--- a/insect_phenology_model.R	Wed Nov 21 11:33:40 2018 -0500
+++ b/insect_phenology_model.R	Thu Dec 20 09:08:50 2018 -0500
@@ -250,50 +250,62 @@
     return(mortality.probability)
 }
 
-mortality.egg = function(temperature, adj=0) {
-    # If no input from adjustment, default
-    # value is 0 (data from Nielsen, 2008).
-    T.mortality = c(15, 17, 20, 25, 27, 30, 33, 35);
-    egg.mortality = c(50, 2, 1, 0, 0, 0, 5, 100);
-    # Calculates slopes and intercepts for lines.
-    slopes = NULL;
-    intercepts = NULL;
-    for (i in 1:length(T.mortality)) {
-        slopes[i] = (egg.mortality[i+1] - egg.mortality[i]) / (T.mortality[i+1] - T.mortality[i]);
-        intercepts[i] = -slopes[i] * T.mortality[i] + egg.mortality[i];
+#mortality.egg = function(temperature, adj=0) {
+#    # If no input from adjustment, default
+#    # value is 0 (data from Nielsen, 2008).
+#    T.mortality = c(15, 17, 20, 25, 27, 30, 33, 35);
+#    egg.mortality = c(50, 2, 1, 0, 0, 0, 5, 100);
+#    # Calculates slopes and intercepts for lines.
+#    slopes = NULL;
+#    intercepts = NULL;
+#    for (i in 1:length(T.mortality)) {
+#        slopes[i] = (egg.mortality[i+1] - egg.mortality[i]) / (T.mortality[i+1] - T.mortality[i]);
+#        intercepts[i] = -slopes[i] * T.mortality[i] + egg.mortality[i];
+#    }
+#    # Calculates mortality based on temperature.
+#    mortality.probability = NULL;
+#    for (j in 1:length(temperature)) {
+#        mortality.probability[j] = if(temperature[j] <= T.mortality[2]) {
+#                           temperature[j] * slopes[1] + intercepts[1];
+#                       } else if (temperature[j] > T.mortality[2] && temperature[j] <= T.mortality[3]) {
+#                           temperature[j] * slopes[2] + intercepts[2];
+#                       } else if (temperature[j] > T.mortality[3] && temperature[j] <= T.mortality[4]) {
+#                           temperature[j] * slopes[3] + intercepts[3];
+#                       } else if (temperature[j] > T.mortality[4] && temperature[j] <= T.mortality[5]) {
+#                           temperature[j] * slopes[4] + intercepts[4];
+#                       } else if (temperature[j] > T.mortality[5] && temperature[j] <= T.mortality[6]) {
+#                           temperature[j] * slopes[5] + intercepts[5];
+#                       } else if (temperature[j] > T.mortality[6] && temperature[j] <= T.mortality[7]) {
+#                           temperature[j] * slopes[6] + intercepts[6];
+#                       } else if (temperature[j] > T.mortality[7]) {
+#                           temperature[j] * slopes[7] + intercepts[7];
+#                       }
+#        # If mortality > 100, make it equal to 100.
+#        mortality.probability[mortality.probability>100] = 100;
+#        # If mortality <0, make equal to 0.
+#        mortality.probability[mortality.probability<0] = 0;
+#    }
+#    # Make mortality adjustments based on adj parameter.
+#    mortality.probability = (100 - mortality.probability) * adj + mortality.probability;
+#    # if mortality > 100, make it equal to 100.
+#    mortality.probability[mortality.probability>100] = 100;
+#    # If mortality <0, make equal to 0.
+#    mortality.probability[mortality.probability<0] = 0;
+#    # Change percent to proportion.
+#    mortality.probability = mortality.probability / 100;
+#    return(mortality.probability)
+#}
+
+mortality.egg = function(temperature) {
+    if (temperature < 12.7) {
+        mortality.probability = 0.8;
+    } else {
+        mortality.probability = 0.8 - temperature / 40.0;
+        if (mortality.probability < 0) {
+            mortality.probability = 0.01;
+        }
     }
-    # Calculates mortality based on temperature.
-    mortality.probability = NULL;
-    for (j in 1:length(temperature)) {
-        mortality.probability[j] = if(temperature[j] <= T.mortality[2]) {
-                           temperature[j] * slopes[1] + intercepts[1];
-                       } else if (temperature[j] > T.mortality[2] && temperature[j] <= T.mortality[3]) {
-                           temperature[j] * slopes[2] + intercepts[2];
-                       } else if (temperature[j] > T.mortality[3] && temperature[j] <= T.mortality[4]) {
-                           temperature[j] * slopes[3] + intercepts[3];
-                       } else if (temperature[j] > T.mortality[4] && temperature[j] <= T.mortality[5]) {
-                           temperature[j] * slopes[4] + intercepts[4];
-                       } else if (temperature[j] > T.mortality[5] && temperature[j] <= T.mortality[6]) {
-                           temperature[j] * slopes[5] + intercepts[5];
-                       } else if (temperature[j] > T.mortality[6] && temperature[j] <= T.mortality[7]) {
-                           temperature[j] * slopes[6] + intercepts[6];
-                       } else if (temperature[j] > T.mortality[7]) {
-                           temperature[j] * slopes[7] + intercepts[7];
-                       }
-        # If mortality > 100, make it equal to 100.
