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Changes to vaccine impact modeling assumptions
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@tjhladish
tjhladish committed Sep 28, 2020
1 parent bbda3cd commit 1afd51c
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Showing 5 changed files with 82 additions and 80 deletions.
2 changes: 1 addition & 1 deletion Community.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -429,7 +429,7 @@ void Community::vaccinate(CatchupVaccinationEvent cve) {

// Valid coverage and age?
assert(cve.coverage >= 0.0 and cve.coverage <= 1.0);
assert(cve.age <= (signed) _personAgeCohort.size());
assert(cve.age <= _personAgeCohort.size());

const size_t duration = cve.campaignDuration;
for (Person* p: _personAgeCohort[cve.age]) {
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56 changes: 18 additions & 38 deletions exp/vac_testing/abc_covid.json
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Original file line number Diff line number Diff line change
@@ -1,10 +1,10 @@
{
"smc_iterations" : 1,
"num_samples" : 9600,
"num_samples" : 24000,
"predictive_prior_fraction" : 1.0,
"pls_training_fraction" : 1.0,

"database_filename" : "covid_vac_v1.2.sqlite",
"database_filename" : "covid_vac_v3.0.sqlite",

"parameters" : [
{"name" : "vaccine",
Expand All @@ -20,7 +20,7 @@
"dist_type" : "PSEUDO",
"num_type" : "FLOAT",
"par1" : 0.1,
"par2" : 0.7,
"par2" : 0.9,
"step" : 0.2},

{"name" : "vaccine_coverage",
Expand All @@ -44,22 +44,30 @@
"dist_type" : "PSEUDO",
"num_type" : "INT",
"par1" : 0,
"par2" : 2,
"step" : 1},
"par2" : 112,
"step" : 56},

{"name" : "vaccine_social_distancing",
"short_name" : "vsd",
"dist_type" : "PSEUDO",
"num_type" : "FLOAT",
"par1" : 0.03,
"par2" : 0.14,
"step" : 0.11},
"par1" : 0.00,
"par2" : 0.3,
"step" : 0.3},

{"name" : "realization",
"dist_type" : "PSEUDO",
"num_type" : "INT",
"par1" : 0,
"par2" : 99}
"par2" : 99},

{"name" : "pre_vac_lockdown",
"short_name" : "pvl",
"dist_type" : "PSEUDO",
"num_type" : "INT",
"par1" : 0,
"par2" : 1,
"step" : 1}
],

"metrics" : [
Expand Down Expand Up @@ -115,20 +123,6 @@
{"name" : "rc49", "num_type" : "INT", "value" : 0},
{"name" : "rc50", "num_type" : "INT", "value" : 0},
{"name" : "rc51", "num_type" : "INT", "value" : 0},
{"name" : "rc52", "num_type" : "INT", "value" : 0},
{"name" : "rc53", "num_type" : "INT", "value" : 0},
{"name" : "rc54", "num_type" : "INT", "value" : 0},
{"name" : "rc55", "num_type" : "INT", "value" : 0},
{"name" : "rc56", "num_type" : "INT", "value" : 0},
{"name" : "rc57", "num_type" : "INT", "value" : 0},
{"name" : "rc58", "num_type" : "INT", "value" : 0},
{"name" : "rc59", "num_type" : "INT", "value" : 0},
{"name" : "rc60", "num_type" : "INT", "value" : 0},
{"name" : "rc61", "num_type" : "INT", "value" : 0},
{"name" : "rc62", "num_type" : "INT", "value" : 0},
{"name" : "rc63", "num_type" : "INT", "value" : 0},
{"name" : "rc64", "num_type" : "INT", "value" : 0},
{"name" : "rc65", "num_type" : "INT", "value" : 0},

