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main.cpp
1793 lines (1618 loc) · 63.5 KB
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main.cpp
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#include <stdio.h>
#include <fstream>
#include <iostream>
#include <vector>
#include <algorithm>
#include <boost/numeric/odeint.hpp>
using namespace std;
using namespace boost::numeric::odeint;
typedef std::vector< double > state_type;
typedef vector<vector<double> > data_type;
void simulation();
void fast_analysis();
void optimisation();
void P3P4_betas();
void compliance();
void vary_Re_P1();
void vary_Re_P2();
void immunity();
void write_simulation(string filename, const data_type &y_vec, const data_type &betas, int v_comps, int h_comps, int r_comps);
void write_phase_matrices(const data_type &beta_ph0,const data_type &beta_ph1,const data_type &beta_ph2,const data_type &beta_ph3);
void write_fast_results(const data_type &fast_results);
void write_optimisations(data_type optim_results);
//Write a vector<vector<class T> > to an output stream. Output is formatted as a matrix.
template < class T >
std::ostream& operator << (std::ostream& os, const std::vector<std::vector<T> >& v)
{
for (typename std::vector<std::vector<T> >::const_iterator i = v.begin(); i != v.end(); ++i){
for (typename std::vector<T>::const_iterator ii = i->begin(); ii != i->end(); ++ii)
{
if (ii == i->begin()){
os << *ii;
} else {
os << "," << *ii;
}
}
os << "\n";
}
return os;
}
template < class T >
std::ostream& operator << (std::ostream& os, const std::vector<T> & v)
{
for (typename std::vector<T>::const_iterator i = v.begin(); i != v.end(); ++i){
if (i == v.begin()){
os << *i;
} else {
os << "," << *i;
}
}
//os << "\n";
return os;
}
double GenTime(double T2, double R0){
double G = T2 * ((R0-1)/log(2));
return(G);
}
data_type parse2DCsvFile(string inputFileName) {
data_type data;
ifstream inputFile(inputFileName);
int l = 0;
while (inputFile) {
l++;
string s;
if (!getline(inputFile, s)) break;
if (s[0] != '#') {
istringstream ss(s);
vector<double> record;
while (ss) {
string line;
if (!getline(ss, line, ','))
break;
try {
record.push_back(stof(line));
}
catch (const std::invalid_argument e) {
cout << "NaN found in file " << inputFileName << " line " << l
<< endl;
e.what();
}
}
data.push_back(record);
}
}
if (!inputFile.eof()) {
cerr << "Could not read file " << inputFileName << "\n";
__throw_invalid_argument("File not found.");
}
return data;
}
double linearBeta(double time, double betaBegin, double betaEnd, double timeBegin, double duration){
double inc = (betaEnd - betaBegin) / duration;
double betaOut = betaBegin + inc * (time - timeBegin);
return(betaOut);
}
data_type calc_beta_3Comp_taper(double t, int num_comps, vector<double> sd, data_type beta_ph0,data_type beta_ph1,data_type beta_ph2,data_type beta_ph3 ){
data_type result;
if (t<=sd[0]){
result = beta_ph0;
} else if ((t>sd[0]) && (t<=sd[1])){
result = beta_ph1;
} else if((t>sd[1]) && (t<=sd[2])) {
for (int i=0; i<num_comps; ++i){
vector<double> temp;
for (int j=0; j<num_comps; ++j){
temp.push_back(linearBeta(t, beta_ph1[i][j], beta_ph2[i][j], sd[1],sd[2]-sd[1]));
}
result.push_back(temp);
}
} else if(t>sd[2] && (t<=sd[3])) {
result = beta_ph3;
} else if(t>sd[3]){
result = beta_ph3;
}
return result;
}
class SIRS_3Comp
{
int m_num_comps;
double m_gamma, m_omega,m_sd1, m_sd2, m_sd3, m_sd4;
