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switch chapter 15/16 recipes, reorganize
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‎QtSLiM/QtSLiMAppDelegate.cpp‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -466,9 +466,9 @@ void QtSLiMAppDelegate::setUpRecipesMenu(QMenu *openRecipesMenu, QAction *findRe
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case 11:chapterName = "Complex mating schemes using mateChoice() callbacks"; break;
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case 12:chapterName = "Direct child modifications using modifyChild() callbacks"; break;
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case 13:chapterName = "Phenotypes, fitness functions, quantitative traits, and QTLs"; break;
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case 14:chapterName = "Advanced models"; break;
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case 15:chapterName = "Continuous-space models and interactions"; break;
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case 16:chapterName = "Going beyond Wright-Fisher models: nonWF model recipes"; break;
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case 14:chapterName = "Advanced WF models"; break;
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case 15:chapterName = "Going beyond Wright-Fisher models: nonWF model recipes"; break;
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case 16:chapterName = "Continuous-space models, interactions, and spatial maps"; break;
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case 17:chapterName = "Tree-sequence recording: tracking population history"; break;
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case 18:chapterName = "Modeling explicit nucleotides"; break;
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case 19:chapterName = "Multispecies modeling"; break;

‎QtSLiM/recipes.qrc‎

Lines changed: 56 additions & 56 deletions
Original file line numberDiff line numberDiff line change
@@ -25,6 +25,8 @@
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<file>recipes/Recipe 5.3.3 - Migration and admixture, A two-dimensional subpopulation matrix.txt</file>
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<file>recipes/Recipe 5.3.4 - Migration and admixture, A random, sparse spatial metapopulation.txt</file>
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<file>recipes/Recipe 5.3.5 - Migration and admixture, Reading a migration matrix from a file.txt</file>
28+
<file>recipes/Recipe 5.4 - The Gravel et al. (2011) model of human evolution I.txt</file>
29+
<file>recipes/Recipe 5.4 - The Gravel et al. (2011) model of human evolution II.txt</file>
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<file>recipes/Recipe 5.5 - Rescaling population sizes to improve simulation performance I.txt</file>
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<file>recipes/Recipe 5.5 - Rescaling population sizes to improve simulation performance II.txt</file>
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<file>recipes/Recipe 6.1.1 - Recombination, Crossing over (Making a random recombination map).txt</file>
@@ -53,6 +55,9 @@
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<file>recipes/Recipe 9.6.2 - A sweep from standing variation at a predetermined locus.txt</file>
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<file>recipes/Recipe 9.7 - Adaptive introgression.txt</file>
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<file>recipes/Recipe 9.8 - Fixation probabilities under Hill-Robertson interference.txt</file>
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<file>recipes/Recipe 9.9 - Keeping a reference to a sweep mutation.txt</file>
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<file>recipes/Recipe 9.10 - Tracking the fate of background mutations.txt</file>
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<file>recipes/Recipe 9.11 - Effective population size versus census population size.txt</file>
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<file>recipes/Recipe 10.1 - Temporally varying selection.txt</file>
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<file>recipes/Recipe 10.2 - Spatially varying selection.txt</file>
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<file>recipes/Recipe 10.3.1 - Fitness as a function of genomic background, Epistasis I.txt</file>
@@ -64,6 +69,7 @@
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<file>recipes/Recipe 10.4.3 - Fitness as a function of population composition, Kin selection and the green-beard effect.txt</file>
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<file>recipes/Recipe 10.5 - Changing selection coefficients with setSelectionCoeff().txt</file>
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<file>recipes/Recipe 10.6 - Varying the dominance coefficient among mutations I.txt</file>
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<file>recipes/Recipe 10.6 - Varying the dominance coefficient among mutations II.txt</file>
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<file>recipes/Recipe 11.1 - Assortative mating.txt</file>
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<file>recipes/Recipe 11.2 - Sequential mate search I.txt</file>
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<file>recipes/Recipe 11.2 - Sequential mate search II.txt</file>
@@ -102,42 +108,55 @@
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<file>recipes/Recipe 14.13 - Modeling opposite ends of a chromosome I.txt</file>
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<file>recipes/Recipe 14.13 - Modeling opposite ends of a chromosome II.txt</file>
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<file>recipes/Recipe 14.14 - Visualizing ancestry and admixture with mutation() callbacks.txt</file>
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<file>recipes/Recipe 15.1 - A simple 2D continuous-space model.txt</file>
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<file>recipes/Recipe 15.2 - Spatial competition.txt</file>
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<file>recipes/Recipe 15.3 - Boundaries and boundary conditions I (stopping boundaries).txt</file>
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<file>recipes/Recipe 15.3 - Boundaries and boundary conditions II (reflecting boundaries).txt</file>
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<file>recipes/Recipe 15.3 - Boundaries and boundary conditions III (absorbing boundaries).txt</file>
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<file>recipes/Recipe 15.3 - Boundaries and boundary conditions IV (reprising boundaries).txt</file>
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<file>recipes/Recipe 15.4 - Mate choice with a spatial kernel.txt</file>
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<file>recipes/Recipe 15.5 - Mate choice with a nearest-neighbor search.txt</file>
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<file>recipes/Recipe 15.6 - Divergence due to phenotypic competition with an interaction() callback.txt</file>
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<file>recipes/Recipe 15.7 - Modeling phenotype as a spatial dimension.txt</file>
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<file>recipes/Recipe 15.8 - Sympatric speciation facilitated by assortative mating.txt</file>
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<file>recipes/Recipe 15.9 - Speciation due to spatial variation in selection.txt</file>
