/
simulator.h
906 lines (785 loc) · 41.3 KB
/
simulator.h
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#include <cstdlib>
#include <cstring>
#include <climits>
#include <iostream>
#include <fstream>
#include <string>
#include <sstream>
#include <assert.h>
#include <gsl/gsl_rng.h>
#include <gsl/gsl_randist.h>
#include "Parameters.h"
#include "Person.h"
#include "Mosquito.h"
#include "Location.h"
#include "Community.h"
#include "Utility.h"
#include "sys/stat.h"
#include "Date.h"
using namespace dengue::standard;
using namespace dengue::util;
enum IncidenceReportingType {
INTRO_INF,
TOTAL_INF,
INTRO_CASE,
TOTAL_CASE,
INTRO_DSS,
TOTAL_DSS,
NUM_OF_INCIDENCE_REPORTING_TYPES
};
enum PrevalenceReportingType {
INTRO_INF_PREV,
TOTAL_INF_PREV,
INTRO_CASE_PREV,
TOTAL_CASE_PREV,
INTRO_DSS_PREV,
TOTAL_DSS_PREV,
NUM_OF_PREVALENCE_REPORTING_TYPES
};
// class Date {
// public:
// Date():_offset(0),_simulation_day(0) {};
// Date(const Parameters* par):_offset(par->startDayOfYear-1),_simulation_day(0) {};
//
// int offset() const { return _offset; }
// inline int day() const { return _simulation_day; } // [0, ...]
// int julianDay() const { return ((day() + offset()) % 365) + 1; } // [1, 365]
// int dayOfMonth() const { return julianMonth() == 1 ? // [1, {29,30,31}]
// julianDay() :
// julianDay() - END_DAY_OF_MONTH[julianMonth()-2]; }
// int nDayPeriod(int n) const { return (int) day()/n; } // [0, ...]
// int week() const { return (int) day()/7; } // [0, ...]
// int julianWeek() const { return (int) ((julianDay()-1)/7) + 1; } // [1, 53]
// int month() const { return _month_ct; } // [0, ...]
// int julianMonth() const { // [1, 12]
// vector<int>::const_iterator it;
// // find first month that hasn't ended (hint: it's this month)
// // julianDay()-1 because this isn't upper_or_equal_bound, which would be convenient
// it = upper_bound(END_DAY_OF_MONTH.begin(), END_DAY_OF_MONTH.end(), julianDay()-1);
// return it - END_DAY_OF_MONTH.begin() + 1; // +1 b/c [1, 12], not [0, 11]
// }
// string monthName() const { return MONTH_NAMES[julianMonth()-1]; }
// int year() const { return (int) (day()/365); }
//
// bool endOfPeriod(int n) const { return (day()+1) % n == 0; }
// bool endOfWeek() const { return (day()+1) % 7 == 0; }
// bool endOfMonth() const {
// vector<int>::const_iterator it;
// // find out if today corresponds to a month-end
// it = find(END_DAY_OF_MONTH.begin(), END_DAY_OF_MONTH.end(), julianDay());
// return it != END_DAY_OF_MONTH.end();
// }
// bool startOfYear() const { return day() % 365 == 0; } // is it beginning of 365 day period
// bool endOfYear() const { return (day()+1) % 365 == 0; } // is it end of 365 day period
// bool startOfJulianYear() const { return julianDay() == 1; } // is it Jan 1
// bool endOfJulianYear() const { return julianDay() == 365; } // is it Dec 31
//
// void increment() {
// if(endOfMonth()) _month_ct++;
// _simulation_day++;
// }
//
// void print() {
// cerr << day() << "\t" << julianDay() << "\t" << year()
// << "\t(" << monthName() << " " << dayOfMonth() << ")\t" << month() << "\t" << julianMonth();
// if (endOfWeek()) cerr << " EoW";
// if (endOfMonth()) cerr << " EoM";
// if (startOfYear()) cerr << " SoY";
// if (endOfYear()) cerr << " EoY";
// if (endOfJulianYear()) cerr << " EoJY";
// cerr << endl;
// }
//
// private:
// const int _offset;
// int _simulation_day;
// int _month_ct;
// };
const gsl_rng* RNG = gsl_rng_alloc (gsl_rng_taus2);
// Predeclare local functions
Community* build_community(const Parameters* par);
void seed_epidemic(const Parameters* par, Community* community);
vector<int> simulate_epidemic(const Parameters* par, Community* community, const string process_id = "0");
void write_immunity_file(const Community* community, const string label, string filename, int runLength);
void write_immunity_by_age_file(const Community* community, const int year, string filename="");
void write_daily_buffer( vector<string>& buffer, const string process_id, string filename);
Community* build_community(const Parameters* par) {
Community* community = new Community(par);
Person::setPar(par);
if (!community->loadLocations(par->locationFilename, par->networkFilename)) {
cerr << "ERROR: Could not load locations" << endl;
exit(-1);
}
if (!community->loadPopulation(par->populationFilename, par->immunityFilename, par->swapProbFilename)) {
