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comoOde.cpp
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comoOde.cpp
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// comomodel.net
// c++ version
// first written by sompob@tropmedre.ac
// modified (from v13.8.1) by bo.gao@ndm.ox.ac.uk
//
// for using with deSolve package in R
#include <Rmath.h>
#include <RcppArmadillo.h>
#include <chrono>
// #include "gperftools/profiler.h"
// #include <iostream>
// [[Rcpp::depends(RcppArmadillo)]]
using namespace Rcpp;
using namespace std::chrono;
// arma::mat getVarmat(std::string m){
// Environment glob = Environment::global_env();
// arma::mat var = as<arma::mat>(glob[m]);
// return(var);
// }
// double SplineFun(NumericVector& a, NumericVector& b, double c){
// Function splinefun("splinefun");
// Function fn = splinefun(a,b, Named("method")="hyman");
// double out = as<double>(fn(c));
// return(out);
// }
double MIN(const arma::vec& a, double m){
arma::vec b = a;
int sz = b.size();
b.resize(sz + 1);
b(sz) = m;
return(min(b));
}
////////////////////////////////////////////////////
// Performance measures
std::chrono::duration<double> duration_a, duration_b, duration_c;
// [[Rcpp::export]]
void covidOdeCpp_print_timing() {
Rcout << "duration_a=" << duration_a.count() << "\n"
<< "duration_b=" << duration_b.count() << "\n"
<< "duration_c=" << duration_c.count() << "\n";
}
bool ask_input = true;
////////////////////////////////////////////////////
// Splinefun
bool is_initialised_splinefun=false;
Environment pkg_stats = Environment::namespace_env("stats");
Function sf=pkg_stats["splinefun"];
// Function sf("splinefun");
NumericVector dummy_a = {1,2,3,4};
NumericVector dummy_b = {1,2,3,4};
Function splinefun_H = sf(dummy_a, dummy_b, Named("method")="hyman");
Function splinefun_ICU = sf(dummy_a, dummy_b, Named("method")="hyman");
Function splinefun_Vent = sf(dummy_a, dummy_b, Named("method")="hyman");
void init_splinefun(
NumericVector& xH,
NumericVector& xICU,
NumericVector& xVent,
NumericVector& f
) {
splinefun_H = sf(xH, f, Named("method")="hyman");
splinefun_ICU = sf(xICU, f, Named("method")="hyman");
splinefun_Vent = sf(xVent, f, Named("method")="hyman");
is_initialised_splinefun=true;
Rcout << "covidOdeCpp: splinefuns updated\n";
// Rcout << "sourceCpp version\n";
}
////////////////////////////////////////////////////
// Static Parameters
bool is_initialised_parameters=false;
// [[Rcpp::export]]
void covidOdeCpp_reset() {
duration_a = std::chrono::duration<double>::zero();
duration_b = std::chrono::duration<double>::zero();
duration_c = std::chrono::duration<double>::zero();
is_initialised_splinefun = false;
is_initialised_parameters = false;
ask_input = true;
}
// [[Rcpp::export]]
List covidOdeCpp(
double t,
const arma::vec& y,
const List& parameters,
const List& input,
int A,
const arma::mat& contact_home,
const arma::mat& contact_school,
const arma::mat& contact_work,
const arma::mat& contact_other,
const arma::vec& popbirth_col2,
const arma::vec& popstruc_col2,
const arma::mat& ageing,
const arma::vec& ifr_col2,
const arma::vec& ihr_col2,
const arma::vec& mort_col,
const List& age_group_vectors
) {
//Rf_PrintValue(parameters);
// auto start_a = high_resolution_clock::now();
////////////////////////////////////////////////////
// Parameters
// Ones selected for fitting
double p = parameters["p"];
double reporth = parameters["reporth"];
double amp = parameters["amp"];
//
// static double p = 0.0;
static double rho = 0.0;
static double omega = 0.0;
static double gamma = 0.0;
static double nui = 0.0;
static double report = 0.0;
static double reportc = 0.0;
static double report_v = 0.0;
static double report_cv = 0.0;
static double report_vr = 0.0;
static double report_cvr = 0.0;
static double report_r = 0.0;
static double report_cr = 0.0;
// static double reporth = 0.0;
static double beds_available = 0.0;
static double icu_beds_available = 0.0;
static double ventilators_available = 0.0;