data_type m_beta_ph0,m_beta_ph1,m_beta_ph2,m_beta_ph3;
vector<double> m_fj;
public:
SIRS_3Comp(int num_comps, double gamma, double omega, double sd1, double sd2, double sd3,double sd4, data_type beta_ph0,data_type beta_ph1,data_type beta_ph2,data_type beta_ph3, vector<double> fj):
m_num_comps(num_comps), m_gamma(gamma), m_omega(omega), m_sd1(sd1), m_sd2(sd2),m_sd3(sd3),m_sd4(sd4),m_beta_ph0(beta_ph0),m_beta_ph1(beta_ph1),m_beta_ph2(beta_ph2),m_beta_ph3(beta_ph3),m_fj(fj) {}
void operator() (const state_type &y, state_type &f, const double t)
{
data_type m_beta = calc_beta_3Comp_taper(t, m_num_comps, {m_sd1,m_sd2,m_sd3,m_sd4}, m_beta_ph0, m_beta_ph1,m_beta_ph2,m_beta_ph3);
for (int i=0;i<m_num_comps;++i){
double sum_beta=0;
for (int j=0;j<m_num_comps; ++j){
sum_beta += m_beta[i][j]*y[i]*y[j+m_num_comps];
}
f[i] = -1.0*sum_beta + m_omega*y[i+(2*m_num_comps)];
f[i+m_num_comps] = sum_beta - m_gamma*y[i+m_num_comps];
f[i+(2*m_num_comps)] = m_gamma*y[i+m_num_comps] - m_omega*y[i+(2*m_num_comps)];
f[i+(3*m_num_comps)] = sum_beta;
}
}
};
struct push_back_state_and_time
{
vector< state_type >& m_states;
vector< double >& m_times;
vector< double > m_fj;
int m_num_comp;
push_back_state_and_time(vector< state_type > &states , vector< double > ×, vector<double> fj, int num_comp)
: m_states( states ) , m_times( times ), m_fj(fj), m_num_comp(num_comp) { }
void operator()( const state_type &x , double t )
{
state_type x1 = x;
x1.insert(x1.begin(),t);
m_states.push_back( x1 );
m_times.push_back( t );
}
};
struct push_back_state_time_pIv_pIh_pIr
{
vector< state_type >& m_states;
vector< double >& m_times;
vector< double > m_fj;
int m_v_comps, m_h_comps, m_r_comps, m_n_comp;
push_back_state_time_pIv_pIh_pIr(vector< state_type > &states , vector< double > ×, vector<double> fj, int v_comps,int h_comps, int r_comps)
: m_states( states ) , m_times( times ), m_fj(fj), m_v_comps(v_comps), m_h_comps(h_comps), m_r_comps(r_comps), m_n_comp(v_comps+h_comps+r_comps) { }
void operator()( const state_type &x , double t )
{
state_type x1 = x;
x1.insert(x1.begin(),t);
//insert sum of comps
//I_comps start at i=n_comp, the first v_comp are Iv, then h_comp Ih and lastly r_comp Ir.
double cumIv,Iv, Ih, Ir;
cumIv = accumulate(x.begin()+3*m_n_comp, x.begin()+3*m_n_comp+m_v_comps, 0.0);
Iv = accumulate(x.begin()+m_n_comp, x.begin()+m_n_comp+m_v_comps, 0.0);
Ih = accumulate(x.begin()+m_n_comp+m_v_comps, x.begin()+m_n_comp+m_v_comps+m_h_comps, 0.0);
Ir = accumulate(x.begin()+m_n_comp+m_v_comps+m_h_comps, x.begin()+m_n_comp+m_n_comp, 0.0);
x1.insert(x1.end(), {cumIv, Iv/m_fj[0],Ih/m_fj[1],Ir/m_fj[2]});
m_states.push_back( x1 );
m_times.push_back( t );
}
};
struct push_back_time_Iv_prop
{
state_type & m_states;
std::vector< double >& m_times;
push_back_time_Iv_prop(state_type &states , vector< double > × )
: m_states( states ) , m_times( times ) { }
void operator()( const state_type &x , double t )
{
m_states.push_back( (x[2]) );
m_times.push_back( t );
}
};
int main(int /* argc */ , char** /* argv */ )
{
simulation();
//fast_analysis();
//optimisation();
//P3P4_betas();
//compliance();
//vary_Re_P1();
//vary_Re_P2();
//immunity();
return 0;
}
void simulation(){
double omega;
double sd1 = 0, sd2 = 0, sd3 = 0,sd4=0;
int simtime;
string output_dir, filename;
double R0 = 2.8;
double T2 = 3.3;
double gamma = 1.0/GenTime(T2,R0);
double beta1_ph0 = 1.7*gamma;
