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timeStep.cpp
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#include <iostream>
#include <fstream>
#include <math.h>
#include <gsl/gsl_rng.h>
#include <gsl/gsl_randist.h>
#include <list>
#include <numeric>
#include <cstring>
#include "seed.h"
#include "parms.h"
#include "functions.h"
#include "timeStep.h"
#include "parameters.h"
struct strainParms;
extern gsl_rng * rgen;
using namespace std;
int switching (int *y, double switching_rate1, double switching_rate2) {
for (int c = 0; c < 32; c++) {
int s1_to_s2 = gsl_ran_binomial(rgen, DTIME*switching_rate1, y[c]);
int s2_to_s1 = gsl_ran_binomial(rgen, DTIME*switching_rate2, y[c+32]);
y[c] = y[c] + s2_to_s1 - s1_to_s2;
y[c+32] = y[c+32] - s2_to_s1 + s1_to_s2;
}
return 0;
}
int timeStep (int *y, int *x, int **bindingVec, bool *currentlyUnbound, strainParms *params, int noSteps, int writeOutFreq, ofstream &outfile) {
// set up counters for output
int stepCounter = 0;
double time = 0;
outputFreq (time, x, outfile);
// initialise pointer arrays
int a[NO_S1_COMPARTMENTS+NO_S2_COMPARTMENTS+1] = {0};
int s[int(0.5*NO_D_COMPARTMENTS)] = {0};
int m[NO_S1_COMPARTMENTS+NO_S2_COMPARTMENTS+1] = {0};
// initialise model compartments
struct strainParms parms = * (struct strainParms *) params;
// PER TIMESTEP CALCULATIONS
for (int step = 0; step < noSteps; step++) {
// strain 1 states
int S1E1E2CX = x[0];
int S1M1E2CX = x[1];
int S1E1M2CX = x[2];
int S1M1M2CX = x[3];
int S1E1E2IX = x[4];
int S1M1E2IX = x[5];
int S1E1M2IX = x[6];
int S1M1M2IX = x[7];
int S1E1E2CY = x[8];
int S1M1E2CY = x[9];
int S1E1M2CY = x[10];
int S1M1M2CY = x[11];
int S1E1E2IY = x[12];
int S1M1E2IY = x[13];
int S1E1M2IY = x[14];
int S1M1M2IY = x[15];
int S1E1E2CXR = x[16];
int S1M1E2CXR = x[17];
int S1E1M2CXR = x[18];
int S1M1M2CXR = x[19];
int S1E1E2IXR = x[20];
int S1M1E2IXR = x[21];
int S1E1M2IXR = x[22];
int S1M1M2IXR = x[23];
int S1E1E2CYR = x[24];
int S1M1E2CYR = x[25];
int S1E1M2CYR = x[26];
int S1M1M2CYR = x[27];
int S1E1E2IYR = x[28];
int S1M1E2IYR = x[29];
int S1E1M2IYR = x[30];
int S1M1M2IYR = x[31];
// strain 2 states
int S2E1E2CX = x[32];
int S2M1E2CX = x[33];
int S2E1M2CX = x[34];
int S2M1M2CX = x[35];
int S2E1E2IX = x[36];
int S2M1E2IX = x[37];
int S2E1M2IX = x[38];
int S2M1M2IX = x[39];
int S2E1E2CY = x[40];
int S2M1E2CY = x[41];
int S2E1M2CY = x[42];
int S2M1M2CY = x[43];
int S2E1E2IY = x[44];
int S2M1E2IY = x[45];
int S2E1M2IY = x[46];
int S2M1M2IY = x[47];
int S2E1E2CXR = x[48];
int S2M1E2CXR = x[49];
int S2E1M2CXR = x[50];
int S2M1M2CXR = x[51];
int S2E1E2IXR = x[52];
int S2M1E2IXR = x[53];
int S2E1M2IXR = x[54];
int S2M1M2IXR = x[55];
int S2E1E2CYR = x[56];
int S2M1E2CYR = x[57];
int S2E1M2CYR = x[58];
int S2M1M2CYR = x[59];
int S2E1E2IYR = x[60];
int S2M1E2IYR = x[61];
int S2E1M2IYR = x[62];
int S2M1M2IYR = x[63];
// DNA compartments
int DE1S1 = x[64];
int DM1S1 = x[65];
int DE2S1 = x[66];
int DM2S1 = x[67];
int DE1S2 = x[68];
int DM1S2 = x[69];
int DE2S2 = x[70];
int DM2S2 = x[71];
int DCS1 = x[72];
int DIS1 = x[73];
int DXS1 = x[74];
int DYS1 = x[75];
int DCS2 = x[76];
int DIS2 = x[77];
int DXS2 = x[78];
int DYS2 = x[79];
// MGE compartments
int M1S1 = x[80];
int M1S2 = x[81];
int M2S1 = x[82];
int M2S2 = x[83];
// R substance compartment
int R1 = x[84];
int R2 = x[85];
// initialise absorption vectors of vectors for DNA
int DNAabsorptionMat[(NO_S1_COMPARTMENTS+NO_S2_COMPARTMENTS+1)][NO_D_COMPARTMENTS] = {{0}};
int DNAtransformationMat[(NO_S1_COMPARTMENTS+NO_S2_COMPARTMENTS)][NO_D_COMPARTMENTS] = {{0}};
// initialise absorption vectors of vectors for MGEs
int MGEabsorptionMat[(NO_S1_COMPARTMENTS+NO_S2_COMPARTMENTS+1)][NO_M_COMPARTMENTS] = {{0}};
int MGEinfectionMat[(NO_S1_COMPARTMENTS+NO_S2_COMPARTMENTS)][NO_M_COMPARTMENTS] = {{0}};
// summarise cell population values and arrays
int totStrain1 = 0;
int totStrain2 = 0;
int cells[NO_S1_COMPARTMENTS+NO_S2_COMPARTMENTS];
for (int i = 0; i < NO_S1_COMPARTMENTS; i++) {
totStrain1+=x[i];
cells[i]=x[i];
}
for (int i = NO_S1_COMPARTMENTS; i < (NO_S1_COMPARTMENTS+NO_S2_COMPARTMENTS); i++) {
totStrain2+=x[i];
cells[i]=x[i];
}
// function for entry into R state
double phi1 = phiFun(int(R1+parms.interstrainR*R2), parms.tR1, parms.gR1);
double phi2 = phiFun(int(R2+parms.interstrainR*R1), parms.tR2, parms.gR2);
/*************************************************
* Absorption of cells to non-cellular components *
*************************************************/
// divide up DNA compartments as those coming from strain 1 and from strain 2
int s1dna[8] = {64,65,66,67,72,73,74,75};
int s2dna[8] = {68,69,70,71,76,77,78,79};
for (int j = 0; j < (0.5*NO_D_COMPARTMENTS); j++) {
// strain 1 DNA binding to bacteria
int bindRet = dnaBinding(x[s1dna[j]], parms.rho1, parms.rhoR1, parms.rho2*parms.interstrainTransformation, parms.rhoR2*parms.interstrainTransformation, parms.deltaD, cells, a);
if (bindRet != 0) {
cerr << "Error with binding subroutine" << endl;
return 1;
}
// fill in relevant compartments of absorption matrix according to cell and DNA type
for (int i = 0; i < (NO_S1_COMPARTMENTS+NO_S2_COMPARTMENTS+1); i++) {
DNAabsorptionMat[i][s1dna[j]-(NO_S1_COMPARTMENTS+NO_S2_COMPARTMENTS)]=a[i];
}
// strain 2 DNA binding to bacteria
bindRet = dnaBinding(x[s2dna[j]], parms.rho1*parms.interstrainTransformation, parms.rhoR1*parms.interstrainTransformation, parms.rho2, parms.rhoR2, parms.deltaD, cells, a);
if (bindRet != 0) {
cerr << "Error with binding subroutine" << endl;
return 1;
}
// fill in relevant compartments of absorption matrix according to cell and DNA type
for (int i = 0; i < (NO_S1_COMPARTMENTS+NO_S2_COMPARTMENTS+1); i++) {
DNAabsorptionMat[i][s2dna[j]-(NO_S1_COMPARTMENTS+NO_S2_COMPARTMENTS)]=a[i];
}
}
// MGE absorption to bacteria
int mgeIndex = NO_S1_COMPARTMENTS+NO_S2_COMPARTMENTS+NO_D_COMPARTMENTS;
// MGE M1S1
int abCheck = 1;
abCheck = mgeAbsorption(x[mgeIndex], parms.beta1, parms.beta1*parms.interstrainMGE, parms.deltaM1, cells, m, parms.rms);
if (abCheck != 0) {
cerr << "Error with MGE absorption subroutine for M1S1" << endl;
return 1;
} else {
for (int i = 0; i < (NO_S1_COMPARTMENTS+NO_S2_COMPARTMENTS+1); i++) {
MGEabsorptionMat[i][mgeIndex-(NO_S1_COMPARTMENTS+NO_S2_COMPARTMENTS+NO_D_COMPARTMENTS)]=m[i];
}
}
// MGE M1S2
abCheck = 1;
++mgeIndex;
abCheck = mgeAbsorption(x[mgeIndex], parms.beta1*parms.interstrainMGE, parms.beta1, parms.deltaM1, cells, m, parms.rms);
if (abCheck != 0) {
cerr << "Error with MGE absorption subroutine M2S1" << endl;
return 1;
} else {