cerr << "ERROR: Could not load population" << endl;
exit(-1);
}
if (!par->abcVerbose) {
cerr << community->getNumPeople() << " people" << endl;
}
if (!par->bSecondaryTransmission) {
community->setNoSecondaryTransmission();
}
return community;
}
void seed_epidemic(const Parameters* par, Community* community) {
// epidemic may be seeded with initial exposure OR initial infection
bool attempt_initial_infection = true;
for (int serotype=0; serotype<NUM_OF_SEROTYPES; serotype++) {
// Normal usage, to simulate epidemic
if (par->nInitialExposed[serotype] > 0) {
attempt_initial_infection = false;
for (int i=0; i<par->nInitialExposed[serotype]; i++)
community->infect(gsl_rng_uniform_int(RNG, community->getNumPeople()), (Serotype) serotype,0);
}
}
if (attempt_initial_infection) {
for (int serotype=0; serotype<NUM_OF_SEROTYPES; serotype++) {
// Useful for estimating R0
if(par->nInitialInfected[serotype] > 0) {
int count = community->getNumInfected(0);
// must infect nInitialInfected persons -- this bit is mysterious
while (community->getNumInfected(0) < count + par->nInitialInfected[serotype]) {
community->infect(gsl_rng_uniform_int(RNG, community->getNumPeople()), (Serotype) serotype,0);
}
}
}
}
return;
}
void write_yearly_people_file(const Parameters* par, const Community* community, int time) {
ofstream yearlyPeopleOutputFile;
ostringstream ssFilename;
ssFilename << par->yearlyPeopleOutputFilename << ((int)(time/365)) << ".csv";
cerr << "outputing yearly people information to " << ssFilename.str() << endl;
yearlyPeopleOutputFile.open(ssFilename.str().c_str());
if(yearlyPeopleOutputFile.fail()) {
cerr << "ERROR: People file '" << par->yearlyPeopleOutputFilename << "' cannot be open for writing." << endl;
exit(-1);
}
yearlyPeopleOutputFile << "pid,serotype,infectiontime,symptomtime,withdrawtime,recoverytime,immdenv1,immdenv2,immdenv3,immdenv4" << endl;
for (Person* p: community->getPeople()) {
for (int j=p->getNumNaturalInfections()-1; j>=0; j--) {
yearlyPeopleOutputFile << p->getID() << ","
<< 1 + (int) p->getSerotype(j) << ","
<< p->getInfectedTime(j) << ","
<< p->getSymptomTime(j) << ","
<< p->getWithdrawnTime(j) << ","
<< p->getRecoveryTime(j) << ",";
for (int s = 0; s < NUM_OF_SEROTYPES - 1; ++s) {
yearlyPeopleOutputFile << (p->isSusceptible((Serotype) s)?0:1) << ",";
}
yearlyPeopleOutputFile << (p->isSusceptible((Serotype) (NUM_OF_SEROTYPES - 1))?0:1) << endl;
}
}
yearlyPeopleOutputFile.close();
return;
}
void initialize_seasonality(const Parameters* par, Community* community, int& nextMosquitoMultiplierIndex, int& nextEIPindex, Date& date) {
const int mosquitoMultiplierTotalDuration = par->getMosquitoMultiplierTotalDuration();
int currentDayOfYearOffset = 0;
if (mosquitoMultiplierTotalDuration > 0) {
nextMosquitoMultiplierIndex = 0;
while (currentDayOfYearOffset <= date.offset()) {
currentDayOfYearOffset += par->mosquitoMultipliers[nextMosquitoMultiplierIndex].duration;
if (currentDayOfYearOffset > date.offset()) {
const double mm = par->mosquitoMultipliers[nextMosquitoMultiplierIndex].value;
community->setMosquitoMultiplier(mm);
}
nextMosquitoMultiplierIndex = (nextMosquitoMultiplierIndex+1)%par->mosquitoMultipliers.size();
}
}
const int EIPtotalDuration = par->getEIPtotalDuration();
currentDayOfYearOffset = 0;
if (EIPtotalDuration > 0) {
nextEIPindex = 0;
while (currentDayOfYearOffset <= date.offset()) {
currentDayOfYearOffset += par->extrinsicIncubationPeriods[nextEIPindex].duration;
if (currentDayOfYearOffset > date.offset()) {
const double eip = par->extrinsicIncubationPeriods[nextEIPindex].value;
community->setExpectedExtrinsicIncubation(eip);
}
nextEIPindex = (nextEIPindex+1)%par->extrinsicIncubationPeriods.size();
}
}
}
void _aggregator(map<string, vector<int> >& periodic_incidence, string key, string daily_key = "daily") {
for (unsigned int i = 0; i < periodic_incidence[daily_key].size(); ++i) periodic_incidence[key][i] += periodic_incidence[daily_key][i];
}
void _reporter(stringstream& ss, map<string, vector<int> > &periodic_incidence, vector<int> &periodic_prevalence, const Parameters* par, const string process_id, const string label, const int value, string key) {
ss << process_id << dec << " " << par->serial << label << value << " ";
for (auto v: periodic_incidence[key]) ss << v << " ";
if(key=="daily") {