double beta2_ph0 = 1.7*gamma;
double beta3_ph0 = 1.7*gamma;
double beta4_ph0 = 1.7*gamma;
double beta1_ph1 = 0.8*gamma;
double beta2_ph1 = 0.9*gamma;
double beta3_ph1 = 0.9*gamma;
double beta4_ph1 = 0.8*gamma;
double beta1_ph2 = 0.4*gamma;
double beta2_ph2 = 1.85*gamma;
double beta3_ph2 = 2.25*gamma;
double beta4_ph2 = 0.4*gamma;
double beta1_ph3 = 0.4*gamma;
double beta2_ph3 = 1.85*gamma;
double beta3_ph3 = 2.25*gamma;
double beta4_ph3 = 0.4*gamma;
int n_comp=5;
//2-2-96 -> 1v-1v-48r
//8-8-84 -> 4v-4h-42r
//14-14-72 -> 7v-7h-36r
//20-20-60 -> 10v-10h-30r or 1v-1h-3r
//20-40-40 -> 1v-2h-2r
//20-10-70 -> 2v-1h-7r
vector<double> fj = {0.2,0.2,0.6};
int v_comps = 1;
int h_comps = 1;
int r_comps = n_comp - v_comps - h_comps;
double fv_per_comp = fj[0]/v_comps;
double fh_per_comp = fj[1]/h_comps;
double fr_per_comp = fj[2]/r_comps;
data_type beta_ph0(n_comp, vector<double>(n_comp,0)),beta_ph1(n_comp, vector<double>(n_comp,0)),beta_ph2(n_comp, vector<double>(n_comp,0)),beta_ph3(n_comp, vector<double>(n_comp,0));
omega = 1.0/365.0;
simtime = 365*2;
sd1 = 71.0;
sd2 = sd1+(6*7);
sd3 = sd2+(12*7);
sd4 = simtime;
double i0=0.0001;
filename = "SIRS_MComp_simulation_20-20-60.csv";
for (int i=0; i<n_comp;++i){
for (int j=0; j<n_comp;++j){
if (i<v_comps){
if (j<v_comps+h_comps){
beta_ph0[i][j] = beta1_ph0;
beta_ph1[i][j] = beta1_ph1;
beta_ph2[i][j] = beta1_ph2;
beta_ph3[i][j] = beta1_ph3;
} else {
beta_ph0[i][j] = beta4_ph0;
beta_ph1[i][j] = beta4_ph1;
beta_ph2[i][j] = beta4_ph2;
beta_ph3[i][j] = beta4_ph3;
}
} else if (i>=v_comps & i<v_comps+h_comps){
if (j<v_comps){
beta_ph0[i][j] = beta1_ph0;
beta_ph1[i][j] = beta1_ph1;
beta_ph2[i][j] = beta1_ph2;
beta_ph3[i][j] = beta1_ph3;
} else if (j>=v_comps & j<v_comps + h_comps){
beta_ph0[i][j] = beta1_ph0;
beta_ph1[i][j] = beta1_ph1;
beta_ph2[i][j] = beta1_ph2;
beta_ph3[i][j] = beta1_ph3;
} else {
beta_ph0[i][j] = beta2_ph0;
beta_ph1[i][j] = beta2_ph1;
beta_ph2[i][j] = beta2_ph2;
beta_ph3[i][j] = beta2_ph3;
}
} else if (i>=v_comps + h_comps){
if (j<v_comps){
beta_ph0[i][j] = beta4_ph0;
beta_ph1[i][j] = beta4_ph1;
beta_ph2[i][j] = beta4_ph2;
beta_ph3[i][j] = beta4_ph3;
} else if (j<v_comps + h_comps){
beta_ph0[i][j] = beta2_ph0;
beta_ph1[i][j] = beta2_ph1;
beta_ph2[i][j] = beta2_ph2;
beta_ph3[i][j] = beta2_ph3;
} else {
beta_ph0[i][j] = beta3_ph0;
beta_ph1[i][j] = beta3_ph1;
beta_ph2[i][j] = beta3_ph2;
beta_ph3[i][j] = beta3_ph3;
}
}
}
}
state_type y(4*n_comp);
for(int i=0;i<v_comps;++i){
y[i]= fv_per_comp - (fv_per_comp*i0);
y[i+n_comp] = fv_per_comp*i0;
y[i+2*n_comp] = 0;
y[i+3*n_comp] = 0;
}
for(int i=v_comps;i<v_comps+h_comps;++i){
y[i]= fh_per_comp - (fh_per_comp*i0);
y[i+n_comp] = fh_per_comp*i0;
y[i+2*n_comp] = 0;
y[i+3*n_comp] = 0;
}
for(int i=v_comps+h_comps; i<n_comp; ++i){
y[i]= fr_per_comp - (fr_per_comp*i0);
y[i+n_comp] = fr_per_comp*i0;
y[i+2*n_comp] = 0;
y[i+3*n_comp] = 0;
}
runge_kutta4< state_type > stepper;
vector<double> times;
SIRS_3Comp vuln(n_comp,gamma,omega,sd1, sd2, sd3, sd4,beta_ph0, beta_ph1,beta_ph2,beta_ph3,fj);
vector<state_type> y_vec;
integrate_n_steps(stepper,vuln, y, 0.0 , 1.0, simtime, push_back_state_time_pIv_pIh_pIr(y_vec, times,fj,v_comps, h_comps,r_comps));
data_type betas;
for (size_t t = 0; t<y_vec.size(); ++t){
data_type tempbetas = calc_beta_3Comp_taper(t,n_comp,{sd1,sd2,sd3,sd4}, beta_ph0, beta_ph1,beta_ph2,beta_ph3);
vector<double> temp;
