# HG changeset patch
# User greg
# Date 1541785915 18000
# Node ID 20c1451d8869891cdb1616ee79d1fc5fc730085e
# Parent  829518206949acbb9b6a115fa899410b3bdfe1e6
Uploaded

diff -r 829518206949 -r 20c1451d8869 insect_phenology_model.R
--- a/insect_phenology_model.R	Mon Nov 05 14:25:19 2018 -0500
+++ b/insect_phenology_model.R	Fri Nov 09 12:51:55 2018 -0500
@@ -250,51 +250,63 @@
     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;
     }
-    # 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;
+    else {
+        mortality.probability = 0.8 - temperature / 40.0;
+        if (mortality.probability < 0) {
+            mortality.probability = 0.01;
+        }
     }
-    # 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.nymph = function(temperature) {
     if (temperature < 12.7) {