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<file>recipes/Recipe 15.10 - A simple biogeographic landscape model.txt</file>
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<file>recipes/Recipe 15.11 - Local adaptation on a heterogeneous landscape map.txt</file>
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<file>recipes/Recipe 15.12 - Periodic spatial boundaries.txt</file>
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<file>recipes/Recipe 16.1 - A simple nonWF model.txt</file>
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<file>recipes/Recipe 16.2 - Age structure (a life table model).txt</file>
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<file>recipes/Recipe 16.3 - Monogamous mating and variation in litter size.txt</file>
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<file>recipes/Recipe 16.4 - Beneficial mutations and absolute fitness.txt</file>
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<file>recipes/Recipe 16.5 - A metapopulation extinction-colonization model.txt</file>
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<file>recipes/Recipe 16.6 - Habitat choice.txt</file>
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<file>recipes/Recipe 16.7 - Evolutionary rescue after environmental change.txt</file>
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<file>recipes/Recipe 16.8 - Pollen flow.txt</file>
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<file>recipes/Recipe 16.9 - Litter size and parental investment.txt</file>
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<file>recipes/Recipe 16.10 - Spatial competition and spatial mate choice in a nonWF model.txt</file>
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<file>recipes/Recipe 16.11 - A spatial model with carrying-capacity density.txt</file>
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<file>recipes/Recipe 16.13 - Forcing a specific pedigree in a nonWF model I.txt</file>
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<file>recipes/Recipe 16.13 - Forcing a specific pedigree in a nonWF model II.txt</file>
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<file>recipes/Recipe 16.14 - Modeling clonal haploids in a nonWF model with addRecombinant().txt</file>
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<file>recipes/Recipe 16.15 - Modeling clonal haploid bacteria with horizontal gene transfer.txt</file>
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<file>recipes/Recipe 16.17 - Alternation of generations.txt</file>
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<file>recipes/Recipe 16.18 - Meiotic drive.txt</file>
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<file>recipes/Recipe 16.19 - A spatial epidemiological S-I-R model.txt</file>
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<file>recipes/Recipe 16.20 - Range expansion in a stepping-stone model I.txt</file>
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<file>recipes/Recipe 16.20 - Range expansion in a stepping-stone model II.txt</file>
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<file>recipes/Recipe 16.21 - Logistic population growth with the Beverton-Holt model.txt</file>
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<file>recipes/Recipe 14.15 - Modeling biallelic loci with a mutation() callback I.txt</file>
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<file>recipes/Recipe 14.15 - Modeling biallelic loci with a mutation() callback II.txt</file>
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<file>recipes/Recipe 14.16 - Modeling biallelic loci in script.txt</file>
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<file>recipes/Recipe 15.1 - A minimal nonWF model.txt</file>
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<file>recipes/Recipe 15.2 - Age structure (a life table model).txt</file>
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<file>recipes/Recipe 15.3 - Monogamous mating and variation in litter size.txt</file>
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<file>recipes/Recipe 15.4 - Beneficial mutations and absolute fitness.txt</file>
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<file>recipes/Recipe 15.5 - A metapopulation extinction-colonization model.txt</file>
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<file>recipes/Recipe 15.6 - Habitat choice.txt</file>
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<file>recipes/Recipe 15.7 - Evolutionary rescue after environmental change.txt</file>
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<file>recipes/Recipe 15.8 - Pollen flow.txt</file>
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<file>recipes/Recipe 15.9 - Litter size and parental investment.txt</file>
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<file>recipes/Recipe 15.10 - Forcing a specific pedigree in a nonWF model I.txt</file>
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<file>recipes/Recipe 15.10 - Forcing a specific pedigree in a nonWF model II.txt</file>
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<file>recipes/Recipe 15.11 - Modeling clonal haploids in a nonWF model with addRecombinant().txt</file>
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<file>recipes/Recipe 15.12 - Modeling clonal haploid bacteria with horizontal gene transfer.txt</file>
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<file>recipes/Recipe 15.13 - Implementing a Wright-Fisher model with a nonWF model I.txt</file>
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<file>recipes/Recipe 15.13 - Implementing a Wright-Fisher model with a nonWF model II.txt</file>
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<file>recipes/Recipe 15.14 - Alternation of generations.txt</file>
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<file>recipes/Recipe 15.15 - Meiotic drive.txt</file>
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<file>recipes/Recipe 15.16 - Range expansion in a stepping-stone model I.txt</file>
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<file>recipes/Recipe 15.16 - Range expansion in a stepping-stone model II.txt</file>
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<file>recipes/Recipe 15.17 - Logistic population growth with the Beverton-Holt model.txt</file>
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<file>recipes/Recipe 15.18 - Dynamic population structure in nonWF models.txt</file>
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<file>recipes/Recipe 15.19 - Sperm storage with a survival() callback.txt</file>
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<file>recipes/Recipe 15.20 - Tracking separate sexes in script, nonWF style.txt</file>
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<file>recipes/Recipe 15.21 - Modeling haplodiploidy with addRecombinant().txt</file>
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<file>recipes/Recipe 16.1 - A simple 2D continuous-space model.txt</file>
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<file>recipes/Recipe 16.2 - Spatial competition.txt</file>
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<file>recipes/Recipe 16.3 - Boundaries and boundary conditions I (stopping boundaries).txt</file>
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<file>recipes/Recipe 16.3 - Boundaries and boundary conditions II (reflecting boundaries).txt</file>
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<file>recipes/Recipe 16.3 - Boundaries and boundary conditions III (absorbing boundaries).txt</file>
