shift some recipes over to using killIndividuals()

Author: bhaller

QtSLiM/recipes/Recipe 16.19 - Range expansion in a stepping-stone model II.txt

@@ -44,14 +44,11 @@ reproduction() {
 early() {
 	// non-overlapping generations; kill off the parental generation
 	inds = sim.subpopulations.individuals;
-	inds[inds.age > 0].fitnessScaling = 0.0;
+	sim.killIndividuals(inds[inds.age > 0]);
 
 	// pre-migration density-dependent fitness for each subpop
 	for (subpop in sim.subpopulations)
-	{
-		juvenileCount = sum(subpop.individuals.age == 0);
-		subpop.fitnessScaling = K / juvenileCount;
-	}
+		subpop.fitnessScaling = K / subpop.individualCount;
 }
 survival() {
 	// honor SLiM's survival decision

QtSLiM/recipes/Recipe 16.5 - A metapopulation extinction-colonization model.txt

@@ -40,7 +40,7 @@ early() {
 	for (subpop in sim.subpopulations)
 	{
 		if (runif(1) < e)
-			subpop.fitnessScaling = 0.0;
+			sim.killIndividuals(subpop.individuals);
 		else
 			subpop.fitnessScaling = K / subpop.individualCount;
 	}

QtSLiM/recipes/Recipe 19.8 - Within-host reproduction in a host-pathogen model.txt

@@ -49,7 +49,6 @@ species pathogen reproduction() {
 
 ticks all 1 early() {
 	monkey.addSubpop("p1", K_MONKEY);
-	monkey.addSubpop("p2", 0);   // temporary graveyard
 
 	// choose initial hosts carrying the infection
 	initial_hosts = p1.sampleIndividuals(5, replace=F);
@@ -128,10 +127,9 @@ ticks all early() {
 		}
 		else if (runif(1) < P_death)
 		{
-			// the host has died; move to the graveyard until the next monkey cycle
+			// the host has died; kill it and its pathogens
 			host = monkey.individualsWithPedigreeIDs(pathogenSubpop.tag);
-			host.color = "black";
-			p2.takeMigrants(host);
+			monkey.killIndividuals(host);
 			pathogenSubpop.removeSubpopulation();
 		}
 	}
@@ -167,9 +165,5 @@ species monkey survival(p1) {
 	}
 	return NULL;
 }
-species monkey survival(p2) {
-	// all monkeys in the temporary graveyard are dead
-	return F;
-}
 
 ticks all 2000 late() { }

SLiMgui/Recipes/Recipe 16.19 - Range expansion in a stepping-stone model II.txt

@@ -44,14 +44,11 @@ reproduction() {
 early() {
 	// non-overlapping generations; kill off the parental generation
 	inds = sim.subpopulations.individuals;
-	inds[inds.age > 0].fitnessScaling = 0.0;
+	sim.killIndividuals(inds[inds.age > 0]);
 
 	// pre-migration density-dependent fitness for each subpop
 	for (subpop in sim.subpopulations)
-	{
-		juvenileCount = sum(subpop.individuals.age == 0);
-		subpop.fitnessScaling = K / juvenileCount;
-	}
+		subpop.fitnessScaling = K / subpop.individualCount;
 }
 survival() {
 	// honor SLiM's survival decision

SLiMgui/Recipes/Recipe 16.5 - A metapopulation extinction-colonization model.txt

@@ -40,7 +40,7 @@ early() {
 	for (subpop in sim.subpopulations)
 	{
 		if (runif(1) < e)
-			subpop.fitnessScaling = 0.0;
+			sim.killIndividuals(subpop.individuals);
 		else
 			subpop.fitnessScaling = K / subpop.individualCount;
 	}

SLiMgui/Recipes/Recipe 19.8 - Within-host reproduction in a host-pathogen model.txt

@@ -49,7 +49,6 @@ species pathogen reproduction() {
 
 ticks all 1 early() {
 	monkey.addSubpop("p1", K_MONKEY);
-	monkey.addSubpop("p2", 0);   // temporary graveyard
 
 	// choose initial hosts carrying the infection
 	initial_hosts = p1.sampleIndividuals(5, replace=F);
@@ -128,10 +127,9 @@ ticks all early() {
 		}
 		else if (runif(1) < P_death)
 		{
-			// the host has died; move to the graveyard until the next monkey cycle
+			// the host has died; kill it and its pathogens
 			host = monkey.individualsWithPedigreeIDs(pathogenSubpop.tag);
-			host.color = "black";
-			p2.takeMigrants(host);
+			monkey.killIndividuals(host);
 			pathogenSubpop.removeSubpopulation();
 		}
 	}
@@ -167,9 +165,5 @@ species monkey survival(p1) {
 	}
 	return NULL;
 }
-species monkey survival(p2) {
-	// all monkeys in the temporary graveyard are dead
-	return F;
-}
 
 ticks all 2000 late() { }

VERSIONS

@@ -125,6 +125,8 @@ development head (in the master branch):
 			change fitness(NULL) callbacks to be called fitnessEffect() callbacks
 			split registerFitnessCallback() into registerMutationEffectCallback() and registerFitnessEffectCallback()
 		add display of the Git SHA-1 hash in slim and SLiMgui, to aid in debugging; works for builds under cmake and qmake, not under Xcode
+		add a "progress indicator" in SLiMgui, in the Tick counter lineedit, that shows the progress towards the last tick the model will execute (assuming it doesn't stop early)
+		shift recipes 16.5, 16.19, and 19.8 to use killIndividuals(), for pedagogical purposes
 
 
 version 3.7.1 (Eidos version 2.7.1):