https://github.com/PublicHealthDynamicsLab/FRED
Revision a45e04ad99c865724a3c2b1a2d3fd979b3c6be88 authored by John Grefenstette on 07 January 2016, 16:32:02 UTC, committed by John Grefenstette on 07 January 2016, 16:32:02 UTC
1 parent 9bc2dce
Tip revision: a45e04ad99c865724a3c2b1a2d3fd979b3c6be88 authored by John Grefenstette on 07 January 2016, 16:32:02 UTC
working markov epidemic model
working markov epidemic model
Tip revision: a45e04a
Neighborhood.cc
/*
This file is part of the FRED system.
Copyright (c) 2010-2015, University of Pittsburgh, John Grefenstette,
Shawn Brown, Roni Rosenfield, Alona Fyshe, David Galloway, Nathan
Stone, Jay DePasse, Anuroop Sriram, and Donald Burke.
Licensed under the BSD 3-Clause license. See the file "LICENSE" for
more information.
*/
//
//
// File: Neighborhood.cc
//
#include "Neighborhood.h"
#include "Global.h"
#include "Params.h"
#include "Random.h"
#include "Person.h"
#include "Disease.h"
#include "Disease_List.h"
//Private static variables that will be set by parameter lookups
double Neighborhood::contacts_per_day = 0.0;
double Neighborhood::same_age_bias = 0.0;
double** Neighborhood::prob_transmission_per_contact = NULL;
double Neighborhood::weekend_contact_rate = 0.0;
Neighborhood::Neighborhood(const char* lab, char _subtype, fred::geo lon, fred::geo lat) : Place(lab, lon, lat) {
this->set_type(Place::TYPE_NEIGHBORHOOD);
this->set_subtype(_subtype);
this->intimacy = 0.0025;
}
void Neighborhood::get_parameters() {
Params::get_param_from_string("neighborhood_contacts", &Neighborhood::contacts_per_day);
Params::get_param_from_string("neighborhood_same_age_bias", &Neighborhood::same_age_bias);
int n = Params::get_param_matrix((char *)"neighborhood_trans_per_contact", &Neighborhood::prob_transmission_per_contact);
if(Global::Verbose > 1) {
printf("\nNeighborhood_contact_prob:\n");
for(int i = 0; i < n; ++i) {
for(int j = 0; j < n; ++j) {
printf("%f ", Neighborhood::prob_transmission_per_contact[i][j]);
}
printf("\n");
}
}
Params::get_param_from_string("weekend_contact_rate", &Neighborhood::weekend_contact_rate);
if(Global::Verbose > 0) {
printf("\nprob_transmission_per_contact before normalization:\n");
for(int i = 0; i < n; ++i) {
for(int j = 0; j < n; ++j) {
printf("%f ", Neighborhood::prob_transmission_per_contact[i][j]);
}
printf("\n");
}
printf("\ncontact rate: %f\n", Neighborhood::contacts_per_day);
}
// normalize contact parameters
// find max contact prob
double max_prob = 0.0;
for(int i = 0; i < n; ++i) {
for(int j = 0; j < n; ++j) {
if(Neighborhood::prob_transmission_per_contact[i][j] > max_prob) {
max_prob = Neighborhood::prob_transmission_per_contact[i][j];
}
}
}
// convert max contact prob to 1.0
if(max_prob > 0) {
for(int i = 0; i < n; ++i) {
for(int j = 0; j < n; ++j) {
Neighborhood::prob_transmission_per_contact[i][j] /= max_prob;
}
}
// compensate contact rate
Neighborhood::contacts_per_day *= max_prob;
// end normalization
if(Global::Verbose > 0) {
printf("\nprob_transmission_per_contact after normalization:\n");
for(int i = 0; i < n; ++i) {
for(int j = 0; j < n; ++j) {
printf("%f ", Neighborhood::prob_transmission_per_contact[i][j]);
}
printf("\n");
}
printf("\ncontact rate: %f\n", Neighborhood::contacts_per_day);
}
// end normalization
}
}
int Neighborhood::get_group(int disease, Person* per) {
int age = per->get_age();
if(age < Global::ADULT_AGE) {
return 0;
} else {
return 1;
}
}
double Neighborhood::get_transmission_probability(int disease, Person* i, Person* s) {
double age_i = i->get_real_age();
double age_s = s->get_real_age();
double diff = fabs(age_i - age_s);
double prob = exp(-Neighborhood::same_age_bias * diff);
return prob;
}
double Neighborhood::get_transmission_prob(int disease, Person* i, Person* s) {
// i = infected agent
// s = susceptible agent
int row = get_group(disease, i);
int col = get_group(disease, s);
double tr_pr = Neighborhood::prob_transmission_per_contact[row][col];
return tr_pr;
}
double Neighborhood::get_contacts_per_day(int disease) {
return Neighborhood::contacts_per_day;
}
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