add terminology autofixes, revise recipes and cal...() functions

QtSLiM/recipes.qrc

@@ -4,7 +4,7 @@
         <file>recipes/Recipe 4.1 - A basic neutral simulation.txt</file>
         <file>recipes/Recipe 4.2.1 - Basic output, Entire population.txt</file>
         <file>recipes/Recipe 4.2.2 - Basic output, Random population sample.txt</file>
-        <file>recipes/Recipe 4.2.3 - Basic output, Sampling individuals rather than genomes.txt</file>
+        <file>recipes/Recipe 4.2.3 - Basic output, Sampling individuals rather than haplosomes.txt</file>
         <file>recipes/Recipe 4.2.4 - Basic output, Substitutions.txt</file>
         <file>recipes/Recipe 4.2.5 - Basic output, Automatic logging with LogFile.txt</file>
         <file>recipes/Recipe 4.2.6 - Basic output, Custom output with Eidos.txt</file>

QtSLiM/recipes/Recipe 10.3.1 - Fitness as a function of genomic background, Epistasis I.txt

@@ -18,9 +18,9 @@ initialize() {
 1 early() { sim.addSubpop("p1", 500); }
 10000 early() { sim.simulationFinished(); }
 mutationEffect(m3) {
-	if (individual.genome1.countOfMutationsOfType(m2))
+	if (individual.haplosomesFromParent1.countOfMutationsOfType(m2))
 		return 0.5;
-	else if (individual.genome2.countOfMutationsOfType(m2))
+	else if (individual.haplosomesFromParent2.countOfMutationsOfType(m2))
 		return 0.5;
 	else
 		return effect;

QtSLiM/recipes/Recipe 10.3.1 - Fitness as a function of genomic background, Epistasis II.txt

@@ -20,9 +20,9 @@ initialize() {
 1 early() { sim.addSubpop("p1", 500); }
 10000 early() { sim.simulationFinished(); }
 mutationEffect(m3) {
-	if (individual.genome1.countOfMutationsOfType(m2))
+	if (individual.haplosomesFromParent1.countOfMutationsOfType(m2))
 		return 0.5;
-	else if (individual.genome2.countOfMutationsOfType(m2))
+	else if (individual.haplosomesFromParent2.countOfMutationsOfType(m2))
 		return 0.5;
 	else
 		return effect;

QtSLiM/recipes/Recipe 10.4.3 - Fitness as a function of population composition, Kin selection and the green-beard effect.txt

@@ -12,7 +12,7 @@ initialize() {
 }
 1 early() { sim.addSubpop("p1", 500); }
 1 late() {
-	target = sample(p1.genomes, 100);
+	target = sample(p1.haplosomes, 100);
 	target.addNewDrawnMutation(m2, 10000);
 }
 1: late() {

QtSLiM/recipes/Recipe 11.1 - Assortative mating.txt

@@ -16,7 +16,7 @@ initialize() {
 	p2.setMigrationRates(p1, 0.1);
 }
 1000 late() {
-	target = sample(p1.genomes, 1);
+	target = sample(p1.haplosomes, 1);
 	target.addNewDrawnMutation(m2, 10000);
 }
 mutationEffect(m2, p2) { return 0.2; }
@@ -40,7 +40,7 @@ mutationEffect(m2, p2) { return 0.2; }
 		return weights * sourceSubpop.getValue("weights2");
 }
 10000: late() {
-	FST = calcFST(p1.genomes, p2.genomes);
+	FST = calcFST(p1.haplosomes, p2.haplosomes);
 	sim.setValue("FST", sim.getValue("FST") + FST);
 }
 19999 late() {