for (auto i : tempbetas){
for (auto j : i){
temp.push_back(j);
}
}
betas.push_back(temp);
}
write_simulation(filename, y_vec, betas,v_comps, h_comps, r_comps);
write_phase_matrices(beta_ph0,beta_ph1, beta_ph2, beta_ph3);
}
void fast_analysis(){
double omega;
double sd1 = 0, sd2 = 0, sd3 = 0,sd4=0;
int simtime;
string output_dir, filename;
double R0 = 2.8;
double T2 = 3.3;
double gamma = 1.0/GenTime(T2,R0);
double beta1_ph0 = 1.7*gamma;
double beta2_ph0 = 1.7*gamma;
double beta3_ph0 = 1.7*gamma;
double beta4_ph0 = 1.7*gamma;
double beta1_ph1 = 0.8*gamma;
double beta2_ph1 = 0.9*gamma;
double beta3_ph1 = 0.9*gamma;
double beta4_ph1 = 0.8*gamma;
double beta1_ph2 = 0.4*gamma;
double beta2_ph2 = 1.85*gamma;
double beta3_ph2 = 2.25*gamma;
double beta4_ph2 = 0.4*gamma;
double beta1_ph3 = 0.4*gamma;
double beta2_ph3 = 1.85*gamma;
double beta3_ph3 = 2.25*gamma;
double beta4_ph3 = 0.4*gamma;
int n_comp=10;
//2-2-96 -> 1v-1v-48r
//8-8-84 -> 4v-4h-42r
//14-14-72 -> 7v-7h-36r
//20-20-60 -> 10v-10h-30r or 1v-1h-3r
//20-40-40 -> 1v-2h-2r
//20-10-70 -> 2v-1h-7r
vector<double> fj = {0.2,0.1,0.7};
int v_comps = 2;
int h_comps = 1;
int r_comps = n_comp - v_comps - h_comps;
double fv_per_comp = fj[0]/v_comps;
double fh_per_comp = fj[1]/h_comps;
double fr_per_comp = fj[2]/r_comps;
data_type beta_ph0(n_comp, vector<double>(n_comp,0)),beta_ph1(n_comp, vector<double>(n_comp,0)),beta_ph2(n_comp, vector<double>(n_comp,0)),beta_ph3(n_comp, vector<double>(n_comp,0));
omega = 1.0/365.0;
simtime = 365*2;
sd1 = 71.0;
sd2 = sd1+(6*7);
sd3 = sd2+(12*7);
sd4 = simtime;
double i0=0.0001;
for (int i=0; i<n_comp;++i){
for (int j=0; j<n_comp;++j){
if (i<v_comps){
if (j<v_comps+h_comps){
beta_ph0[i][j] = beta1_ph0;
beta_ph1[i][j] = beta1_ph1;
beta_ph2[i][j] = beta1_ph2;
beta_ph3[i][j] = beta1_ph3;
} else {
beta_ph0[i][j] = beta4_ph0;
beta_ph1[i][j] = beta4_ph1;
beta_ph2[i][j] = beta4_ph2;
beta_ph3[i][j] = beta4_ph3;
}
} else if (i>=v_comps & i<v_comps+h_comps){
if (j<v_comps){
beta_ph0[i][j] = beta1_ph0;
beta_ph1[i][j] = beta1_ph1;
beta_ph2[i][j] = beta1_ph2;
beta_ph3[i][j] = beta1_ph3;
} else if (j>=v_comps & j<v_comps + h_comps){
beta_ph0[i][j] = beta1_ph0;
beta_ph1[i][j] = beta1_ph1;
beta_ph2[i][j] = beta1_ph2;
beta_ph3[i][j] = beta1_ph3;
} else {
beta_ph0[i][j] = beta2_ph0;
beta_ph1[i][j] = beta2_ph1;
beta_ph2[i][j] = beta2_ph2;
beta_ph3[i][j] = beta2_ph3;
}
} else if (i>=v_comps + h_comps){
if (j<v_comps){
beta_ph0[i][j] = beta4_ph0;
beta_ph1[i][j] = beta4_ph1;
beta_ph2[i][j] = beta4_ph2;
beta_ph3[i][j] = beta4_ph3;
} else if (j<v_comps + h_comps){
beta_ph0[i][j] = beta2_ph0;
beta_ph1[i][j] = beta2_ph1;
beta_ph2[i][j] = beta2_ph2;
beta_ph3[i][j] = beta2_ph3;
} else {
beta_ph0[i][j] = beta3_ph0;
beta_ph1[i][j] = beta3_ph1;
beta_ph2[i][j] = beta3_ph2;
beta_ph3[i][j] = beta3_ph3;
}
}
}
}
state_type y(4*n_comp);
data_type fast_results;
string file("FAST_paras.csv");
vector<vector<double> > paras = parse2DCsvFile(file);
for (size_t i=0; i<paras.size();++i){
for(int i=0;i<v_comps;++i){
y[i]= fv_per_comp - (fv_per_comp*i0);
y[i+n_comp] = fv_per_comp*i0;
y[i+2*n_comp] = 0;
y[i+3*n_comp] = 0;
}
for(int i=v_comps;i<v_comps+h_comps;++i){
y[i]= fh_per_comp - (fh_per_comp*i0);
y[i+n_comp] = fh_per_comp*i0;
y[i+2*n_comp] = 0;
y[i+3*n_comp] = 0;
}
for(int i=v_comps+h_comps; i<n_comp; ++i){
y[i]= fr_per_comp - (fr_per_comp*i0);
y[i+n_comp] = fr_per_comp*i0;
