# HG changeset patch
# User greg
# Date 1520361554 18000
# Node ID f5ecff4800f2be87a96bbc624d4915f201d124de
# Parent  6f31ade9a0f4245b88a154447976b3f6c67ade35
Uploaded

diff -r 6f31ade9a0f4 -r f5ecff4800f2 insect_phenology_model.R
--- a/insect_phenology_model.R	Tue Mar 06 08:26:50 2018 -0500
+++ b/insect_phenology_model.R	Tue Mar 06 13:39:14 2018 -0500
@@ -53,16 +53,22 @@
 }
 
 dev.egg = function(temperature) {
+    # This function is not used, but was
+    # in the original, so keep it for now.
     dev.rate = -0.9843 * temperature + 33.438;
     return(dev.rate);
 }
 
 dev.emerg = function(temperature) {
+    # This function is not used, but was
+    # in the original, so keep it for now.
     emerg.rate = -0.5332 * temperature + 24.147;
     return(emerg.rate);
 }
 
 dev.old = function(temperature) {
+    # This function is not used, but was
+    # in the original, so keep it for now.
     n34 = -0.6119 * temperature + 17.602;
     n45 = -0.4408 * temperature + 19.036;
     dev.rate = mean(n34 + n45);
@@ -70,6 +76,8 @@
 }
 
 dev.young = function(temperature) {
+    # This function is not used, but was
+    # in the original, so keep it for now.
     n12 = -0.3728 * temperature + 14.68;
     n23 = -0.6119 * temperature + 25.249;
     dev.rate = mean(n12 + n23);
@@ -95,6 +103,35 @@
     return(c(unlist(month_labels)));
 }
 
+get_life_stage_index = function(life_stage, life_stage_nymph=NULL, life_stage_adult=NULL) {
+    # Name collection elements so that they
+    # are displayed in logical order.
+    if (life_stage=="Egg") {
+        lsi = "01";
+    } else if (life_stage=="Nymph") {
+        if (life_stage_nymph=="Young") {
+            lsi = "02";
+        } else if (life_stage_nymph=="Old") {
+            lsi = "03";
+        } else if (life_stage_nymph=="Total") {
+            lsi="04";
+        }
+    } else if (life_stage=="Adult") {
+        if (life_stage_adult=="Pre-vittelogenic") {
+            lsi = "05";
+        } else if (life_stage_adult=="Vittelogenic") {
+            lsi = "06";
+        } else if (life_stage_adult=="Diapausing") {
+            lsi = "07";
+        } else if (life_stage_adult=="Total") {
+            lsi = "08";
+        }
+    } else if (life_stage=="Total") {
+        lsi = "09";
+    }
+    return(lsi);
+}
+
 get_temperature_at_hour = function(latitude, temperature_data_frame, row, num_days) {
     # Base development threshold for Brown Marmorated Stink Bug
     # insect phenology model.
@@ -218,8 +255,8 @@
 
 
 render_chart = function(date_labels, chart_type, plot_std_error, insect, location, latitude, start_date, end_date, days, maxval,
-    replications, life_stage, group, group_std_error, group2=NULL, group2_std_error=NULL, group3=NULL, group3_std_error=NULL,
-    life_stages_adult=NULL, life_stages_nymph=NULL) {
+            replications, life_stage, group, group_std_error, group2=NULL, group2_std_error=NULL, group3=NULL, group3_std_error=NULL,
+            life_stages_adult=NULL, life_stages_nymph=NULL) {
     if (chart_type=="pop_size_by_life_stage") {
         if (life_stage=="Total") {
             title = paste(insect, ": Reps", replications, ":", life_stage, "Pop :", location, ": Lat", latitude, ":", start_date, "-", end_date, sep=" ");
@@ -389,7 +426,7 @@
 population.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
 