QtSLiM/recipes/Recipe 11.3 - Gametophytic self-incompatibility.txt

@@ -17,9 +17,9 @@ initialize() {
 	cat("m2 mutation count: " + sim.countOfMutationsOfType(m2) + "\n");
 }
 modifyChild(p1) {
-	pollenSMuts = child.genome2.mutationsOfType(m2);
-	styleSMuts1 = parent1.genome1.mutationsOfType(m2);
-	styleSMuts2 = parent1.genome2.mutationsOfType(m2);
+	pollenSMuts = child.haplosomesFromParent2.mutationsOfType(m2);
+	styleSMuts1 = parent1.haplosomesFromParent1.mutationsOfType(m2);
+	styleSMuts2 = parent1.haplosomesFromParent2.mutationsOfType(m2);
 	if (identical(pollenSMuts, styleSMuts1))
 		if (runif(1) < 0.99)
 			return F;

QtSLiM/recipes/Recipe 12.2 - Lethal epistasis I.txt

@@ -15,12 +15,12 @@ initialize() {
 	sim.addSubpop("p1", 500);
 }
 1 late() {
-	sample(p1.genomes, 20).addNewDrawnMutation(m2, 10000);  // add A
-	sample(p1.genomes, 20).addNewDrawnMutation(m3, 20000);  // add B
+	sample(p1.haplosomes, 20).addNewDrawnMutation(m2, 10000);  // add A
+	sample(p1.haplosomes, 20).addNewDrawnMutation(m3, 20000);  // add B
 }
 modifyChild() {
-	hasMutA = any(child.genomes.countOfMutationsOfType(m2) > 0);
-	hasMutB = any(child.genomes.countOfMutationsOfType(m3) > 0);
+	hasMutA = any(child.haplosomes.countOfMutationsOfType(m2) > 0);
+	hasMutB = any(child.haplosomes.countOfMutationsOfType(m3) > 0);
 	if (hasMutA & hasMutB)
 		return F;
 	return T;

QtSLiM/recipes/Recipe 12.2 - Lethal epistasis II.txt

@@ -15,12 +15,12 @@ initialize() {
 	sim.addSubpop("p1", 500);
 }
 1 late() {
-	sample(p1.genomes, 20).addNewDrawnMutation(m2, 10000);  // add A
-	sample(p1.genomes, 20).addNewDrawnMutation(m3, 20000);  // add B
+	sample(p1.haplosomes, 20).addNewDrawnMutation(m2, 10000);  // add A
+	sample(p1.haplosomes, 20).addNewDrawnMutation(m3, 20000);  // add B
 }
 modifyChild() {
-	mutACount = sum(child.genomes.countOfMutationsOfType(m2));
-	mutBCount = sum(child.genomes.countOfMutationsOfType(m3));
+	mutACount = sum(child.haplosomes.countOfMutationsOfType(m2));
+	mutBCount = sum(child.haplosomes.countOfMutationsOfType(m3));
 	if ((mutACount == 2) & (mutBCount == 2))
 		return F;
 	return T;

QtSLiM/recipes/Recipe 12.3 - Simulating gene drive.txt

@@ -17,7 +17,7 @@ initialize() {
 		sim.subpopulations[i].setMigrationRates(i+1, 0.1);
 }
 100 late() {
-	p0.genomes[0:49].addNewDrawnMutation(m2, 10000);
+	p0.haplosomes[0:49].addNewDrawnMutation(m2, 10000);
 }
 100:10000 late() {
 	if (sim.countOfMutationsOfType(m2) == 0)
@@ -34,12 +34,12 @@ mutationEffect(m2) {
 	mut = sim.mutationsOfType(m2);
 	if (size(mut) == 1)
 	{
-		hasMutOnChromosome1 = child.genome1.containsMutations(mut);
-		hasMutOnChromosome2 = child.genome2.containsMutations(mut);
+		hasMutOnChromosome1 = child.haplosomesFromParent1.containsMutations(mut);
+		hasMutOnChromosome2 = child.haplosomesFromParent2.containsMutations(mut);
 		if (hasMutOnChromosome1 & !hasMutOnChromosome2)
-			child.genome2.addMutations(mut);
+			child.haplosomesFromParent2.addMutations(mut);
 		else if (hasMutOnChromosome2 & !hasMutOnChromosome1)
-			child.genome1.addMutations(mut);
+			child.haplosomesFromParent1.addMutations(mut);
 	}
 	return T;
 }

