# HG changeset patch
# User greg
# Date 1545315352 18000
# Node ID 39308558943830362cebab3948531b935f6268c4
# Parent  892cf703be62dd123a1e07cda360c036eca8d08e
Uploaded

diff -r 892cf703be62 -r 393085589438 insect_phenology_model.R
--- a/insect_phenology_model.R	Wed Nov 21 11:42:37 2018 -0500
+++ b/insect_phenology_model.R	Thu Dec 20 09:15:52 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) {
@@ -366,13 +378,6 @@
                 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$DOY[end_date_ytd_row]);
-                if (end_doy_ytd > end_date_ytd_row + 1) {
-                    # The input year-to-date dataset is missing 1 or more
-                    # days of data.
-                    days_missing = end_doy_ytd - end_date_ytd_row;
-                    msg = cat("The year-to-date dataset is missing ", days_missing, " days of data.\n");
-                    stop_err(msg);
-                }
             } else {
                 end_date_ytd_row = 0;
             }
@@ -396,13 +401,6 @@
             # Save the first DOY to later check if start_date is Jan 1.
             start_doy_ytd = as.integer(temperature_data_frame$DOY[1]);
             end_doy_ytd = as.integer(temperature_data_frame$DOY[num_ytd_rows]);
-            if (end_doy_ytd > end_date_ytd_row + 1) {
-                # The input year-to-date dataset is missing 1 or more
-                # days of data.
-                days_missing = end_doy_ytd - end_date_ytd_row;
-                msg = cat("The year-to-date dataset is missing ", days_missing, " days of data.\n");
-                stop_err(msg);
-            }
         }
     } else {
         # We're processing only the 30 year normals data, so create an empty
@@ -557,6 +555,8 @@
             }
         }
     }
+    # Ensure all DOY values are consectuive integers.
+    validate_doys(temperature_data_frame);
     # Add a column containing the daylight length for each day.
     temperature_data_frame = add_daylight_length(temperature_data_frame);
     return(list(temperature_data_frame, start_date, end_date, prepend_end_doy_norm, append_start_doy_norm, is_leap_year, location));
@@ -856,7 +856,8 @@
                 }
                 if (vector.individual[2] == 0) {
                     # Egg.
-                    death.probability = opt$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.
diff -r 892cf703be62 -r 393085589438 insect_phenology_model.xml
--- a/insect_phenology_model.xml	Wed Nov 21 11:42:37 2018 -0500
+++ b/insect_phenology_model.xml	Thu Dec 20 09:15:52 2018 -0500
@@ -66,13 +66,13 @@
             <validator type="expression" message="30 year normals temperature data must have 10 columns and 366 rows">value is not None and value.metadata.columns==10 and value.metadata.data_lines==366</validator>
         </param>
         <conditional name="merge_ytd_temperature_data_cond">
-            <param name="merge_ytd_temperature_data" type="select" label="Merge year-to-date temperature data with 30 year normals temperature data?">
+            <param name="merge_ytd_temperature_data" type="select" label="Merge daily actuals temperature data with 30 year normals temperature data?">
                 <option value="yes" selected="true">Yes</option>
                 <option value="no">No</option>
             </param>
             <when value="yes">
-                <param name="input_ytd" type="data" format="csv" label="Year-to-date temperature data">
-                    <validator type="expression" message="Year-to-date temperature data must have 6 columns">value is not None and value.metadata.columns==6</validator>
+                <param name="input_ytd" type="data" format="csv" label="Daily actuals temperature data">
+                    <validator type="expression" message="Daily actuals temperature data must have 6 columns">value is not None and value.metadata.columns==6</validator>
                 </param>
                 <param name="location" type="text" value="" optional="true" label="Location" help="Enter the location or leave blank to use the station name from 30 year normals data."/>
             </when>
@@ -81,7 +81,7 @@
         <param name="insect" type="select" label="Select insect">
             <option value="BMSB" selected="True">Brown Marmorated Stink Bug</option>
         </param>
-        <param name="replications" type="integer" value="10" min="2" label="Number of replications"/>
+        <param name="replications" type="integer" value="5" min="2" label="Number of replications"/>
         <param name="insects_per_replication" type="integer" value="1000" min="100" label="Number of insects with which to start each replication"/>
         <param name="photoperiod" type="float" value="13.5" min="0" label="Critical photoperiod for diapause induction/termination"/>
         <param name="egg_mortality" type="float" value="1" min="0" max="1" label="Adjustment rate for egg mortality" help="Floating point value between 0 and 1"/>
@@ -242,7 +242,7 @@
  * **30 year normals temperature data** - the dataset from your history containing the 30-year normals temperature data (available at http://pestwatch.psu.edu/ghcn).
  * **Merge year-to-date temperature data with 30 year normals temperature data** - select Yes to merge a year-to-date temperature dataset from your history into the selected 30 year normals temperature data.
 
-  * **Year-to-date temperature data** - the dataset from your history containing the year-to-date temperature data (available at http://pestwatch.psu.edu/minmax).
