Merge branch 'multichrom' into multi_ts

Author: bhaller

QtSLiM/recipes.qrc

@@ -2,6 +2,7 @@
     <qresource prefix="/">
         <file>recipes/_README.txt</file>
         <file>recipes/Recipe 4.1 - A basic neutral simulation.txt</file>
+        <file>recipes/Recipe 4.1.10 - Using symbolic constants for model parameters.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 haplosomes.txt</file>
@@ -29,21 +30,25 @@
         <file>recipes/Recipe 5.4 - The Gravel et al. (2011) model of human evolution II.txt</file>
         <file>recipes/Recipe 5.5 - Rescaling population sizes to improve simulation performance I.txt</file>
         <file>recipes/Recipe 5.5 - Rescaling population sizes to improve simulation performance II.txt</file>
-        <file>recipes/Recipe 6.1.1 - Recombination, Crossing over (Making a random recombination map).txt</file>
-        <file>recipes/Recipe 6.1.2 - Recombination, Crossing over (Reading a recombination map from a file).txt</file>
-        <file>recipes/Recipe 6.1.3 - Recombination, Gene conversion.txt</file>
-        <file>recipes/Recipe 6.1.4 - Recombination, Multiple chromosomes.txt</file>
-        <file>recipes/Recipe 6.2.1 - Separate sexes, Enabling separate sexes.txt</file>
-        <file>recipes/Recipe 6.2.2 - Separate sexes, Sex ratios I.txt</file>
-        <file>recipes/Recipe 6.2.2 - Separate sexes, Sex ratios II.txt</file>
-        <file>recipes/Recipe 6.2.3 - Separate sexes, Modeling sex-chromosome evolution.txt</file>
-        <file>recipes/Recipe 6.3.1 - Selfing and cloning, Selfing in hermaphroditic populations.txt</file>
-        <file>recipes/Recipe 6.3.2 - Selfing and cloning, Cloning I.txt</file>
-        <file>recipes/Recipe 6.3.2 - Selfing and cloning, Cloning II.txt</file>
-        <file>recipes/Recipe 7.1 - Genomic structure, Part I (Mutation types and fitness effects).txt</file>
-        <file>recipes/Recipe 7.2 - Genomic structure, Part II (Genomic element types).txt</file>
-        <file>recipes/Recipe 7.3 - Genomic structure, Part III (Chromosome organization).txt</file>
-        <file>recipes/Recipe 7.4 - Genomic structure, Part IV (Custom display colors in SLiMgui).txt</file>
+        <file>recipes/Recipe 6.1 - Genomic structure, Part I (Mutation types and fitness effects).txt</file>
+        <file>recipes/Recipe 6.2 - Genomic structure, Part II (Genomic element types).txt</file>
+        <file>recipes/Recipe 6.3 - Genomic structure, Part III (Chromosome organization).txt</file>
+        <file>recipes/Recipe 6.4 - Genomic structure, Part IV (Custom display colors in SLiMgui).txt</file>
+        <file>recipes/Recipe 8.1.1 - Reproduction, Enabling separate sexes.txt</file>
+        <file>recipes/Recipe 8.1.2 - Reproduction, Sex ratios I.txt</file>
+        <file>recipes/Recipe 8.1.2 - Reproduction, Sex ratios II.txt</file>
+        <file>recipes/Recipe 8.1.3 - Reproduction, Selfing in hermaphroditic populations.txt</file>
+        <file>recipes/Recipe 8.1.4 - Reproduction, Cloning I.txt</file>
+        <file>recipes/Recipe 8.1.4 - Reproduction, Cloning II.txt</file>
+        <file>recipes/Recipe 8.2.1 - Recombination, Making a random recombination map.txt</file>
+        <file>recipes/Recipe 8.2.2 - Recombination, Reading a recombination map from a file.txt</file>
+        <file>recipes/Recipe 8.2.3 - Recombination, Unlinked loci.txt</file>
+        <file>recipes/Recipe 8.2.4 - Recombination, Gene conversion.txt</file>
+        <file>recipes/Recipe 8.3.1 - Multiple diploid autosomes.txt</file>
+        <file>recipes/Recipe 8.3.2 - Clonal haploids and chromosome types.txt</file>
+        <file>recipes/Recipe 8.3.3 - Haploids with recombination.txt</file>
+        <file>recipes/Recipe 8.3.4 - Sex-chromosome evolution and null haplosomes.txt</file>
+        <file>recipes/Recipe 8.3.5 - Modeling the full human genome.txt</file>
         <file>recipes/Recipe 9.1 - Introducing adaptive mutations.txt</file>
         <file>recipes/Recipe 9.2 - Making sweeps conditional on fixation.txt</file>
         <file>recipes/Recipe 9.3 - Making sweeps conditional on establishment.txt</file>
@@ -203,6 +208,5 @@
         <file>recipes/Recipe 19.6 - A coevolutionary host-parasitoid trait-matching model.txt</file>
         <file>recipes/Recipe 19.7 - A coevolutionary host-parasite matching-allele model.txt</file>
         <file>recipes/Recipe 19.8 - Within-host reproduction in a host-pathogen model.txt</file>
-        <file>recipes/Recipe 4.1.10 - Using symbolic constants for model parameters.txt</file>
     </qresource>
 </RCC>

