progressDisease.cpp

#include <iostream>
#include <vector>
#include <time.h>
#include <eigen3/Eigen/Dense>
#include "csvUtil.h"
#include "globals.h"

inline
double exp2(double x) {
  x = 1.0 + x / 1024.0;
  x *= x; x *= x; x *= x; x *= x;
  x *= x; x *= x; x *= x; x *= x;
  x *= x; x *= x;
  return x;
}

void progressDisease() {

    double count;
    int hiv = 1;
    // cd4 > 0 special handling inside loop
    // vl > 0 special handling inside loop
    int art = 0;
    // CD4 Influx - need to get counts from previous CD4 and VL categories, calculate how many people leave the category, increment the category by 1,
    // and merge back to the original data frame and add that number of people.  Probably a cleaner way of doing this
    for (int age : ageBins){
        for (int male : maleBins){
            for (int risk : riskBins){
                for (int cd4 = 1; cd4 < nCD4; cd4++){
                    for (int vl = 1; vl < nVl; vl++){
                        for (int circ : circBins){
                            for (int prep : prepBins){
                                for (int condom : condomBins){
                                    // do stuff
                                    count = popCount[hiv][age][male][risk][cd4][vl][circ][prep][condom][art];
                                    if (cd4 < 5){
                                        popDiff[hiv][age][male][risk][cd4][vl][circ][prep][condom][art] -= count * (1- exp(-time_step/cd4_prog[male][vl-1][cd4-1]));
                                    }
                                    if (vl < 5){
                                        popDiff[hiv][age][male][risk][cd4][vl][circ][prep][condom][art] -= count * (1- exp(-time_step/vl_prog[male][vl-1][cd4-1]));
                                    }
                                    // influx
                                    // CD4
                                    if(cd4 < (nCD4 - 1)) {
                                        // check this allen!!!!, seems ok to me.
                                        popDiff[hiv][age][male][risk][cd4+1][vl][circ][prep][condom][art] += count * (1- exp(-time_step/cd4_prog[male][vl-1][cd4-1]));
                                    }
                                    // VL
                                    if(vl < (nVl - 1)) {
                                        popDiff[hiv][age][male][risk][cd4][vl+1][circ][prep][condom][art] += count * (1- exp(-time_step/vl_prog[male][vl-1][cd4-1]));
                                    }
                                }
                            }
                        }
                    }
                }
            }
        }
    }

}




// clang++ -O3 -std=c++11 -g progressDisease.cpp csvUtil.cpp globals.cpp
// int main(){

//     int timeIndex = 0;
//     clock_t tStart;
//     clock_t tEnd;
//     initPop("agePop_0.out");
//     tStart = clock();

//     progressDisease(); //0 based

//     tEnd = clock();
//     std::cout << "time took: " << (double)(tEnd - tStart)/CLOCKS_PER_SEC << std::endl;

//     std::stringstream filename;
//     filename << "progressDisease_" << timeIndex << ".cout";

//     writePop(filename.str(), timeIndex);
//     return 0;
// }