for (int i = 0; i < (NO_S1_COMPARTMENTS+NO_S2_COMPARTMENTS+1); i++) {
MGEabsorptionMat[i][mgeIndex-(NO_S1_COMPARTMENTS+NO_S2_COMPARTMENTS+NO_D_COMPARTMENTS)]=m[i];
}
}
// MGE M2S1
abCheck = 1;
++mgeIndex;
abCheck = mgeAbsorption(x[mgeIndex], parms.beta2, parms.beta2*parms.interstrainMGE, parms.deltaM2, cells, m, parms.rms);
if (abCheck != 0) {
cerr << "Error with MGE absorption subroutine M2S1" << endl;
return 1;
} else {
for (int i = 0; i < (NO_S1_COMPARTMENTS+NO_S2_COMPARTMENTS+1); i++) {
MGEabsorptionMat[i][mgeIndex-(NO_S1_COMPARTMENTS+NO_S2_COMPARTMENTS+NO_D_COMPARTMENTS)]=m[i];
}
}
// MGE M2S2
abCheck = 1;
++mgeIndex;
abCheck = mgeAbsorption(x[mgeIndex], parms.beta2*parms.interstrainMGE, parms.beta2, parms.deltaM2, cells, m, parms.rms);
if (abCheck != 0) {
cerr << "Error with MGE absorption subroutine M2S2" << endl;
return 1;
} else {
for (int i = 0; i < (NO_S1_COMPARTMENTS+NO_S2_COMPARTMENTS+1); i++) {
MGEabsorptionMat[i][mgeIndex-(NO_S1_COMPARTMENTS+NO_S2_COMPARTMENTS+NO_D_COMPARTMENTS)]=m[i];
}
}
// DNA import, and MGE infection, of bacteria
// iterate through cell compartments
for (int i = 0; i < (NO_S1_COMPARTMENTS+NO_S2_COMPARTMENTS); i++) {
// check if number of cells in compartment is too high for model
if (x[i] > MAX_CELLS) {
cerr << "Number of cells in compartment i=" << i << " (" << x[i] << ") is greater than " << MAX_CELLS << "; model should be recompiled" << endl;
return 1;
}
// count up bound non-cellular compartments
int elementsTotal = 0;
for (int e = 0; e < NO_D_COMPARTMENTS; e++) {
elementsTotal+=DNAabsorptionMat[i][e];
}
for (int e = 0; e < NO_M_COMPARTMENTS; e++) {
elementsTotal+=MGEabsorptionMat[i][e];
}
// only assign binding if there are both cells and non-cellular elements to be bound
if (x[i] > 0 && elementsTotal > 0) {
// set currentlyBound as being false
memset(currentlyUnbound,true,MAX_CELLS);
// record if any cells in this compartment bind an extracellular component
bool anyBound = false;
// iterate through absorbed DNA types and attach to individual cells
for (int j = 0; j < NO_D_COMPARTMENTS; j++) {
for (int k = 0; k < DNAabsorptionMat[i][j]; k++) {
int cellIndex = rand() % x[i];
// cell is now bound to an extracellular component
if (currentlyUnbound[cellIndex] && true) {
std::fill_n(bindingVec[cellIndex],MAX_MOLS,-1);
currentlyUnbound[cellIndex] = false;
anyBound = true;
// if the number of bound molecules exceeds MAX_MOLS, then die
} else if (bindingVec[cellIndex][MAX_MOLS-1] != -1) {
cerr << "Too many non-cellular agents bound to a single cell!" << endl;
exit(29);
}
int l = 0;
while (bindingVec[cellIndex][l] != -1 && l < MAX_MOLS) {
l++;
}
bindingVec[cellIndex][l] = j;
}
}
// iterate through absorbed MGE types and attach to individual cells
for (int j = 0; j < NO_M_COMPARTMENTS; j++) {
for (int k = 0; k < MGEabsorptionMat[i][j]; k++) {
int cellIndex = rand() % x[i];
// cell is now bound to an extracellular component
if (currentlyUnbound[cellIndex] && true) {
std::fill_n(bindingVec[cellIndex],MAX_MOLS,-1);
currentlyUnbound[cellIndex] = false;
anyBound = true;
// if the number of bound molecules exceeds MAX_MOLS, then die
} else if (bindingVec[cellIndex][MAX_MOLS-1] != -1) {
cerr << "Too many non-cellular agents bound to a single cell!" << endl;
exit(30);
}
int l = 0;
while (bindingVec[cellIndex][l] != -1 && l < MAX_MOLS) {
l++;
}
bindingVec[cellIndex][l] = j+NO_D_COMPARTMENTS;
}
}
// check if any cells in the compartment have bound an extracellular component
if (anyBound && true) {
// iterate through cells with bound elements
for (int p = 0; p < x[i]; ++p) {
// only look at currently bound cells
if (!(currentlyUnbound[p]) && true) {
// identify cells with multiple molecules bound
int boundTotal = 0;
for (int q = 0; q < MAX_MOLS; q++) {
if (bindingVec[p][q] > -1) {
boundTotal++;
}
}
// now select a single molecule to remain bound to a cell
int molIndex = 0;
// if multiple cell types bound, pick one either at random or with a bias to MGE
if (boundTotal > 1 && parms.phageFirst == 0) {
molIndex = rand () % boundTotal;
} else if (boundTotal > 1 && parms.phageFirst == 1) {
// selectively bind phage if present; otherwise bind DNA
int justPhage[MAX_MOLS];
int boundPhage = 0;
// iterate through bound molecules and select phage
for (int r = 0; r < boundTotal; ++r) {
if (bindingVec[p][r] >= NO_D_COMPARTMENTS) {
justPhage[boundPhage] = r;
++boundPhage;
}
}
// select one phage index, convert to molIndex
if (boundPhage > 0) {
int phageIndex = rand () % boundPhage;
molIndex = justPhage[phageIndex];
// unless there are no phage bound
} else {
molIndex = rand () % boundTotal;
}
}
if (boundTotal > 0) {
if (bindingVec[p][molIndex] < NO_D_COMPARTMENTS) {
DNAtransformationMat[i][bindingVec[p][molIndex]]++;
} else {
MGEinfectionMat[i][bindingVec[p][molIndex]-NO_D_COMPARTMENTS]++;
}
}
}
}
}
}
}
// washout and degradation of non-cellular components
int DE1S1_death = DNAabsorptionMat[NO_S1_COMPARTMENTS+NO_S2_COMPARTMENTS][0];
int DM1S1_death = DNAabsorptionMat[NO_S1_COMPARTMENTS+NO_S2_COMPARTMENTS][1];
int DE2S1_death = DNAabsorptionMat[NO_S1_COMPARTMENTS+NO_S2_COMPARTMENTS][2];
int DM2S1_death = DNAabsorptionMat[NO_S1_COMPARTMENTS+NO_S2_COMPARTMENTS][3];
int DE1S2_death = DNAabsorptionMat[NO_S1_COMPARTMENTS+NO_S2_COMPARTMENTS][4];
int DM1S2_death = DNAabsorptionMat[NO_S1_COMPARTMENTS+NO_S2_COMPARTMENTS][5];
int DE2S2_death = DNAabsorptionMat[NO_S1_COMPARTMENTS+NO_S2_COMPARTMENTS][6];
int DM2S2_death = DNAabsorptionMat[NO_S1_COMPARTMENTS+NO_S2_COMPARTMENTS][7];
int DCS1_death = DNAabsorptionMat[NO_S1_COMPARTMENTS+NO_S2_COMPARTMENTS][8];
int DIS1_death = DNAabsorptionMat[NO_S1_COMPARTMENTS+NO_S2_COMPARTMENTS][9];
int DXS1_death = DNAabsorptionMat[NO_S1_COMPARTMENTS+NO_S2_COMPARTMENTS][10];
int DYS1_death = DNAabsorptionMat[NO_S1_COMPARTMENTS+NO_S2_COMPARTMENTS][11];
int DCS2_death = DNAabsorptionMat[NO_S1_COMPARTMENTS+NO_S2_COMPARTMENTS][12];
int DIS2_death = DNAabsorptionMat[NO_S1_COMPARTMENTS+NO_S2_COMPARTMENTS][13];
int DXS2_death = DNAabsorptionMat[NO_S1_COMPARTMENTS+NO_S2_COMPARTMENTS][14];
int DYS2_death = DNAabsorptionMat[NO_S1_COMPARTMENTS+NO_S2_COMPARTMENTS][15];
int M1S1_death = MGEabsorptionMat[NO_S1_COMPARTMENTS+NO_S2_COMPARTMENTS][0];
int M1S2_death = MGEabsorptionMat[NO_S1_COMPARTMENTS+NO_S2_COMPARTMENTS][1];
int M2S1_death = MGEabsorptionMat[NO_S1_COMPARTMENTS+NO_S2_COMPARTMENTS][2];
int M2S2_death = MGEabsorptionMat[NO_S1_COMPARTMENTS+NO_S2_COMPARTMENTS][3];
/*******************************
* Processes affecting strain 1 *
*******************************/
// rates for strain 1