static double nus = 0.0;
static double rhos = 0.0;
// static double amp = 0.0;
static double phi = 0.0;
// static double ihr_scaling = 0.0;
static double give = 0.0;
static double pdeath_h = 0.0;
static double pdeath_ho = 0.0;
static double pdeath_hc = 0.0;
static double pdeath_hco = 0.0;
static double pdeath_icu = 0.0;
static double pdeath_icuo = 0.0;
static double pdeath_icuc = 0.0;
static double pdeath_icuco = 0.0;
static double pdeath_vent = 0.0;
static double pdeath_ventc = 0.0;
static double nusc = 0.0;
static double nu_icu = 0.0;
static double nu_icuc = 0.0;
static double nu_vent = 0.0;
static double nu_ventc = 0.0;
static double pclin = 0.0;
static double prob_icu = 0.0;
static double prob_vent = 0.0;
//interventions
// self isolation
static double selfis_eff = 0.0;
// social distance
static double dist_eff = 0.0;
// hand washing
static double hand_eff = 0.0;
// mask wearing
static double mask_eff = 0.0;
// working at home
static double work_eff = 0.0;
static double w2h = 0.0;
// school closures
// static double school_eff = 0.0;
static double s2h = 0.0;
// cocooning the elderly
static double cocoon_eff = 0.0;
static double age_cocoon = 0.0;
// vaccination
static double vaccine_eff = 0.0;
static double vaccine_eff_r = 0.0;
static double vac_campaign = 0.0;
// imported cases
static double mean_imports = 0.0;
// screening
static double screen_test_sens = 0.0;
static double screen_overdispersion = 0.0;
// quarantine
static double quarantine_days = 0.0;
static double quarantine_effort = 0.0;
static double quarantine_eff_home = 0.0;
static double quarantine_eff_other = 0.0;
// lockdown
// mean household size
static double household_size = 0.0;
static double mass_test_sens = 0.0;
static double isolation_days = 0.0;
static double propo2 = 0.0;
static double pa_dexo2 = 0.0;
static double pa_dexo2c = 0.0;
static double pa_dexv = 0.0;
static double pa_dexvc = 0.0;
static double vent_dex = 0.0;
static double prob_icu_v = 0.0;
static double prob_icu_vr = 0.0;
static double prob_icu_r = 0.0;
static double prob_v_v = 0.0;
static double prob_v_r = 0.0;
static double prob_v_vr = 0.0;
static double pclin_v = 0.0;
static double pclin_vr = 0.0;
static double pclin_r = 0.0;
static double sigmaEV = 0.0;
static double sigmaER = 0.0;
static double sigmaEVR = 0.0;
static double sigmaR = 0.0;
static double vac_dur = 0.0;
static double vac_dur_r = 0.0;
static double report_natdeathI = 0.0;
static double report_natdeathCL = 0.0;
static double report_death_HC = 0.0;
static double reporth_ICU = 0.0;
static double pre = 0.0;
static double pdeath_vent_hc = 0.0;
static double pdeath_icu_hc = 0.0;
static double pdeath_icu_hco = 0.0;
static double reporth_g = 0.0;
static double seroneg = 0.0;
if (!is_initialised_parameters) {
// p = parameters["p"];
rho = parameters["rho"];
omega = parameters["omega"];
gamma = parameters["gamma"];
nui = parameters["nui"];
report = parameters["report"];
reportc = parameters["reportc"];
report_v = parameters["report_v"];
report_cv = parameters["report_cv"];
report_vr = parameters["report_vr"];
report_cvr = parameters["report_cvr"];
report_r = parameters["report_r"];
report_cr = parameters["report_cr"];
// reporth = parameters["reporth"];
beds_available = parameters["beds_available"];
icu_beds_available = parameters["icu_beds_available"];
ventilators_available = parameters["ventilators_available"];
nus = parameters["nus"];
rhos = parameters["rhos"];
// amp = parameters["amp"];
phi = parameters["phi"];
// ihr_scaling = parameters["ihr_scaling"];
give = parameters["give"];
pdeath_h = parameters["pdeath_h"];
pdeath_ho = parameters["pdeath_ho"];
pdeath_hc = parameters["pdeath_hc"];
pdeath_hco = parameters["pdeath_hco"];
pdeath_icu = parameters["pdeath_icu"];
pdeath_icuo = parameters["pdeath_icuo"];
pdeath_icuc = parameters["pdeath_icuc"];
pdeath_icuco = parameters["pdeath_icuco"];
pdeath_vent = parameters["pdeath_vent"];
pdeath_ventc = parameters["pdeath_ventc"];
nusc = parameters["nusc"];
