# HG changeset patch
# User greg
# Date 1573047047 18000
# Node ID 734f8e4dfbe5b2e12f349486e1cc8bf541fda833
# Parent  39308558943830362cebab3948531b935f6268c4
Uploaded

diff -r 393085589438 -r 734f8e4dfbe5 insect_phenology_model.R
--- a/insect_phenology_model.R	Thu Dec 20 09:15:52 2018 -0500
+++ b/insect_phenology_model.R	Wed Nov 06 08:30:47 2019 -0500
@@ -250,62 +250,50 @@
     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];
-#    }
-#    # 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;
-        }
+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];
     }
-    return (mortality.probability);
+    # 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.nymph = function(temperature) {