double strain1_deathR = parms.mu1*(double(totStrain1)+parms.interstrainCompetition*double(totStrain2))/parms.kappa1;
double strain1_killR = parms.kR1*(S1E1E2CXR + S1M1E2CXR + S1E1M2CXR + S1M1M2CXR + S1E1E2IXR + S1M1E2IXR + S1E1M2IXR + S1M1M2IXR + S1E1E2CYR + S1M1E2CYR + S1E1M2CYR + S1M1M2CYR + S1E1E2IYR + S1M1E2IYR + S1E1M2IYR + S1M1M2IYR)+parms.interstrainKill*parms.kR2*(S2E1E2CXR + S2M1E2CXR + S2E1M2CXR + S2M1M2CXR + S2E1E2IXR + S2M1E2IXR + S2E1M2IXR + S2M1M2IXR + S2E1E2CYR + S2M1E2CYR + S2E1M2CYR + S2M1M2CYR + S2E1E2IYR + S2M1E2IYR + S2E1M2IYR + S2M1M2IYR);
double strain1_recoveryR = parms.rR1;
double strain1_recruitR = phi1;
double strain1_m1activR = parms.f1;
double strain1_m2activR = parms.f2;
double strain1_m1activRR = parms.fR1;
double strain1_m2activRR = parms.fR2;
double strain1_mutateR = parms.mutate1;
/*
------- S1E1E2CX cells -------
*/
int cellIndex = 0;
// initialise values
int S1E1E2CX_in, S1E1E2CX_rec, S1E1E2CX_DE1S1, S1E1E2CX_DM1S1, S1E1E2CX_DE2S1, S1E1E2CX_DM2S1, S1E1E2CX_DCS1, S1E1E2CX_DIS1, S1E1E2CX_DXS1, S1E1E2CX_DYS1, S1E1E2CX_DE1S2, S1E1E2CX_DM1S2, S1E1E2CX_DE2S2, S1E1E2CX_DM2S2, S1E1E2CX_DCS2, S1E1E2CX_DIS2, S1E1E2CX_DXS2, S1E1E2CX_DYS2, S1E1E2CX_DE1S1_asymmetry, S1E1E2CX_DE1S2_asymmetry, S1E1E2CX_DM1S1_asymmetry, S1E1E2CX_DM1S2_asymmetry, S1E1E2CX_DE2S1_asymmetry, S1E1E2CX_DE2S2_asymmetry, S1E1E2CX_DM2S1_asymmetry, S1E1E2CX_DM2S2_asymmetry, S1E1E2CX_M1S1_inf, S1E1E2CX_M1S2_inf, S1E1E2CX_M2S1_inf, S1E1E2CX_M2S2_inf;
int S1E1E2CX_out, S1E1E2CX_mutate, S1E1E2CX_recruit, S1E1E2CX_kill, S1E1E2CX_death;
if (S1E1E2CX > 0) {
// S1E1E2CX cell growth
S1E1E2CX_in = gsl_ran_binomial(rgen, DTIME*parms.mu1*parms.xfit, S1E1E2CX);
// S1E1E2CX/DNA complexes
S1E1E2CX_rec = 0;
for (int i = 0; i < NO_D_COMPARTMENTS; i++) {
S1E1E2CX_rec+=DNAtransformationMat[cellIndex][i];
}
S1E1E2CX_DE1S1 = DNAtransformationMat[cellIndex][0];
S1E1E2CX_DM1S1 = DNAtransformationMat[cellIndex][1];
S1E1E2CX_DE2S1 = DNAtransformationMat[cellIndex][2];
S1E1E2CX_DM2S1 = DNAtransformationMat[cellIndex][3];
S1E1E2CX_DE1S2 = DNAtransformationMat[cellIndex][4];
S1E1E2CX_DM1S2 = DNAtransformationMat[cellIndex][5];
S1E1E2CX_DE2S2 = DNAtransformationMat[cellIndex][6];
S1E1E2CX_DM2S2 = DNAtransformationMat[cellIndex][7];
S1E1E2CX_DCS1 = DNAtransformationMat[cellIndex][8];
S1E1E2CX_DIS1 = DNAtransformationMat[cellIndex][9];
S1E1E2CX_DXS1 = DNAtransformationMat[cellIndex][10];
S1E1E2CX_DYS1 = DNAtransformationMat[cellIndex][11];
S1E1E2CX_DCS2 = DNAtransformationMat[cellIndex][12];
S1E1E2CX_DIS2 = DNAtransformationMat[cellIndex][13];
S1E1E2CX_DXS2 = DNAtransformationMat[cellIndex][14];
S1E1E2CX_DYS2 = DNAtransformationMat[cellIndex][15];
// DNA asymmetry
dnaAsymmetry(parms.sigmaM11,parms.sigmaM21,S1E1E2CX_DE1S1,S1E1E2CX_DE1S2,S1E1E2CX_DM1S1,S1E1E2CX_DM1S2,S1E1E2CX_DE2S1,S1E1E2CX_DE2S2,S1E1E2CX_DM2S1,S1E1E2CX_DM2S2,s);
S1E1E2CX_DE1S1_asymmetry = s[0]; S1E1E2CX_DE1S2_asymmetry = s[1]; S1E1E2CX_DM1S1_asymmetry = s[2]; S1E1E2CX_DM1S2_asymmetry = s[3]; S1E1E2CX_DE2S1_asymmetry = s[4]; S1E1E2CX_DE2S2_asymmetry = s[5]; S1E1E2CX_DM2S1_asymmetry = s[6]; S1E1E2CX_DM2S2_asymmetry = s[7];
// S1E1E2CX/MGE complexes
int S1E1E2CX_total_inf = 0;
for (int m = 0; m < NO_M_COMPARTMENTS; m++) {
S1E1E2CX_total_inf+=MGEinfectionMat[cellIndex][m];
}
S1E1E2CX_M1S1_inf = MGEinfectionMat[cellIndex][0];
S1E1E2CX_M1S2_inf = MGEinfectionMat[cellIndex][1];
S1E1E2CX_M2S1_inf = MGEinfectionMat[cellIndex][2];
S1E1E2CX_M2S2_inf = MGEinfectionMat[cellIndex][3];
// S1E1E2CX cellular processes
S1E1E2CX_out = gsl_ran_binomial(rgen, DTIME*(strain1_deathR + strain1_killR + strain1_recruitR + strain1_mutateR), S1E1E2CX - S1E1E2CX_rec - S1E1E2CX_total_inf);
S1E1E2CX_mutate = gsl_ran_binomial(rgen, strain1_mutateR/(strain1_deathR + strain1_killR + strain1_recruitR + strain1_mutateR), S1E1E2CX_out);
S1E1E2CX_recruit = gsl_ran_binomial(rgen, strain1_recruitR/(strain1_deathR + strain1_killR + strain1_recruitR), S1E1E2CX_out - S1E1E2CX_mutate);
S1E1E2CX_kill = gsl_ran_binomial(rgen, strain1_killR/(strain1_deathR + strain1_killR), S1E1E2CX_out - S1E1E2CX_mutate - S1E1E2CX_recruit);
S1E1E2CX_death = S1E1E2CX_out - S1E1E2CX_mutate - S1E1E2CX_recruit - S1E1E2CX_kill;
} else {
S1E1E2CX_in = S1E1E2CX_rec = S1E1E2CX_DE1S1 = S1E1E2CX_DM1S1 = S1E1E2CX_DE2S1 = S1E1E2CX_DM2S1 = S1E1E2CX_DCS1 = S1E1E2CX_DIS1 = S1E1E2CX_DXS1 = S1E1E2CX_DYS1 = S1E1E2CX_DE1S2 = S1E1E2CX_DM1S2 = S1E1E2CX_DE2S2 = S1E1E2CX_DM2S2 = S1E1E2CX_DCS2 = S1E1E2CX_DIS2 = S1E1E2CX_DXS2 = S1E1E2CX_DYS2 = S1E1E2CX_DE1S1_asymmetry = S1E1E2CX_DE1S2_asymmetry = S1E1E2CX_DM1S1_asymmetry = S1E1E2CX_DM1S2_asymmetry = S1E1E2CX_DE2S1_asymmetry = S1E1E2CX_DE2S2_asymmetry = S1E1E2CX_DM2S1_asymmetry = S1E1E2CX_DM2S2_asymmetry = S1E1E2CX_M1S1_inf = S1E1E2CX_M1S2_inf = S1E1E2CX_M2S1_inf = S1E1E2CX_M2S2_inf = S1E1E2CX_out = S1E1E2CX_mutate = S1E1E2CX_recruit = S1E1E2CX_kill = S1E1E2CX_death = 0;
}
/*
------- S1E1E2CXR cells -------
*/
cellIndex = 16;
// initialise values
int S1E1E2CXR_in, S1E1E2CXR_rec, S1E1E2CXR_DE1S1, S1E1E2CXR_DM1S1, S1E1E2CXR_DE2S1, S1E1E2CXR_DM2S1, S1E1E2CXR_DCS1, S1E1E2CXR_DIS1, S1E1E2CXR_DXS1, S1E1E2CXR_DYS1, S1E1E2CXR_DE1S2, S1E1E2CXR_DM1S2, S1E1E2CXR_DE2S2, S1E1E2CXR_DM2S2, S1E1E2CXR_DCS2, S1E1E2CXR_DIS2, S1E1E2CXR_DXS2, S1E1E2CXR_DYS2, S1E1E2CXR_DE1S1_asymmetry, S1E1E2CXR_DE1S2_asymmetry, S1E1E2CXR_DM1S1_asymmetry, S1E1E2CXR_DM1S2_asymmetry, S1E1E2CXR_DE2S1_asymmetry, S1E1E2CXR_DE2S2_asymmetry, S1E1E2CXR_DM2S1_asymmetry, S1E1E2CXR_DM2S2_asymmetry, S1E1E2CXR_M1S1_inf, S1E1E2CXR_M1S2_inf, S1E1E2CXR_M2S1_inf, S1E1E2CXR_M2S2_inf;
int S1E1E2CXR_out, S1E1E2CXR_mutate, S1E1E2CXR_recovery, S1E1E2CXR_death;
if (S1E1E2CXR > 0) {
// S1E1E2CXR cell growth
S1E1E2CXR_in = gsl_ran_binomial(rgen, DTIME*parms.mu1*parms.xfit*(1-parms.cR1), S1E1E2CXR);
// S1E1E2CXR/DNA complexes
S1E1E2CXR_rec = 0;
for (int i = 0; i < NO_D_COMPARTMENTS; i++) {
S1E1E2CXR_rec+=DNAtransformationMat[cellIndex][i];
}
S1E1E2CXR_DE1S1 = DNAtransformationMat[cellIndex][0];
S1E1E2CXR_DM1S1 = DNAtransformationMat[cellIndex][1];
S1E1E2CXR_DE2S1 = DNAtransformationMat[cellIndex][2];
S1E1E2CXR_DM2S1 = DNAtransformationMat[cellIndex][3];
S1E1E2CXR_DE1S2 = DNAtransformationMat[cellIndex][4];
S1E1E2CXR_DM1S2 = DNAtransformationMat[cellIndex][5];
S1E1E2CXR_DE2S2 = DNAtransformationMat[cellIndex][6];
S1E1E2CXR_DM2S2 = DNAtransformationMat[cellIndex][7];
S1E1E2CXR_DCS1 = DNAtransformationMat[cellIndex][8];
S1E1E2CXR_DIS1 = DNAtransformationMat[cellIndex][9];
S1E1E2CXR_DXS1 = DNAtransformationMat[cellIndex][10];
S1E1E2CXR_DYS1 = DNAtransformationMat[cellIndex][11];
