--- a/insect_phenology_model.R	Mon Nov 13 10:42:31 2017 -0500
+++ b/insect_phenology_model.R	Mon Nov 13 10:53:31 2017 -0500
@@ -60,7 +60,8 @@
     dxp <- temperature_data[row, 6]
     # Mean temperature for current row.
     dmean <- 0.5 * (dnp + dxp)
-    dd <- 0  # initialize degree day accumulation
+    # Initialize degree day accumulation
+    dd <- 0
     if (dxp < threshold) {
         dd <- 0
     }
@@ -239,7 +240,7 @@
         temp.profile <- get_temperature_at_hour(latitude, temperature_data, daylight_length_vector, row, opt$num_days)
         mean.temp <- temp.profile[1]
         dd.temp <- temp.profile[2]
-        dd.day[day] <- dd.temp
+        dd.day[row] <- dd.temp
         # Trash bin for death.
         death.vec <- NULL
         # Newborn.
@@ -268,7 +269,7 @@
             }
             else if (vec.ind[2] == 3 | vec.ind[2] == 4 | vec.ind[2] == 5) {
                 # For adult.
-                if (day < day.kill) {
+                if (doy < day.kill) {
                     death.prob = opt$adult_mort * mortality.adult(mean.temp)
                 }
                 else {
@@ -286,7 +287,7 @@
                 # Event 1 end of diapause.
                 if (vec.ind[1] == 0 && vec.ind[2] == 3) {
                     # Overwintering adult (previttelogenic).
-                    if (photoperiod > opt$photoperiod && vec.ind[3] > 68 && day < 180) {
+                    if (photoperiod > opt$photoperiod && vec.ind[3] > 68 && doy < 180) {
                         # Add 68C to become fully reproductively matured.
                         # Transfer to vittelogenic.
                         vec.ind <- c(0, 4, 0, 0, 0)
@@ -352,7 +353,7 @@
                 }
 
                 # Event 2 oviposition -- for gen 1.
-                if (vec.ind[2] == 4 && vec.ind[1] == 1 && mean.temp > 12.5 && day < 222) {
+                if (vec.ind[2] == 4 && vec.ind[1] == 1 && mean.temp > 12.5 && doy < 222) {
                     # Vittelogenic stage, 1st generation
                     if (vec.ind[4] == 0) {
                         # Just turned in vittelogenic stage.
@@ -413,7 +414,7 @@
                         current.gen <- vec.ind[1]
                         # Transfer to old nym stage.
                         vec.ind <- c(current.gen, 2, 0, 0, 0)
-                        if (photoperiod < opt$photoperiod && day > 180) {
+                        if (photoperiod < opt$photoperiod && doy > 180) {
                             vec.ind[5] <- 1
                         } # Prepare for diapausing.
                     }
@@ -491,26 +492,30 @@
         gen2 <- sum(vec.mat[,1] == 2)
         # Sum of all adults.
         n.adult <- sum(vec.mat[,2] == 3) + sum(vec.mat[,2] == 4) + sum(vec.mat[,2] == 5)
-        # Gen eration 0 pop size.
-        gen0.pop[day] <- gen0
-        gen1.pop[day] <- gen1
-        gen2.pop[day] <- gen2
-        S0[day] <- s0
-        S1[day] <- s1
-        S2[day] <- s2
-        S3[day] <- s3
-        S4[day] <- s4
-        S5[day] <- s5
-        g0.adult[day] <- sum(vec.mat[,1] == 0)
-        g1.adult[day] <- sum((vec.mat[,1] == 1 & vec.mat[,2] == 3) | (vec.mat[,1] == 1 & vec.mat[,2] == 4) | (vec.mat[,1] == 1 & vec.mat[,2] == 5))
-        g2.adult[day] <- sum((vec.mat[,1]== 2 & vec.mat[,2] == 3) | (vec.mat[,1] == 2 & vec.mat[,2] == 4) | (vec.mat[,1] == 2 & vec.mat[,2] == 5))
+
+        # Generation 0 pop size.
+        gen0.pop[row] <- gen0
+        gen1.pop[row] <- gen1
+        gen2.pop[row] <- gen2
 
-        N.newborn[day] <- n.newborn
-        N.death[day] <- n.death
-        N.adult[day] <- n.adult
+        S0[row] <- s0
+        S1[row] <- s1
+        S2[row] <- s2
+        S3[row] <- s3
+        S4[row] <- s4
+        S5[row] <- s5
+
+        g0.adult[row] <- sum(vec.mat[,1] == 0)
+        g1.adult[row] <- sum((vec.mat[,1] == 1 & vec.mat[,2] == 3) | (vec.mat[,1] == 1 & vec.mat[,2] == 4) | (vec.mat[,1] == 1 & vec.mat[,2] == 5))
+        g2.adult[row] <- sum((vec.mat[,1]== 2 & vec.mat[,2] == 3) | (vec.mat[,1] == 2 & vec.mat[,2] == 4) | (vec.mat[,1] == 2 & vec.mat[,2] == 5))
+
+        N.newborn[row] <- n.newborn
+        N.death[row] <- n.death
+        N.adult[row] <- n.adult
     }   # end of days specified in the input temperature data
 
     dd.cum <- cumsum(dd.day)
+
     # Collect all the outputs.
     S0.rep[,N.rep] <- S0
     S1.rep[,N.rep] <- S1