 # Process replications.
-for (N.replications in 1:opt$replications) {
+for (current_replication in 1:opt$replications) {
     # Start with the user-defined number of insects per replication.
     num_insects = opt$insects_per_replication;
     # Generation, Stage, degree-days, T, Diapause.
@@ -474,6 +511,7 @@
                 death.probability = opt$egg_mortality * mortality.egg(mean.temp);
             }
             else if (vector.individual[2] == 1 | vector.individual[2] == 2) {
+                # Nymph.
                 death.probability = opt$nymph_mortality * mortality.nymph(mean.temp);
             }
             else if (vector.individual[2] == 3 | vector.individual[2] == 4 | vector.individual[2] == 5) {
@@ -711,7 +749,7 @@
 
         if (plot_generations_separately) {
             if (process_eggs) {
-                # For egg life stage of generation F1 population size,
+                # For egg life stage of generation P population size,
                 # column 1 (generation) is 0 and column 2 (Stage) is 0.
                 P.egg[row] = sum(vector.matrix[,1]==0 & vector.matrix[,2]==0);
                 # For egg life stage of generation F1 population size,
@@ -722,7 +760,7 @@
                 F2.egg[row] = sum(vector.matrix[,1]==2 & vector.matrix[,2]==0);
             }
             if (process_nymphs) {
-                # For nymph life stage of generation F1 population
+                # For nymph life stage of generation P population
                 # size, one of the following combinations is required:
                 # - column 1 (Generation) is 0 and column 2 (Stage) is 1 (Young nymph)
                 # - column 1 (Generation) is 0 and column 2 (Stage) is 2 (Old nymph)
@@ -765,44 +803,45 @@
 
     # Define the output values.
     if (process_eggs) {
-        Eggs.replications[,N.replications] = Eggs;
+        Eggs.replications[,current_replication] = Eggs;
     }
     if (process_nymphs) {
-        YoungNymphs.replications[,N.replications] = YoungNymphs;
-        OldNymphs.replications[,N.replications] = OldNymphs;
+        YoungNymphs.replications[,current_replication] = YoungNymphs;
+        OldNymphs.replications[,current_replication] = OldNymphs;
     }
     if (process_adults) {
-        Previtellogenic.replications[,N.replications] = Previtellogenic;
-        Vitellogenic.replications[,N.replications] = Vitellogenic;
-        Diapausing.replications[,N.replications] = Diapausing;
+        Previtellogenic.replications[,current_replication] = Previtellogenic;
+        Vitellogenic.replications[,current_replication] = Vitellogenic;
+        Diapausing.replications[,current_replication] = Diapausing;
     }
-    newborn.replications[,N.replications] = N.newborn;
-    adult.replications[,N.replications] = N.adult;
-    death.replications[,N.replications] = N.death;
+    newborn.replications[,current_replication] = N.newborn;
+    adult.replications[,current_replication] = N.adult;
+    death.replications[,current_replication] = N.death;
     if (plot_generations_separately) {
         # P is Parental, or overwintered adults.
-        P.replications[,N.replications] = overwintering_adult.population;
+        P.replications[,current_replication] = overwintering_adult.population;
         # F1 is the first field-produced generation.
-        F1.replications[,N.replications] = first_generation.population;
+        F1.replications[,current_replication] = first_generation.population;
         # F2 is the second field-produced generation.
-        F2.replications[,N.replications] = second_generation.population;
+        F2.replications[,current_replication] = second_generation.population;
         if (process_eggs) {
-            P_eggs.replications[,N.replications] = P.egg;
-            F1_eggs.replications[,N.replications] = F1.egg;
-            F2_eggs.replications[,N.replications] = F2.egg;
+            P_eggs.replications[,current_replication] = P.egg;
+            F1_eggs.replications[,current_replication] = F1.egg;
+            F2_eggs.replications[,current_replication] = F2.egg;
         }
         if (process_nymphs) {
-            P_nymphs.replications[,N.replications] = P.nymph;
-            F1_nymphs.replications[,N.replications] = F1.nymph;
-            F2_nymphs.replications[,N.replications] = F2.nymph;
+            P_nymphs.replications[,current_replication] = P.nymph;
+            F1_nymphs.replications[,current_replication] = F1.nymph;
+            F2_nymphs.replications[,current_replication] = F2.nymph;
         }
         if (process_adults) {
-            P_adults.replications[,N.replications] = P.adult;
-            F1_adults.replications[,N.replications] = F1.adult;
-            F2_adults.replications[,N.replications] = F2.adult;
+            P_adults.replications[,current_replication] = P.adult;
+            F1_adults.replications[,current_replication] = F1.adult;
+            F2_adults.replications[,current_replication] = F2.adult;
         }
     }
-    population.replications[,N.replications] = total.population;
+    population.replications[,current_replication] = total.population;
+    # End processing replications.
 }
 