S1E1E2CXR_DCS2 = DNAtransformationMat[cellIndex][12];
S1E1E2CXR_DIS2 = DNAtransformationMat[cellIndex][13];
S1E1E2CXR_DXS2 = DNAtransformationMat[cellIndex][14];
S1E1E2CXR_DYS2 = DNAtransformationMat[cellIndex][15];
// DNA asymmetry
dnaAsymmetry(parms.sigmaM11,parms.sigmaM21,S1E1E2CXR_DE1S1,S1E1E2CXR_DE1S2,S1E1E2CXR_DM1S1,S1E1E2CXR_DM1S2,S1E1E2CXR_DE2S1,S1E1E2CXR_DE2S2,S1E1E2CXR_DM2S1,S1E1E2CXR_DM2S2,s);
S1E1E2CXR_DE1S1_asymmetry = s[0]; S1E1E2CXR_DE1S2_asymmetry = s[1]; S1E1E2CXR_DM1S1_asymmetry = s[2]; S1E1E2CXR_DM1S2_asymmetry = s[3]; S1E1E2CXR_DE2S1_asymmetry = s[4]; S1E1E2CXR_DE2S2_asymmetry = s[5]; S1E1E2CXR_DM2S1_asymmetry = s[6]; S1E1E2CXR_DM2S2_asymmetry = s[7];
// S1E1E2CXR/MGE complexes
int S1E1E2CXR_total_inf = 0;
for (int m = 0; m < NO_M_COMPARTMENTS; m++) {
S1E1E2CXR_total_inf+=MGEinfectionMat[cellIndex][m];
}
S1E1E2CXR_M1S1_inf = MGEinfectionMat[cellIndex][0];
S1E1E2CXR_M1S2_inf = MGEinfectionMat[cellIndex][1];
S1E1E2CXR_M2S1_inf = MGEinfectionMat[cellIndex][2];
S1E1E2CXR_M2S2_inf = MGEinfectionMat[cellIndex][3];
// S1E1E2CXR cellular processes
S1E1E2CXR_out = gsl_ran_binomial(rgen, DTIME*(strain1_deathR + strain1_recoveryR + strain1_mutateR), S1E1E2CXR - S1E1E2CXR_rec - S1E1E2CXR_total_inf);
S1E1E2CXR_mutate = gsl_ran_binomial(rgen, strain1_mutateR/(strain1_deathR + strain1_recoveryR + strain1_mutateR), S1E1E2CXR_out);
S1E1E2CXR_recovery = gsl_ran_binomial(rgen, strain1_recoveryR/(strain1_deathR + strain1_recoveryR), S1E1E2CXR_out - S1E1E2CXR_mutate);
S1E1E2CXR_death = S1E1E2CXR_out - S1E1E2CXR_mutate - S1E1E2CXR_recovery;
} else {
S1E1E2CXR_in = S1E1E2CXR_rec = S1E1E2CXR_DE1S1 = S1E1E2CXR_DM1S1 = S1E1E2CXR_DE2S1 = S1E1E2CXR_DM2S1 = S1E1E2CXR_DCS1 = S1E1E2CXR_DIS1 = S1E1E2CXR_DXS1 = S1E1E2CXR_DYS1 = S1E1E2CXR_DE1S2 = S1E1E2CXR_DM1S2 = S1E1E2CXR_DE2S2 = S1E1E2CXR_DM2S2 = S1E1E2CXR_DCS2 = S1E1E2CXR_DIS2 = S1E1E2CXR_DXS2 = S1E1E2CXR_DYS2 = S1E1E2CXR_DE1S1_asymmetry = S1E1E2CXR_DE1S2_asymmetry = S1E1E2CXR_DM1S1_asymmetry = S1E1E2CXR_DM1S2_asymmetry = S1E1E2CXR_DE2S1_asymmetry = S1E1E2CXR_DE2S2_asymmetry = S1E1E2CXR_DM2S1_asymmetry = S1E1E2CXR_DM2S2_asymmetry = S1E1E2CXR_M1S1_inf = S1E1E2CXR_M1S2_inf = S1E1E2CXR_M2S1_inf = S1E1E2CXR_M2S2_inf = S1E1E2CXR_out = S1E1E2CXR_mutate = S1E1E2CXR_recovery = S1E1E2CXR_death = 0;
}
/*
------- S1E1E2CY cells -------
*/
cellIndex = 8;
// initialise values
int S1E1E2CY_in, S1E1E2CY_rec, S1E1E2CY_DE1S1, S1E1E2CY_DM1S1, S1E1E2CY_DE2S1, S1E1E2CY_DM2S1, S1E1E2CY_DCS1, S1E1E2CY_DIS1, S1E1E2CY_DXS1, S1E1E2CY_DYS1, S1E1E2CY_DE1S2, S1E1E2CY_DM1S2, S1E1E2CY_DE2S2, S1E1E2CY_DM2S2, S1E1E2CY_DCS2, S1E1E2CY_DIS2, S1E1E2CY_DXS2, S1E1E2CY_DYS2, S1E1E2CY_DE1S1_asymmetry, S1E1E2CY_DE1S2_asymmetry, S1E1E2CY_DM1S1_asymmetry, S1E1E2CY_DM1S2_asymmetry, S1E1E2CY_DE2S1_asymmetry, S1E1E2CY_DE2S2_asymmetry, S1E1E2CY_DM2S1_asymmetry, S1E1E2CY_DM2S2_asymmetry, S1E1E2CY_M1S1_inf, S1E1E2CY_M1S2_inf, S1E1E2CY_M2S1_inf, S1E1E2CY_M2S2_inf;
int S1E1E2CY_out, S1E1E2CY_mutate, S1E1E2CY_recruit, S1E1E2CY_kill, S1E1E2CY_death;
if (S1E1E2CY > 0) {
// S1E1E2CY cell growth
S1E1E2CY_in = gsl_ran_binomial(rgen, DTIME*parms.mu1*parms.yfit, S1E1E2CY);
// S1E1E2CY/DNA complexes
S1E1E2CY_rec = 0;
for (int i = 0; i < NO_D_COMPARTMENTS; i++) {
S1E1E2CY_rec+=DNAtransformationMat[cellIndex][i];
}
S1E1E2CY_DE1S1 = DNAtransformationMat[cellIndex][0];
S1E1E2CY_DM1S1 = DNAtransformationMat[cellIndex][1];
S1E1E2CY_DE2S1 = DNAtransformationMat[cellIndex][2];
S1E1E2CY_DM2S1 = DNAtransformationMat[cellIndex][3];
S1E1E2CY_DE1S2 = DNAtransformationMat[cellIndex][4];
S1E1E2CY_DM1S2 = DNAtransformationMat[cellIndex][5];
S1E1E2CY_DE2S2 = DNAtransformationMat[cellIndex][6];
S1E1E2CY_DM2S2 = DNAtransformationMat[cellIndex][7];
S1E1E2CY_DCS1 = DNAtransformationMat[cellIndex][8];
S1E1E2CY_DIS1 = DNAtransformationMat[cellIndex][9];
S1E1E2CY_DXS1 = DNAtransformationMat[cellIndex][10];
S1E1E2CY_DYS1 = DNAtransformationMat[cellIndex][11];
S1E1E2CY_DCS2 = DNAtransformationMat[cellIndex][12];
S1E1E2CY_DIS2 = DNAtransformationMat[cellIndex][13];
S1E1E2CY_DXS2 = DNAtransformationMat[cellIndex][14];
S1E1E2CY_DYS2 = DNAtransformationMat[cellIndex][15];
// DNA asymmetry
dnaAsymmetry(parms.sigmaM11,parms.sigmaM21,S1E1E2CY_DE1S1,S1E1E2CY_DE1S2,S1E1E2CY_DM1S1,S1E1E2CY_DM1S2,S1E1E2CY_DE2S1,S1E1E2CY_DE2S2,S1E1E2CY_DM2S1,S1E1E2CY_DM2S2,s);
S1E1E2CY_DE1S1_asymmetry = s[0]; S1E1E2CY_DE1S2_asymmetry = s[1]; S1E1E2CY_DM1S1_asymmetry = s[2]; S1E1E2CY_DM1S2_asymmetry = s[3]; S1E1E2CY_DE2S1_asymmetry = s[4]; S1E1E2CY_DE2S2_asymmetry = s[5]; S1E1E2CY_DM2S1_asymmetry = s[6]; S1E1E2CY_DM2S2_asymmetry = s[7];
// S1E1E2CY/MGE complexes
int S1E1E2CY_total_inf = 0;
for (int m = 0; m < NO_M_COMPARTMENTS; m++) {
S1E1E2CY_total_inf+=MGEinfectionMat[cellIndex][m];
}
S1E1E2CY_M1S1_inf = MGEinfectionMat[cellIndex][0];
S1E1E2CY_M1S2_inf = MGEinfectionMat[cellIndex][1];
S1E1E2CY_M2S1_inf = MGEinfectionMat[cellIndex][2];
S1E1E2CY_M2S2_inf = MGEinfectionMat[cellIndex][3];
// S1E1E2CY cellular processes
S1E1E2CY_out = gsl_ran_binomial(rgen, DTIME*(strain1_deathR + strain1_killR + strain1_recruitR + strain1_mutateR), S1E1E2CY - S1E1E2CY_rec - S1E1E2CY_total_inf);
S1E1E2CY_mutate = gsl_ran_binomial(rgen, strain1_mutateR/(strain1_deathR + strain1_killR + strain1_recruitR + strain1_mutateR), S1E1E2CY_out);
S1E1E2CY_recruit = gsl_ran_binomial(rgen, strain1_recruitR/(strain1_deathR + strain1_killR + strain1_recruitR), S1E1E2CY_out - S1E1E2CY_mutate);
S1E1E2CY_kill = gsl_ran_binomial(rgen, strain1_killR/(strain1_deathR + strain1_killR), S1E1E2CY_out - S1E1E2CY_mutate - S1E1E2CY_recruit);
S1E1E2CY_death = S1E1E2CY_out - S1E1E2CY_mutate - S1E1E2CY_recruit - S1E1E2CY_kill;
} else {
S1E1E2CY_in = S1E1E2CY_rec = S1E1E2CY_DE1S1 = S1E1E2CY_DM1S1 = S1E1E2CY_DE2S1 = S1E1E2CY_DM2S1 = S1E1E2CY_DCS1 = S1E1E2CY_DIS1 = S1E1E2CY_DXS1 = S1E1E2CY_DYS1 = S1E1E2CY_DE1S2 = S1E1E2CY_DM1S2 = S1E1E2CY_DE2S2 = S1E1E2CY_DM2S2 = S1E1E2CY_DCS2 = S1E1E2CY_DIS2 = S1E1E2CY_DXS2 = S1E1E2CY_DYS2 = S1E1E2CY_DE1S1_asymmetry = S1E1E2CY_DE1S2_asymmetry = S1E1E2CY_DM1S1_asymmetry = S1E1E2CY_DM1S2_asymmetry = S1E1E2CY_DE2S1_asymmetry = S1E1E2CY_DE2S2_asymmetry = S1E1E2CY_DM2S1_asymmetry = S1E1E2CY_DM2S2_asymmetry = S1E1E2CY_M1S1_inf = S1E1E2CY_M1S2_inf = S1E1E2CY_M2S1_inf = S1E1E2CY_M2S2_inf = S1E1E2CY_out = S1E1E2CY_mutate = S1E1E2CY_recruit = S1E1E2CY_kill = S1E1E2CY_death = 0;
}
/*
------- S1E1E2CYR cells -------
*/
cellIndex = 24;
// initialise values