nu_icu = parameters["nu_icu"];
nu_icuc = parameters["nu_icuc"];
nu_vent = parameters["nu_vent"];
nu_ventc = parameters["nu_ventc"];
pclin = parameters["pclin"];
prob_icu = parameters["prob_icu"];
prob_vent = parameters["prob_vent"];
//interventions
// self isolation
selfis_eff = parameters["selfis_eff"];
// social distance
dist_eff = parameters["dist_eff"];
// hand washing
hand_eff = parameters["hand_eff"];
// mask wearing
mask_eff = parameters["mask_eff"];
// working at home
work_eff = parameters["work_eff"];
w2h = parameters["w2h"];
// school closures
s2h = parameters["s2h"];
// cocooning the elderly
cocoon_eff = parameters["cocoon_eff"];
age_cocoon = parameters["age_cocoon"];
// vaccination
vaccine_eff = parameters["vaccine_eff"];
vaccine_eff_r = parameters["vaccine_eff_r"];
vac_campaign = parameters["vac_campaign"];
// imported cases
mean_imports = parameters["mean_imports"];
// screening
screen_test_sens = parameters["screen_test_sens"];
screen_overdispersion = parameters["screen_overdispersion"];
// quarantine
quarantine_days = parameters["quarantine_days"];
quarantine_effort = parameters["quarantine_effort"];
quarantine_eff_home = parameters["quarantine_eff_home"];
quarantine_eff_other = parameters["quarantine_eff_other"];
// lockdown
// mean household size
household_size = parameters["household_size"];
mass_test_sens = parameters["mass_test_sens"];
isolation_days = parameters["isolation_days"];
propo2 = parameters["propo2"];
pa_dexo2 = parameters["dexo2"];
pa_dexo2c = parameters["dexo2c"];
pa_dexv = parameters["dexv"];
pa_dexvc = parameters["dexvc"];
vent_dex = parameters["vent_dex"];
prob_icu_v = parameters["prob_icu_v"];
prob_icu_vr = parameters["prob_icu_vr"];
prob_icu_r = parameters["prob_icu_r"];
prob_v_v = parameters["prob_v_v"];
prob_v_r = parameters["prob_v_r"];
prob_v_vr = parameters["prob_v_vr"];
pclin_v = parameters["pclin_v"];
pclin_vr = parameters["pclin_vr"];
pclin_r = parameters["pclin_r"];
sigmaEV = parameters["sigmaEV"];
sigmaER = parameters["sigmaER"];
sigmaEVR = parameters["sigmaEVR"];
sigmaR = parameters["sigmaR"];
vac_dur = parameters["vac_dur"];
vac_dur_r = parameters["vac_dur_r"];
report_natdeathI = parameters["report_natdeathI"];
report_natdeathCL = parameters["report_natdeathCL"];
report_death_HC = parameters["report_death_HC"];
reporth_ICU = parameters["reporth_ICU"];
pre = parameters["pre"];
pdeath_vent_hc = parameters["pdeath_vent_hc"];
pdeath_icu_hc = parameters["pdeath_icu_hc"];
pdeath_icu_hco = parameters["pdeath_icu_hco"];
reporth_g = parameters["reporth_g"];
seroneg = parameters["seroneg"];
is_initialised_parameters=true;
}
// int A = 21;
// duration_a += high_resolution_clock::now()-start_a;
// auto start_b = high_resolution_clock::now();
int ii = 0;
arma::vec S = y.subvec(ii*A,(ii+1)*A-1); ii++;
arma::vec SR = y.subvec(ii*A,(ii+1)*A-1); ii++;
arma::vec E = y.subvec(ii*A,(ii+1)*A-1); ii++;
arma::vec I = y.subvec(ii*A,(ii+1)*A-1); ii++;
arma::vec R = y.subvec(ii*A,(ii+1)*A-1); ii++;
arma::vec X = y.subvec(ii*A,(ii+1)*A-1); ii++;
arma::vec H = y.subvec(ii*A,(ii+1)*A-1); ii++;
arma::vec HC = y.subvec(ii*A,(ii+1)*A-1); ii++;
arma::vec C = y.subvec(ii*A,(ii+1)*A-1); ii++;
arma::vec CM = y.subvec(ii*A,(ii+1)*A-1); ii++;
arma::vec V = y.subvec(ii*A,(ii+1)*A-1); ii++;
arma::vec QS = y.subvec(ii*A,(ii+1)*A-1); ii++;
arma::vec QSR = y.subvec(ii*A,(ii+1)*A-1); ii++;
arma::vec QE = y.subvec(ii*A,(ii+1)*A-1); ii++;
arma::vec QI = y.subvec(ii*A,(ii+1)*A-1); ii++;
arma::vec QR = y.subvec(ii*A,(ii+1)*A-1); ii++;
arma::vec CL = y.subvec(ii*A,(ii+1)*A-1); ii++;
arma::vec QC = y.subvec(ii*A,(ii+1)*A-1); ii++;
arma::vec ICU = y.subvec(ii*A,(ii+1)*A-1); ii++;
arma::vec ICUC = y.subvec(ii*A,(ii+1)*A-1); ii++;
arma::vec ICUCV = y.subvec(ii*A,(ii+1)*A-1); ii++;
arma::vec Vent = y.subvec(ii*A,(ii+1)*A-1); ii++;
arma::vec VentC = y.subvec(ii*A,(ii+1)*A-1); ii++;
arma::vec CMC = y.subvec(ii*A,(ii+1)*A-1); ii++;
arma::vec Z = y.subvec(ii*A,(ii+1)*A-1); ii++;
arma::vec EV = y.subvec(ii*A,(ii+1)*A-1); ii++;