 if (process_eggs) {
@@ -814,17 +853,17 @@
 if (process_nymphs) {
     # Calculate nymph populations for selected life stage.
     for (life_stage_nymph in life_stages_nymph) {
-        if (life_stages_nymph=="Total") {
+        if (life_stage_nymph=="Total") {
             # Mean value for all nymphs.
             total_nymphs = apply((YoungNymphs.replications+OldNymphs.replications), 1, mean);
             # Standard error for all nymphs.
             total_nymphs.std_error = apply((YoungNymphs.replications+OldNymphs.replications) / sqrt(opt$replications), 1, sd);
-        } else if (life_stages_nymph=="Young") {
+        } else if (life_stage_nymph=="Young") {
             # Mean value for young nymphs.
             young_nymphs = apply(YoungNymphs.replications, 1, mean);
             # Standard error for young nymphs.
             young_nymphs.std_error = apply(YoungNymphs.replications / sqrt(opt$replications), 1, sd);
-        } else if (life_stages_nymph=="Old") {
+        } else if (life_stage_nymph=="Old") {
             # Mean value for old nymphs.
             old_nymphs = apply(OldNymphs.replications, 1, mean);
             # Standard error for old nymphs.
@@ -835,22 +874,22 @@
 if (process_adults) {
     # Calculate adult populations for selected life stage.
     for (life_stage_adult in life_stages_adult) {
-        if (life_stages_adult=="Total") {
+        if (life_stage_adult=="Total") {
             # Mean value for all adults.
             total_adults = apply((Previtellogenic.replications+Vitellogenic.replications+Diapausing.replications), 1, mean);
             # Standard error for all adults.
             total_adults.std_error = apply((Previtellogenic.replications+Vitellogenic.replications+Diapausing.replications), 1, sd) / sqrt(opt$replications);
-        } else if (life_stages_adult == "Pre-vittelogenic") {
+        } else if (life_stage_adult == "Pre-vittelogenic") {
             # Mean value for previtellogenic adults.
             previttelogenic_adults = apply(Previtellogenic.replications, 1, mean);
             # Standard error for previtellogenic adults.
             previttelogenic_adults.std_error = apply(Previtellogenic.replications, 1, sd) / sqrt(opt$replications);
-        } else if (life_stages_adult == "Vittelogenic") {
+        } else if (life_stage_adult == "Vittelogenic") {
             # Mean value for vitellogenic adults.
             vittelogenic_adults = apply(Vitellogenic.replications, 1, mean);
             # Standard error for vitellogenic adults.
             vittelogenic_adults.std_error = apply(Vitellogenic.replications, 1, sd) / sqrt(opt$replications);
-        } else if (life_stages_adult == "Diapausing") {
+        } else if (life_stage_adult == "Diapausing") {
             # Mean value for vitellogenic adults.
             diapausing_adults = apply(Diapausing.replications, 1, mean);
             # Standard error for vitellogenic adults.
@@ -929,11 +968,13 @@
         if (life_stage == "Egg") {
             # Start PDF device driver.
             dev.new(width=20, height=30);
-            file_path = paste(output_dir, "egg_pop_by_generation.pdf", sep="/");
+            lsi = get_life_stage_index(life_stage);
+            file_name = paste(lsi, "egg_pop_by_generation.pdf", sep="_");
+            file_path = paste(output_dir, file_name, sep="/");
             pdf(file=file_path, width=20, height=30, bg="white");
             par(mar=c(5, 6, 4, 4), mfrow=c(3, 1));
             # Egg population size by generation.
-            maxval = max(F2_eggs) + 100;
+            maxval = max(P_eggs+F1_eggs+F2_eggs) + 100;