y[i+2*n_comp] = 0;
y[i+3*n_comp] = 0;
}
beta_ph0 = {
{beta1_ph0*paras[i][0], beta1_ph0*paras[i][1], beta4_ph0*paras[i][2],beta4_ph0*paras[i][2],beta4_ph0*paras[i][2]},
{beta1_ph0*paras[i][3], beta1_ph0*paras[i][4], beta2_ph0*paras[i][5],beta2_ph0*paras[i][5],beta2_ph0*paras[i][5]},
{beta4_ph0*paras[i][6], beta2_ph0*paras[i][7], beta3_ph0*paras[i][8],beta3_ph0*paras[i][8],beta3_ph0*paras[i][8]},
{beta4_ph0*paras[i][6], beta2_ph0*paras[i][7], beta3_ph0*paras[i][8],beta3_ph0*paras[i][8],beta3_ph0*paras[i][8]},
{beta4_ph0*paras[i][6], beta2_ph0*paras[i][7], beta3_ph0*paras[i][8],beta3_ph0*paras[i][8],beta3_ph0*paras[i][8]}
};
beta_ph1 = {
{beta1_ph1*paras[i][0], beta1_ph1*paras[i][1], beta4_ph1*paras[i][2],beta4_ph1*paras[i][2],beta4_ph1*paras[i][2]},
{beta1_ph1*paras[i][3], beta1_ph1*paras[i][4], beta2_ph1*paras[i][5],beta2_ph1*paras[i][5],beta2_ph1*paras[i][5]},
{beta4_ph1*paras[i][6], beta2_ph1*paras[i][7], beta3_ph1*paras[i][8],beta3_ph1*paras[i][8],beta3_ph1*paras[i][8]},
{beta4_ph1*paras[i][6], beta2_ph1*paras[i][7], beta3_ph1*paras[i][8],beta3_ph1*paras[i][8],beta3_ph1*paras[i][8]},
{beta4_ph1*paras[i][6], beta2_ph1*paras[i][7], beta3_ph1*paras[i][8],beta3_ph1*paras[i][8],beta3_ph1*paras[i][8]}
};
beta_ph2 = {
{beta1_ph2*paras[i][0], beta1_ph2*paras[i][1], beta4_ph2*paras[i][2],beta4_ph2*paras[i][2],beta4_ph2*paras[i][2]},
{beta1_ph2*paras[i][3], beta1_ph2*paras[i][4], beta2_ph2*paras[i][5],beta2_ph2*paras[i][5],beta2_ph2*paras[i][5]},
{beta4_ph2*paras[i][6], beta2_ph2*paras[i][7], beta3_ph2*paras[i][8],beta3_ph2*paras[i][8],beta3_ph2*paras[i][8]},
{beta4_ph2*paras[i][6], beta2_ph2*paras[i][7], beta3_ph2*paras[i][8],beta3_ph2*paras[i][8],beta3_ph2*paras[i][8]},
{beta4_ph2*paras[i][6], beta2_ph2*paras[i][7], beta3_ph2*paras[i][8],beta3_ph2*paras[i][8],beta3_ph2*paras[i][8]}
};
beta_ph3 = beta_ph2;
runge_kutta4< state_type > stepper;
vector<double> times;
SIRS_3Comp vuln(n_comp,gamma,omega,sd1, sd2, sd3, sd4,beta_ph0, beta_ph1,beta_ph2,beta_ph3,fj);
vector<state_type> y_vec;
integrate_n_steps(stepper,vuln, y, 0.0 , 1.0, simtime, push_back_state_and_time(y_vec, times,fj,n_comp));
std::vector<double> temp;
for (size_t i=0; i<y_vec.size();++i){
temp.push_back(y_vec[i][24]);
}
double incrIv = 0;
int sd_2nd_peak_Iv = static_cast<int>(sd1)+300;
for (size_t i=72; i<sd1+400;++i){
if (temp[i]>=temp[i-1]){
incrIv=1;
sd_2nd_peak_Iv = i;
break;
}
}
auto it = *max_element(std::begin(temp)+sd_2nd_peak_Iv, std::begin(temp)+(sd1+365));
double higher;
if (it>temp[71]){
higher = 1.0;
} else {
higher = 0.0;
}
vector<double> temp1 = {it,y_vec[71+365][16]/fj[0], higher};
fast_results.push_back(temp1);
}
write_fast_results(fast_results);
}
void optimisation(){
double omega;
double sd1 = 0, sd2 = 0, sd3 = 0,sd4=0;
int simtime;
string output_dir, filename;
double R0 = 2.8;
double T2 = 3.3;
double gamma = 1.0/GenTime(T2,R0);
double beta1_ph0 = 1.7*gamma;
double beta2_ph0 = 1.7*gamma;
double beta3_ph0 = 1.7*gamma;
double beta4_ph0 = 1.7*gamma;
double beta1_ph1 = 0.8*gamma;
double beta2_ph1 = 0.9*gamma;
double beta3_ph1 = 0.9*gamma;
double beta4_ph1 = 0.8*gamma;
double beta1_ph2 = 0.4*gamma;
double beta2_ph2 = 1.85*gamma;
double beta3_ph2 = 2.25*gamma;
double beta4_ph2 = 0.4*gamma;
double beta1_ph3 = 0.4*gamma;
double beta2_ph3 = 1.85*gamma;
double beta3_ph3 = 2.25*gamma;
double beta4_ph3 = 0.4*gamma;
int n_comp=10;
//2-2-96 -> 1v-1v-48r
//8-8-84 -> 4v-4h-42r