arma::vec ER = y.subvec(ii*A,(ii+1)*A-1); ii++;
arma::vec EVR = y.subvec(ii*A,(ii+1)*A-1); ii++;
arma::vec VR = y.subvec(ii*A,(ii+1)*A-1); ii++;
arma::vec QV = y.subvec(ii*A,(ii+1)*A-1); ii++;
arma::vec QEV = y.subvec(ii*A,(ii+1)*A-1); ii++;
arma::vec QEVR= y.subvec(ii*A,(ii+1)*A-1); ii++;
arma::vec QER = y.subvec(ii*A,(ii+1)*A-1); ii++;
arma::vec QVR = y.subvec(ii*A,(ii+1)*A-1); ii++;
arma::vec HCICU = y.subvec(ii*A,(ii+1)*A-1); ii++;
arma::vec HCV = y.subvec(ii*A,(ii+1)*A-1); ii++;
arma::vec Ab = y.subvec(ii*A,(ii+1)*A-1); ii++;
// Zindex<-(22*A+1):(23*A)
// Rcout << "cpp: ii: "<<ii<<"\n";
// Rcout << "cpp: 1\n";
arma::vec P = (S+SR+E+I+R+X+Z+V+H+HC+ICU+ICUC+ICUCV+Vent+VentC+EV+ER+EVR+VR+HCICU+HCV+
QS+QSR+QE+QI+QR+CL+QC+QEV+QV+QER+QEVR+QVR);
// Rcout << "cpp: 1.1\n";
double Q = double((sum(QS)+sum(QSR)+sum(QE)+sum(QI)+sum(QC)+sum(QR)+sum(QV)+sum(QER)+sum(QEVR)+sum(QEV)+sum(QVR)))/double(sum(P));
// Rcout << "Q=" << Q << "\n";
// Environment base = Environment("package:base");
// Function readline = base["readline"];
// Function as_numeric = base["as.numeric"];
// if (ask_input) {
// int drink = as<int>(as_numeric(readline("input: ")));
// if (drink == 4) {
// ask_input=false;
// }
// }
// duration_b += high_resolution_clock::now()-start_b;
// auto start_c = high_resolution_clock::now();
// health system performance
if (!is_initialised_splinefun) {
NumericVector f = {1.0,(1.0+give)/2.0,(1.0-give)/2.0,0.0};
double KH = beds_available;
double KICU = icu_beds_available + ventilators_available;
double Kvent = ventilators_available;
NumericVector xH = {0.0,(1.0+give)*KH/2.0,(3.0-give)*KH/2.0,2.0*KH};
NumericVector xICU = {0.0,(1.0+give)*KICU/2.0,(3.0-give)*KICU/2.0,2.0*KICU};
NumericVector xVent = {0.0,(1.0+give)*Kvent/2.0,(3.0-give)*Kvent/2.0,2.0*Kvent};
// double critH = std::min(1.0 - SplineFun(xH, f,sum(H)+sum(ICUC)+sum(ICUCV)),1.0);
// double crit = std::min(1.0-SplineFun(xICU, f,sum(ICU)+sum(Vent)+sum(VentC)),1.0);
// double critV = std::min(1.0-SplineFun(xVent, f,sum(Vent)),1.0);
init_splinefun(xH, xICU, xVent, f);
}
double sum_H=sum(H);
double sum_ICUC=sum(ICUC);
double sum_ICUCV=sum(ICUCV);
double sum_ICU=sum(ICU);
double sum_Vent=sum(Vent);
double sum_VentC=sum(VentC);
// double critH = std::min(1.0 - SplineFun(xH, f,sum_H+sum_ICUC+sum_ICUCV),1.0);
// double crit = std::min(1.0-SplineFun(xICU, f,sum_ICU+sum_Vent+sum_VentC),1.0);
// double critV = std::min(1.0-SplineFun(xVent, f,sum_Vent),1.0);
double critH = std::min(1.0 - as<double>(splinefun_H(sum_H+sum_ICUC+sum_ICUCV)), 1.0);
double crit = std::min(1.0 - as<double>(splinefun_ICU(sum_ICU+sum_Vent+sum_VentC)), 1.0);
double critV = std::min(1.0 - as<double>(splinefun_Vent(sum_Vent)),1.0);
int to_keep = 10000000;
critH = round(critH * to_keep) / to_keep;
crit = round(crit * to_keep) / to_keep;
critV = round(critV * to_keep) / to_keep;
// if (t == (int)t) {
// Rcout << "t=" << t
// << std::setprecision(15)
// << ", " << critH
// << ", " << crit
// << ", " << critV << "\n";
// }
// interventions
// int isolation = (t>=selfis_on)*(t<=selfis_on+selfis_dur);
// int distancing = (t>=dist_on)*(t<=(dist_on+dist_dur));
// int handwash = (t>=hand_on)*(t<=(hand_on+hand_dur));
// int workhome = (t>=work_on)*(t<=(work_on+work_dur));
// int schoolclose = (t>=school_on)*(t<=(school_on+school_dur));
// int cocoon = (t>=cocoon_on)*(t<=(cocoon_on+cocoon_dur))*cocoon_cov;
// int vaccine = (t>=(vaccine_on))*(t<=vaccine_on+vac_campaign);
// int travelban = (t>=travelban_on)*(t<=(travelban_on+travelban_dur));
// int screen = (t>=screen_on)*(t<=(screen_on+screen_dur));
// int quarantine = (t>=quarantine_on)*(t<=(quarantine_on+quarantine_dur));
// int lockdown_low = (t>=lockdown_low_on)*(t<=(lockdown_low_on+lockdown_low_dur));
// int lockdown_mid = (t>=lockdown_mid_on)*(t<=(lockdown_mid_on+lockdown_mid_dur));
// int lockdown_high = (t>=lockdown_high_on)*(t<=(lockdown_high_on+lockdown_high_dur));
int my_t = t*20;
int isolation = as<NumericVector>(input["isolation"])[my_t];