ss << "| ";
for (auto v: periodic_prevalence) { ss << v << " "; }
}
ss << "| ";
for (auto v: par->reportedFraction) { ss << v << " "; }
}
void periodic_output(const Parameters* par, const Community* community, map<string, vector<int> > &periodic_incidence, vector<int> &periodic_prevalence, const Date& date, const string process_id, vector<int>& proto_metrics) {
stringstream ss;
//if (date.day() >= 25*365 and date.day() < 36*365) {
//if (date.day() >= 116*365) { // daily output starting in 1995, assuming Jan 1, 1879 simulation start
//if (date.day() >= 99*365 and date.day() < 105*365) { // daily output for summer/winter IRS comparison
if (par->dailyOutput) {
_reporter(ss, periodic_incidence, periodic_prevalence, par, process_id, " day: ", date.day(), "daily");
ss << community->getExpectedExtrinsicIncubation() << " " << community->getMosquitoMultiplier()*par->nDefaultMosquitoCapacity << endl;
}
//}
vector<int> dummy;
if (par->periodicOutput) {
_aggregator(periodic_incidence, "n_day");
const int n = par->periodicOutputInterval;
if (date.endOfPeriod(n)) {
_reporter(ss, periodic_incidence, dummy, par, process_id, " " + to_string(n) + "_day: ", date.nDayPeriod(n), "n_day"); ss << endl;
periodic_incidence["n_day"] = vector<int>(NUM_OF_INCIDENCE_REPORTING_TYPES, 0);
}
}
if (par->weeklyOutput) {
_aggregator(periodic_incidence, "weekly");
if (date.endOfWeek()) {
_reporter(ss, periodic_incidence, dummy, par, process_id, " week: ", date.week(), "weekly"); ss << endl;
periodic_incidence["weekly"] = vector<int>(NUM_OF_INCIDENCE_REPORTING_TYPES, 0);
}
}
if (par->monthlyOutput) {
_aggregator(periodic_incidence, "monthly");
if (date.endOfMonth()) {
_reporter(ss, periodic_incidence, dummy, par, process_id, " month: ", date.julianMonth(), "monthly"); ss << endl;
periodic_incidence["monthly"] = vector<int>(NUM_OF_INCIDENCE_REPORTING_TYPES, 0);
}
}
/* if (par->simulateTrial) {
_reporter(ss, periodic_incidence, periodic_prevalence, par, process_id, " day (arm 1 ): ", date.day(), "daily-arm1");
ss << endl;
_reporter(ss, periodic_incidence, periodic_prevalence, par, process_id, " day (arm 2 ): ", date.day(), "daily-arm2");
ss << endl;
}*/
// handle several things that happen yearly
_aggregator(periodic_incidence, "yearly");
if (par->simulateTrial) {
_aggregator(periodic_incidence, "yearly-arm1", "daily-arm1");
_aggregator(periodic_incidence, "yearly-arm2", "daily-arm2");
}
if (date.endOfYear()) {
if (par->abcVerbose) {
cout << process_id << dec << " " << par->serial << " T: " << date.day() << " annual: ";
for (auto v: periodic_incidence["yearly"]) { cout << v << " "; } cout << endl;
}
if (par->yearlyOutput) {
_reporter(ss, periodic_incidence, dummy, par, process_id, " year ( total ): ", date.year(), "yearly"); ss << endl;
}
periodic_incidence["yearly"] = vector<int>(NUM_OF_INCIDENCE_REPORTING_TYPES, 0);
if (par->simulateTrial) {
proto_metrics.push_back(periodic_incidence["yearly-arm1"][TOTAL_INF]);
proto_metrics.push_back(periodic_incidence["yearly-arm1"][TOTAL_CASE]);
proto_metrics.push_back(periodic_incidence["yearly-arm1"][TOTAL_DSS]);
proto_metrics.push_back(periodic_incidence["yearly-arm2"][TOTAL_INF]);
proto_metrics.push_back(periodic_incidence["yearly-arm2"][TOTAL_CASE]);
proto_metrics.push_back(periodic_incidence["yearly-arm2"][TOTAL_DSS]);
if (par->yearlyOutput) {
_reporter(ss, periodic_incidence, dummy, par, process_id, " year ( arm_1 ): ", date.year(), "yearly-arm1"); ss << endl;
_reporter(ss, periodic_incidence, dummy, par, process_id, " year ( arm_2 ): ", date.year(), "yearly-arm2"); ss << endl;
}
periodic_incidence["yearly-arm1"] = vector<int>(NUM_OF_INCIDENCE_REPORTING_TYPES, 0);
periodic_incidence["yearly-arm2"] = vector<int>(NUM_OF_INCIDENCE_REPORTING_TYPES, 0);
} else {
proto_metrics.push_back(periodic_incidence["yearly"][2]);
}
if (par->yearlyPeopleOutputFilename.length() > 0) write_yearly_people_file(par, community, date.day());
}
periodic_incidence["daily"] = vector<int>(NUM_OF_INCIDENCE_REPORTING_TYPES, 0);
if (par->simulateTrial) {
periodic_incidence["daily-arm1"] = vector<int>(NUM_OF_INCIDENCE_REPORTING_TYPES, 0);
periodic_incidence["daily-arm2"] = vector<int>(NUM_OF_INCIDENCE_REPORTING_TYPES, 0);
}
periodic_prevalence = vector<int>(NUM_OF_PREVALENCE_REPORTING_TYPES, 0);
string output = ss.str();
fputs(output.c_str(), stderr);