+  * **Daily actuals temperature data** - the dataset from your history containing the daily actuals temperature data (available at http://pestwatch.psu.edu/minmax).
 
  * **Location** - the location associated with the selected temperature data.
  * **Select insect** - currently only the Brown Marmorated Stink Bug can be analyzed.
diff -r 892cf703be62 -r 393085589438 test-data/output_combined1.csv
--- a/test-data/output_combined1.csv	Wed Nov 21 11:42:37 2018 -0500
+++ b/test-data/output_combined1.csv	Thu Dec 20 09:15:52 2018 -0500
@@ -1,1 +1,1 @@
-"LATITUDE","LONGITUDE","DATE","DOY","TMIN","TMAX","DAYLEN","YOUNGNYMPH","YOUNGNYMPHSE","PRE.VITADULT","PRE.VITADULTSE"
+"LATITUDE","LONGITUDE","DATE","DOY","TMIN","TMAX","DAYLEN","DEGREE.DAYS","YOUNGNYMPH","YOUNGNYMPHSE","PRE.VITADULT","PRE.VITADULTSE"
diff -r 892cf703be62 -r 393085589438 test-data/output_combined2.csv
--- a/test-data/output_combined2.csv	Wed Nov 21 11:42:37 2018 -0500
+++ b/test-data/output_combined2.csv	Thu Dec 20 09:15:52 2018 -0500
@@ -1,1 +1,1 @@
-"LATITUDE","LONGITUDE","DATE","DOY","TMIN","TMAX","DAYLEN","EGG","EGGSE","TOTALNYMPH","TOTALNYMPHSE","TOTALADULT","TOTALADULTSE"
+"LATITUDE","LONGITUDE","DATE","DOY","TMIN","TMAX","DAYLEN","DEGREE.DAYS","EGG","EGGSE","TOTALNYMPH","TOTALNYMPHSE","TOTALADULT","TOTALADULTSE"
diff -r 892cf703be62 -r 393085589438 test-data/output_combined3.csv
--- a/test-data/output_combined3.csv	Wed Nov 21 11:42:37 2018 -0500
+++ b/test-data/output_combined3.csv	Thu Dec 20 09:15:52 2018 -0500
@@ -1,1 +1,1 @@
-"LATITUDE","LONGITUDE","DATE","DOY","TMIN","TMAX","DAYLEN","OLDNYMPH","OLDNYMPHSE"
+"LATITUDE","LONGITUDE","DATE","DOY","TMIN","TMAX","DAYLEN","DEGREE.DAYS","OLDNYMPH","OLDNYMPHSE"
diff -r 892cf703be62 -r 393085589438 test-data/output_combined4.csv
--- a/test-data/output_combined4.csv	Wed Nov 21 11:42:37 2018 -0500
+++ b/test-data/output_combined4.csv	Thu Dec 20 09:15:52 2018 -0500
@@ -1,1 +1,1 @@
-"LATITUDE","LONGITUDE","DATE","DOY","TMIN","TMAX","DAYLEN","EGG","EGGSE","TOTALNYMPH","TOTALNYMPHSE","TOTALADULT","TOTALADULTSE"
+"LATITUDE","LONGITUDE","DATE","DOY","TMIN","TMAX","DAYLEN","DEGREE.DAYS","EGG","EGGSE","TOTALNYMPH","TOTALNYMPHSE","TOTALADULT","TOTALADULTSE"
diff -r 892cf703be62 -r 393085589438 test-data/output_f1_3.csv
--- a/test-data/output_f1_3.csv	Wed Nov 21 11:42:37 2018 -0500
+++ b/test-data/output_f1_3.csv	Thu Dec 20 09:15:52 2018 -0500
@@ -1,1 +1,1 @@
-"LATITUDE","LONGITUDE","DATE","DOY","TMIN","TMAX","DAYLEN","OLDNYMPH.F1","OLDNYMPH.F1.SE"
+"LATITUDE","LONGITUDE","DATE","DOY","TMIN","TMAX","DAYLEN","DEGREE.DAYS","OLDNYMPH","OLDNYMPHSE","OLDNYMPH.F1","OLDNYMPH.F1.SE"
diff -r 892cf703be62 -r 393085589438 test-data/output_f1_4.csv
--- a/test-data/output_f1_4.csv	Wed Nov 21 11:42:37 2018 -0500
+++ b/test-data/output_f1_4.csv	Thu Dec 20 09:15:52 2018 -0500
@@ -1,1 +1,1 @@
-"LATITUDE","LONGITUDE","DATE","DOY","TMIN","TMAX","DAYLEN","EGG.F1","EGG.F1.SE","TOTALNYMPH.F1","TOTALNYMPH.F1.SE","TOTALADULT.F1","TOTALADULT.F1.SE"