int distancing = as<NumericVector>(input["distancing"])[my_t];
int handwash = as<NumericVector>(input["handwash"])[my_t];
int masking = as<NumericVector>(input["masking"])[my_t];
int workhome = as<NumericVector>(input["workhome"])[my_t];
int schoolclose = as<NumericVector>(input["schoolclose"])[my_t];
int schoolclosep = as<NumericVector>(input["schoolclosepartial"])[my_t];
// int cocoon = as<NumericVector>(input["cocoon"])[my_t];
int vaccine = as<NumericVector>(input["vaccine"])[my_t];
int travelban = as<NumericVector>(input["travelban"])[my_t];
int screen = as<NumericVector>(input["screen"])[my_t];
int quarantine = as<NumericVector>(input["quarantine"])[my_t];
// int lockdown_low = as<NumericVector>(input["lockdown_low"])[my_t];
// int lockdown_mid = as<NumericVector>(input["lockdown_mid"])[my_t];
// int lockdown_high = as<NumericVector>(input["lockdown_high"])[my_t];
int masstesting = as<NumericVector>(input["masstesting"])[my_t];
int dexamethasone = as<NumericVector>(input["dex"])[my_t];
int pmod = as<NumericVector>(input["pmod"])[my_t];
int dmod = as<NumericVector>(input["dmod"])[my_t];
int cmod = as<NumericVector>(input["cmod"])[my_t];
double screen_eff = 0.0;
double selfis = 0.0;
double school = 1.0;
double school2 = 1.0;
double dist = 1.0;
double hand = 0.0;
double mask = 0.0;
double vaccinate = 0.0;
double trvban_eff = 0.0;
double quarantine_rate = 0.0;
double rate_q = 0.0;
double work;
double vac_rate;
double selfis_cov = (as<NumericVector>(input["si_vector"])[my_t])/100.0;
double screen_contacts = (as<NumericVector>(input["scr_vector"])[my_t])/10.0;
double school_eff = (as<NumericVector>(input["sc_vector"])[my_t])/100.0;
double school_effp = (as<NumericVector>(input["scp_vector"])[my_t])/100.0;
double dist_cov = (as<NumericVector>(input["sd_vector"])[my_t])/100.0;
double hand_cov = (as<NumericVector>(input["hw_vector"])[my_t])/100.0;
double mask_cov = (as<NumericVector>(input["msk_vector"])[my_t])/100.0;
double cocoon = (as<NumericVector>(input["cte_vector"])[my_t])/100.0;
double work_cov = (as<NumericVector>(input["wah_vector"])[my_t])/100.0;
double travelban_eff = (as<NumericVector>(input["tb_vector"])[my_t])/100.0;
double vaccine_cov = (as<NumericVector>(input["vc_vector"])[my_t])/100.0;
// vaccine_covp
double quarantine_cov = (as<NumericVector>(input["q_vector"])[my_t])/100.0;
double tests_per_day = (as<NumericVector>(input["mt_vector"])[my_t]);
// double min_age_testing = floor((as<NumericVector>(input["minas_vector"])[my_t])/5.0 + 1.0);
// double max_age_testing = floor((as<NumericVector>(input["maxas_vector"])[my_t])/5.0 + 1.0);
// double min_age_vaccine = floor((as<NumericVector>(input["minav_vector"])[my_t])/5.0 + 1.0);
// double max_age_vaccine = floor((as<NumericVector>(input["maxav_vector"])[my_t])/5.0 + 1.0);
int vaccineage = as<NumericVector>(input["vaccineage"])[my_t];
// vaccineagep
int testage = as<NumericVector>(input["testage"])[my_t];
double dmod_vector = as<NumericVector>(input["dmod_vector"])[my_t];
double pmod_vector = as<NumericVector>(input["pmod_vector"])[my_t];
double cmod_vector = as<NumericVector>(input["cmod_vector"])[my_t]/100.0;
double dm = 1.0;
double pm = 1.0;
double sigmaR_mod = sigmaR;
// double sig = sigmaR;
if (dmod) {
dm = dmod_vector;
}
if (pmod) {
pm = pmod_vector;
}
if (cmod) {
sigmaR_mod = cmod_vector;
}
// arma::vec age_testing_vector = arma::join_cols(
// arma::vec(min_age_testing-1, arma::fill::zeros),
// arma::vec(max_age_testing-min_age_testing+1, arma::fill::ones),
// arma::vec(A-max_age_testing, arma::fill::zeros)
// );
arma::vec age_vaccine_vector = arma::vec(A, arma::fill::zeros);
if (vaccine) {
// age_vaccine_vector = arma::join_cols(
// arma::vec(min_age_vaccine-1, arma::fill::zeros),
// arma::vec(max_age_vaccine-min_age_vaccine+1, arma::fill::ones),
// arma::vec(A-max_age_vaccine, arma::fill::zeros)
// );
age_vaccine_vector = as<arma::vec>(age_group_vectors[vaccineage-1]);
vac_rate = -log(1.0-vaccine_cov)/vac_campaign;
