Manually updating files (removing comments and unnecessary outputs) d…

…ue to error when using git subtree push command -> maybe I am doing it in a wrong order and first do a git subtree push and the a git push?

Genome.cpp

@@ -124,14 +124,12 @@ void Chromosome::inherit(const Chromosome* parentChr, const short posn, const sh
 	for (int i = 0; i < nloc; i++) {
 		if (diploid) {
 			pLoci[i].allele[posn] = parentChr->pLoci[i].allele[ix];
-		    if (probcross >1) Rcpp::Rcout << "Crossover probability: " << probcross << std::endl;
 			if (pRandom->Bernoulli(probcross)) { // crossover occurs
 				if (ix == 0) ix = 1; else ix = 0;
 			}
 		}
 		else
 			pLoci[i].allele[posn] = parentChr->pLoci[i].allele[0];
-		if (probmutn >1) Rcpp::Rcout << "Mutation probability: " << probmutn << std::endl;
 		if (pRandom->Bernoulli(probmutn)) { // mutation occurs
 			double intbase = INTBASE;
 #if RSDEBUG

Individual.cpp

@@ -37,7 +37,6 @@ Individual::Individual(Cell* pCell, Patch* pPatch, short stg, short a, short rep
 	indCounter++; // unique identifier for each individual
 
 	stage = stg;
-	if (probmale > 1) Rcpp::Rcout << "probmale = " << probmale << std::endl;
 	if (probmale <= 0.0) sex = 0;
 	else sex = pRandom->Bernoulli(probmale);
 	age = a;
@@ -922,7 +921,6 @@ int Individual::moveKernel(Landscape* pLandscape, Species* pSpecies,
 	// scale the appropriate kernel mean to the cell size
 	if (trfr.twinKern)
 	{
-	    if (kern.probKern1 > 1) Rcpp::Rcout << "probKern1 = " << kern.probKern1<< std::endl;
 		if (pRandom->Bernoulli(kern.probKern1))
 			meandist = kern.meanDist1 / (float)land.resol;
 		else
@@ -1051,7 +1049,6 @@ int Individual::moveKernel(Landscape* pLandscape, Species* pSpecies,
 		else {
 			dispmort = mort.fixedMort;
 		}
-		if(dispmort > 1) Rcpp::Rcout << "dispmort = " << dispmort << std::endl;
 		if (pRandom->Bernoulli(dispmort)) {
 			status = 7; // dies
 			dispersing = 0;
@@ -1113,7 +1110,6 @@ int Individual::moveStep(Landscape* pLandscape, Species* pSpecies,
 	if (pPatch == pNatalPatch && path->out == 0 && path->year == path->total) {
 		mortprob = 0.0;
 	}
-	if (mortprob > 1) Rcpp::Rcout << "mortprob = " << mortprob << std::endl;
 	if (pRandom->Bernoulli(mortprob)) { // individual dies
 		status = 7;
 		dispersing = 0;

Population.cpp

@@ -475,7 +475,6 @@ void Population::reproduction(const float localK, const float envval, const int
 					// determine whether she must miss current breeding attempt
 					ind = inds[i]->getStats();
 					if (ind.fallow >= sstruct.repInterval) {
-					    if(sstruct.probRep > 1) Rcpp::Rcout << "probRep: " << sstruct.probRep << std::endl;
 						if (pRandom->Bernoulli(sstruct.probRep)) skipbreeding = false;
 						else skipbreeding = true;
 					}
@@ -540,7 +539,6 @@ void Population::reproduction(const float localK, const float envval, const int
 						// determine whether she must miss current breeding attempt
 						ind = inds[i]->getStats();
 						if (ind.fallow >= sstruct.repInterval) {
-						    if(sstruct.probRep > 1) Rcpp::Rcout << "probRep: " << sstruct.probRep << std::endl;
 							if (pRandom->Bernoulli(sstruct.probRep)) skipbreeding = false;
 							else skipbreeding = true;
 						}
@@ -757,7 +755,6 @@ void Population::emigration(float localK)
 
 
 			} // end of no individual variability
-			if (disp > 1) Rcpp::Rcout << "disp: " << disp << std::endl;
 			disp = pRandom->Bernoulli(Pdisp);
 
 			if (disp == 1) { // emigrant
@@ -955,8 +952,6 @@ int Population::transfer(Landscape* pLandscape, short landIx)
 								settprob = settDD.s0 /
 									(1.0 + exp(-(popsize / localK - (double)settDD.beta) * (double)settDD.alpha));
 
-								if (settprob > 1) Rcpp::Rcout << "settprob: " << settprob << std::endl;
-
 								if (pRandom->Bernoulli(settprob)) { // settlement allowed
 									densdepOK = true;
 									settle.settleStatus = 2;
@@ -1238,13 +1233,11 @@ void Population::survival0(float localK, short option0, short option1)
 			if (ind.status < 6 || ind.status == 10) { // not already doomed
 				double probsurv = surv[ind.stage][ind.sex];
 				// does the individual survive?
-				if (probsurv > 1) Rcpp::Rcout << "probsurv at stage: " << ind.stage << " and sex " << ind.sex << " : " << probsurv << std::endl;
 				if (pRandom->Bernoulli(probsurv)) { // survives
 					// does the individual develop?
 					double probdev = dev[ind.stage][ind.sex];
 					if (ind.stage < nStages - 1) { // not final stage
 						if (ind.age >= minAge[ind.stage + 1][ind.sex]) { // old enough to enter next stage
-						    if (probdev > 1) Rcpp::Rcout << "probdev: " << probdev << std::endl;
 							if (pRandom->Bernoulli(probdev)) {
 								inds[i]->developing();
 							}
@@ -1833,18 +1826,6 @@ Individual* Population::catchIndividual( // Translocate a set of individuals wit
     }
 }
 
-// ---------------------------------------------------------------------------
-// // Add a specified individual to the new or current population of a patch
-// void Population::recruitTranslocated(Individual* catched_individual) {
-//     Rcpp::Rcout << "Recruit translocated individual" << endl;
-//     Rcpp::Rcout << "Individual ID: " << catched_individual->getId() << endl;
-//     Rcpp::Rcout << "Size of population" << getNInds() << endl;
-//     inds.push_back(catched_individual);
-//     Rcpp::Rcout << "Size of population after translocation" << getNInds() << endl;
-//     indStats ind = catched_individual->getStats();
-//     nInds[ind.stage][ind.sex]++;
-// }
-
 // ---------------------------------------------------------------------------
 bool Population::getSizeSampledInds(
 ){