//fputs(output.c_str(), stdout);
}
void update_vaccinations(const Parameters* par, Community* community, const Date &date) {
const int doseInterval = par->vaccineDoseInterval;
assert(doseInterval > 0); // neg is nonsensical, 0 is disallowed due to mod operation
//const int boostInterval = par->vaccineBoostingInterval;
for (CatchupVaccinationEvent cve: par->catchupVaccinationEvents) {
// Normal, initial vaccination -- boosting, multiple doses handled in Community::tick()
if (date.day() == cve.simDay) {
if (not par->abcVerbose) cerr << "vaccinating " << cve.coverage*100 << "% of age " << cve.age << " on day " << cve.simDay << endl;
community->vaccinate(cve);
}
}
}
void schedule_vector_control(const Parameters* par, Community* community) {
for (VectorControlEvent vce: par->vectorControlEvents) {
const string loc_label = vce.locationType == 0 ? "houses" : vce.locationType == 1 ? "workplaces" : vce.locationType == 2 ? "schools" : "unknown location type";
if (not par->abcVerbose) cerr << "will start treating " << vce.coverage*100 << "% of " << loc_label << " on day " << vce.campaignStart << endl;
double rho = par->calculate_daily_vector_control_mortality(vce.efficacy);
if (vce.strategy == UNIFORM_STRATEGY) {
for (Location* loc: community->getLocations() ) {
if (loc->getType() == vce.locationType and gsl_rng_uniform(RNG) < vce.coverage) {
// location will be treated
const int loc_treatment_date = vce.campaignStart + gsl_rng_uniform_int(RNG, vce.campaignDuration);
loc->scheduleVectorControlEvent(vce.efficacy, rho, loc_treatment_date, vce.efficacyDuration);
}
}
} else if (vce.strategy == TIRS_STUDY_STRATEGY) {
for (Location* loc: community->getLocations() ) {
if (loc->getType() == vce.locationType and loc->getTrialArm() == 2) {
// location will be treated
const int loc_treatment_date = vce.campaignStart + gsl_rng_uniform_int(RNG, vce.campaignDuration);
loc->scheduleVectorControlEvent(vce.efficacy, rho, loc_treatment_date, vce.efficacyDuration);
}
}
} else if (vce.strategy == MAX_MOSQUITOES_STRATEGY) { // TODO - implement me
cerr << "ERROR: MAX_MOSQUITOES_STRATEGY is not yet implemented\n";
exit(-831);
} else {
cerr << "ERROR: Unsupported vector control strategy\n";
exit(-832);
}
}
}
int seed_epidemic(const Parameters* par, Community* community, const Date &date) {
int introduced_infection_ct = 0;
const int numperson = community->getNumPeople();
for (int serotype=0; serotype<NUM_OF_SEROTYPES; serotype++) {
const int ai_year_lookup = date.year() % par->annualIntroductions.size();
const double intros = par->annualIntroductions[ai_year_lookup];
const int de_year_lookup = date.year() % par->nDailyExposed.size();
const double serotype_weight = par->nDailyExposed[de_year_lookup][serotype];
const double annual_intros_weight = par->annualIntroductionsCoef;
const double expected_num_exposed = serotype_weight * annual_intros_weight * intros;
if (expected_num_exposed <= 0) continue;
assert(expected_num_exposed <= numperson);
const int num_exposed = gsl_ran_poisson(RNG, expected_num_exposed);
for (int i=0; i<num_exposed; i++) {
// gsl_rng_uniform_int returns on [0, numperson-1]
int transmit_to_id = gsl_rng_uniform_int(RNG, numperson);
if (community->infect(transmit_to_id, (Serotype) serotype, date.day())) {
introduced_infection_ct++;
}
}
}
return introduced_infection_ct;
}
void update_mosquito_population(const Parameters* par, Community* community, const Date &date, int& nextMosquitoMultiplierIndex) {
const int mosquitoMultiplierTotalDuration = par->getMosquitoMultiplierTotalDuration();
// should the mosquito population change?
if (par->mosquitoMultipliers.size() > 0) {
const int nextMosquitoStart = par->mosquitoMultipliers[nextMosquitoMultiplierIndex].start;
if ( ((date.day()+date.offset())%mosquitoMultiplierTotalDuration) == nextMosquitoStart) {
//cerr << "updating mosquitoes on day " << date.day() << ", which is day " << date.julianDay()
// << " of the year. Using index " << nextMosquitoMultiplierIndex << endl;
community->applyMosquitoMultiplier(par->mosquitoMultipliers[nextMosquitoMultiplierIndex].value);
nextMosquitoMultiplierIndex = (nextMosquitoMultiplierIndex+1)%par->mosquitoMultipliers.size();
}
}
}
void update_extrinsic_incubation_period(const Parameters* par, Community* community, const Date &date, int& nextEIPindex) {
// should the EIP change?