//14-14-72 -> 7v-7h-36r
//20-20-60 -> 10v-10h-30r or 1v-1h-3r
//20-40-40 -> 1v-2h-2r
//20-10-70 -> 2v-1h-7r
vector<double> fj = {0.2,0.1,0.7};
int v_comps = 2;
int h_comps = 1;
int r_comps = n_comp - v_comps - h_comps;
double fv_per_comp = fj[0]/v_comps;
double fh_per_comp = fj[1]/h_comps;
double fr_per_comp = fj[2]/r_comps;
data_type beta_ph0(n_comp, vector<double>(n_comp,0)),beta_ph1(n_comp, vector<double>(n_comp,0)),beta_ph2(n_comp, vector<double>(n_comp,0)),beta_ph3(n_comp, vector<double>(n_comp,0));
omega = 1.0/365.0;
simtime = 365*2;
sd1 = 71.0;
sd2 = sd1+(6*7);
sd3 = sd2+(12*7);
sd4 = simtime;
double i0=0.0001;
for (int i=0; i<n_comp;++i){
for (int j=0; j<n_comp;++j){
if (i<v_comps){
if (j<v_comps+h_comps){
beta_ph0[i][j] = beta1_ph0;
beta_ph1[i][j] = beta1_ph1;
beta_ph2[i][j] = beta1_ph2;
beta_ph3[i][j] = beta1_ph3;
} else {
beta_ph0[i][j] = beta4_ph0;
beta_ph1[i][j] = beta4_ph1;
beta_ph2[i][j] = beta4_ph2;
beta_ph3[i][j] = beta4_ph3;
}
} else if (i>=v_comps & i<v_comps+h_comps){
if (j<v_comps){
beta_ph0[i][j] = beta1_ph0;
beta_ph1[i][j] = beta1_ph1;
beta_ph2[i][j] = beta1_ph2;
beta_ph3[i][j] = beta1_ph3;
} else if (j>=v_comps & j<v_comps + h_comps){
beta_ph0[i][j] = beta1_ph0;
beta_ph1[i][j] = beta1_ph1;
beta_ph2[i][j] = beta1_ph2;
beta_ph3[i][j] = beta1_ph3;
} else {
beta_ph0[i][j] = beta2_ph0;
beta_ph1[i][j] = beta2_ph1;
beta_ph2[i][j] = beta2_ph2;
beta_ph3[i][j] = beta2_ph3;
}
} else if (i>=v_comps + h_comps){
if (j<v_comps){
beta_ph0[i][j] = beta4_ph0;
beta_ph1[i][j] = beta4_ph1;
beta_ph2[i][j] = beta4_ph2;
beta_ph3[i][j] = beta4_ph3;
} else if (j<v_comps + h_comps){
beta_ph0[i][j] = beta2_ph0;
beta_ph1[i][j] = beta2_ph1;
beta_ph2[i][j] = beta2_ph2;
beta_ph3[i][j] = beta2_ph3;
} else {
beta_ph0[i][j] = beta3_ph0;
beta_ph1[i][j] = beta3_ph1;
beta_ph2[i][j] = beta3_ph2;
beta_ph3[i][j] = beta3_ph3;
}
}
}
}
state_type y(4*n_comp);
data_type optim_results;
//for 3 values of beta1 (0.0, 0.4, 0.8) and 3 values of beta2 (0.9, 1.85, 2.8) vary beta3 from 0.9 to 2.8 and beta2 from 0.0 to 0.8
for (double beta1=0.0; beta1<0.81;beta1+=0.4){
for (double beta2=0.9; beta2<2.81;beta2+=0.95){
for (double beta3=0.9; beta3<2.801;beta3+=0.01){
for (double beta4=0.0; beta4<0.81;beta4+=0.01){
for (int i=0; i<n_comp;++i){
for (int j=0; j<n_comp;++j){
if (i<v_comps){
if (j<v_comps+h_comps){
beta_ph2[i][j] = beta1*gamma;
beta_ph3[i][j] = beta1*gamma;
} else {
beta_ph2[i][j] = beta4*gamma;
beta_ph3[i][j] = beta4*gamma;
}
} else if (i>=v_comps & i<v_comps+h_comps){
if (j<v_comps){
beta_ph2[i][j] = beta1*gamma;
beta_ph3[i][j] = beta1*gamma;
} else if (j>=v_comps & j<v_comps + h_comps){
beta_ph2[i][j] = beta1*gamma;
beta_ph3[i][j] = beta1*gamma;
} else {
beta_ph2[i][j] = beta2*gamma;
beta_ph3[i][j] = beta2*gamma;
}
} else if (i>=v_comps + h_comps){
if (j<v_comps){
beta_ph2[i][j] = beta4*gamma;
beta_ph3[i][j] = beta4*gamma;
} else if (j<v_comps + h_comps){
beta_ph2[i][j] = beta2*gamma;
beta_ph3[i][j] = beta2*gamma;
} else {
beta_ph2[i][j] = beta3*gamma;
beta_ph3[i][j] = beta3*gamma;
}
}
}
}
//Initialise starting values
for(int i=0;i<v_comps;++i){
y[i]= fv_per_comp - (fv_per_comp*i0);
y[i+n_comp] = fv_per_comp*i0;
y[i+2*n_comp] = 0;
y[i+3*n_comp] = 0;
}
for(int i=v_comps;i<v_comps+h_comps;++i){
y[i]= fh_per_comp - (fh_per_comp*i0);
y[i+n_comp] = fh_per_comp*i0;
y[i+2*n_comp] = 0;
y[i+3*n_comp] = 0;
}
for(int i=v_comps+h_comps; i<n_comp; ++i){
