (herds, i);
gsl_histogram_increment (histogram, (double) (herd->size));
}
herd_size_dist = PDF_new_histogram_dist (histogram);
g_assert (herd_size_dist != NULL);
#if DEBUG
s = PDF_dist_to_string (herd_size_dist);
g_log (G_LOG_DOMAIN, G_LOG_LEVEL_DEBUG, "herd size distribution =\n%s", s);
free (s);
#endif
/* Compute the herd size factors. */
for (i = 0; i < nherds; i++)
{
herd = HRD_herd_list_get (herds, i);
size_factor[i] = PDF_cdf (herd->size, herd_size_dist) * 2;
}
#if DEBUG
g_log (G_LOG_DOMAIN, G_LOG_LEVEL_DEBUG, "herd size factors");
for (i = 0; i < nherds; i++)
{
herd = HRD_herd_list_get (herds, i);
g_log (G_LOG_DOMAIN, G_LOG_LEVEL_DEBUG, "herd #%u (size %u) = %g",
i, herd->size, size_factor[i]);
}
#endif
/* The following line also frees the histogram. */
PDF_free_dist (herd_size_dist);
#if DEBUG
g_log (G_LOG_DOMAIN, G_LOG_LEVEL_DEBUG, "----- EXIT build_size_factor_list");
#endif
return size_factor;
}
