adjust ids versus indices in recipe 5.3.1

Author: bhaller

QtSLiM/recipes/Recipe 5.3.1 - Migration and admixture, A linear stepping-stone model.txt

@@ -1,19 +1,19 @@
 // Keywords: migration, dispersal
 
 initialize() {
+	defineConstant("COUNT", 10);
 	initializeMutationRate(1e-7);
 	initializeMutationType("m1", 0.5, "f", 0.0);
 	initializeGenomicElementType("g1", m1, 1.0);
 	initializeGenomicElement(g1, 0, 99999);
 	initializeRecombinationRate(1e-8);
 }
 1 early() {
-	subpopCount = 10;
-	for (i in 1:subpopCount)
+	for (i in 0:(COUNT-1))
 		sim.addSubpop(i, 500);
-	for (i in 2:subpopCount)
-		sim.subpopulations[i-1].setMigrationRates(i-1, 0.2);
-	for (i in 1:(subpopCount-1))
-		sim.subpopulations[i-1].setMigrationRates(i+1, 0.05);
+	
+	subpops = sim.subpopulations;
+	for (i in 1:(COUNT-1)) subpops[i].setMigrationRates(i-1, 0.2);
+	for (i in 0:(COUNT-2)) subpops[i].setMigrationRates(i+1, 0.05);
 }
 10000 late() { sim.outputFixedMutations(); }

SLiMgui/Recipes/Recipe 5.3.1 - Migration and admixture, A linear stepping-stone model.txt

@@ -1,19 +1,19 @@
 // Keywords: migration, dispersal
 
 initialize() {
+	defineConstant("COUNT", 10);
 	initializeMutationRate(1e-7);
 	initializeMutationType("m1", 0.5, "f", 0.0);
 	initializeGenomicElementType("g1", m1, 1.0);
 	initializeGenomicElement(g1, 0, 99999);
 	initializeRecombinationRate(1e-8);
 }
 1 early() {
-	subpopCount = 10;
-	for (i in 1:subpopCount)
+	for (i in 0:(COUNT-1))
 		sim.addSubpop(i, 500);
-	for (i in 2:subpopCount)
-		sim.subpopulations[i-1].setMigrationRates(i-1, 0.2);
-	for (i in 1:(subpopCount-1))
-		sim.subpopulations[i-1].setMigrationRates(i+1, 0.05);
+	
+	subpops = sim.subpopulations;
+	for (i in 1:(COUNT-1)) subpops[i].setMigrationRates(i-1, 0.2);
+	for (i in 0:(COUNT-2)) subpops[i].setMigrationRates(i+1, 0.05);
 }
 10000 late() { sim.outputFixedMutations(); }

VERSIONS

@@ -41,6 +41,7 @@ development head (in the master branch):
 	fix a bug that would cause failures to write buffered compressed data from writeFile(), only in SLiMgui; these failures were not reported to the user well (only through SLiMgui's stderr)
 	recipe 14.7 is a ground-up rewrite, to show the utility of using marker mutations to track true local ancestry, including live plotting in SLiMgui
 	add estimatedLastTick() method to Community; useful for custom plotting where you want to know the span of the model up front, to set an axis range, for example
+	adjusted recipe 5.3.1 to use zero-based subpopulation ids, simplifying the logic; the workshop uses this recipe and it was a common source of confusion
 
 
 version 4.1 (Eidos version 3.1):