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<file>recipes/Recipe 16.3 - Boundaries and boundary conditions IV (reprising boundaries).txt</file>
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<file>recipes/Recipe 16.3 - Boundaries and boundary conditions V (dispersal kernels).txt</file>
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<file>recipes/Recipe 16.4 - Mate choice with a spatial kernel.txt</file>
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<file>recipes/Recipe 16.5 - Mate choice with a nearest-neighbor search.txt</file>
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<file>recipes/Recipe 16.6 - Divergence due to phenotypic competition with an interaction() callback.txt</file>
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<file>recipes/Recipe 16.7 - Modeling phenotype as a spatial dimension.txt</file>
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<file>recipes/Recipe 16.8 - Sympatric speciation facilitated by assortative mating.txt</file>
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<file>recipes/Recipe 16.9 - Speciation due to spatial variation in selection.txt</file>
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<file>recipes/Recipe 16.10 - A simple biogeographic landscape model.txt</file>
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<file>recipes/Recipe 16.11 - Local adaptation on a heterogeneous landscape map.txt</file>
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<file>recipes/Recipe 16.12 - Periodic spatial boundaries.txt</file>
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<file>recipes/Recipe 16.13 - Density-dependent fecundity with summarizeIndividuals().txt</file>
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<file>recipes/Recipe 16.14 - Directed dispersal with the SpatialMap class.txt</file>
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<file>recipes/Recipe 16.15 - Spatial competition and spatial mate choice in a nonWF model.txt</file>
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<file>recipes/Recipe 16.16 - A spatial model with carrying-capacity density.txt</file>
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<file>recipes/Recipe 16.17 - A spatial epidemiological S-I-R model.txt</file>
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<file>recipes/Recipe 16.18 - A sexual, age-structured spatial model.txt</file>
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<file>recipes/Recipe 17.1 - A minimal tree-seq model.txt</file>
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<file>recipes/Recipe 17.2 - Overlaying neutral mutations.py</file>
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<file>recipes/Recipe 17.3 - Simulation conditional upon fixation of a sweep, preserving ancestry I.txt</file>
@@ -173,19 +192,7 @@
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<file>recipes/Recipe 18.13 - Tree-sequence recording and nucleotide-based models II.py</file>
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<file>recipes/Recipe 18.13 - Tree-sequence recording and nucleotide-based models III.py</file>
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<file>recipes/Recipe 18.14 - Modeling identity by state (IBS) (uniquing mutations with a mutation() callback).txt</file>
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<file>recipes/Recipe 10.6 - Varying the dominance coefficient among mutations II.txt</file>
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<file>recipes/Recipe 5.4 - The Gravel et al. (2011) model of human evolution I.txt</file>
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<file>recipes/Recipe 5.4 - The Gravel et al. (2011) model of human evolution II.txt</file>
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<file>recipes/Recipe 9.9 - Keeping a reference to a sweep mutation.txt</file>
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<file>recipes/Recipe 9.10 - Tracking the fate of background mutations.txt</file>
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<file>recipes/Recipe 16.22 - Dynamic population structure in nonWF models.txt</file>
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<file>recipes/Recipe 16.23 - Sperm storage with a survival() callback.txt</file>
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<file>recipes/Recipe 16.24 - Tracking separate sexes in script, nonWF style.txt</file>
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<file>recipes/Recipe 15.13 - Density-dependent fecundity with summarizeIndividuals().txt</file>
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<file>recipes/Recipe 16.25 - Modeling haplodiploidy with addRecombinant().txt</file>
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<file>recipes/Recipe 16.16 - Implementing a Wright-Fisher model with a nonWF model I.txt</file>
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<file>recipes/Recipe 16.16 - Implementing a Wright-Fisher model with a nonWF model II.txt</file>
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<file>recipes/Recipe 9.11 - Effective population size versus census population size.txt</file>
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<file>recipes/Recipe 18.15 - Modeling identity by state (IBS) (uniquing back-mutations to the ancestral state).txt</file>
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<file>recipes/Recipe 19.1 - A simple multispecies model.txt</file>
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<file>recipes/Recipe 19.2 - A two-species model.txt</file>
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<file>recipes/Recipe 19.3 - A deterministic host-parasitoid model.txt</file>
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<file>recipes/Recipe 19.5 - A continuous-space host-parasitoid model.txt</file>
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<file>recipes/Recipe 19.6 - A coevolutionary host-parasitoid trait-matching model.txt</file>
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<file>recipes/Recipe 19.7 - A coevolutionary host-parasite matching-allele model.txt</file>
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<file>recipes/Recipe 18.15 - Modeling identity by state (IBS) (uniquing back-mutations to the ancestral state).txt</file>
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<file>recipes/Recipe 14.15 - Modeling biallelic loci with a mutation() callback I.txt</file>
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<file>recipes/Recipe 14.15 - Modeling biallelic loci with a mutation() callback II.txt</file>
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<file>recipes/Recipe 14.16 - Modeling biallelic loci in script.txt</file>
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<file>recipes/Recipe 19.8 - Within-host reproduction in a host-pathogen model.txt</file>
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<file>recipes/Recipe 22.7 - Parallelizing nonWF reproduction and spatial interactions.txt</file>
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<file>recipes/Recipe 15.3 - Boundaries and boundary conditions V (dispersal kernels).txt</file>
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<file>recipes/Recipe 15.14 - Directed dispersal with the SpatialMap class.txt</file>
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<file>recipes/Recipe 16.12 - A sexual, age-structured spatial model.txt</file>
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</qresource>
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</RCC>