int S1E1E2CYR_in, S1E1E2CYR_rec, S1E1E2CYR_DE1S1, S1E1E2CYR_DM1S1, S1E1E2CYR_DE2S1, S1E1E2CYR_DM2S1, S1E1E2CYR_DCS1, S1E1E2CYR_DIS1, S1E1E2CYR_DXS1, S1E1E2CYR_DYS1, S1E1E2CYR_DE1S2, S1E1E2CYR_DM1S2, S1E1E2CYR_DE2S2, S1E1E2CYR_DM2S2, S1E1E2CYR_DCS2, S1E1E2CYR_DIS2, S1E1E2CYR_DXS2, S1E1E2CYR_DYS2, S1E1E2CYR_DE1S1_asymmetry, S1E1E2CYR_DE1S2_asymmetry, S1E1E2CYR_DM1S1_asymmetry, S1E1E2CYR_DM1S2_asymmetry, S1E1E2CYR_DE2S1_asymmetry, S1E1E2CYR_DE2S2_asymmetry, S1E1E2CYR_DM2S1_asymmetry, S1E1E2CYR_DM2S2_asymmetry, S1E1E2CYR_M1S1_inf, S1E1E2CYR_M1S2_inf, S1E1E2CYR_M2S1_inf, S1E1E2CYR_M2S2_inf;
int S1E1E2CYR_out, S1E1E2CYR_mutate, S1E1E2CYR_recovery, S1E1E2CYR_death;
if (S1E1E2CYR > 0) {
// S1E1E2CYR cell growth
S1E1E2CYR_in = gsl_ran_binomial(rgen, DTIME*parms.mu1*parms.yfit*(1-parms.cR1), S1E1E2CYR);
// S1E1E2CYR/DNA complexes
S1E1E2CYR_rec = 0;
for (int i = 0; i < NO_D_COMPARTMENTS; i++) {
S1E1E2CYR_rec+=DNAtransformationMat[cellIndex][i];
}
S1E1E2CYR_DE1S1 = DNAtransformationMat[cellIndex][0];
S1E1E2CYR_DM1S1 = DNAtransformationMat[cellIndex][1];
S1E1E2CYR_DE2S1 = DNAtransformationMat[cellIndex][2];
S1E1E2CYR_DM2S1 = DNAtransformationMat[cellIndex][3];
S1E1E2CYR_DE1S2 = DNAtransformationMat[cellIndex][4];
S1E1E2CYR_DM1S2 = DNAtransformationMat[cellIndex][5];
S1E1E2CYR_DE2S2 = DNAtransformationMat[cellIndex][6];
S1E1E2CYR_DM2S2 = DNAtransformationMat[cellIndex][7];
S1E1E2CYR_DCS1 = DNAtransformationMat[cellIndex][8];
S1E1E2CYR_DIS1 = DNAtransformationMat[cellIndex][9];
S1E1E2CYR_DXS1 = DNAtransformationMat[cellIndex][10];
S1E1E2CYR_DYS1 = DNAtransformationMat[cellIndex][11];
S1E1E2CYR_DCS2 = DNAtransformationMat[cellIndex][12];
S1E1E2CYR_DIS2 = DNAtransformationMat[cellIndex][13];
S1E1E2CYR_DXS2 = DNAtransformationMat[cellIndex][14];
S1E1E2CYR_DYS2 = DNAtransformationMat[cellIndex][15];
// DNA asymmetry
dnaAsymmetry(parms.sigmaM11,parms.sigmaM21,S1E1E2CYR_DE1S1,S1E1E2CYR_DE1S2,S1E1E2CYR_DM1S1,S1E1E2CYR_DM1S2,S1E1E2CYR_DE2S1,S1E1E2CYR_DE2S2,S1E1E2CYR_DM2S1,S1E1E2CYR_DM2S2,s);
S1E1E2CYR_DE1S1_asymmetry = s[0]; S1E1E2CYR_DE1S2_asymmetry = s[1]; S1E1E2CYR_DM1S1_asymmetry = s[2]; S1E1E2CYR_DM1S2_asymmetry = s[3]; S1E1E2CYR_DE2S1_asymmetry = s[4]; S1E1E2CYR_DE2S2_asymmetry = s[5]; S1E1E2CYR_DM2S1_asymmetry = s[6]; S1E1E2CYR_DM2S2_asymmetry = s[7];
// S1E1E2CYR/MGE complexes
int S1E1E2CYR_total_inf = 0;
for (int m = 0; m < NO_M_COMPARTMENTS; m++) {
S1E1E2CYR_total_inf+=MGEinfectionMat[cellIndex][m];
}
S1E1E2CYR_M1S1_inf = MGEinfectionMat[cellIndex][0];
S1E1E2CYR_M1S2_inf = MGEinfectionMat[cellIndex][1];
S1E1E2CYR_M2S1_inf = MGEinfectionMat[cellIndex][2];
S1E1E2CYR_M2S2_inf = MGEinfectionMat[cellIndex][3];
// S1E1E2CYR cellular processes
S1E1E2CYR_out = gsl_ran_binomial(rgen, DTIME*(strain1_deathR + strain1_recoveryR + strain1_mutateR), S1E1E2CYR - S1E1E2CYR_rec - S1E1E2CYR_total_inf);
S1E1E2CYR_mutate = gsl_ran_binomial(rgen, strain1_mutateR/(strain1_deathR + strain1_recoveryR + strain1_mutateR), S1E1E2CYR_out);
S1E1E2CYR_recovery = gsl_ran_binomial(rgen, strain1_recoveryR/(strain1_deathR + strain1_recoveryR), S1E1E2CYR_out - S1E1E2CYR_mutate);
S1E1E2CYR_death = S1E1E2CYR_out - S1E1E2CYR_mutate - S1E1E2CYR_recovery;
} else {
S1E1E2CYR_in = S1E1E2CYR_rec = S1E1E2CYR_DE1S1 = S1E1E2CYR_DM1S1 = S1E1E2CYR_DE2S1 = S1E1E2CYR_DM2S1 = S1E1E2CYR_DCS1 = S1E1E2CYR_DIS1 = S1E1E2CYR_DXS1 = S1E1E2CYR_DYS1 = S1E1E2CYR_DE1S2 = S1E1E2CYR_DM1S2 = S1E1E2CYR_DE2S2 = S1E1E2CYR_DM2S2 = S1E1E2CYR_DCS2 = S1E1E2CYR_DIS2 = S1E1E2CYR_DXS2 = S1E1E2CYR_DYS2 = S1E1E2CYR_DE1S1_asymmetry = S1E1E2CYR_DE1S2_asymmetry = S1E1E2CYR_DM1S1_asymmetry = S1E1E2CYR_DM1S2_asymmetry = S1E1E2CYR_DE2S1_asymmetry = S1E1E2CYR_DE2S2_asymmetry = S1E1E2CYR_DM2S1_asymmetry = S1E1E2CYR_DM2S2_asymmetry = S1E1E2CYR_M1S1_inf = S1E1E2CYR_M1S2_inf = S1E1E2CYR_M2S1_inf = S1E1E2CYR_M2S2_inf = S1E1E2CYR_out = S1E1E2CYR_mutate = S1E1E2CYR_recovery = S1E1E2CYR_death = 0;
}
/*
------- S1M1E2CX cells -------
*/
cellIndex = 1;
// initialise values
int S1M1E2CX_in, S1M1E2CX_rec, S1M1E2CX_DE1S1, S1M1E2CX_DM1S1, S1M1E2CX_DE2S1, S1M1E2CX_DM2S1, S1M1E2CX_DCS1, S1M1E2CX_DIS1, S1M1E2CX_DXS1, S1M1E2CX_DYS1, S1M1E2CX_DE1S2, S1M1E2CX_DM1S2, S1M1E2CX_DE2S2, S1M1E2CX_DM2S2, S1M1E2CX_DCS2, S1M1E2CX_DIS2, S1M1E2CX_DXS2, S1M1E2CX_DYS2, S1M1E2CX_DE1S1_asymmetry, S1M1E2CX_DE1S2_asymmetry, S1M1E2CX_DM1S1_asymmetry, S1M1E2CX_DM1S2_asymmetry, S1M1E2CX_DE2S1_asymmetry, S1M1E2CX_DE2S2_asymmetry, S1M1E2CX_DM2S1_asymmetry, S1M1E2CX_DM2S2_asymmetry, S1M1E2CX_M1S1_inf, S1M1E2CX_M1S2_inf, S1M1E2CX_M2S1_inf, S1M1E2CX_M2S2_inf;
int S1M1E2CX_out, S1M1E2CX_kill, S1M1E2CX_mutate, S1M1E2CX_M1_activation, S1M1E2CX_recruit, S1M1E2CX_death;
if (S1M1E2CX > 0) {
// S1M1E2CX cell growth
S1M1E2CX_in = gsl_ran_binomial(rgen, DTIME*parms.mu1*parms.xfit*(1-parms.cM1), S1M1E2CX);
if (parms.mgerec1 == 1) {
// S1M1E2CX/DNA complexes
S1M1E2CX_rec = 0;
for (int i = 0; i < NO_D_COMPARTMENTS; i++) {
S1M1E2CX_rec+=DNAtransformationMat[cellIndex][i];
}
S1M1E2CX_DE1S1 = DNAtransformationMat[cellIndex][0];
S1M1E2CX_DM1S1 = DNAtransformationMat[cellIndex][1];
S1M1E2CX_DE2S1 = DNAtransformationMat[cellIndex][2];
S1M1E2CX_DM2S1 = DNAtransformationMat[cellIndex][3];
S1M1E2CX_DE1S2 = DNAtransformationMat[cellIndex][4];
S1M1E2CX_DM1S2 = DNAtransformationMat[cellIndex][5];
S1M1E2CX_DE2S2 = DNAtransformationMat[cellIndex][6];
S1M1E2CX_DM2S2 = DNAtransformationMat[cellIndex][7];
S1M1E2CX_DCS1 = DNAtransformationMat[cellIndex][8];
S1M1E2CX_DIS1 = DNAtransformationMat[cellIndex][9];
S1M1E2CX_DXS1 = DNAtransformationMat[cellIndex][10];
S1M1E2CX_DYS1 = DNAtransformationMat[cellIndex][11];
S1M1E2CX_DCS2 = DNAtransformationMat[cellIndex][12];
S1M1E2CX_DIS2 = DNAtransformationMat[cellIndex][13];
S1M1E2CX_DXS2 = DNAtransformationMat[cellIndex][14];
S1M1E2CX_DYS2 = DNAtransformationMat[cellIndex][15];
// DNA asymmetry
dnaAsymmetry(parms.sigmaM11,parms.sigmaM21,S1M1E2CX_DE1S1,S1M1E2CX_DE1S2,S1M1E2CX_DM1S1,S1M1E2CX_DM1S2,S1M1E2CX_DE2S1,S1M1E2CX_DE2S2,S1M1E2CX_DM2S1,S1M1E2CX_DM2S2,s);
S1M1E2CX_DE1S1_asymmetry = s[0]; S1M1E2CX_DE1S2_asymmetry = s[1]; S1M1E2CX_DM1S1_asymmetry = s[2]; S1M1E2CX_DM1S2_asymmetry = s[3]; S1M1E2CX_DE2S1_asymmetry = s[4]; S1M1E2CX_DE2S2_asymmetry = s[5]; S1M1E2CX_DM2S1_asymmetry = s[6]; S1M1E2CX_DM2S2_asymmetry = s[7];
} else {
S1M1E2CX_rec = S1M1E2CX_DE1S1 = S1M1E2CX_DM1S1 = S1M1E2CX_DE2S1 = S1M1E2CX_DM2S1 = S1M1E2CX_DCS1 = S1M1E2CX_DIS1 = S1M1E2CX_DXS1 = S1M1E2CX_DYS1 = S1M1E2CX_DE1S2 = S1M1E2CX_DM1S2 = S1M1E2CX_DE2S2 = S1M1E2CX_DM2S2 = S1M1E2CX_DCS2 = S1M1E2CX_DIS2 = S1M1E2CX_DXS2 = S1M1E2CX_DYS2 = S1M1E2CX_DE1S1_asymmetry = S1M1E2CX_DE1S2_asymmetry = S1M1E2CX_DM1S1_asymmetry = S1M1E2CX_DM1S2_asymmetry = S1M1E2CX_DE2S1_asymmetry = S1M1E2CX_DE2S2_asymmetry = S1M1E2CX_DM2S1_asymmetry = S1M1E2CX_DM2S2_asymmetry = 0;