{"name" : "Rt00", "num_type" : "INT", "value" : 0},
{"name" : "Rt01", "num_type" : "INT", "value" : 0},
Expand Down Expand Up @@ -181,20 +175,6 @@
{"name" : "Rt48", "num_type" : "INT", "value" : 0},
{"name" : "Rt49", "num_type" : "INT", "value" : 0},
{"name" : "Rt50", "num_type" : "INT", "value" : 0},
{"name" : "Rt51", "num_type" : "INT", "value" : 0},
{"name" : "Rt52", "num_type" : "INT", "value" : 0},
{"name" : "Rt53", "num_type" : "INT", "value" : 0},
{"name" : "Rt54", "num_type" : "INT", "value" : 0},
{"name" : "Rt55", "num_type" : "INT", "value" : 0},
{"name" : "Rt56", "num_type" : "INT", "value" : 0},
{"name" : "Rt57", "num_type" : "INT", "value" : 0},
{"name" : "Rt58", "num_type" : "INT", "value" : 0},
{"name" : "Rt59", "num_type" : "INT", "value" : 0},
{"name" : "Rt60", "num_type" : "INT", "value" : 0},
{"name" : "Rt61", "num_type" : "INT", "value" : 0},
{"name" : "Rt62", "num_type" : "INT", "value" : 0},
{"name" : "Rt63", "num_type" : "INT", "value" : 0},
{"name" : "Rt64", "num_type" : "INT", "value" : 0},
{"name" : "Rt65", "num_type" : "INT", "value" : 0}
{"name" : "Rt51", "num_type" : "INT", "value" : 0}
]
}
98 changes: 59 additions & 39 deletions exp/vac_testing/main_abc.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -24,27 +24,31 @@ const string output_dir("/ufrc/longini/tjhladish/");
//const string imm_dir(output_dir + "");

const int RESTART_BURNIN = 0;
const int FORECAST_DURATION = 462;
const int FORECAST_DURATION = 364;
const int OVERRUN = 14; // to get accurate Rt estimates near the end of the forecast duration
const bool RUN_FORECAST = true;
const int TOTAL_DURATION = RUN_FORECAST ? RESTART_BURNIN + FORECAST_DURATION : RESTART_BURNIN;
const size_t JULIAN_TALLY_DATE = 146; // intervention julian date - 1
const int TOTAL_DURATION = RUN_FORECAST ? RESTART_BURNIN + FORECAST_DURATION + OVERRUN : RESTART_BURNIN;
//const size_t JULIAN_TALLY_DATE = 146; // intervention julian date - 1
const size_t JULIAN_START_YEAR = 2020;

//Parameters* define_simulator_parameters(vector<double> args, const unsigned long int rng_seed) {
Parameters* define_simulator_parameters(vector<double> args, const unsigned long int rng_seed, const unsigned long int serial, const string /*process_id*/) {
Parameters* define_simulator_parameters(vector<double> /*args*/, const unsigned long int rng_seed, const unsigned long int serial, const string /*process_id*/) {
Parameters* par = new Parameters();
par->define_defaults();
par->serial = serial;

const float T = 0.225;
const float T = 0.205;

par->household_transmissibility = T;
par->workplace_transmissibility = T;
par->school_transmissibility = T;
par->social_transmissibility = T/10.0;
par->household_transmissibility = T;
par->social_transmissibility = T/10.0; // assumes complete graphs between households
par->workplace_transmissibility = T;
par->school_transmissibility = T;
par->hospital_transmissibility = T/10.0;
par->nursinghome_transmissibility = 2*T;
//hospitalizedFraction = {0.0, 0.15, 0.9};
//par->reportedFraction = {0.0, 0.01, 0.5, 0.8, 1.0}; // fraction of asymptomatic, mild, severe, critical, and deaths reported
par->reportedFraction = {0.0, 0.2, 0.75, 0.75, 0.75}; // fraction of asymptomatic, mild, severe, critical, and deaths reported
//par->reportedFraction = {0.0, 0.2, 0.75, 0.75, 0.75}; // fraction of asymptomatic, mild, severe, critical, and deaths reported
par->probFirstDetection = {0.0, 0.15, 0.6, 0.1, 0.01}; // probability of being detected while {asymp, mild, severe, crit, dead} if not detected previously
par->randomseed = rng_seed;
par->dailyOutput = false; // turn on for daily prevalence figure, probably uncomment filter in simulator.h for daily output to get only rel. days
par->periodicOutput = false;
Expand All @@ -56,49 +60,43 @@ Parameters* define_simulator_parameters(vector<double> args, const unsigned long
par->runLength = TOTAL_DURATION;
par->julianYear = JULIAN_START_YEAR;
par->startDayOfYear = 45;
// par->startDayOfYear = 1;
par->annualIntroductionsCoef = 1;

//par->pathogenicityModel = ORIGINAL_LOGISTIC;
par->traceContacts = true;
//par->mmodsScenario = ms; // MMODS_CLOSED, MMODS_2WEEKS, MMODS_1PERCENT, MMODS_OPEN

