--- a/insect_phenology_model.R	Tue Dec 05 11:21:30 2017 -0500
+++ b/insect_phenology_model.R	Tue Dec 05 11:32:33 2017 -0500
@@ -505,28 +505,20 @@
                 }
             } # Else if it is still alive.
         } # End of the individual bug loop.
-        # Find the number of deaths.
+
+        # Number of deaths.
         num_insects.death <- length(death.vector)
         if (num_insects.death > 0) {
             # Remove record of dead.
             vector.matrix <- vector.matrix[-death.vector, ]
         }
-        # Find the number of births.
+        # Number of births.
         num_insects.newborn <- length(birth.vector[,1])
         vector.matrix <- rbind(vector.matrix, birth.vector)
         # Update population size for the next day.
         num_insects <- num_insects - num_insects.death + num_insects.newborn
 
         # Aggregate results by day.
-        total.population <- c(total.population, num_insects)
-        # All adults population size.
-        num_insects.adult <- sum(vector.matrix[,2]==3)+sum(vector.matrix[,2]==4)+sum(vector.matrix[,2]==5)
-        # Overwintering adult population size.
-        overwintering_adult.population[row] <- sum(vector.matrix[,1]==0)
-        # First generation population size.
-        first_generation.population[row] <- sum(vector.matrix[,1]==1)
-        # Second generation population size.
-        second_generation.population[row] <- sum(vector.matrix[,1]==2)
         # Egg population size.
         Eggs[row] <- sum(vector.matrix[,2]==0)
         # Young nymph population size.
@@ -539,18 +531,29 @@
         Vitellogenic[row] <- sum(vector.matrix[,2]==4)
         # Diapausing population size.
         Diapausing[row] <- sum(vector.matrix[,2]==5)
+
+        # Newborn population size.
+        N.newborn[row] <- num_insects.newborn
+        # Adult population size.
+        N.adult[row] <- sum(vector.matrix[,2]==3) + sum(vector.matrix[,2]==4) + sum(vector.matrix[,2]==5)
+        # Dead population size.
+        N.death[row] <- num_insects.death
+
+        total.population <- c(total.population, num_insects)
+
+        # Overwintering adult population size.
+        overwintering_adult.population[row] <- sum(vector.matrix[,1]==0)
+        # First generation population size.
+        first_generation.population[row] <- sum(vector.matrix[,1]==1)
+        # Second generation population size.
+        second_generation.population[row] <- sum(vector.matrix[,1]==2)
+
         # P adult population size.
         P.adult[row] <- sum(vector.matrix[,1]==0)
         # F1 adult population size.
         F1.adult[row] <- sum((vector.matrix[,1]==1 & vector.matrix[,2]==3) | (vector.matrix[,1]==1 & vector.matrix[,2]==4) | (vector.matrix[,1]==1 & vector.matrix[,2]==5))
         # F2 adult population size
         F2.adult[row] <- sum((vector.matrix[,1]==2 & vector.matrix[,2]==3) | (vector.matrix[,1]==2 & vector.matrix[,2]==4) | (vector.matrix[,1]==2 & vector.matrix[,2]==5))
-        # Newborn population size.
-        N.newborn[row] <- num_insects.newborn
-        # Dead population size.
-        N.death[row] <- num_insects.death
-        # Adult population size.
-        N.adult[row] <- num_insects.adult
     }   # End of days specified in the input temperature data.
 
     averages.cum <- cumsum(averages.day)
@@ -562,16 +565,19 @@
     Previtellogenic.replications[,N.replications] <- Previtellogenic
     Vitellogenic.replications[,N.replications] <- Vitellogenic
     Diapausing.replications[,N.replications] <- Diapausing
+
     newborn.replications[,N.replications] <- N.newborn
+    adult.replications[,N.replications] <- N.adult
     death.replications[,N.replications] <- N.death
-    adult.replications[,N.replications] <- N.adult
-    population.replications[,N.replications] <- total.population
+
     P.replications[,N.replications] <- overwintering_adult.population
     F1.replications[,N.replications] <- first_generation.population
     F2.replications[,N.replications] <- second_generation.population
     P_adults.replications[,N.replications] <- P.adult
     F1_adults.replications[,N.replications] <- F1.adult
     F2_adults.replications[,N.replications] <- F2.adult
+
+    population.replications[,N.replications] <- total.population
 }
 
 # Mean value for eggs.
@@ -645,7 +651,7 @@
 # Subfigure 3: adult population size by generation
 maxval <- max(F2_adults) + 100
 render_chart("adult_pop_size_by_generation", opt$insect, opt$location, latitude, start_date, end_date, days, maxval,
-             opt$std_error_plot, P_adults, F1_adults, F2_adults, P_adults.std_error, F1_adults.std_error, F2_adults2.std_error)
+             opt$std_error_plot, P_adults, F1_adults, F2_adults, P_adults.std_error, F1_adults.std_error, F2_adults.std_error)
 
 # Turn off device driver to flush output.
 dev.off()