y[i]= fr_per_comp - (fr_per_comp*i0);
y[i+n_comp] = fr_per_comp*i0;
y[i+2*n_comp] = 0;
y[i+3*n_comp] = 0;
}
runge_kutta4< state_type > stepper;
vector<double> times;
SIRS_3Comp vuln(n_comp,gamma,omega,sd1, sd2, sd3, sd4,beta_ph0, beta_ph1,beta_ph2,beta_ph3,fj);
vector<state_type> y_vec;
integrate_n_steps(stepper,vuln, y, 0.0 , 1.0, simtime, push_back_state_time_pIv_pIh_pIr(y_vec, times,fj,v_comps, h_comps,r_comps));
std::vector<double> tempIv, tempIh,tempIr;
//last three cells of y_vec are pIv, pIh & pIr
//Outputs of interest:
//1) peak 2 Iv <= peak 1 Iv;
//2) peak 2 Iv <= peak 1 Iv & peak 2 Is <= peak 1 Is & peak 2 Ir <= peak 1 Ir;
//3) No increase at all in Iv, Is or Ir after peak 1
int end = y_vec[0].size();
for (size_t i=0; i<y_vec.size();++i){
tempIv.push_back(y_vec[i][end-3]);
tempIh.push_back(y_vec[i][end-2]);
tempIr.push_back(y_vec[i][end-1]);
}
double incrIv = 0,incrIh = 0, incrIr =0;
int sd_2nd_peak_Iv = static_cast<int>(sd1)+300,sd_2nd_peak_Ih = static_cast<int>(sd1)+300,sd_2nd_peak_Ir = static_cast<int>(sd1)+300;
for (size_t i=72; i<sd1+365;++i){
if (tempIv[i]>=tempIv[i-1]){
incrIv=1;
sd_2nd_peak_Iv = i;
break;
}
}
for (size_t i=72; i<sd1+365;++i){
if (tempIh[i]>=tempIh[i-1]){
incrIh=1;
sd_2nd_peak_Ih = i;
break;
}
}
for (size_t i=72; i<sd1+365;++i){
if (tempIr[i]>=tempIr[i-1]){
incrIr=1;
sd_2nd_peak_Ir = i;
break;
}
}
auto maxIv = *max_element(std::begin(tempIv)+sd_2nd_peak_Iv, std::begin(tempIv)+(sd1+365));
auto maxIh = *max_element(std::begin(tempIh)+sd_2nd_peak_Ih, std::begin(tempIh)+(sd1+365));
auto maxIr = *max_element(std::begin(tempIr)+sd_2nd_peak_Ir, std::begin(tempIr)+(sd1+365));
vector<double> temp = {beta1, beta2, beta3, beta4,y_vec[71+365][end-4]/fj[0], tempIv[71], maxIv,tempIh[71], maxIh,tempIr[71], maxIr, incrIv,incrIh,incrIr};
optim_results.push_back(temp);
//cout << ".";
}
}
}
}
write_optimisations(optim_results);
}
void P3P4_betas(){
double omega;
double sd1 = 0, sd2 = 0, sd3 = 0,sd4=0;
int simtime;
string output_dir, filename;
double R0 = 2.8;
double T2 = 3.3;
double gamma = 1.0/GenTime(T2,R0);
double beta1_ph0 = 1.7*gamma;
double beta2_ph0 = 1.7*gamma;
double beta3_ph0 = 1.7*gamma;
double beta4_ph0 = 1.7*gamma;
double beta1_ph1 = 0.8*gamma;
double beta2_ph1 = 0.9*gamma;
double beta3_ph1 = 0.9*gamma;
double beta4_ph1 = 0.8*gamma;
double beta1_ph2 = 0.4*gamma;
double beta2_ph2 = 1.85*gamma;
double beta3_ph2 = 2.25*gamma;
double beta4_ph2 = 0.4*gamma;
double beta1_ph3 = 0.4*gamma;
double beta2_ph3 = 1.85*gamma;
double beta3_ph3 = 2.25*gamma;
double beta4_ph3 = 0.4*gamma;
int n_comp=5;
//2-2-96 -> 1v-1v-48r
//8-8-84 -> 4v-4h-42r
//14-14-72 -> 7v-7h-36r
//20-20-60 -> 10v-10h-30r or 1v-1h-3r
//20-40-40 -> 1v-2h-2r
//20-10-70 -> 2v-1h-7r
vector<double> fj = {0.2,0.2,0.6};
int v_comps = 1;
int h_comps = 1;
int r_comps = n_comp - v_comps - h_comps;
double fv_per_comp = fj[0]/v_comps;
double fh_per_comp = fj[1]/h_comps;
double fr_per_comp = fj[2]/r_comps;
data_type beta_ph0(n_comp, vector<double>(n_comp,0)),beta_ph1(n_comp, vector<double>(n_comp,0)),beta_ph2(n_comp, vector<double>(n_comp,0)),beta_ph3(n_comp, vector<double>(n_comp,0));
omega = 1.0/365.0;
simtime = 365*2;
sd1 = 71.0;
sd2 = sd1+(6*7);
sd3 = sd2+(12*7);
sd4 = simtime;
data_type results;
double i0=0.0001;
for (double perc=0.75; perc<1.251; perc+=0.01){
for (int i=0; i<n_comp;++i){
for (int j=0; j<n_comp;++j){
