// test of genetic entropy
initialize() {
	initializeSLiMModelType("nonWF");
	defineConstant("K", 1000);	// carrying capacity
	
	// set up mutation
	initializeMutationType("m1", 0.5, "f", 0.0); //neutral
	m1.convertToSubstitution = T;
	initializeMutationType("m2", 0.5, "g", -0.5, 0.5); //deleterious
	m2.convertToSubstitution = F;
	initializeMutationType("m3", 0.5, "e", 0.001); //beneficial
	m3.convertToSubstitution = F;
	
	initializeGenomicElementType("g1", c(m1, m2, m3), c(0, 0.99, 0.01)); //fraction of each mut type
	initializeGenomicElement(g1, 0, 5e6); //genome size
	initializeMutationRate(1e-7); 
	initializeRecombinationRate(1e-6);
}

// each individual reproduces once with someone else at random
reproduction() {
	subpop.addCrossed(individual, subpop.sampleIndividuals(1));
}

// create an initial population of 1000 individuals
1 early() {
	sim.addSubpop("p1", 1000);
	log = community.createLogFile("GE_run5.txt", logInterval=100);
	log.addCycle();
	log.addCustomColumn("Population_size", "p1.individualCount;");
	//log.addCustomColumn("Neutral_muts", "sim.countOfMutationsOfType(m1);");
	log.addCustomColumn("Deleterious_muts", "sim.countOfMutationsOfType(m2);");
	log.addCustomColumn("Beneficial_muts", "sim.countOfMutationsOfType(m3);");
	log.addCustomColumn("Mean_fitness", "mean(p1.cachedFitness(NULL));");
	
	
}

// provide density-dependent selection
early() {
	p1.fitnessScaling = K / p1.individualCount;
}

// finish at 50k gens
50000 late() { sim.outputFull(); }