const int EIPtotalDuration = par->getEIPtotalDuration();
if (par->extrinsicIncubationPeriods.size() > 0) {
const int nextEIPstart = par->extrinsicIncubationPeriods[nextEIPindex].start;
if ( ((date.day()+date.offset())%EIPtotalDuration) == nextEIPstart) {
community->setExpectedExtrinsicIncubation(par->extrinsicIncubationPeriods[nextEIPindex].value);
nextEIPindex = (nextEIPindex+1)%par->extrinsicIncubationPeriods.size();
}
}
}
void advance_simulator(const Parameters* par, Community* community, Date &date, const string process_id, map<string, vector<int> > &periodic_incidence, vector<int> &periodic_prevalence, int &nextMosquitoMultiplierIndex, int &nextEIPindex, vector<int> &proto_metrics) {
update_mosquito_population(par, community, date, nextMosquitoMultiplierIndex);
update_extrinsic_incubation_period(par, community, date, nextEIPindex);
community->tick(date);
seed_epidemic(par, community, date);
for (Person* p: community->getPeople()) {
if (p->isInfected(date.day())) {
const Infection* infec = p->getInfection();
bool intro = not infec->isLocallyAcquired();
bool symp = infec->isSymptomatic();
bool severe = infec->isSevere();
// Prevalence
periodic_prevalence[INTRO_INF_PREV] += intro;
periodic_prevalence[INTRO_CASE_PREV] += intro and symp;
periodic_prevalence[INTRO_DSS_PREV] += intro and severe;
periodic_prevalence[TOTAL_INF_PREV] += 1;
periodic_prevalence[TOTAL_CASE_PREV] += symp;
periodic_prevalence[TOTAL_DSS_PREV] += severe;
// Incidence
if (p->isNewlyInfected(date.day())) {
periodic_incidence["daily"][INTRO_INF] += intro;
periodic_incidence["daily"][INTRO_CASE] += intro and symp;
periodic_incidence["daily"][INTRO_DSS] += intro and severe;
periodic_incidence["daily"][TOTAL_INF] += 1;
periodic_incidence["daily"][TOTAL_CASE] += symp;
periodic_incidence["daily"][TOTAL_DSS] += severe;
const Location* home = p->getLocation(HOME_MORNING);
if (par->simulateTrial) { // TODO check whether p is a surveilled person (e.g. a child, for TIRS study)
const int age = p->getAge();
const TrialArmState arm = home->isSurveilled() and age >= 2 and age <= 15 ? home->getTrialArm() : NOT_IN_TRIAL;
if (arm == TRIAL_ARM_1) {
periodic_incidence["daily-arm1"][INTRO_INF] += intro;
periodic_incidence["daily-arm1"][INTRO_CASE] += intro and symp;
periodic_incidence["daily-arm1"][INTRO_DSS] += intro and severe;
periodic_incidence["daily-arm1"][TOTAL_INF] += 1;
periodic_incidence["daily-arm1"][TOTAL_CASE] += symp;
periodic_incidence["daily-arm1"][TOTAL_DSS] += severe;
} else if (arm == TRIAL_ARM_2) {
periodic_incidence["daily-arm2"][INTRO_INF] += intro;
periodic_incidence["daily-arm2"][INTRO_CASE] += intro and symp;
periodic_incidence["daily-arm2"][INTRO_DSS] += intro and severe;
periodic_incidence["daily-arm2"][TOTAL_INF] += 1;
periodic_incidence["daily-arm2"][TOTAL_CASE] += symp;
periodic_incidence["daily-arm2"][TOTAL_DSS] += severe;
}
}
}
}
}
periodic_output(par, community, periodic_incidence, periodic_prevalence, date, process_id, proto_metrics);
return;
}
map<string, vector<int> > construct_tally() {
// { introductions, local transmission, total, case, severe}
map<string, vector<int> > periodic_incidence { {"daily", vector<int>(NUM_OF_INCIDENCE_REPORTING_TYPES,0)},
{"n_day", vector<int>(NUM_OF_INCIDENCE_REPORTING_TYPES,0)},
{"weekly", vector<int>(NUM_OF_INCIDENCE_REPORTING_TYPES,0)},
{"monthly", vector<int>(NUM_OF_INCIDENCE_REPORTING_TYPES,0)},
{"yearly", vector<int>(NUM_OF_INCIDENCE_REPORTING_TYPES,0)},
{"yearly-arm1", vector<int>(NUM_OF_INCIDENCE_REPORTING_TYPES,0)},
{"yearly-arm2", vector<int>(NUM_OF_INCIDENCE_REPORTING_TYPES,0)},
{"daily-arm1", vector<int>(NUM_OF_INCIDENCE_REPORTING_TYPES,0)},
{"daily-arm2", vector<int>(NUM_OF_INCIDENCE_REPORTING_TYPES,0)}};
return periodic_incidence;
}
vector<int> simulate_epidemic_with_seroprev(const Parameters* par, Community* community, const string process_id, bool capture_sero_prev, vector< vector<double> > &sero_prev, int sero_prev_aggregation_julian_start=0) {
sero_prev = vector< vector<double> > (5, vector<double>(par->nRunLength/365, 0.0)); // rows are infection history: 0, 1, and 2+ infections
vector<int> proto_metrics;
Date date(par);
int nextMosquitoMultiplierIndex = 0;
int nextEIPindex = 0;
initialize_seasonality(par, community, nextMosquitoMultiplierIndex, nextEIPindex, date);
schedule_vector_control(par, community);