‎QtSLiM/recipes/Recipe 16.1 - A simple nonWF model.txt‎ renamed to ‎QtSLiM/recipes/Recipe 15.1 - A minimal nonWF model.txt‎

File renamed without changes.

‎QtSLiM/recipes/Recipe 16.13 - Forcing a specific pedigree in a nonWF model I.txt‎ renamed to ‎QtSLiM/recipes/Recipe 15.10 - Forcing a specific pedigree in a nonWF model I.txt‎

File renamed without changes.

‎QtSLiM/recipes/Recipe 16.13 - Forcing a specific pedigree in a nonWF model II.txt‎ renamed to ‎QtSLiM/recipes/Recipe 15.10 - Forcing a specific pedigree in a nonWF model II.txt‎

File renamed without changes.

‎QtSLiM/recipes/Recipe 16.14 - Modeling clonal haploids in a nonWF model with addRecombinant().txt‎ renamed to ‎QtSLiM/recipes/Recipe 15.11 - Modeling clonal haploids in a nonWF model with addRecombinant().txt‎

File renamed without changes.

‎QtSLiM/recipes/Recipe 16.15 - Modeling clonal haploid bacteria with horizontal gene transfer.txt‎ renamed to ‎QtSLiM/recipes/Recipe 15.12 - Modeling clonal haploid bacteria with horizontal gene transfer.txt‎

File renamed without changes.

‎QtSLiM/recipes/Recipe 16.16 - Implementing a Wright-Fisher model with a nonWF model I.txt‎ renamed to ‎QtSLiM/recipes/Recipe 15.13 - Implementing a Wright-Fisher model with a nonWF model I.txt‎

File renamed without changes.

‎QtSLiM/recipes/Recipe 16.16 - Implementing a Wright-Fisher model with a nonWF model II.txt‎ renamed to ‎QtSLiM/recipes/Recipe 15.13 - Implementing a Wright-Fisher model with a nonWF model II.txt‎

File renamed without changes.

‎QtSLiM/recipes/Recipe 16.17 - Alternation of generations.txt‎ renamed to ‎QtSLiM/recipes/Recipe 15.14 - Alternation of generations.txt‎

File renamed without changes.

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