}
// S1M1E2CX/MGE complexes
int S1M1E2CX_total_inf = 0;
for (int m = 0; m < NO_M_COMPARTMENTS; m++) {
S1M1E2CX_total_inf+=MGEinfectionMat[cellIndex][m];
}
S1M1E2CX_M1S1_inf = MGEinfectionMat[cellIndex][0];
S1M1E2CX_M1S2_inf = MGEinfectionMat[cellIndex][1];
S1M1E2CX_M2S1_inf = MGEinfectionMat[cellIndex][2];
S1M1E2CX_M2S2_inf = MGEinfectionMat[cellIndex][3];
// S1M1E2CX cellular processes
S1M1E2CX_out = gsl_ran_binomial(rgen, DTIME*(strain1_deathR + strain1_recruitR + strain1_m1activR + strain1_mutateR + strain1_killR), S1M1E2CX - S1M1E2CX_rec - S1M1E2CX_total_inf);
S1M1E2CX_kill = gsl_ran_binomial(rgen, strain1_killR/(strain1_deathR + strain1_recruitR + strain1_m1activR + strain1_mutateR + strain1_killR), S1M1E2CX_out);
S1M1E2CX_mutate = gsl_ran_binomial(rgen, strain1_mutateR/(strain1_deathR + strain1_recruitR + strain1_m1activR + strain1_mutateR), S1M1E2CX_out - S1M1E2CX_kill);
S1M1E2CX_M1_activation = gsl_ran_binomial(rgen, strain1_m1activR/(strain1_deathR + strain1_recruitR + strain1_m1activR), S1M1E2CX_out - S1M1E2CX_kill - S1M1E2CX_mutate);
S1M1E2CX_recruit = gsl_ran_binomial(rgen, strain1_recruitR/(strain1_deathR + strain1_recruitR), S1M1E2CX_out - S1M1E2CX_kill - S1M1E2CX_mutate - S1M1E2CX_M1_activation);
S1M1E2CX_death = S1M1E2CX_out - S1M1E2CX_kill - S1M1E2CX_mutate - S1M1E2CX_M1_activation - S1M1E2CX_recruit;
} else {
S1M1E2CX_in = S1M1E2CX_rec = S1M1E2CX_DE1S1 = S1M1E2CX_DM1S1 = S1M1E2CX_DE2S1 = S1M1E2CX_DM2S1 = S1M1E2CX_DCS1 = S1M1E2CX_DIS1 = S1M1E2CX_DXS1 = S1M1E2CX_DYS1 = S1M1E2CX_DE1S2 = S1M1E2CX_DM1S2 = S1M1E2CX_DE2S2 = S1M1E2CX_DM2S2 = S1M1E2CX_DCS2 = S1M1E2CX_DIS2 = S1M1E2CX_DXS2 = S1M1E2CX_DYS2 = S1M1E2CX_DE1S1_asymmetry = S1M1E2CX_DE1S2_asymmetry = S1M1E2CX_DM1S1_asymmetry = S1M1E2CX_DM1S2_asymmetry = S1M1E2CX_DE2S1_asymmetry = S1M1E2CX_DE2S2_asymmetry = S1M1E2CX_DM2S1_asymmetry = S1M1E2CX_DM2S2_asymmetry = S1M1E2CX_M1S1_inf = S1M1E2CX_M1S2_inf = S1M1E2CX_M2S1_inf = S1M1E2CX_M2S2_inf = S1M1E2CX_out = S1M1E2CX_kill = S1M1E2CX_mutate = S1M1E2CX_M1_activation = S1M1E2CX_recruit = S1M1E2CX_death = 0;
}
/*
------- S1M1E2CXR cells -------
*/
cellIndex = 17;
// initialise values
int S1M1E2CXR_in, S1M1E2CXR_rec, S1M1E2CXR_DE1S1, S1M1E2CXR_DM1S1, S1M1E2CXR_DE2S1, S1M1E2CXR_DM2S1, S1M1E2CXR_DCS1, S1M1E2CXR_DIS1, S1M1E2CXR_DXS1, S1M1E2CXR_DYS1, S1M1E2CXR_DE1S2, S1M1E2CXR_DM1S2, S1M1E2CXR_DE2S2, S1M1E2CXR_DM2S2, S1M1E2CXR_DCS2, S1M1E2CXR_DIS2, S1M1E2CXR_DXS2, S1M1E2CXR_DYS2, S1M1E2CXR_DE1S1_asymmetry, S1M1E2CXR_DE1S2_asymmetry, S1M1E2CXR_DM1S1_asymmetry, S1M1E2CXR_DM1S2_asymmetry, S1M1E2CXR_DE2S1_asymmetry, S1M1E2CXR_DE2S2_asymmetry, S1M1E2CXR_DM2S1_asymmetry, S1M1E2CXR_DM2S2_asymmetry, S1M1E2CXR_M1S1_inf, S1M1E2CXR_M1S2_inf, S1M1E2CXR_M2S1_inf, S1M1E2CXR_M2S2_inf;
int S1M1E2CXR_death, S1M1E2CXR_out, S1M1E2CXR_mutate, S1M1E2CXR_M1_activation, S1M1E2CXR_recovery;
if (S1M1E2CXR > 0) {
// S1M1E2CXR cell growth
S1M1E2CXR_in = gsl_ran_binomial(rgen, DTIME*parms.mu1*parms.xfit*(1-parms.cR1)*(1-parms.cM1), S1M1E2CXR);
if (parms.mgerec1 == 1) {
// S1M1E2CXR/DNA complexes
S1M1E2CXR_rec = 0;
for (int i = 0; i < NO_D_COMPARTMENTS; i++) {
S1M1E2CXR_rec+=DNAtransformationMat[cellIndex][i];
}
S1M1E2CXR_DE1S1 = DNAtransformationMat[cellIndex][0];
S1M1E2CXR_DM1S1 = DNAtransformationMat[cellIndex][1];
S1M1E2CXR_DE2S1 = DNAtransformationMat[cellIndex][2];
S1M1E2CXR_DM2S1 = DNAtransformationMat[cellIndex][3];
S1M1E2CXR_DE1S2 = DNAtransformationMat[cellIndex][4];
S1M1E2CXR_DM1S2 = DNAtransformationMat[cellIndex][5];
S1M1E2CXR_DE2S2 = DNAtransformationMat[cellIndex][6];
S1M1E2CXR_DM2S2 = DNAtransformationMat[cellIndex][7];
S1M1E2CXR_DCS1 = DNAtransformationMat[cellIndex][8];
S1M1E2CXR_DIS1 = DNAtransformationMat[cellIndex][9];
S1M1E2CXR_DXS1 = DNAtransformationMat[cellIndex][10];
S1M1E2CXR_DYS1 = DNAtransformationMat[cellIndex][11];
S1M1E2CXR_DCS2 = DNAtransformationMat[cellIndex][12];
S1M1E2CXR_DIS2 = DNAtransformationMat[cellIndex][13];
S1M1E2CXR_DXS2 = DNAtransformationMat[cellIndex][14];
S1M1E2CXR_DYS2 = DNAtransformationMat[cellIndex][15];
// DNA asymmetry
dnaAsymmetry(parms.sigmaM11,parms.sigmaM21,S1M1E2CXR_DE1S1,S1M1E2CXR_DE1S2,S1M1E2CXR_DM1S1,S1M1E2CXR_DM1S2,S1M1E2CXR_DE2S1,S1M1E2CXR_DE2S2,S1M1E2CXR_DM2S1,S1M1E2CXR_DM2S2,s);
S1M1E2CXR_DE1S1_asymmetry = s[0]; S1M1E2CXR_DE1S2_asymmetry = s[1]; S1M1E2CXR_DM1S1_asymmetry = s[2]; S1M1E2CXR_DM1S2_asymmetry = s[3]; S1M1E2CXR_DE2S1_asymmetry = s[4]; S1M1E2CXR_DE2S2_asymmetry = s[5]; S1M1E2CXR_DM2S1_asymmetry = s[6]; S1M1E2CXR_DM2S2_asymmetry = s[7];
} else {
S1M1E2CXR_rec = S1M1E2CXR_DE1S1 = S1M1E2CXR_DM1S1 = S1M1E2CXR_DE2S1 = S1M1E2CXR_DM2S1 = S1M1E2CXR_DCS1 = S1M1E2CXR_DIS1 = S1M1E2CXR_DXS1 = S1M1E2CXR_DYS1 = S1M1E2CXR_DE1S2 = S1M1E2CXR_DM1S2 = S1M1E2CXR_DE2S2 = S1M1E2CXR_DM2S2 = S1M1E2CXR_DCS2 = S1M1E2CXR_DIS2 = S1M1E2CXR_DXS2 = S1M1E2CXR_DYS2 = S1M1E2CXR_DE1S1_asymmetry = S1M1E2CXR_DE1S2_asymmetry = S1M1E2CXR_DM1S1_asymmetry = S1M1E2CXR_DM1S2_asymmetry = S1M1E2CXR_DE2S1_asymmetry = S1M1E2CXR_DE2S2_asymmetry = S1M1E2CXR_DM2S1_asymmetry = S1M1E2CXR_DM2S2_asymmetry = 0;
}
// S1M1E2CXR/MGE complexes
int S1M1E2CXR_total_inf = 0;
for (int m = 0; m < NO_M_COMPARTMENTS; m++) {
S1M1E2CXR_total_inf+=MGEinfectionMat[cellIndex][m];
}
S1M1E2CXR_M1S1_inf = MGEinfectionMat[cellIndex][0];
S1M1E2CXR_M1S2_inf = MGEinfectionMat[cellIndex][1];
S1M1E2CXR_M2S1_inf = MGEinfectionMat[cellIndex][2];
S1M1E2CXR_M2S2_inf = MGEinfectionMat[cellIndex][3];
// S1M1E2CXR cellular processes
S1M1E2CXR_out = gsl_ran_binomial(rgen, DTIME*(strain1_deathR + strain1_recoveryR + strain1_m1activRR + strain1_mutateR), S1M1E2CXR - S1M1E2CXR_rec - S1M1E2CXR_total_inf);
S1M1E2CXR_mutate = gsl_ran_binomial(rgen, strain1_mutateR/(strain1_deathR + strain1_recoveryR + strain1_m1activRR + strain1_mutateR), S1M1E2CXR_out);
S1M1E2CXR_M1_activation = gsl_ran_binomial(rgen, strain1_m1activRR/(strain1_deathR + strain1_recoveryR + strain1_m1activRR), S1M1E2CXR_out - S1M1E2CXR_mutate);
S1M1E2CXR_recovery = gsl_ran_binomial(rgen, strain1_recoveryR/(strain1_deathR + strain1_recoveryR), S1M1E2CXR_out - S1M1E2CXR_mutate - S1M1E2CXR_M1_activation);
S1M1E2CXR_death = S1M1E2CXR_out - S1M1E2CXR_mutate - S1M1E2CXR_M1_activation - S1M1E2CXR_recovery;
} else {