vaccinate = vac_rate;
// if (t < 0.1){
// Rcout << "age_vaccine_vector\n" << age_vaccine_vector << "\n";
// Rcout << "t\n" << t << "\n";
// }
}
// Rcout << "cpp: 2\n";
arma::vec age_testing_vector = arma::vec(A, arma::fill::zeros);
if (masstesting) {
age_testing_vector = as<arma::vec>(age_group_vectors[testage-1]);
}
arma::vec schoolclose2 = arma::vec(A, arma::fill::zeros);
// if (schoolclose >= 1) {
// school = school_eff;
// schoolclose2 = as<arma::vec>(age_group_vectors[schoolclose-1]);
// }
arma::vec schoolclose2p = arma::vec(A, arma::fill::zeros);
arma::vec schoolclose3 = arma::vec(A, arma::fill::zeros);
arma::vec schoolclose4 = arma::vec(A, arma::fill::zeros);
school = school_eff;
school2 = school_effp;
if (schoolclose >=1) {
schoolclose2 = as<arma::vec>(age_group_vectors[schoolclose-1]);
}
if (schoolclosep >= 1) {
schoolclose2p = as<arma::vec>(age_group_vectors[schoolclosep-1]);
}
schoolclose3 = arma::max(school * schoolclose2, school2 * schoolclose2p);
schoolclose4 = arma::max((1-school) * schoolclose2, (1-school2) * schoolclose2p);
if (workhome){
work = work_cov*work_eff;
}else{work = 1.0;}
if (isolation){
selfis = selfis_cov;
if(screen){
// screen_eff = MIN((report*I + reportc*CL + H+ICU+Vent+ reporth*HC + ICUC+VentC) *screen_contacts*(screen_overdispersion*I/P)*screen_cov/P,1.0);
screen_eff = MIN(sum(report*I + reportc*CL + H+ICU+Vent+ reporth*(HC+ICUC+ICUCV+VentC+HCICU+HCV)) *screen_contacts*(screen_overdispersion*I/P)*screen_test_sens/P,1.0);
}
}
if(distancing){
dist = dist_cov*dist_eff;
}
if(handwash){
hand = hand_eff*hand_cov;
}
if (masking) {
mask = mask_eff*mask_cov;
}
if(travelban){
trvban_eff = travelban_eff;
}
if(quarantine){
rate_q = std::min(std::min(sum((CL+H+ICU+Vent+HC+ICUC+ICUCV+VentC+HCV+HCICU))*(household_size-1.0)/sum(P),1.0) * quarantine_effort, quarantine_cov/2.0);
quarantine_rate = rate_q/(1.0+exp(-10.0*(quarantine_cov/2.0-Q)));
}
double prob_v;
double dexo2;
double dexo2c;
double dexv;
double dexvc;
if (dexamethasone) {
prob_v = prob_vent*vent_dex;
dexo2 = pa_dexo2;
dexo2c = pa_dexo2c;
dexv = pa_dexv;
dexvc = pa_dexvc;
} else {
prob_v = prob_vent;
dexo2 = 1.0;
dexo2c = 1.0;
dexv = 1.0;
dexvc = 1.0;
}
// testing rates
double sum_I = sum(I);
double sum_P = sum(P);
double sum_CL = sum(CL);
double sum_E = sum(E);
double sum_EV = sum(EV);
double sum_ER = sum(ER);
double sum_EVR = sum(EVR);
double sum_HC = sum(HC);
double sum_HCICU = sum(HCICU);
double sum_HCV = sum(HCV);
double propI = sum_I/sum_P;
double propC = sum_CL/sum_P;
double propE = sum_E/sum_P;
double propEV = sum_EV/sum_P;
double propER = sum_ER/sum_P;
double propEVR = sum_EVR/sum_P;
double propHC = sum_HC/sum_P;
double propHCICU = sum_HCICU/sum_P;
double propHCV = sum_HCV/sum_P;
double testE = tests_per_day * propE;
double testEV = tests_per_day * propEV;
double testER = tests_per_day * propER;
double testEVR = tests_per_day * propEVR;
double testI = tests_per_day * propI;
double testC = tests_per_day * propC;
double testHC = tests_per_day * propHC;
double testHCICU = tests_per_day * propHCICU;
double testHCV = tests_per_day * propHCV;
double ratetestI = 0.0;
double ratetestC = 0.0;
double ratetestE = 0.0;
double ratetestEV = 0.0;
double ratetestER = 0.0;
double ratetestEVR = 0.0;
double ratetestHC = 0.0;
double ratetestHCICU = 0.0;
double ratetestHCV = 0.0;
if(sum_I > 1){
ratetestI = mass_test_sens * testI / sum_I;
}
if(sum_CL > 1){
ratetestC = mass_test_sens * testC / sum_CL;
}
if(sum_E > 1){
ratetestE = mass_test_sens * testE / sum_E;
}
if(sum_EV > 1){
ratetestEV = mass_test_sens * testEV / sum_EV;
}
if(sum_ER > 1){
ratetestER = mass_test_sens * testER / sum_ER;
}
if(sum_EVR > 1){
ratetestEVR = mass_test_sens * testEVR / sum_EVR;
}
if(sum_HC > 1){
ratetestHC = mass_test_sens * testHC / sum_HC;
}
if(sum_HCICU > 1){
ratetestHCICU = mass_test_sens * testHCICU / sum_HCICU;
}
if(sum_HCV > 1){
ratetestHCV = mass_test_sens * testHCV / sum_HCV;
}
// cocooning the elderly
// arma::mat cocoon_mat(21,21);
