Mercurial > repos > greg > insect_phenology_model

changeset 63:c5df0777fa31 draft

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Uploaded
author greg
date Fri, 08 Nov 2019 13:01:48 -0500
parents 3116ddd4c26d
children 883d812611b3
files insect_phenology_model.R
diffstat 1 files changed, 39 insertions(+), 41 deletions(-) [+]
line wrap: on
line diff
--- a/insect_phenology_model.R	Fri Nov 08 12:49:57 2019 -0500
+++ b/insect_phenology_model.R	Fri Nov 08 13:01:48 2019 -0500
@@ -251,51 +251,49 @@
 }
 
 mortality.egg = function(temperature, adj=0) {
-    if (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;
-        }
-    } else {
-        # Make mortality adjustments based on adj parameter.
-        mortality.probability = (100 - mortality.probability) * adj + mortality.probability;
-        # if mortality > 100, make it equal to 100.
+    # 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;
-        # Change percent to proportion.
-        mortality.probability = mortality.probability / 100;
     }
+    # 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)
 }