// These are only initial values for time-structured interventions. They can be changed dynamically.
par->timedInterventions[SCHOOL_CLOSURE].clear();
par->timedInterventions[SCHOOL_CLOSURE].resize(30, 0.0);
const size_t aug31 = 243 - par->startDayOfYear;
// const size_t school_closed_duration = aug31 < par->runLength ? aug31 : par->runLength;
// par->timedInterventions[SCHOOL_CLOSURE].resize(school_closed_duration, 1.0);
par->timedInterventions[SCHOOL_CLOSURE].resize(aug31, 1.0);
par->timedInterventions[SCHOOL_CLOSURE].resize(par->runLength, 0.0);

par->timedInterventions[NONESSENTIAL_BUSINESS_CLOSURE].clear();
par->timedInterventions[NONESSENTIAL_BUSINESS_CLOSURE].resize(45, 0.0);
par->timedInterventions[NONESSENTIAL_BUSINESS_CLOSURE].resize(75, 1.0);
par->timedInterventions[NONESSENTIAL_BUSINESS_CLOSURE].resize(par->runLength, 0.0);

const float mobility_logit_shift = -2.7;
const float mobility_logit_stretch = 2;
//const float mobility_logit_shift = -2.7;
//const float mobility_logit_stretch = 2;
// using createSocialDistancingModel() defines timedInterventions[SOCIAL_DISTANCING] values
// NB: startDayOfYear, runLength, and julianYear must be defined in par before a social distancing model can be meaningfully created!
// TODO - make that dependency something the user doesn't have to know or think about
//par->createSocialDistancingModel(pop_dir + "/safegraph_mobility_index.csv", mobility_logit_shift, mobility_logit_stretch);
// plot(as.Date(d$date), shiftstretch(1-d$smooth_ma7, shift=-2.7, stretch=2), ylim=c(0,1), type='l')
par->createSocialDistancingModel(pop_dir + "/sgmi_fl_comp.csv", mobility_logit_shift, mobility_logit_stretch);
//par->createSocialDistancingModel(pop_dir + "/../florida/sgmi_fl_comp.csv", mobility_logit_shift, mobility_logit_stretch);
//par->createSocialDistancingModel(pop_dir + "/sgmi_escambia_comp.csv", mobility_logit_shift, mobility_logit_stretch);
//par->createSocialDistancingModel(pop_dir + "/sgmi_dade_comp.csv", mobility_logit_shift, mobility_logit_stretch);

//par->defaultReportingLag = 14;
par->createReportingLagModel(pop_dir + "/case_report_delay.csv");
par->symptomToTestLag = 2;
par->deathReportingLag = 4;
par->deathReportingLag = 7;

const double max_icu_mortality_reduction = 1.0/3.0; // primarily due to use of dexamethasone
const size_t icu_mortality_inflection_sim_day = Date::to_julian_day("2020-06-25") - par->startDayOfYear;
const double icu_mortality_reduction_slope = 0.5; // 0.5 -> change takes ~2 weeks
par->createIcuMortalityReductionModel(max_icu_mortality_reduction, icu_mortality_inflection_sim_day, icu_mortality_reduction_slope);
par->icuMortalityFraction = 0.5; // to be fit; fraction of all deaths that occur in ICUs;
// used for interpreting empirical mortality data, *not within simulation*
par->define_susceptibility_and_pathogenicity();

par->daysImmune = 730;
par->VES = 0.0;

//par->hospitalizedFraction = 0.25; // fraction of cases assumed to be hospitalized
par->numInitialInfected = 1;
par->probDailyExposure = {1.0e-05};
par->probInitialExposure = {1.0e-04};
par->probDailyExposure = {1.0e-05};

par->populationFilename = pop_dir + "/population-" + SIM_POP + ".txt";
par->comorbidityFilename = pop_dir + "/comorbidity-" + SIM_POP + ".txt";
par->locationFilename = pop_dir + "/locations-" + SIM_POP + ".txt";
par->networkFilename = pop_dir + "/network-" + SIM_POP + ".txt";

Expand Down Expand Up @@ -172,7 +170,7 @@ int julian_to_sim_day (const Parameters* par, const size_t julian, const int int


vector<double> tally_counts(const Parameters* par, Community* community, int discard_days) {
const size_t num_weeks = (par->runLength - discard_days)/7;
const size_t num_weeks = (par->runLength - discard_days - OVERRUN)/7;