if (i<v_comps){
if (j<v_comps+h_comps){
beta_ph0[i][j] = beta1_ph0;
beta_ph1[i][j] = beta1_ph1;
beta_ph2[i][j] = perc*beta1_ph2;
beta_ph3[i][j] = perc*beta1_ph3;
} else {
beta_ph0[i][j] = beta4_ph0;
beta_ph1[i][j] = beta4_ph1;
beta_ph2[i][j] = perc*beta4_ph2;
beta_ph3[i][j] = perc*beta4_ph3;
}
} else if (i>=v_comps & i<v_comps+h_comps){
if (j<v_comps){
beta_ph0[i][j] = beta1_ph0;
beta_ph1[i][j] = beta1_ph1;
beta_ph2[i][j] = perc*beta1_ph2;
beta_ph3[i][j] = perc*beta1_ph3;
} else if (j>=v_comps & j<v_comps + h_comps){
beta_ph0[i][j] = beta1_ph0;
beta_ph1[i][j] = beta1_ph1;
beta_ph2[i][j] = perc*beta1_ph2;
beta_ph3[i][j] = perc*beta1_ph3;
} else {
beta_ph0[i][j] = beta2_ph0;
beta_ph1[i][j] = beta2_ph1;
beta_ph2[i][j] = perc*beta2_ph2;
beta_ph3[i][j] = perc*beta2_ph3;
}
} else if (i>=v_comps + h_comps){
if (j<v_comps){
beta_ph0[i][j] = beta4_ph0;
beta_ph1[i][j] = beta4_ph1;
beta_ph2[i][j] = perc*beta4_ph2;
beta_ph3[i][j] = perc*beta4_ph3;
} else if (j<v_comps + h_comps){
beta_ph0[i][j] = beta2_ph0;
beta_ph1[i][j] = beta2_ph1;
beta_ph2[i][j] = perc*beta2_ph2;
beta_ph3[i][j] = perc*beta2_ph3;
} else {
beta_ph0[i][j] = beta3_ph0;
beta_ph1[i][j] = beta3_ph1;
beta_ph2[i][j] = perc*beta3_ph2;
beta_ph3[i][j] = perc*beta3_ph3;
}
}
}
}
state_type y(4*n_comp);
//Initialise starting values
for(int i=0;i<v_comps;++i){
y[i]= fv_per_comp - (fv_per_comp*i0);
y[i+n_comp] = fv_per_comp*i0;
y[i+2*n_comp] = 0;
y[i+3*n_comp] = 0;
}
for(int i=v_comps;i<v_comps+h_comps;++i){
y[i]= fh_per_comp - (fh_per_comp*i0);
y[i+n_comp] = fh_per_comp*i0;
y[i+2*n_comp] = 0;
y[i+3*n_comp] = 0;
}
for(int i=v_comps+h_comps; i<n_comp; ++i){
y[i]= fr_per_comp - (fr_per_comp*i0);
y[i+n_comp] = fr_per_comp*i0;
y[i+2*n_comp] = 0;
y[i+3*n_comp] = 0;
}
runge_kutta4< state_type > stepper;
vector<double> times;
SIRS_3Comp vuln(n_comp,gamma,omega,sd1, sd2, sd3, sd4,beta_ph0, beta_ph1,beta_ph2,beta_ph3,fj);
vector<state_type> y_vec;
integrate_n_steps(stepper,vuln, y, 0.0 , 1.0, simtime, push_back_state_time_pIv_pIh_pIr(y_vec, times,fj,v_comps, h_comps,r_comps));
//Calc height first peak and second peak
vector<double> tempIv;
int end = y_vec[0].size();
for (size_t i=0; i<y_vec.size();++i){
tempIv.push_back(y_vec[i][end-3]);
}
double incrIv = 0;
int sd_2nd_peak_Iv = static_cast<int>(sd1)+300;
for (size_t i=72; i<sd1+365;++i){
if (tempIv[i]>=tempIv[i-1]){
incrIv=1;
sd_2nd_peak_Iv = i;
break;
}
}
auto maxIv = *max_element(std::begin(tempIv)+sd_2nd_peak_Iv, std::begin(tempIv)+(sd1+365));
auto rel_height = maxIv/tempIv[71];
results.push_back({perc,rel_height});
}
cout << results;
}
void compliance(){
double omega;
double sd1 = 0, sd2 = 0, sd3 = 0,sd4=0;
int simtime;
string output_dir, filename;
double R0 = 2.8;
double T2 = 3.3;
double gamma = 1.0/GenTime(T2,R0);
double beta1_ph0 = 1.7*gamma;
double beta2_ph0 = 1.7*gamma;
double beta3_ph0 = 1.7*gamma;
double beta4_ph0 = 1.7*gamma;
double beta1_ph1 = 0.8*gamma;
double beta2_ph1 = 0.9*gamma;
double beta3_ph1 = 0.9*gamma;
double beta4_ph1 = 0.8*gamma;
double beta1_ph2 = 0.4*gamma;
double beta2_ph2 = 1.85*gamma;
double beta3_ph2 = 2.25*gamma;
double beta4_ph2 = 0.4*gamma;
double beta1_ph3 = 0.4*gamma;
double beta2_ph3 = 1.85*gamma;
double beta3_ph3 = 2.25*gamma;
double beta4_ph3 = 0.4*gamma;
int n_comp=5;
//2-2-96 -> 1v-1v-48r
//8-8-84 -> 4v-4h-42r
//14-14-72 -> 7v-7h-36r
//20-20-60 -> 10v-10h-30r or 1v-1h-3r
//20-40-40 -> 1v-2h-2r