QtSLiM/recipes/Recipe 13.1 - Polygenic selection.txt

@@ -15,7 +15,7 @@ initialize() {
 }
 1 early() { sim.addSubpop("p1", 500); }
 fitnessEffect() {
-	phenotype = sum(individual.genomes.countOfMutationsOfType(m2));
+	phenotype = sum(individual.haplosomes.countOfMutationsOfType(m2));
 	return 1.5 - (phenotype - 10.0)^2 * 0.005;
 }
 5000 late() {

QtSLiM/recipes/Recipe 13.3 - A model of discrete QTL effects with a structured chromosome.txt

@@ -52,7 +52,7 @@ initialize() {
 	community.registerEarlyEvent("s2", s1.source, 2, 2);
 
 	// optional: give m2 mutations to everyone, as standing variation
-	g = sim.subpopulations.genomes;
+	g = sim.subpopulations.haplosomes;
 
 	for (q in Q)
 	{

QtSLiM/recipes/Recipe 13.5 - A QTL-based model with two quantitative phenotypic traits and pleiotropy.txt

@@ -71,7 +71,7 @@ late() {
 	for (ind in sim.subpopulations.individuals)
 	{
 		// construct phenotypes from additive effects of QTL mutations
-		muts = ind.genomes.mutationsOfType(m2);
+		muts = ind.haplosomes.mutationsOfType(m2);
 		phenotype0 = size(muts) ? sum(muts.getValue("e0")) else 0.0;
 		phenotype1 = size(muts) ? sum(muts.getValue("e1")) else 0.0;
 		ind.setValue("phenotype0", phenotype0);

QtSLiM/recipes/Recipe 14.1 - Relatedness, inbreeding, and heterozygosity.txt

@@ -17,6 +17,6 @@ mateChoice() {
 }
 1000 late() {
 	// Print mean heterozygosity across the population
-	heterozygosity = calcHeterozygosity(p1.genomes);
+	heterozygosity = calcHeterozygosity(p1.haplosomes);
 	cat("Mean heterozygosity = " + heterozygosity + "\n");
 }

QtSLiM/recipes/Recipe 14.11 - Modeling microsatellites.txt

@@ -21,14 +21,14 @@ initialize() {
 	sim.addSubpop("p1", 500);
 
 	// create some microsatellites at random positions
-	genomes = sim.subpopulations.genomes;
+	haplosomes = sim.subpopulations.haplosomes;
 	positions = rdunif(msatCount, 0, L-1);
 	repeats = rpois(msatCount, 20) + 5;
 
 	for (msatIndex in 0:(msatCount-1))
 	{
 		pos = positions[msatIndex];
-		mut = genomes.addNewDrawnMutation(m2, pos);
+		mut = haplosomes.addNewDrawnMutation(m2, pos);
 		mut.tag = repeats[msatIndex];
 	}
 
@@ -37,14 +37,14 @@ initialize() {
 }
 modifyChild() {
 	// mutate microsatellites with rate msatMu
-	for (genome in child.genomes)
+	for (haplosome in child.haplosomes)
 	{
 		mutCount = rpois(1, msatMu * msatCount);
 
 		if (mutCount)
 		{
 			mutSites = sample(msatPositions, mutCount);
-			msats = genome.mutationsOfType(m2);
+			msats = haplosome.mutationsOfType(m2);
 
 			for (mutSite in mutSites)
 			{
@@ -66,15 +66,15 @@ modifyChild() {
 
 					if (matchingMut.size() == 1)
 					{
-						genome.removeMutations(msat);
-						genome.addMutations(matchingMut);
+						haplosome.removeMutations(msat);
+						haplosome.addMutations(matchingMut);
 						next;
 					}
 				}
 