             render_chart(date_labels, "pop_size_by_generation", opt$plot_std_error, opt$insect, opt$location, latitude, start_date, end_date, days, maxval,
                 opt$replications, life_stage, group=P_eggs, group_std_error=P_eggs.std_error, group2=F1_eggs, group2_std_error=F1_eggs.std_error, group3=F2_eggs,
                 group3_std_error=F2_eggs.std_error);
@@ -943,15 +984,16 @@
             for (life_stage_nymph in life_stages_nymph) {
                 # Start PDF device driver.
                 dev.new(width=20, height=30);
-                file_name = paste(tolower(life_stage_nymph), "nymph_pop_by_generation.pdf", sep="_");
+                lsi = get_life_stage_index(life_stage, life_stage_nymph=life_stage_nymph);
+                file_name = paste(lsi, tolower(life_stage_nymph), "nymph_pop_by_generation.pdf", sep="_");
                 file_path = paste(output_dir, file_name, sep="/");
                 pdf(file=file_path, width=20, height=30, bg="white");
                 par(mar=c(5, 6, 4, 4), mfrow=c(3, 1));
                 # Nymph population size by generation.
-                maxval = max(F2_nymphs) + 100;
+                maxval = max(P_nymphs+F1_nymphs+F2_nymphs) + 100;
                 render_chart(date_labels, "pop_size_by_generation", opt$plot_std_error, opt$insect, opt$location, latitude, start_date, end_date, days, maxval,
-                    opt$replications, life_stage, group=P_nymphs, group_std_error=P_nymphs.std_error, group2=F1_nymphs, group2_std_error=F1_nymphs.std_error,
-                    group3=F2_nymphs, group3_std_error=F2_nymphs.std_error, life_stages_nymph=life_stage_nymph);
+                                            opt$replications, life_stage, group=P_nymphs, group_std_error=P_nymphs.std_error, group2=F1_nymphs, group2_std_error=F1_nymphs.std_error,
+                                            group3=F2_nymphs, group3_std_error=F2_nymphs.std_error, life_stages_nymph=life_stage_nymph);
                 # Turn off device driver to flush output.
                 dev.off();
             }
@@ -959,12 +1001,13 @@
             for (life_stage_adult in life_stages_adult) {
                 # Start PDF device driver.
                 dev.new(width=20, height=30);
-                file_name = paste(tolower(life_stage_adult), "adult_pop_by_generation.pdf", sep="_");
+                lsi = get_life_stage_index(life_stage, life_stage_adult=life_stage_adult);
+                file_name = paste(lsi, tolower(life_stage_adult), "adult_pop_by_generation.pdf", sep="_");
                 file_path = paste(output_dir, file_name, sep="/");
                 pdf(file=file_path, width=20, height=30, bg="white");
                 par(mar=c(5, 6, 4, 4), mfrow=c(3, 1));
                 # Adult population size by generation.
-                maxval = max(F2_adults) + 100;
+                maxval = max(P_adults+F1_adults+F2_adults) + 100;
                 render_chart(date_labels, "pop_size_by_generation", opt$plot_std_error, opt$insect, opt$location, latitude, start_date, end_date, days, maxval,
                     opt$replications, life_stage, group=P_adults, group_std_error=P_adults.std_error, group2=F1_adults, group2_std_error=F1_adults.std_error,
                     group3=F2_adults, group3_std_error=F2_adults.std_error, life_stages_adult=life_stage_adult);
@@ -973,12 +1016,16 @@
             }
         } else if (life_stage == "Total") {
             # Start PDF device driver.
+            # Name collection elements so that they
+            # are displayed in logical order.
             dev.new(width=20, height=30);
-            file_path = paste(output_dir, "total_pop_by_generation.pdf", sep="/");
+            lsi = get_life_stage_index(life_stage);