-        mortality.probability[mortality.probability>100] = 100;
-        # If mortality <0, make equal to 0.
-        mortality.probability[mortality.probability<0] = 0;
-    }
-    # Make mortality adjustments based on adj parameter.
-    mortality.probability = (100 - mortality.probability) * adj + mortality.probability;
-    # if mortality > 100, make it equal to 100.
-    mortality.probability[mortality.probability>100] = 100;
-    # If mortality <0, make equal to 0.
-    mortality.probability[mortality.probability<0] = 0;
-    # Change percent to proportion.
-    mortality.probability = mortality.probability / 100;
-    return(mortality.probability)
+    return (mortality.probability);
 }
 
 mortality.nymph = function(temperature) {
@@ -311,6 +323,8 @@
     prepend_end_doy_norm = 0;
     # The start DOY for norm data appended to ytd data.
     append_start_doy_norm = 0;
+    cat("start_date: ", start_date, "\n");
+    cat("end_date: ", end_date, "\n");
     if (is.null(start_date) && is.null(end_date)) {
         # We're not dealing with a date interval.
         date_interval = FALSE;
@@ -326,6 +340,7 @@
         start_date_doy = as.integer(strftime(start_date, format="%j"));
         end_date_doy = as.integer(strftime(end_date, format="%j"));
     }
+    cat("date_interval: ", date_interval, "\n");
     if (is.null(input_ytd)) {
         # We're processing only the 30 year normals data.
         processing_year_to_date_data = FALSE;
@@ -363,16 +378,13 @@
             }
             end_date_ytd_row = which(temperature_data_frame$DATE==end_date);
             if (length(end_date_ytd_row) > 0) {
+                cat("I'm here...\n");
                 end_date_ytd_row = end_date_ytd_row[1];
                 # The end date is contained within the input_ytd data.
                 end_doy_ytd = as.integer(temperature_data_frame$DOY[end_date_ytd_row]);
-                if (end_doy_ytd > end_date_ytd_row + 1) {
-                    # The input year-to-date dataset is missing 1 or more
-                    # days of data.
-                    days_missing = end_doy_ytd - end_date_ytd_row;
-                    msg = cat("The year-to-date dataset is missing ", days_missing, " days of data.\n");
-                    stop_err(msg);
-                }
+                cat("end_doy_ytd: ", end_doy_ytd, "\n");
+                cat("end_date_ytd_row: ", end_date_ytd_row, "\n");
+                cat("start_date_ytd_row: ", start_date_ytd_row, "\n");
             } else {
                 end_date_ytd_row = 0;
             }
@@ -396,13 +408,10 @@
             # Save the first DOY to later check if start_date is Jan 1.
             start_doy_ytd = as.integer(temperature_data_frame$DOY[1]);
             end_doy_ytd = as.integer(temperature_data_frame$DOY[num_ytd_rows]);
-            if (end_doy_ytd > end_date_ytd_row + 1) {
-                # The input year-to-date dataset is missing 1 or more
-                # days of data.
-                days_missing = end_doy_ytd - end_date_ytd_row;
-                msg = cat("The year-to-date dataset is missing ", days_missing, " days of data.\n");
-                stop_err(msg);
-            }
+            cat("I'm here 2...\n");
+            cat("end_doy_ytd: ", end_doy_ytd, "\n");
+            cat("end_date_ytd_row: ", end_date_ytd_row, "\n");
+            cat("start_date_ytd_row: ", start_date_ytd_row, "\n");
         }
     } else {
         # We're processing only the 30 year normals data, so create an empty
@@ -557,6 +566,8 @@
             }
         }
     }
+    # Ensure all DOY values are consectuive integers.
+    validate_doys(temperature_data_frame);
     # Add a column containing the daylight length for each day.
     temperature_data_frame = add_daylight_length(temperature_data_frame);
     return(list(temperature_data_frame, start_date, end_date, prepend_end_doy_norm, append_start_doy_norm, is_leap_year, location));
@@ -856,7 +867,8 @@
                 }
                 if (vector.individual[2] == 0) {
                     # Egg.
-                    death.probability = opt$egg_mortality * mortality.egg(mean.temp, adj=opt$egg_mortality);
+                    # death.probability = opt$egg_mortality * mortality.egg(mean.temp, adj=opt$egg_mortality);
+                    death.probability = opt$egg_mortality * mortality.egg(mean.temp);
                 }
                 else if (vector.individual[2] == 1 | vector.individual[2] == 2) {
                     # Nymph.