# HG changeset patch
# User greg
# Date 1512412468 18000
# Node ID 691b677d8f83610bd03c20f475e9e6fed32a5310
# Parent  52114847afffdc4e6aa3195cd5e05b41662984d4
Uploaded

diff -r 52114847afff -r 691b677d8f83 insect_phenology_model.R
--- a/insect_phenology_model.R	Mon Dec 04 13:21:20 2017 -0500
+++ b/insect_phenology_model.R	Mon Dec 04 13:34:28 2017 -0500
@@ -231,10 +231,10 @@
     # Complete matrix for the population.
     vector.matrix <- base::t(matrix(vector.matrix, nrow=5))
     # Time series of population size.
-    tot.pop <- NULL
-    gen0.pop <- rep(0, opt$num_days)
-    gen1.pop <- rep(0, opt$num_days)
-    gen2.pop <- rep(0, opt$num_days)
+    total.population <- NULL
+    overwintering_adult.population <- rep(0, opt$num_days)
+    first_generation.population <- rep(0, opt$num_days)
+    second_generation.population <- rep(0, opt$num_days)
     S0 <- rep(0, opt$num_days)
     S1 <- rep(0, opt$num_days)
     S2 <- rep(0, opt$num_days)
@@ -480,34 +480,34 @@
         num_insects <- num_insects - num_insects.death + num_insects.newborn
 
         # Aggregate results by day.
-        tot.pop <- c(tot.pop, num_insects)
+        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.
-        gen0.pop[row] <- sum(vector.matrix[,1] == 0)
+        overwintering_adult.population[row] <- sum(vector.matrix[,1] == 0)
         # First generation population size.
-        gen1.pop[row] <- sum(vector.matrix[,1] == 1)
+        first_generation.population[row] <- sum(vector.matrix[,1] == 1)
         # Second generation population size.
-        gen2.pop[row] <- sum(vector.matrix[,1] == 2)
+        second_generation.population[row] <- sum(vector.matrix[,1] == 2)
 
         # Egg population size.
-        S0[row] <- sum(vector.matrix[,2] == 0)
+        S0[row] <- sum(vector.matrix[,2]==0)
         # Young nymph population size.
-        S1[row] <- sum(vector.matrix[,2] == 1)
+        S1[row] <- sum(vector.matrix[,2]==1)
         # Old nymph population size.
-        S2[row] <- sum(vector.matrix[,2] == 2)
+        S2[row] <- sum(vector.matrix[,2]==2)
         # Previtellogenic population size.
-        S3[row] <- sum(vector.matrix[,2] == 3)
+        S3[row] <- sum(vector.matrix[,2]==3)
         # Vitellogenic population size.
-        S4[row] <- sum(vector.matrix[,2] == 4)
+        S4[row] <- sum(vector.matrix[,2]==4)
         # Diapausing population size.
-        S5[row] <- sum(vector.matrix[,2] == 5)
+        S5[row] <- sum(vector.matrix[,2]==5)
 
-        P.adult[row] <- sum(vector.matrix[,1] == 0)
-        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[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))
+        P.adult[row] <- sum(vector.matrix[,1]==0)
+        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[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))
 
         N.newborn[row] <- num_insects.newborn
         N.death[row] <- num_insects.death
@@ -526,10 +526,10 @@
     newborn.replications[,N.replications] <- N.newborn
     death.replications[,N.replications] <- N.death
     adult.replications[,N.replications] <- N.adult
-    pop.replications[,N.replications] <- tot.pop
-    P.replications[,N.replications] <- gen0.pop
-    F1.replications[,N.replications] <- gen1.pop
-    F2.replications[,N.replications] <- gen2.pop
+    pop.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