handle single animal in breed()

Author: Poissonfish

src/interface/interface.jl

@@ -175,7 +175,6 @@ function breed(cohort_A         ::Cohort,
         else
             # Mate
             progenies = mate(cohort_A, cohort_B; silent=true, args...)
-            println(progenies)
             # Select
             if n_select > 0
                 progenies = select(progenies, n_select; silent=true, args...)
@@ -189,12 +188,19 @@ function breed(cohort_A         ::Cohort,
                 cohort_A = progenies
                 cohort_B = progenies
             end
-            println(progenies)
 
         end
 
+        if length(cohort_A) == 1
+            cohort_A = Cohort(cohort_A)
+        end
+        if length(cohort_B) == 1
+            cohort_B = Cohort(cohort_B)
+        end
+
         # LOG
-        sm = summary(cohort_A + cohort_B)
+        sum_cohort = cohort_A + cohort_B
+        sm = summary(sum_cohort)
         LOG("Gen $i -> Mean of BVs: $(sm["mu_g"]), Variance of BVs: $(sm["var_g"])")
     end
 

test/paper_cases.jl

@@ -89,19 +89,24 @@ for parent in diverse_parents
 end
 # Each family produce 200 progenies by selfing
 args = Dict(# Mating
-            :n_per_mate => 1, # single-seed decent (SSD)
+            :n_per_mate => 10,
             :scheme     => "selfing",
             # Selection
             :criteria   => "phenotypes",
             # Breed
             :n_gens     => 4,
-            :n_select   => 200)
+            # single-seed decent
+            :n_select   => 1)
 NAM = Cohort()
 for family in F1
-    F2 = mate(family, n_per_mate=200)
-    NAM += breed(F2; args...)
+    F2 = mate(family, n_per_mate=200, scheme="selfing")
+    for seed in F2
+        NAM += breed(seed; args...)
+    end
 end
 
+family=F1[1]
+get_genotypes(F2)
 
 #----- Methods ----------------
 path = PATH("map")