vector<string> daily_output_buffer;
if (par->bSecondaryTransmission and not par->abcVerbose) {
daily_output_buffer.push_back("day,year,id,age,location,vaccinated,serotype,symptomatic,severity");
}
map<string, vector<int> > periodic_incidence = construct_tally();
vector<int> periodic_prevalence(NUM_OF_PREVALENCE_REPORTING_TYPES, 0);
for (; date.day() < par->nRunLength; date.increment()) {
update_vaccinations(par, community, date);
advance_simulator(par, community, date, process_id, periodic_incidence, periodic_prevalence, nextMosquitoMultiplierIndex, nextEIPindex, proto_metrics);
if (capture_sero_prev and ((int) date.julianDay() == ((sero_prev_aggregation_julian_start+364) % 365 ) + 1)) { // +1 because julianDay is [1,365])), avg(avg(interventions are specified on [0,364]
// tally current seroprevalence stats
int vaccinated_tally = 0;
vector<double> inf_ct_tally(5,0.0); // [0,4] past infections
for (Person* p: community->getPeople()) {
// ignoring possible seroconversion due to vaccine
vaccinated_tally += p->isVaccinated();
const int ct = p->getNumNaturalInfections();
++inf_ct_tally[ct];
}
double N = community->getNumPeople();
for (unsigned int i = 0; i < inf_ct_tally.size(); ++i) sero_prev[i][date.year()] = inf_ct_tally[i] / N;
cerr << "vaccinated N, fraction: " << vaccinated_tally << " " << (double) vaccinated_tally / N << endl;
}
}
/*
stringstream ss_filename;
ss_filename << "/scratch/lfs/thladish/who-feb-2016/daily." << process_id << "." << par->randomseed;
string dailyfilename = ss_filename.str();
write_daily_buffer(daily_output_buffer, process_id, dailyfilename);
*/
return proto_metrics;
}
vector<int> simulate_epidemic(const Parameters* par, Community* community, const string process_id) {
vector< vector<double> > sero_prev;
bool capture_sero_prev = false;
return simulate_epidemic_with_seroprev(par, community, process_id, capture_sero_prev, sero_prev);
}
vector<long double> simulate_who_fitting(const Parameters* par, Community* community, const string process_id, vector<int> &serotested_ids) {
assert(serotested_ids.size() > 0);
vector<long double> metrics;
vector<int> proto_metrics;
Date date(par);
int nextMosquitoMultiplierIndex = 0;
int nextEIPindex = 0;
initialize_seasonality(par, community, nextMosquitoMultiplierIndex, nextEIPindex, date);
vector<string> daily_output_buffer;
if (par->bSecondaryTransmission and not par->abcVerbose) {
daily_output_buffer.push_back("time,type,id,location,serotype,symptomatic,withdrawn,new_infection");
//cout << "time,type,id,location,serotype,symptomatic,withdrawn,new_infection" << endl;
}
map<string, vector<int> > periodic_incidence = construct_tally();
vector<int> periodic_prevalence(NUM_OF_PREVALENCE_REPORTING_TYPES, 0);
for (; date.day() < par->nRunLength; date.increment()) {
if ( date.julianDay() == 99 ) {
// for a 135 year simulation
// calculate seroprevalence among 9 year old merida residents
double seropos_9yo = 0.0;
for (int id: serotested_ids) {
const double seropos = community->getPersonByID(id)->getNumNaturalInfections() > 0 ? 1.0 : 0.0;
seropos_9yo += seropos;
}
seropos_9yo /= serotested_ids.size();
metrics.push_back(seropos_9yo);
}
advance_simulator(par, community, date, process_id, periodic_incidence, periodic_prevalence, nextMosquitoMultiplierIndex, nextEIPindex, proto_metrics);
}
return metrics;
}
//c('0-4', '5-9', '10-14', '15-19', '20-29', '30-39', '40-49', '50-59', '60+')
vector<int> simulate_abc(const Parameters* par, Community* community, const string process_id, vector<int> &serotested_ids_87, double &seropos_87, vector<int> &serotested_ids_14, vector<double> &seropos_14_by_age) {
assert(serotested_ids_87.size() > 0);
vector<int> proto_metrics;
Date date(par);
int nextMosquitoMultiplierIndex = 0;
int nextEIPindex = 0;
initialize_seasonality(par, community, nextMosquitoMultiplierIndex, nextEIPindex, date);
vector<string> daily_output_buffer;
if (par->bSecondaryTransmission and not par->abcVerbose) {
daily_output_buffer.push_back("day,year,id,age,location,vaccinated,serotype,symptomatic,severe");
}
map<string, vector<int> > periodic_incidence = construct_tally();
vector<int> periodic_prevalence(NUM_OF_PREVALENCE_REPORTING_TYPES, 0);
const vector<int> upper_age_bound_14 = {4, 9, 14, 19, 29, 39, 49, 59, INT_MAX};
vector<int> seropos_14_sample_size(upper_age_bound_14.size(), 0);
