-
Notifications
You must be signed in to change notification settings - Fork 10
/
simulator.h
906 lines (785 loc) · 41.3 KB
/
simulator.h
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
#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"; }
}