 				// make a new mutation with the new repeat count
-				genome.removeMutations(msat);
-				msat = genome.addNewDrawnMutation(m2, mutSite);
+				haplosome.removeMutations(msat);
+				msat = haplosome.addNewDrawnMutation(m2, mutSite);
 				msat.tag = repeats;
 			}
 		}

QtSLiM/recipes/Recipe 14.12 - Modeling transposable elements.txt

@@ -28,22 +28,22 @@ initialize() {
 	sim.tag = 0;	// the next unique tag value to use for TEs
 
 	// create some transposons at random positions
-	genomes = sim.subpopulations.genomes;
+	haplosomes = sim.subpopulations.haplosomes;
 	positions = rdunif(teInitialCount, 0, L-1);
 
 	for (teIndex in 0:(teInitialCount-1))
 	{
 		pos = positions[teIndex];
-		mut = genomes.addNewDrawnMutation(m2, pos);
+		mut = haplosomes.addNewDrawnMutation(m2, pos);
 		mut.tag = sim.tag;
 		sim.tag = sim.tag + 1;
 	}
 }
 modifyChild() {
 	// disable transposons with rate teDisableP
-	for (genome in child.genomes)
+	for (haplosome in child.haplosomes)
 	{
-		tes = genome.mutationsOfType(m2);
+		tes = haplosome.mutationsOfType(m2);
 		teCount = tes.size();
 		mutatedCount = teCount ? rpois(1, teCount * teDisableP) else 0;
 
@@ -59,14 +59,14 @@ modifyChild() {
 				if (size(disabledTE))
 				{
 					// use the existing disabled TE mutation
-					genome.removeMutations(te);
-					genome.addMutations(disabledTE);
+					haplosome.removeMutations(te);
+					haplosome.addMutations(disabledTE);
 					next;
 				}
 
 				// make a new disabled TE mutation with the right tag
-				genome.removeMutations(te);
-				disabledTE = genome.addNewDrawnMutation(m3, te.position);
+				haplosome.removeMutations(te);
+				disabledTE = haplosome.addNewDrawnMutation(m3, te.position);
 				disabledTE.tag = te.tag;
 			}
 		}
@@ -78,9 +78,9 @@ late() {
 	// make active transposons copy themselves with rate teJumpP
 	for (individual in sim.subpopulations.individuals)
 	{
-		for (genome in individual.genomes)
+		for (haplosome in individual.haplosomes)
 		{
-			tes = genome.mutationsOfType(m2);
+			tes = haplosome.mutationsOfType(m2);
 			teCount = tes.size();
 			jumpCount = teCount ? rpois(1, teCount * teJumpP) else 0;
 
@@ -92,7 +92,7 @@ late() {
 				{
 					// make a new TE mutation
 					pos = rdunif(1, 0, L-1);
-					jumpTE = genome.addNewDrawnMutation(m2, pos);
+					jumpTE = haplosome.addNewDrawnMutation(m2, pos);
 					jumpTE.tag = sim.tag;
 					sim.tag = sim.tag + 1;
 				}
@@ -104,7 +104,7 @@ late() {
 	// print information on each TE, including the fraction of it disabled
 	all_tes = sortBy(sim.mutationsOfType(m2), "position");
 	all_disabledTEs = sortBy(sim.mutationsOfType(m3), "position");
-	genomeCount = size(sim.subpopulations.genomes);
+	haplosomeCount = size(sim.subpopulations.haplosomes);
 
 	catn("Active TEs:");
 	for (te in all_tes)
@@ -126,7 +126,7 @@ late() {
 
 		total = active + disabled;
 
-		cat("frequency " + format("%0.3f", total / genomeCount) + ", ");
+		cat("frequency " + format("%0.3f", total / haplosomeCount) + ", ");
 		catn(round(active / total * 100) + "% active");
 	}
 

