Merge pull request #16 from rscherrer/develop

Develop

README.md

@@ -159,7 +159,7 @@ The following variables are saved every `tsave` timepoint:
 * `genome_freqs`: the allele frequencies for each locus within each ecotype
 * `genome_hobs`: the observed heterozygosity for each locus within each ecotype
 * `network_corgen`, `network_corbreed`, `network_corfreq`: respectively the pairwise correlations in genetic value, breeding value and allele frequency between the two interacting loci for each edge in all three networks (ordered by trait)
-* `network_avgi`, `network_avgj`: the expected epistatic variance in average effect (define that maybe?) of the first and second interacting loci, respectively, for each edge
+* `network_avgi`, `network_avgj`: the expected epistatic variance in average effect of the first and second interacting loci, respectively, for each edge. `network_avgi` corresponds to the expected effect of genetic variation at locus i on the variation in the additive effect of allele substitutions at locus j, and vice versa for `network_avgj`. This is mostly for plotting purposes, to detect genes that are expected to modify the additive effects of their interacting partners.
 * `individual_ecotype`, `individual_habitat`: the ecotype and habitat of each individual
 * `individual_trait`: the value of each trait for each individual
 * `individual_midparent`: the midparent phenotype (i.e. the mean between maternal and paternal values) for each trait for each individual 

src/MetaPop.cpp

@@ -24,26 +24,6 @@ std::vector<Individual> MetaPop::populate(const Param &p, const GenArch &arch)
 
 }
 
-
-// Life cycle of the population
-
-void MetaPop::cycle(const Param &p, const GenArch &arch)
-{
-
-    // Dispersal
-    if (!isburnin) disperse(p);
-
-    // Consumption
-    consume(p);
-
-    // Reproduction
-    reproduce(p, arch);
-
-    // Survival
-    survive(p);
-
-}
-
 void MetaPop::disperse(const Param &p)
 {
     // Sample migrants across the population
@@ -470,6 +450,7 @@ void MetaPop::resetTraits(const size_t &trait, const double &x, const Param &p)
         population[i].resetTrait(trait, x, p);
     }
 }
+
 void MetaPop::resetTraits(const size_t &trait, const size_t &h, const double &x,
  const Param &p)
 {
@@ -478,9 +459,18 @@ void MetaPop::resetTraits(const size_t &trait, const size_t &h, const double &x,
             population[i].resetTrait(trait, x, p);
     }
 }
+
 void MetaPop::resetGenders(const bool &sex)
 {
     for (size_t i = 0u; i < population.size(); ++i) {
         population[i].resetGender(sex);
     }
 }
+
+void MetaPop::resetGenders(const size_t &h, const bool &sex)
+{
+    for (size_t i = 0u; i < population.size(); ++i) {
+        if (population[i].getHabitat() == h)
+            population[i].resetGender(sex);
+    }
+}

src/MetaPop.h

@@ -32,7 +32,6 @@ class MetaPop
 
     ~MetaPop() {}
 
-    void cycle(const Param&, const GenArch&);
     void exitburnin();
     void complete(); // complete speciation (no more reproduction allowed)
     bool isextinct() const;
@@ -63,6 +62,7 @@ class MetaPop
     void resetTraits(const size_t&, const double&, const Param&);
     void resetTraits(const size_t&, const size_t&, const double&, const Param&);
     void resetGenders(const bool&);
+    void resetGenders(const size_t&, const bool&);
 
 private:
 

src/Simul.cpp

@@ -62,10 +62,9 @@ int simulate(const std::vector<std::string> &args)
             if (pars.talkative) std::cout << t << '\n';
 
             // Life cycle of the metapopulation
-            metapop.disperse(pars);
             metapop.consume(pars);
 
-            const bool timetosave = t % pars.tsave;
+            const bool timetosave = t % pars.tsave == 0;
 
             // Analyze the metapopulation if needed
             if (pars.datsave && (t >= 0 || pars.burninsave) && timetosave) {
@@ -89,6 +88,8 @@ int simulate(const std::vector<std::string> &args)
                 std::cout << "The population went extinct at t = " << t << '\n';
                 break;
             }
+
+            metapop.disperse(pars);
         }
 
         std::cout << "Simulation ended.\n";