S1M1E2CXR_in = S1M1E2CXR_rec = S1M1E2CXR_DE1S1 = S1M1E2CXR_DM1S1 = S1M1E2CXR_DE2S1 = S1M1E2CXR_DM2S1 = S1M1E2CXR_DCS1 = S1M1E2CXR_DIS1 = S1M1E2CXR_DXS1 = S1M1E2CXR_DYS1 = S1M1E2CXR_DE1S2 = S1M1E2CXR_DM1S2 = S1M1E2CXR_DE2S2 = S1M1E2CXR_DM2S2 = S1M1E2CXR_DCS2 = S1M1E2CXR_DIS2 = S1M1E2CXR_DXS2 = S1M1E2CXR_DYS2 = S1M1E2CXR_DE1S1_asymmetry = S1M1E2CXR_DE1S2_asymmetry = S1M1E2CXR_DM1S1_asymmetry = S1M1E2CXR_DM1S2_asymmetry = S1M1E2CXR_DE2S1_asymmetry = S1M1E2CXR_DE2S2_asymmetry = S1M1E2CXR_DM2S1_asymmetry = S1M1E2CXR_DM2S2_asymmetry = S1M1E2CXR_M1S1_inf = S1M1E2CXR_M1S2_inf = S1M1E2CXR_M2S1_inf = S1M1E2CXR_M2S2_inf = S1M1E2CXR_death = S1M1E2CXR_out = S1M1E2CXR_mutate = S1M1E2CXR_M1_activation = S1M1E2CXR_recovery = 0;
}
/*
------- S1M1E2CY cells -------
*/
cellIndex = 9;
// initialise values
int S1M1E2CY_in, S1M1E2CY_rec, S1M1E2CY_DE1S1, S1M1E2CY_DM1S1, S1M1E2CY_DE2S1, S1M1E2CY_DM2S1, S1M1E2CY_DCS1, S1M1E2CY_DIS1, S1M1E2CY_DXS1, S1M1E2CY_DYS1, S1M1E2CY_DE1S2, S1M1E2CY_DM1S2, S1M1E2CY_DE2S2, S1M1E2CY_DM2S2, S1M1E2CY_DCS2, S1M1E2CY_DIS2, S1M1E2CY_DXS2, S1M1E2CY_DYS2, S1M1E2CY_DE1S1_asymmetry, S1M1E2CY_DE1S2_asymmetry, S1M1E2CY_DM1S1_asymmetry, S1M1E2CY_DM1S2_asymmetry, S1M1E2CY_DE2S1_asymmetry, S1M1E2CY_DE2S2_asymmetry, S1M1E2CY_DM2S1_asymmetry, S1M1E2CY_DM2S2_asymmetry, S1M1E2CY_M1S1_inf, S1M1E2CY_M1S2_inf, S1M1E2CY_M2S1_inf, S1M1E2CY_M2S2_inf;
int S1M1E2CY_death, S1M1E2CY_out, S1M1E2CY_kill, S1M1E2CY_mutate, S1M1E2CY_M1_activation, S1M1E2CY_recruit;
if (S1M1E2CY > 0) {
// S1M1E2CY cell growth
S1M1E2CY_in = gsl_ran_binomial(rgen, DTIME*parms.mu1*parms.yfit*(1-parms.cM1), S1M1E2CY);
if (parms.mgerec1 == 1) {
// S1M1E2CY/DNA complexes
S1M1E2CY_rec = 0;
for (int i = 0; i < NO_D_COMPARTMENTS; i++) {
S1M1E2CY_rec+=DNAtransformationMat[cellIndex][i];
}
S1M1E2CY_DE1S1 = DNAtransformationMat[cellIndex][0];
S1M1E2CY_DM1S1 = DNAtransformationMat[cellIndex][1];
S1M1E2CY_DE2S1 = DNAtransformationMat[cellIndex][2];
S1M1E2CY_DM2S1 = DNAtransformationMat[cellIndex][3];
S1M1E2CY_DE1S2 = DNAtransformationMat[cellIndex][4];
S1M1E2CY_DM1S2 = DNAtransformationMat[cellIndex][5];
S1M1E2CY_DE2S2 = DNAtransformationMat[cellIndex][6];
S1M1E2CY_DM2S2 = DNAtransformationMat[cellIndex][7];
S1M1E2CY_DCS1 = DNAtransformationMat[cellIndex][8];
S1M1E2CY_DIS1 = DNAtransformationMat[cellIndex][9];
S1M1E2CY_DXS1 = DNAtransformationMat[cellIndex][10];
S1M1E2CY_DYS1 = DNAtransformationMat[cellIndex][11];
S1M1E2CY_DCS2 = DNAtransformationMat[cellIndex][12];
S1M1E2CY_DIS2 = DNAtransformationMat[cellIndex][13];
S1M1E2CY_DXS2 = DNAtransformationMat[cellIndex][14];
S1M1E2CY_DYS2 = DNAtransformationMat[cellIndex][15];
// DNA asymmetry
dnaAsymmetry(parms.sigmaM11,parms.sigmaM21,S1M1E2CY_DE1S1,S1M1E2CY_DE1S2,S1M1E2CY_DM1S1,S1M1E2CY_DM1S2,S1M1E2CY_DE2S1,S1M1E2CY_DE2S2,S1M1E2CY_DM2S1,S1M1E2CY_DM2S2,s);
S1M1E2CY_DE1S1_asymmetry = s[0]; S1M1E2CY_DE1S2_asymmetry = s[1]; S1M1E2CY_DM1S1_asymmetry = s[2]; S1M1E2CY_DM1S2_asymmetry = s[3]; S1M1E2CY_DE2S1_asymmetry = s[4]; S1M1E2CY_DE2S2_asymmetry = s[5]; S1M1E2CY_DM2S1_asymmetry = s[6]; S1M1E2CY_DM2S2_asymmetry = s[7];
} else {
S1M1E2CY_rec = S1M1E2CY_DE1S1 = S1M1E2CY_DM1S1 = S1M1E2CY_DE2S1 = S1M1E2CY_DM2S1 = S1M1E2CY_DCS1 = S1M1E2CY_DIS1 = S1M1E2CY_DXS1 = S1M1E2CY_DYS1 = S1M1E2CY_DE1S2 = S1M1E2CY_DM1S2 = S1M1E2CY_DE2S2 = S1M1E2CY_DM2S2 = S1M1E2CY_DCS2 = S1M1E2CY_DIS2 = S1M1E2CY_DXS2 = S1M1E2CY_DYS2 = S1M1E2CY_DE1S1_asymmetry = S1M1E2CY_DE1S2_asymmetry = S1M1E2CY_DM1S1_asymmetry = S1M1E2CY_DM1S2_asymmetry = S1M1E2CY_DE2S1_asymmetry = S1M1E2CY_DE2S2_asymmetry = S1M1E2CY_DM2S1_asymmetry = S1M1E2CY_DM2S2_asymmetry = 0;
}
// S1M1E2CY/MGE complexes
int S1M1E2CY_total_inf = 0;
for (int m = 0; m < NO_M_COMPARTMENTS; m++) {
S1M1E2CY_total_inf+=MGEinfectionMat[cellIndex][m];
}
S1M1E2CY_M1S1_inf = MGEinfectionMat[cellIndex][0];
S1M1E2CY_M1S2_inf = MGEinfectionMat[cellIndex][1];
S1M1E2CY_M2S1_inf = MGEinfectionMat[cellIndex][2];
S1M1E2CY_M2S2_inf = MGEinfectionMat[cellIndex][3];
// S1M1E2CY cellular processes
S1M1E2CY_out = gsl_ran_binomial(rgen, DTIME*(strain1_deathR + strain1_recruitR + strain1_m1activR + strain1_mutateR + strain1_killR), S1M1E2CY - S1M1E2CY_rec - S1M1E2CY_total_inf);
S1M1E2CY_kill = gsl_ran_binomial(rgen, strain1_killR/(strain1_deathR + strain1_recruitR + strain1_m1activR + strain1_mutateR + strain1_killR), S1M1E2CY_out);
S1M1E2CY_mutate = gsl_ran_binomial(rgen, strain1_mutateR/(strain1_deathR + strain1_recruitR + strain1_m1activR + strain1_mutateR), S1M1E2CY_out - S1M1E2CY_kill);
S1M1E2CY_M1_activation = gsl_ran_binomial(rgen, strain1_m1activR/(strain1_deathR + strain1_recruitR + strain1_m1activR), S1M1E2CY_out - S1M1E2CY_kill - S1M1E2CY_mutate);
S1M1E2CY_recruit = gsl_ran_binomial(rgen, strain1_recruitR/(strain1_deathR + strain1_recruitR), S1M1E2CY_out - S1M1E2CY_kill - S1M1E2CY_mutate - S1M1E2CY_M1_activation);
S1M1E2CY_death = S1M1E2CY_out - S1M1E2CY_kill - S1M1E2CY_mutate - S1M1E2CY_M1_activation - S1M1E2CY_recruit;
} else {
S1M1E2CY_in = S1M1E2CY_rec = S1M1E2CY_DE1S1 = S1M1E2CY_DM1S1 = S1M1E2CY_DE2S1 = S1M1E2CY_DM2S1 = S1M1E2CY_DCS1 = S1M1E2CY_DIS1 = S1M1E2CY_DXS1 = S1M1E2CY_DYS1 = S1M1E2CY_DE1S2 = S1M1E2CY_DM1S2 = S1M1E2CY_DE2S2 = S1M1E2CY_DM2S2 = S1M1E2CY_DCS2 = S1M1E2CY_DIS2 = S1M1E2CY_DXS2 = S1M1E2CY_DYS2 = S1M1E2CY_DE1S1_asymmetry = S1M1E2CY_DE1S2_asymmetry = S1M1E2CY_DM1S1_asymmetry = S1M1E2CY_DM1S2_asymmetry = S1M1E2CY_DE2S1_asymmetry = S1M1E2CY_DE2S2_asymmetry = S1M1E2CY_DM2S1_asymmetry = S1M1E2CY_DM2S2_asymmetry = S1M1E2CY_M1S1_inf = S1M1E2CY_M1S2_inf = S1M1E2CY_M2S1_inf = S1M1E2CY_M2S2_inf = S1M1E2CY_death = S1M1E2CY_out = S1M1E2CY_kill = S1M1E2CY_mutate = S1M1E2CY_M1_activation = S1M1E2CY_recruit = 0;
}
/*
------- S1M1E2CYR cells -------
*/
cellIndex = 25;
// initialise values
int S1M1E2CYR_in, S1M1E2CYR_rec, S1M1E2CYR_DE1S1, S1M1E2CYR_DM1S1, S1M1E2CYR_DE2S1, S1M1E2CYR_DM2S1, S1M1E2CYR_DCS1, S1M1E2CYR_DIS1, S1M1E2CYR_DXS1, S1M1E2CYR_DYS1, S1M1E2CYR_DE1S2, S1M1E2CYR_DM1S2, S1M1E2CYR_DE2S2, S1M1E2CYR_DM2S2, S1M1E2CYR_DCS2, S1M1E2CYR_DIS2, S1M1E2CYR_DXS2, S1M1E2CYR_DYS2, S1M1E2CYR_DE1S1_asymmetry, S1M1E2CYR_DE1S2_asymmetry, S1M1E2CYR_DM1S1_asymmetry, S1M1E2CYR_DM1S2_asymmetry, S1M1E2CYR_DE2S1_asymmetry, S1M1E2CYR_DE2S2_asymmetry, S1M1E2CYR_DM2S1_asymmetry, S1M1E2CYR_DM2S2_asymmetry, S1M1E2CYR_M1S1_inf, S1M1E2CYR_M1S2_inf, S1M1E2CYR_M2S1_inf, S1M1E2CYR_M2S2_inf;
int S1M1E2CYR_death, S1M1E2CYR_out, S1M1E2CYR_mutate, S1M1E2CYR_M1_activation, S1M1E2CYR_recovery;
if (S1M1E2CYR > 0) {
// S1M1E2CYR cell growth
S1M1E2CYR_in = gsl_ran_binomial(rgen, DTIME*parms.mu1*parms.yfit*(1-parms.cR1)*(1-parms.cM1), S1M1E2CYR);
if (parms.mgerec1 == 1) {
// S1M1E2CYR/DNA complexes
S1M1E2CYR_rec = 0;
for (int i = 0; i < NO_D_COMPARTMENTS; i++) {
S1M1E2CYR_rec+=DNAtransformationMat[cellIndex][i];
}
S1M1E2CYR_DE1S1 = DNAtransformationMat[cellIndex][0];
S1M1E2CYR_DM1S1 = DNAtransformationMat[cellIndex][1];
S1M1E2CYR_DE2S1 = DNAtransformationMat[cellIndex][2];