assert(upper_age_bound_14.size() == seropos_14_by_age.size());
for (; date.day() < par->nRunLength; date.increment()) {
if ( date.julianDay() == 99 and date.year() == 108 ) { // This corresponds to April 9 (day 99) of 1987
// for a simulation starting Jan 1, 1879
cerr << "1987 serosurvey\n";
// calculate seroprevalence among 8-14 year old merida residents
for (int id: serotested_ids_87) {
const double seropos = community->getPersonByID(id)->getNumNaturalInfections() > 0 ? 1.0 : 0.0;
seropos_87 += seropos;
}
seropos_87 /= serotested_ids_87.size();
} else if ( date.julianDay() == 99 and date.year() == 135 ) { // This corresponds to April 9 (day 99) of 2014
cerr << "2014 serosurvey\n";
// calculate seroprevalence among all merida residents
for (int id: serotested_ids_14) {
const Person* p = community->getPersonByID(id);
const int age = p->getAge();
assert(age >= 0);
unsigned int age_cat;
for (age_cat = 0; age_cat<upper_age_bound_14.size() and age>upper_age_bound_14[age_cat]; ++age_cat) {/*this space intentionally left blank*/}
const double seropos = p->getNumNaturalInfections() > 0 ? 1.0 : 0.0;
seropos_14_by_age[age_cat] += seropos;
seropos_14_sample_size[age_cat]++;
}
for (unsigned int age_cat = 0; age_cat < seropos_14_by_age.size(); ++age_cat) {
seropos_14_by_age[age_cat] /= seropos_14_sample_size[age_cat];
}
}
advance_simulator(par, community, date, process_id, periodic_incidence, periodic_prevalence, nextMosquitoMultiplierIndex, nextEIPindex, proto_metrics);
/* if ( date.julianDay() == 365 and date.year() == 121 ) { // December 31 (day 365) of 2000
string imm_filename = "/ufrc/longini/tjhladish/imm_1000_yucatan-irs_refit/immunity2000." + process_id;
write_immunity_file(community, process_id, imm_filename, date.day());
}
if ( date.julianDay() == 99 and date.year() == 135 ) { // April 9 (day 99) of 2014
string imm_filename = "/ufrc/longini/tjhladish/imm_1000_yucatan-irs_refit/immunity2014_04_09." + process_id;
write_immunity_file(community, process_id, imm_filename, date.day());
}*/
}
//string dailyfilename = "";
//write_daily_buffer(daily_output_buffer, process_id, dailyfilename);
return proto_metrics;
}
bool fileExists(const std::string& filename) {
struct stat buf;
return stat(filename.c_str(), &buf) != -1;
}
void write_daily_buffer( vector<string>& buffer, const string process_id, string filename = "" ) {
if (filename == "") {
stringstream ss_filename;
ss_filename << "daily_output." << process_id;
filename = ss_filename.str();
}
string all_output;
for (const auto &line : buffer) all_output += (line + "\n");
if (fileExists(filename)) {
cerr << "WARNING: Daily output file already exists: " << filename << endl << "WARNING: Aborting write.\n";
return;
}
ofstream file;
file.open(filename);
if (file.is_open()) { // TODO - add this check everywhere a file is opened
file << all_output;
file.close();
} else {
cerr << "ERROR: Could not open daily buffer file for output: " << filename << endl;
exit(-842);
}
}
void write_immunity_by_age_file(const Community* community, const int year, string filename) {
if (filename == "") {
stringstream ss_filename;
ss_filename << "imm_vs_age.year" << year;
filename = ss_filename.str();
}
// total count, denv1, denv2, denv3, denv4, imm_to_one, imm_to_all
vector< vector<int> > tally(NUM_AGE_CLASSES, vector<int>(NUM_OF_SEROTYPES+3, 0));
for (Person* p: community->getPeople()) {
const int age = p->getAge();
tally[age][0]++;
const int numInfections = p->getNumNaturalInfections();
for (int k = 0; k<numInfections; ++k) {
const int s = (int) p->getSerotype(k);
tally[age][s+1]++;
}
if (numInfections > 0) tally[age][NUM_OF_SEROTYPES+1]++;
if (numInfections == NUM_OF_SEROTYPES) tally[age][NUM_OF_SEROTYPES+2]++;
}
ofstream file;
file.open(filename);
for (int a = 0; a<NUM_AGE_CLASSES; ++a) {
file << a;
for (int i: tally[a]) file << " " << i;
file << endl;
}
file.close();
}
void write_immunity_file(const Community* community, const string label, string filename, int runLength) {
if (filename == "") {
stringstream ss_filename;
ss_filename << "immunity." << label;
filename = ss_filename.str();
}
ofstream file;
file.open(filename);
file << "pid age imm1 imm2 imm3 imm4\n";
for (Person* p: community->getPeople()) {
vector<int> infection_history(NUM_OF_SEROTYPES, 0); // 0 is no infection; -1 means yesterday, -2 means 2 days ago ...
