#include <Rcpp.h>

using namespace Rcpp;

//' Calculate the event rate of contact model based on SEIR vector.

//'

//' @param SEIR_vector The numeric vector of current SEIR status.

//' @param numpatch length of location list.

//' @param Di The duration of infectious period (days).

//' @param De The duration of exposed period (days).

//' @param R0_matrix The matrix of R0 between two locations.

//' @param N The vector of population at each location.

//' @return A vector of event rate.

// [[Rcpp::export]]

NumericVector event_rate_coloc_cpp(NumericVector SEIR_vector, int numpatch, float Di, float De,

NumericMatrix R0_matrix, IntegerVector N){

double *S = &SEIR_vector[0], *E = &SEIR_vector[numpatch], *I = &SEIR_vector[numpatch*2];

// things that can happen, S->E, E->I, I->R

NumericVector event (numpatch*3);

for(int i=0; i < numpatch; i++){

double eventSE = 0;

for (int j=0; j < numpatch; j++) {

//if(j == i) continue;

eventSE += S[j] * I[j] * R0_matrix(j,i) / N[j] / Di;

}

event[i] = eventSE;

event[i+numpatch] = E[i] / De;

event[i+2*numpatch] = I[i] / Di;

}

return event;

}