+"LATITUDE","LONGITUDE","DATE","DOY","TMIN","TMAX","DAYLEN","DEGREE.DAYS","EGG","EGGSE","TOTALNYMPH","TOTALNYMPHSE","TOTALADULT","TOTALADULTSE","EGG.F1","EGG.F1.SE","TOTALNYMPH.F1","TOTALNYMPH.F1.SE","TOTALADULT.F1","TOTALADULT.F1.SE","ALL.TOTAL.F1","ALL.TOTAL.F1.SE"
diff -r 892cf703be62 -r 393085589438 test-data/output_f2_3.csv
--- a/test-data/output_f2_3.csv	Wed Nov 21 11:42:37 2018 -0500
+++ b/test-data/output_f2_3.csv	Thu Dec 20 09:15:52 2018 -0500
@@ -1,1 +1,1 @@
-"LATITUDE","LONGITUDE","DATE","DOY","TMIN","TMAX","DAYLEN","OLDNYMPH.F2","OLDNYMPH.F2.SE"
+"LATITUDE","LONGITUDE","DATE","DOY","TMIN","TMAX","DAYLEN","DEGREE.DAYS","OLDNYMPH","OLDNYMPHSE","OLDNYMPH.F2","OLDNYMPH.F2.SE"
diff -r 892cf703be62 -r 393085589438 test-data/output_f2_4.csv
--- a/test-data/output_f2_4.csv	Wed Nov 21 11:42:37 2018 -0500
+++ b/test-data/output_f2_4.csv	Thu Dec 20 09:15:52 2018 -0500
@@ -1,1 +1,1 @@
-"LATITUDE","LONGITUDE","DATE","DOY","TMIN","TMAX","DAYLEN","EGG.F2","EGG.F2.SE","TOTALNYMPH.F2","TOTALNYMPH.F2.SE","TOTALADULT.F2","TOTALADULT.F2.SE"
+"LATITUDE","LONGITUDE","DATE","DOY","TMIN","TMAX","DAYLEN","DEGREE.DAYS","EGG","EGGSE","TOTALNYMPH","TOTALNYMPHSE","TOTALADULT","TOTALADULTSE","EGG.F2","EGG.F2.SE","TOTALNYMPH.F2","TOTALNYMPH.F2.SE","TOTALADULT.F2","TOTALADULT.F2.SE","ALL.TOTAL.F2","ALL.TOTAL.F2.SE"
diff -r 892cf703be62 -r 393085589438 test-data/output_p_3.csv
--- a/test-data/output_p_3.csv	Wed Nov 21 11:42:37 2018 -0500
+++ b/test-data/output_p_3.csv	Thu Dec 20 09:15:52 2018 -0500
@@ -1,1 +1,1 @@
-"LATITUDE","LONGITUDE","DATE","DOY","TMIN","TMAX","DAYLEN","OLDNYMPH.P","OLDNYMPH.P.SE"
+"LATITUDE","LONGITUDE","DATE","DOY","TMIN","TMAX","DAYLEN","DEGREE.DAYS","OLDNYMPH","OLDNYMPHSE","OLDNYMPH.P","OLDNYMPH.P.SE"
diff -r 892cf703be62 -r 393085589438 test-data/output_p_4.csv
--- a/test-data/output_p_4.csv	Wed Nov 21 11:42:37 2018 -0500
+++ b/test-data/output_p_4.csv	Thu Dec 20 09:15:52 2018 -0500
@@ -1,1 +1,1 @@
-"LATITUDE","LONGITUDE","DATE","DOY","TMIN","TMAX","DAYLEN","EGG.P","EGG.P.SE","TOTALNYMPH.P","TOTALNYMPH.P.SE","TOTALADULT.P","TOTALADULT.P.SE","ALL.TOTAL.P","ALL.TOTAL.P.SE"
+"LATITUDE","LONGITUDE","DATE","DOY","TMIN","TMAX","DAYLEN","DEGREE.DAYS","EGG","EGGSE","TOTALNYMPH","TOTALNYMPHSE","TOTALADULT","TOTALADULTSE","EGG.P","EGG.P.SE","TOTALNYMPH.P","TOTALNYMPH.P.SE","TOTALADULT.P","TOTALADULT.P.SE","ALL.TOTAL.P","ALL.TOTAL.P.SE"
diff -r 892cf703be62 -r 393085589438 utils.R
--- a/utils.R	Wed Nov 21 11:42:37 2018 -0500
+++ b/utils.R	Thu Dec 20 09:15:52 2018 -0500
@@ -333,3 +333,21 @@
     }
     return(valid_date);
 }
+
+validate_doys = function(temperature_data_frame) {
+    # Ensure all DOY values are consecutive integers.
+    last_doy = 0;
+    num_rows = dim(temperature_data_frame)[1];
+    for (i in 1:num_rows) {
+        doy = as.integer(temperature_data_frame$DOY[i]);
+        if (last_doy == 0) {
+            last_doy = doy;
+        } else {
+            if (doy != last_doy + 1) {
+                msg = paste("DOY ", doy, " is not consecutive (previous DOY is ", last_doy, ".", sep="");
+                stop_err(msg);
+            }
+            last_doy = doy;
+        }
+    }
+}