arma::mat cocoon_mat(A,A);
cocoon_mat.fill((1.0-cocoon_eff));
arma::mat cc_sub(age_cocoon-1,age_cocoon-1);
cc_sub.fill(1.0);
cocoon_mat.submat(0,0,cc_sub.n_rows-1,cc_sub.n_rows-1) = cc_sub;
// arma::mat contact_home = getVarmat("contact_home");
// arma::mat contact_other = getVarmat("contact_other");
// arma::mat contact_school = getVarmat("contact_school");
// arma::mat contact_work = getVarmat("contact_work");
// contact matrices
arma::mat cts = (contact_home+distancing*(1.0-dist)*contact_other+(1.0-distancing)*contact_other
+(1.0-schoolclose3)%contact_school.each_col() //# school on
+schoolclose4%contact_school.each_col() //# school close
+(schoolclose3%contact_home.each_col())*s2h //# inflating contacts at home when school closes
+(1.0-workhome)*contact_work //# normal work
+workhome*(1.0-work)*contact_work //# people not working from home when homework is active
+contact_home*workhome*work*w2h //# inflating contacts at home when working from home
);
// Final transmission related parameters
arma::mat contacts = (1.0-cocoon)*cts+cocoon*cts%cocoon_mat+(cocoon*(1.0+schoolclose3*(1.0-school_eff)+workhome*(1.0-work_eff))%contact_home.each_col())%(1.0-cocoon_mat);
double seas = 1.0+amp*cos(2.0*3.14*(t-(phi*365.25/12.0))/365.25);
double importation = mean_imports*(1.0-trvban_eff);
arma::vec HH = H+ICU+Vent+ICUC+ICUCV+VentC;
arma::vec HHC = HC+HCICU+HCV;
// std::cout << "std::max(hand,mask)=" << std::max(hand,mask) << "\n";
arma::vec lam = (1.0-std::max(hand,mask))*p*pm*seas*(contacts*((rho*E+(I+CL+importation)+(1.0-selfis_eff)*(X+HHC)+rhos*(HH))/P))
+ (1.0-std::max(hand,mask))*p*pm*seas*(1.0-quarantine*quarantine_eff_other)*(contact_other*((rho*QE+QI+QC+QEV+QEVR+QER)/P));
// # contacts under home quarantine
arma::vec lamq = (1.0-std::max(hand,mask))*p*pm*seas*((1.0-quarantine_eff_home)*contact_home*(((1.0-selfis_eff)*(X+HHC+rho*QE+QI+QC+QEV+QEVR+QER))/P))
+ (1.0-std::max(hand,mask))*p*pm*seas*(1.0-quarantine_eff_other)*(contact_other*((rho*E+(I+CL+importation)+(1.0-selfis_eff)*(X+HHC+rho*QE+QI+QC+QEV+QEVR+QER)+rhos*(HH))/P));
// if (t < 0.4){
// // Rcout << std::setprecision(15) << "lam:" << lam << "lam[0]:" << lam[0] << "\n";
// // Rcout << std::setprecision(15) << "lamq:" << lamq << "lamq[0]:" << lamq[0] << "\n";
// Rcout << std::setprecision(15) << "vaccinate:" << vaccinate << "\n";
// }
// # birth/death
double b1 = sum(popbirth_col2 % popstruc_col2);
arma::vec birth = 0.0*popbirth_col2;
birth(0) = b1;
// Rcout << "cpp: before ODE sys\n";
//# ODE system
arma::vec dSdt = -S%lam
- vaccinate*age_vaccine_vector%S
+ vac_dur*V
+ ageing*S
- mort_col%S
+ birth
- quarantine_rate*S
+ (1.0/quarantine_days)*QS
;
arma::vec dSRdt = -SR%lam
+ omega*R
- quarantine_rate*SR
+ (1.0/quarantine_days)*QSR
+ ageing*SR
- mort_col%SR
;
arma::vec dEdt = S%lam
+ SR%lam
- gamma*E
+ ageing*E
- vaccinate*age_vaccine_vector%E
- mort_col%E
- quarantine_rate*E
+ (1.0/quarantine_days)*QE
;
arma::vec dIdt = gamma*(1.0-pclin )*(1.0-screen_eff)*(1.0-ihr_col2)%(1.0-age_testing_vector*ratetestE)%E
+ gamma*(1.0-pclin_v )*(1.0-screen_eff)*(1.0-sigmaEV *ihr_col2)%(1.0-age_testing_vector*ratetestEV )%EV
+ gamma*(1.0-pclin_vr)*(1.0-screen_eff)*(1.0-sigmaEVR*ihr_col2)%(1.0-age_testing_vector*ratetestEVR)%EVR
+ gamma*(1.0-pclin_r )*(1.0-screen_eff)*(1.0-sigmaER *ihr_col2)%(1.0-age_testing_vector*ratetestER )%ER
- vaccinate*age_vaccine_vector%I
- nui*I
+ ageing*I
- mort_col%I
+ (1.0/quarantine_days)*QI
- quarantine_rate*I
- ratetestI*age_testing_vector%I
;
arma::vec dCLdt = gamma*pclin*(1.0-age_testing_vector*ratetestE)*(1.0-selfis)%(1.0-ihr_col2)*(1.0-quarantine_rate)%E
+ gamma*pclin_v *(1.0-age_testing_vector*ratetestEV )*(1.0-selfis)%(1.0-sigmaEV* ihr_col2)*(1.0-quarantine_rate)%EV
+ gamma*pclin_vr*(1.0-age_testing_vector*ratetestEVR)*(1.0-selfis)%(1.0-sigmaEVR*ihr_col2)*(1.0-quarantine_rate)%EVR
+ gamma*pclin_r *(1.0-age_testing_vector*ratetestER )*(1.0-selfis)%(1.0-sigmaER* ihr_col2)*(1.0-quarantine_rate)%ER
- nui*CL+ageing*CL
- mort_col%CL