QtSLiM/recipes/Recipe 14.15 - Modeling biallelic loci with a mutation() callback I.txt

@@ -24,7 +24,7 @@ initialize() {
 	sim.addSubpop("p1", 100);
 
 	// create the canonical mutation objects
-	target = p1.genomes[0];
+	target = p1.haplosomes[0];
 	target.addNewDrawnMutation(m2, 0:99);
 	defineConstant("MUT2", target.mutations);
 	target.removeMutations();
@@ -33,7 +33,7 @@ initialize() {
 	target.removeMutations();
 
 	// start homozygous "aa" at every position
-	p1.genomes.addMutations(MUT3);
+	p1.haplosomes.addMutations(MUT3);
 
 	// log results
 	log = community.createLogFile("freq.csv", logInterval=10);

QtSLiM/recipes/Recipe 14.15 - Modeling biallelic loci with a mutation() callback II.txt

@@ -22,7 +22,7 @@ initialize() {
 	sim.addSubpop("p1", 100);
 
 	// create the permanent m2 mutation objects we will use
-	target = p1.genomes[0];
+	target = p1.haplosomes[0];
 	target.addNewDrawnMutation(m2, 0:99);
 	defineConstant("MUT", target.mutations);
 
@@ -37,7 +37,7 @@ initialize() {
 mutation(m3) {
 	// if we already have an m2 mutation at the site, allow
 	// the new m3 mutation; we will remove the stack below
-	if (genome.containsMarkerMutation(m2, mut.position))
+	if (haplosome.containsMarkerMutation(m2, mut.position))
 		return T;
 
 	// no m2 mutation is present, so unique down
@@ -51,18 +51,18 @@ late() {
 	// if so, we have m2/m3 stacked mutations to remove
 	if (m3muts.length() > 0)
 	{
-		genomes = sim.subpopulations.genomes;
-		counts = genomes.countOfMutationsOfType(m3);
-		hasStacked = genomes[counts > 0];
+		haplosomes = sim.subpopulations.haplosomes;
+		counts = haplosomes.countOfMutationsOfType(m3);
+		hasStacked = haplosomes[counts > 0];
 
-		for (genome in hasStacked)
+		for (haplosome in hasStacked)
 		{
-			stacked_m3 = genome.mutationsOfType(m3);
+			stacked_m3 = haplosome.mutationsOfType(m3);
 			stackPositions = stacked_m3.position;
-			all_m2 = genome.mutationsOfType(m2);
+			all_m2 = haplosome.mutationsOfType(m2);
 			s = (match(all_m2.position, stackPositions) >= 0);
 			stacked_m2 = all_m2[s];
-			genome.removeMutations(c(stacked_m3, stacked_m2));
+			haplosome.removeMutations(c(stacked_m3, stacked_m2));
 		}
 	}
 }

QtSLiM/recipes/Recipe 14.3 - Reading initial simulation state from an MS output file II.txt

@@ -38,15 +38,15 @@ initialize() {
 	if (parts[0] != "positions:") stop("Missing positions.");
 	positions = asFloat(parts[1:(size(parts)-1)]);
 
-	// create all mutations in a genome in a dummy subpopulation
+	// create all mutations in a haplosome in a dummy subpopulation
 	sim.addSubpop("p2", 1);
-	g = p2.genomes[0];
-	L = sim.chromosome.lastPosition;
+	g = p2.haplosomes[0];
+	L = sim.chromosomes.lastPosition;
 	intPositions = asInteger(round(positions * L));
 	muts = g.addNewMutation(m1, 0.0, intPositions);
 
-	// add the appropriate mutations to each genome
-	for (g in p1.genomes)
+	// add the appropriate mutations to each haplosome
+	for (g in p1.haplosomes)
 	{
 		f = asLogical(asInteger(strsplit(lines[index], "")));
 		index = index + 1;