…(Mutation types and fitness effects).txt …(Mutation types and fitness effects).txtQtSLiM/recipes/Recipe 7.1 - Genomic structure, Part I (Mutation types and fitness effects).txt renamed to QtSLiM/recipes/Recipe 6.1 - Genomic structure, Part I (Mutation types and fitness effects).txt QtSLiM/recipes/Recipe 7.1 - Genomic structure, Part I (Mutation types and fitness effects).txt renamed to QtSLiM/recipes/Recipe 6.1 - Genomic structure, Part I (Mutation types and fitness effects).txt

@@ -1,12 +1,12 @@
 // Keywords: sexual
 
 initialize() {
+	initializeSex();
 	initializeMutationRate(1e-7);
 	initializeMutationType("m1", 0.5, "f", 0.0);
 	initializeGenomicElementType("g1", m1, 1.0);
 	initializeGenomicElement(g1, 0, 99999);
 	initializeRecombinationRate(1e-8);
-	initializeSex("X");
 }
 1 early() { sim.addSubpop("p1", 500); }
 10000 early() { sim.simulationFinished(); }

QtSLiM/recipes/Recipe 6.1.4 - Recombination, Multiple chromosomes.txt

@@ -1,12 +1,12 @@
 // Keywords: sexual, sex ratio
 
 initialize() {
+	initializeSex();
 	initializeMutationRate(1e-7);
 	initializeMutationType("m1", 0.5, "f", 0.0);
 	initializeGenomicElementType("g1", m1, 1.0);
 	initializeGenomicElement(g1, 0, 99999);
 	initializeRecombinationRate(1e-8);
-	initializeSex("A");
 }
 1 early() { sim.addSubpop("p1", 500, 0.6); }
 10000 early() { sim.simulationFinished(); }

…ure, Part II (Genomic element types).txt …ure, Part II (Genomic element types).txtQtSLiM/recipes/Recipe 7.2 - Genomic structure, Part II (Genomic element types).txt renamed to QtSLiM/recipes/Recipe 6.2 - Genomic structure, Part II (Genomic element types).txt QtSLiM/recipes/Recipe 7.2 - Genomic structure, Part II (Genomic element types).txt renamed to QtSLiM/recipes/Recipe 6.2 - Genomic structure, Part II (Genomic element types).txt

@@ -1,12 +1,12 @@
 // Keywords: sexual, sex ratio
 
 initialize() {
+	initializeSex();
 	initializeMutationRate(1e-7);
 	initializeMutationType("m1", 0.5, "f", 0.0);
 	initializeGenomicElementType("g1", m1, 1.0);
 	initializeGenomicElement(g1, 0, 99999);
 	initializeRecombinationRate(1e-8);
-	initializeSex("A");
 }
 1 early() { sim.addSubpop("p1", 500); }
 1: early() { p1.setSexRatio(runif(1, 0.3, 0.7)); }