for (int k = 0; k<p->getNumNaturalInfections(); ++k) {
int s = (int) p->getSerotype(k);
infection_history[s] = p->getInfectedTime(k) - runLength;
}
file << p->getID() << " " << p->getAge() << " ";
for (auto sero: infection_history) file << sero << " ";
file << endl;
}
file.close();
}
void daily_detailed_output(Community* community, int t) {
// print out infectious mosquitoes
/* for (int i=community->getNumInfectiousMosquitoes()-1; i>=0; i--) {
Mosquito *p = community->getInfectiousMosquito(i);
cout << t << ",mi," << p->getID() << "," << p->getLocation()->getID() << "," << "," << "," << endl;
}
// print out exposed mosquitoes
for (int i=community->getNumExposedMosquitoes()-1; i>=0; i--) {
Mosquito *p = community->getExposedMosquito(i);
// "current" location
cout << t << ",me," << p->getID() << "," << p->getLocation()->getID() << "," << 1 + (int) p->getSerotype() << "," << "," << "," << endl;
}*/
// print out infected people
for (Person *p: community->getPeople()) {
if (p->isInfected(t)) {
// home location
cout << t
<< ",p,"
<< p->getID() << ","
<< p->getLocation(HOME_MORNING)->getID() << ","
<< 1 + (int) p->getSerotype() << ","
<< (p->isSymptomatic(t)?1:0) << ","
<< (p->isWithdrawn(t)?1:0) << ","
<< (p->isNewlyInfected(t)?1:0) << endl;
}
}
}
void write_mosquito_location_data(const Community* community, string mos_filename, string loc_filename) {
ofstream mos_file;
mos_file.open(mos_filename);
mos_file << "locID sero queue idx ageInfd ageInfs ageDead\n";
const vector< vector<Mosquito*> > exposed = community->getExposedMosquitoes();
// Exposed mosquitoes, by incubation days left
for (unsigned int i = 0; i < exposed.size(); ++i) {
const vector<Mosquito*>& mosquitoes = exposed[i];
for (const Mosquito* m: mosquitoes) {
mos_file << m->getLocation()->getID() << " " << m->getSerotype() << " "
<< "e " << i << " " << m->getAgeInfected() << " "
<< m->getAgeInfectious() << " " << m->getAgeDeath() << endl;
}
}
const vector< vector<Mosquito*> > infectious = community->getInfectiousMosquitoes();
// Infectious mosquitoes, by days left to live
for (unsigned int i = 0; i < infectious.size(); ++i) {
const vector<Mosquito*>& mosquitoes = infectious[i];
for (const Mosquito* m: mosquitoes) {
mos_file << m->getLocation()->getID() << " " << m->getSerotype() << " "
<< "i " << i << " " << m->getAgeInfected() << " "
<< m->getAgeInfectious() << " " << m->getAgeDeath() << endl;
}
}
mos_file.close();
ofstream loc_file;
loc_file.open(loc_filename);
loc_file << "locID baseMos infdMos\n";
// Mosquitoes by location
const vector<Location*> locations = community->getLocations();
for (Location* loc: locations) {
loc_file << loc->getID() << " ";
loc_file << loc->getBaseMosquitoCapacity() << " ";
loc_file << loc->getCurrentInfectedMosquitoes() << endl;
}
loc_file.close();
}
void import_csv_to_db(string filename, string table, string db) {
stringstream ss;
ss << "sqlite3 " << db << " '.mode csv' '.import " << filename << ' ' << table << "'";
string cmd_str = ss.str();
int retval = system(cmd_str.c_str());
if (retval == -1) { cerr << "System failed to import " << table << " data to db\n"; }
return;
}
void generate_sim_data_db(const Parameters* /*par*/, const Community* community, const unsigned long int serial, vector<string> tables) {
vector<stringstream> filenames(tables.size());
for (size_t i = 0; i < tables.size(); ++i) {
filenames[i] << "./" << tables[i] << "_" << serial << ".csv";
}
map<string, ofstream> ofiles;
for (size_t i = 0; i < tables.size(); ++i) {
ofiles[tables[i]] = ofstream(filenames[i].str(), std::ios::trunc);
}
bool all_files_open = true;
for (const auto& [table, ofile] : ofiles) {
all_files_open = all_files_open and (bool)ofile;
}
if (not all_files_open) { cerr << "FILES FAILED TO OPEN" << endl; exit(-1); }
for (Person* p : community->getPeople()) {
for (Infection* inf : p->getInfectionHistory()) {
if (not inf) { continue; }
int inf_place_id = inf->getInfectedLoc() ? inf->getInfectedLoc()->getID() : -1;
int inf_by_id = inf->getInfectedBy() ? inf->getInfectedBy()->getID() : -1;
int inf_owner_id = inf->getInfectionOwner() ? inf->getInfectionOwner()->getID() : -1;
ofiles["infection_history"] << inf << ','
<< inf_place_id << ','
<< inf_by_id << ','
<< inf_owner_id << ','
<< inf->getInfectedTime() << ','
<< inf->getInfectiousTime() << ','
<< inf->getSymptomTime() << ','
<< inf->getRecoveryTime() << ','
<< inf->getWithdrawnTime() << ','
<< inf->isSevere() << ','
<< inf->serotype() << endl;
}
}
for (auto& [table, ofile] : ofiles) { ofile.close(); }
stringstream ss, db;
db << "sim_data_" << serial << ".sqlite";
ss << "sqlite3 " << db.str() << " '.read gen_sim_db.sql'";
string cmd_str = ss.str();
int retval = system(cmd_str.c_str());
if (retval == -1) { cerr << "System call to `sqlite3 " << db.str() << " '.read gen_sim_db.sql'` failed\n"; }
for (size_t i = 0; i < tables.size(); ++i) {
import_csv_to_db(filenames[i].str(), tables[i], db.str());
}
ss.str(string());
ss << "rm";
for (size_t i = 0; i < filenames.size(); ++i) { ss << ' ' << filenames[i].str(); }
cmd_str = ss.str();
retval = system(cmd_str.c_str());
if (retval == -1) { cerr << "System call to delete infection csv files failed\n"; }
}