+ (1.0/quarantine_days)*QC
- ratetestC*age_testing_vector%CL
;
arma::vec dRdt = nui*I
+ nui*X
+ nui*CL
+ ageing*R
- mort_col%R
+ (1.0/isolation_days)*Z
+ (1.0/quarantine_days)*QR
+ nus*propo2*(1.0-dexo2*pdeath_ho*dm)*ifr_col2%H
+ nus*(1.0-propo2)*(1.0-pdeath_h*dm)*ifr_col2%H
+ nusc*propo2*(1.0-pdeath_hco*dm)*ifr_col2%HC
+ nusc*(1.0-propo2)*(1.0-pdeath_hc*dm)*ifr_col2%HC
+ nusc*propo2*(1.0-pdeath_icu_hco*dm)*ifr_col2%HCICU
+ nusc*(1.0-propo2)*(1.0-pdeath_icu_hc*dm)*ifr_col2%HCICU
+ nu_icu*propo2*(1.0-dexo2*pdeath_icuo*dm)*ifr_col2%ICU
+ nu_icu*(1.0-propo2)*(1.0-pdeath_icu*dm)*ifr_col2%ICU
+ nu_icuc*propo2*(1.0-dexo2c*pdeath_icuco*dm)*ifr_col2%ICUC
+ nu_icuc*(1.0-propo2)*(1.0-pdeath_icuc*dm)*ifr_col2%ICUC
+ nu_vent*(1.0-dexv*pdeath_vent*dm)*ifr_col2%Vent
+ nu_ventc*(1.0-pdeath_vent_hc*dm)*ifr_col2%HCV
+ nu_ventc*(1.0-dexvc*pdeath_ventc*dm)*ifr_col2%VentC
+ nu_ventc*(1.0-dexvc*pdeath_ventc*dm)*ifr_col2%ICUCV
+ vac_dur_r*VR
- omega*R
- vaccinate*age_vaccine_vector%R
- lam*sigmaR_mod%R
- quarantine_rate*R
;
arma::vec dXdt = (gamma*selfis*(1.0-age_testing_vector*ratetestE)*pclin%(1.0-ihr_col2))%E
+ (gamma*(1.0-pclin)*(1.0-age_testing_vector*ratetestE)*screen_eff%(1.0-ihr_col2))%E
- nui*X
+ ageing*X
- mort_col%X
+ gamma*selfis *(1.0-age_testing_vector*ratetestEV) *pclin_v %(1.0-sigmaEV*ihr_col2 )%EV
+ gamma*(1.0-pclin_v) *(1.0-age_testing_vector*ratetestEV) *screen_eff%(1.0-sigmaEV*ihr_col2 )%EV
+ gamma*selfis *(1.0-age_testing_vector*ratetestEVR)*pclin_v %(1.0-sigmaEVR*ihr_col2)%EVR
+ gamma*(1.0-pclin_vr)*(1.0-age_testing_vector*ratetestEVR)*screen_eff%(1.0-sigmaEVR*ihr_col2)%EVR
+ gamma*selfis *(1.0-age_testing_vector*ratetestER) *pclin_r %(1.0-sigmaER*ihr_col2 )%ER
+ gamma*(1.0-pclin_r) *(1.0-age_testing_vector*ratetestER) *screen_eff%(1.0-sigmaER*ihr_col2 )%ER
;
arma::vec dVdt = vaccinate*age_vaccine_vector%S
- ((1.0-vaccine_eff)*lam)%V
+ ageing*V
- mort_col%V
+ omega*VR
- vac_dur*V
- quarantine_rate*V
;
arma::vec dEVdt = (1.0-vaccine_eff)*lam%V
- gamma*EV
+ ageing*EV
- mort_col%EV
- quarantine_rate*EV
+ (1.0/quarantine_days)*QEV
;
arma::vec dERdt = lam*sigmaR_mod%R
- gamma*ER
+ ageing*ER
- mort_col%ER
- quarantine_rate*ER
+ (1.0/quarantine_days)*QER
;
arma::vec dVRdt = vaccinate*age_vaccine_vector%E
+ vaccinate*age_vaccine_vector%I
+ vaccinate*age_vaccine_vector%R
- (1.0-vaccine_eff_r)*lam%VR
- vac_dur_r*VR
+ ageing*VR
- mort_col%VR
- omega*VR
- quarantine_rate*VR
+ (1.0/quarantine_days)*QVR
;
arma::vec dEVRdt= (1.0-vaccine_eff_r)*lam%VR
- gamma*EVR
+ ageing*EVR
- mort_col%EVR
- quarantine_rate*EVR
+ (1.0/quarantine_days)*QEVR
;
arma::vec dQSdt = quarantine_rate*S+ ageing*QS-mort_col%QS - (1.0/quarantine_days)*QS - lamq%QS;
arma::vec dQEdt = quarantine_rate*E - gamma*QE + ageing*QE-mort_col%QE - (1.0/quarantine_days)*QE
+ lamq%QS
+ lamq%QSR
;
arma::vec dQSRdt = quarantine_rate*SR + ageing*QSR - mort_col%QSR - (1.0/quarantine_days)*QSR
- lamq%QSR
;
arma::vec dQIdt = quarantine_rate*I
+ (gamma*(1.0-ihr_col2)*(1.0-pclin))%QE
- nui*QI
+ ageing*QI
- mort_col%QI
- (1.0/quarantine_days)*QI
+ gamma*(1.0-sigmaEV*ihr_col2 )*(1.0-pclin_v )%QEV
+ gamma*(1.0-sigmaER*ihr_col2 )*(1.0-pclin_r )%QER
+ gamma*(1.0-sigmaEVR*ihr_col2)*(1.0-pclin_vr)%QEVR
;
arma::vec dQCdt = (gamma*pclin*(1.0-selfis)*(1.0-age_testing_vector*ratetestE)%(1.0-ihr_col2))*quarantine_rate%E
+ (gamma*(1.0-ihr_col2))%(pclin*QE)
- nui*QC
+ ageing*QC-mort_col%QC
- (1.0/quarantine_days)*QC
+ gamma*pclin_v *(1.0-age_testing_vector*ratetestEV) *(1.0-selfis)%(1.0-sigmaEV *ihr_col2)*quarantine_rate%EV
+ gamma*pclin_vr*(1.0-age_testing_vector*ratetestEVR)*(1.0-selfis)%(1.0-sigmaEVR*ihr_col2)*quarantine_rate%EVR
+ gamma*pclin_r *(1.0-age_testing_vector*ratetestER) *(1.0-selfis)%(1.0-sigmaER *ihr_col2)*quarantine_rate%ER
+ gamma*(1.0-sigmaEV* ihr_col2)*pclin_v %QEV
+ gamma*(1.0-sigmaER* ihr_col2)*pclin_r %QER
+ gamma*(1.0-sigmaEVR*ihr_col2)*pclin_vr%QEVR
;
arma::vec dQRdt = nui*QI
+ nui*QC
+ ageing*QR
- mort_col%QR
- (1.0/quarantine_days)*QR
- sigmaR_mod*lamq%QR