//vector<size_t> infected = community->getNumNewlyInfected();
//vector< vector<int> > severe = community->getNumSevereCases();
Expand All @@ -183,7 +181,7 @@ vector<double> tally_counts(const Parameters* par, Community* community, int dis
vector<size_t> Rt_incidence_tally(num_weeks, 0);

vector<double> metrics(num_weeks*2, 0.0);
for (size_t t = discard_days; t < par->runLength; t++) {
for (size_t t = discard_days; t < par->runLength - OVERRUN; t++) {
const size_t w = (t-discard_days)/7; // which reporting week are we in?
metrics[w] += symptomatic[t];
metrics[num_weeks + w] += R[t].first > 0 ? R[t].first*R[t].second : 0;
Expand Down Expand Up @@ -214,20 +212,42 @@ vector<double> simulator(vector<double> args, const unsigned long int rng_seed,
cerr << "SCENARIO " << rng_seed;
for (auto _p: args) { cerr << " " << _p; } cerr << endl;

const vector<size_t> VAC_DATES = {56, 140, 200};
// const vector<size_t> VAC_DATES = {56, 140, 200}; // julian dates

Parameters* par = define_simulator_parameters(args, rng_seed, serial, process_id);
vector<double> reported_frac = par->toReportedFraction(par->probFirstDetection);
cerr_vector(reported_frac); cerr << endl;
const bool vaccine = (bool) args[0];
const double vac_efficacy = args[1];
const double vac_coverage = args[2];
const int vac_mech = (int) args[3];
const int vac_date = VAC_DATES[(size_t) args[4]];
//const int vac_date = VAC_DATES[(size_t) args[4]];
const int vac_sim_day = (int) args[4];
const double vac_soc_dist = args[5]; // social distancing in effect post vaccination campaign
const int vac_sim_day = vac_date - par->startDayOfYear + 1;
//const int vac_sim_day = vac_date - par->startDayOfYear + 1;
const bool pre_vac_lockdown = (bool) args[7];
assert(vac_sim_day >= 0);
const size_t vac_campaign_duration = 30;

par->timedInterventions[SOCIAL_DISTANCING].resize(vac_sim_day);
const double pandemic_soc_dist = 0.3;
par->timedInterventions[SCHOOL_CLOSURE].clear();
par->timedInterventions[NONESSENTIAL_BUSINESS_CLOSURE].clear();
par->timedInterventions[SOCIAL_DISTANCING].clear();

const size_t lockdown_duration = 14;
if (pre_vac_lockdown and vac_sim_day >= (signed) lockdown_duration) {
par->timedInterventions[SCHOOL_CLOSURE].resize(vac_sim_day - lockdown_duration, 0.0);
par->timedInterventions[NONESSENTIAL_BUSINESS_CLOSURE].resize(vac_sim_day - lockdown_duration, 0.0);
par->timedInterventions[SOCIAL_DISTANCING].resize(vac_sim_day - lockdown_duration, pandemic_soc_dist);

par->timedInterventions[SCHOOL_CLOSURE].resize(vac_sim_day, 1.0);
par->timedInterventions[NONESSENTIAL_BUSINESS_CLOSURE].resize(vac_sim_day, 1.0);
par->timedInterventions[SOCIAL_DISTANCING].resize(vac_sim_day, 1.0);
}

par->timedInterventions[SCHOOL_CLOSURE].resize(par->runLength, 0.0);
par->timedInterventions[NONESSENTIAL_BUSINESS_CLOSURE].resize(par->runLength, 0.0);
par->timedInterventions[SOCIAL_DISTANCING].resize(vac_sim_day, pandemic_soc_dist);
par->timedInterventions[SOCIAL_DISTANCING].resize(par->runLength, vac_soc_dist);

Community* community = build_community(par);
Expand Down
4 changes: 3 additions & 1 deletion exp/vac_testing/remove_nonsensical_particles.sql
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Original file line number Diff line number Diff line change
@@ -1,3 +1,5 @@
delete from par where vac = 0 and (vac_eff != 0.1 or vac_cov != 0.5);
delete from par where vac = 0 and (vac_eff != 0.5 or vac_cov != 0.5);
delete from par where pvl = 1 and vac_day = 0;
delete from job where serial not in (select serial from par);
delete from met where serial not in (select serial from par);
update par set seed = realization;
2 changes: 1 addition & 1 deletion exp/vac_testing/run_model.sh
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
for i in `seq 1 540`
for i in `seq 1 660`
do
./abc_sql abc_covid.json --simulate -n 2 2> /dev/null
done

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