S1M1E2CYR_DM2S1 = DNAtransformationMat[cellIndex][3];
S1M1E2CYR_DE1S2 = DNAtransformationMat[cellIndex][4];
S1M1E2CYR_DM1S2 = DNAtransformationMat[cellIndex][5];
S1M1E2CYR_DE2S2 = DNAtransformationMat[cellIndex][6];
S1M1E2CYR_DM2S2 = DNAtransformationMat[cellIndex][7];
S1M1E2CYR_DCS1 = DNAtransformationMat[cellIndex][8];
S1M1E2CYR_DIS1 = DNAtransformationMat[cellIndex][9];
S1M1E2CYR_DXS1 = DNAtransformationMat[cellIndex][10];
S1M1E2CYR_DYS1 = DNAtransformationMat[cellIndex][11];
S1M1E2CYR_DCS2 = DNAtransformationMat[cellIndex][12];
S1M1E2CYR_DIS2 = DNAtransformationMat[cellIndex][13];
S1M1E2CYR_DXS2 = DNAtransformationMat[cellIndex][14];
S1M1E2CYR_DYS2 = DNAtransformationMat[cellIndex][15];
// DNA asymmetry
dnaAsymmetry(parms.sigmaM11,parms.sigmaM21,S1M1E2CYR_DE1S1,S1M1E2CYR_DE1S2,S1M1E2CYR_DM1S1,S1M1E2CYR_DM1S2,S1M1E2CYR_DE2S1,S1M1E2CYR_DE2S2,S1M1E2CYR_DM2S1,S1M1E2CYR_DM2S2,s);
S1M1E2CYR_DE1S1_asymmetry = s[0]; S1M1E2CYR_DE1S2_asymmetry = s[1]; S1M1E2CYR_DM1S1_asymmetry = s[2]; S1M1E2CYR_DM1S2_asymmetry = s[3]; S1M1E2CYR_DE2S1_asymmetry = s[4]; S1M1E2CYR_DE2S2_asymmetry = s[5]; S1M1E2CYR_DM2S1_asymmetry = s[6]; S1M1E2CYR_DM2S2_asymmetry = s[7];
} else {
S1M1E2CYR_rec = S1M1E2CYR_DE1S1 = S1M1E2CYR_DM1S1 = S1M1E2CYR_DE2S1 = S1M1E2CYR_DM2S1 = S1M1E2CYR_DCS1 = S1M1E2CYR_DIS1 = S1M1E2CYR_DXS1 = S1M1E2CYR_DYS1 = S1M1E2CYR_DE1S2 = S1M1E2CYR_DM1S2 = S1M1E2CYR_DE2S2 = S1M1E2CYR_DM2S2 = S1M1E2CYR_DCS2 = S1M1E2CYR_DIS2 = S1M1E2CYR_DXS2 = S1M1E2CYR_DYS2 = S1M1E2CYR_DE1S1_asymmetry = S1M1E2CYR_DE1S2_asymmetry = S1M1E2CYR_DM1S1_asymmetry = S1M1E2CYR_DM1S2_asymmetry = S1M1E2CYR_DE2S1_asymmetry = S1M1E2CYR_DE2S2_asymmetry = S1M1E2CYR_DM2S1_asymmetry = S1M1E2CYR_DM2S2_asymmetry = 0;
}
// S1M1E2CYR/MGE complexes
int S1M1E2CYR_total_inf = 0;
for (int m = 0; m < NO_M_COMPARTMENTS; m++) {
S1M1E2CYR_total_inf+=MGEinfectionMat[cellIndex][m];
}
S1M1E2CYR_M1S1_inf = MGEinfectionMat[cellIndex][0];
S1M1E2CYR_M1S2_inf = MGEinfectionMat[cellIndex][1];
S1M1E2CYR_M2S1_inf = MGEinfectionMat[cellIndex][2];
S1M1E2CYR_M2S2_inf = MGEinfectionMat[cellIndex][3];
// S1M1E2CYR cellular processes
S1M1E2CYR_out = gsl_ran_binomial(rgen, DTIME*(strain1_deathR + strain1_recoveryR + strain1_m1activRR + strain1_mutateR), S1M1E2CYR - S1M1E2CYR_rec - S1M1E2CYR_total_inf);
S1M1E2CYR_mutate = gsl_ran_binomial(rgen, strain1_mutateR/(strain1_deathR + strain1_recoveryR + strain1_m1activRR + strain1_mutateR), S1M1E2CYR_out);
S1M1E2CYR_M1_activation = gsl_ran_binomial(rgen, strain1_m1activRR/(strain1_deathR + strain1_recoveryR + strain1_m1activRR), S1M1E2CYR_out - S1M1E2CYR_mutate);
S1M1E2CYR_recovery = gsl_ran_binomial(rgen, strain1_recoveryR/(strain1_deathR + strain1_recoveryR), S1M1E2CYR_out - S1M1E2CYR_mutate - S1M1E2CYR_M1_activation);
S1M1E2CYR_death = S1M1E2CYR_out - S1M1E2CYR_mutate - S1M1E2CYR_M1_activation - S1M1E2CYR_recovery;
} else {
S1M1E2CYR_in = S1M1E2CYR_rec = S1M1E2CYR_DE1S1 = S1M1E2CYR_DM1S1 = S1M1E2CYR_DE2S1 = S1M1E2CYR_DM2S1 = S1M1E2CYR_DCS1 = S1M1E2CYR_DIS1 = S1M1E2CYR_DXS1 = S1M1E2CYR_DYS1 = S1M1E2CYR_DE1S2 = S1M1E2CYR_DM1S2 = S1M1E2CYR_DE2S2 = S1M1E2CYR_DM2S2 = S1M1E2CYR_DCS2 = S1M1E2CYR_DIS2 = S1M1E2CYR_DXS2 = S1M1E2CYR_DYS2 = S1M1E2CYR_DE1S1_asymmetry = S1M1E2CYR_DE1S2_asymmetry = S1M1E2CYR_DM1S1_asymmetry = S1M1E2CYR_DM1S2_asymmetry = S1M1E2CYR_DE2S1_asymmetry = S1M1E2CYR_DE2S2_asymmetry = S1M1E2CYR_DM2S1_asymmetry = S1M1E2CYR_DM2S2_asymmetry = S1M1E2CYR_M1S1_inf = S1M1E2CYR_M1S2_inf = S1M1E2CYR_M2S1_inf = S1M1E2CYR_M2S2_inf = S1M1E2CYR_death = S1M1E2CYR_out = S1M1E2CYR_mutate = S1M1E2CYR_M1_activation = S1M1E2CYR_recovery = 0;
}
/*
------- S1E1M2CX cells -------
*/
cellIndex = 2;
// initialise values
int S1E1M2CX_in, S1E1M2CX_rec, S1E1M2CX_DE1S1, S1E1M2CX_DM1S1, S1E1M2CX_DE2S1, S1E1M2CX_DM2S1, S1E1M2CX_DCS1, S1E1M2CX_DIS1, S1E1M2CX_DXS1, S1E1M2CX_DYS1, S1E1M2CX_DE1S2, S1E1M2CX_DM1S2, S1E1M2CX_DE2S2, S1E1M2CX_DM2S2, S1E1M2CX_DCS2, S1E1M2CX_DIS2, S1E1M2CX_DXS2, S1E1M2CX_DYS2, S1E1M2CX_DE1S1_asymmetry, S1E1M2CX_DE1S2_asymmetry, S1E1M2CX_DM1S1_asymmetry, S1E1M2CX_DM1S2_asymmetry, S1E1M2CX_DE2S1_asymmetry, S1E1M2CX_DE2S2_asymmetry, S1E1M2CX_DM2S1_asymmetry, S1E1M2CX_DM2S2_asymmetry, S1E1M2CX_M1S1_inf, S1E1M2CX_M1S2_inf, S1E1M2CX_M2S1_inf, S1E1M2CX_M2S2_inf;
int S1E1M2CX_death, S1E1M2CX_out, S1E1M2CX_kill, S1E1M2CX_mutate, S1E1M2CX_M2_activation, S1E1M2CX_recruit;
if (S1E1M2CX > 0) {
// S1E1M2CX cell growth
S1E1M2CX_in = gsl_ran_binomial(rgen, DTIME*parms.mu1*parms.xfit*(1-parms.cM2), S1E1M2CX);
if (parms.mgerec2 == 1) {
// S1E1M2CX/DNA complexes
S1E1M2CX_rec = 0;
for (int i = 0; i < NO_D_COMPARTMENTS; i++) {
S1E1M2CX_rec+=DNAtransformationMat[cellIndex][i];
}
S1E1M2CX_DE1S1 = DNAtransformationMat[cellIndex][0];
S1E1M2CX_DM1S1 = DNAtransformationMat[cellIndex][1];
S1E1M2CX_DE2S1 = DNAtransformationMat[cellIndex][2];
S1E1M2CX_DM2S1 = DNAtransformationMat[cellIndex][3];
S1E1M2CX_DE1S2 = DNAtransformationMat[cellIndex][4];
S1E1M2CX_DM1S2 = DNAtransformationMat[cellIndex][5];
S1E1M2CX_DE2S2 = DNAtransformationMat[cellIndex][6];
S1E1M2CX_DM2S2 = DNAtransformationMat[cellIndex][7];
S1E1M2CX_DCS1 = DNAtransformationMat[cellIndex][8];
S1E1M2CX_DIS1 = DNAtransformationMat[cellIndex][9];
S1E1M2CX_DXS1 = DNAtransformationMat[cellIndex][10];
S1E1M2CX_DYS1 = DNAtransformationMat[cellIndex][11];
S1E1M2CX_DCS2 = DNAtransformationMat[cellIndex][12];
S1E1M2CX_DIS2 = DNAtransformationMat[cellIndex][13];
S1E1M2CX_DXS2 = DNAtransformationMat[cellIndex][14];
S1E1M2CX_DYS2 = DNAtransformationMat[cellIndex][15];
// DNA asymmetry
dnaAsymmetry(parms.sigmaM11,parms.sigmaM21,S1E1M2CX_DE1S1,S1E1M2CX_DE1S2,S1E1M2CX_DM1S1,S1E1M2CX_DM1S2,S1E1M2CX_DE2S1,S1E1M2CX_DE2S2,S1E1M2CX_DM2S1,S1E1M2CX_DM2S2,s);
S1E1M2CX_DE1S1_asymmetry = s[0]; S1E1M2CX_DE1S2_asymmetry = s[1]; S1E1M2CX_DM1S1_asymmetry = s[2]; S1E1M2CX_DM1S2_asymmetry = s[3]; S1E1M2CX_DE2S1_asymmetry = s[4]; S1E1M2CX_DE2S2_asymmetry = s[5]; S1E1M2CX_DM2S1_asymmetry = s[6]; S1E1M2CX_DM2S2_asymmetry = s[7];
} else {
S1E1M2CX_rec = S1E1M2CX_DE1S1 = S1E1M2CX_DM1S1 = S1E1M2CX_DE2S1 = S1E1M2CX_DM2S1 = S1E1M2CX_DCS1 = S1E1M2CX_DIS1 = S1E1M2CX_DXS1 = S1E1M2CX_DYS1 = S1E1M2CX_DE1S2 = S1E1M2CX_DM1S2 = S1E1M2CX_DE2S2 = S1E1M2CX_DM2S2 = S1E1M2CX_DCS2 = S1E1M2CX_DIS2 = S1E1M2CX_DXS2 = S1E1M2CX_DYS2 = S1E1M2CX_DE1S1_asymmetry = S1E1M2CX_DE1S2_asymmetry = S1E1M2CX_DM1S1_asymmetry = S1E1M2CX_DM1S2_asymmetry = S1E1M2CX_DE2S1_asymmetry = S1E1M2CX_DE2S2_asymmetry = S1E1M2CX_DM2S1_asymmetry = S1E1M2CX_DM2S2_asymmetry = 0;
}
// S1E1M2CX/MGE complexes
int S1E1M2CX_total_inf = 0;
for (int m = 0; m < NO_M_COMPARTMENTS; m++) {