+            file_name = paste(lsi, "total_pop_by_generation.pdf", sep="_");
+            file_path = paste(output_dir, file_name, sep="/");
             pdf(file=file_path, width=20, height=30, bg="white");
             par(mar=c(5, 6, 4, 4), mfrow=c(3, 1));
             # Total population size by generation.
-            maxval = max(F2);
+            maxval = max(P+F1+F2) + 100;
             render_chart(date_labels, "pop_size_by_generation", opt$plot_std_error, opt$insect, opt$location, latitude, start_date, end_date, days, maxval,
                 opt$replications, life_stage, group=P, group_std_error=P.std_error, group2=F1, group2_std_error=F1.std_error, group3=F2, group3_std_error=F2.std_error);
             # Turn off device driver to flush output.
@@ -990,11 +1037,13 @@
         if (life_stage == "Egg") {
             # Start PDF device driver.
             dev.new(width=20, height=30);
-            file_path = paste(output_dir, "egg_pop.pdf", sep="/");
+            lsi = get_life_stage_index(life_stage);
+            file_name = paste(lsi, "egg_pop.pdf", sep="_");
+            file_path = paste(output_dir, file_name, sep="/");
             pdf(file=file_path, width=20, height=30, bg="white");
             par(mar=c(5, 6, 4, 4), mfrow=c(3, 1));
             # Egg population size.
-            maxval = max(eggs+eggs.std_error);
+            maxval = max(eggs+eggs.std_error) + 100;
             render_chart(date_labels, "pop_size_by_life_stage", opt$plot_std_error, opt$insect, opt$location, latitude, start_date, end_date, days, maxval,
                 opt$replications, life_stage, group=eggs, group_std_error=eggs.std_error);
             # Turn off device driver to flush output.
@@ -1003,7 +1052,8 @@
             for (life_stage_nymph in life_stages_nymph) {
                 # Start PDF device driver.
                 dev.new(width=20, height=30);
-                file_name = paste(tolower(life_stage_nymph), "nymph_pop.pdf", sep="_");
+                lsi = get_life_stage_index(life_stage, life_stage_nymph=life_stage_nymph);
+                file_name = paste(lsi, tolower(life_stage_nymph), "nymph_pop.pdf", sep="_");
                 file_path = paste(output_dir, file_name, sep="/");
                 pdf(file=file_path, width=20, height=30, bg="white");
                 par(mar=c(5, 6, 4, 4), mfrow=c(3, 1));
@@ -1020,7 +1070,7 @@
                     group = old_nymphs;
                     group_std_error = old_nymphs.std_error;
                 }
-                maxval = max(group+group.std_error);
+                maxval = max(group+group_std_error) + 100;
                 render_chart(date_labels, "pop_size_by_life_stage", opt$plot_std_error, opt$insect, opt$location, latitude, start_date, end_date, days, maxval,
                     opt$replications, life_stage, group=group, group_std_error=group_std_error, life_stages_nymph=life_stage_nymph);
                 # Turn off device driver to flush output.
@@ -1030,7 +1080,8 @@
             for (life_stage_adult in life_stages_adult) {
                 # Start PDF device driver.
                 dev.new(width=20, height=30);
-                file_name = paste(tolower(life_stages_adult), "adult_pop.pdf", sep="_");
+                lsi = get_life_stage_index(life_stage, life_stage_adult=life_stage_adult);
+                file_name = paste(lsi, tolower(life_stage_adult), "adult_pop.pdf", sep="_");
                 file_path = paste(output_dir, file_name, sep="/");
                 pdf(file=file_path, width=20, height=30, bg="white");
                 par(mar=c(5, 6, 4, 4), mfrow=c(3, 1));
@@ -1051,7 +1102,7 @@
                     group = diapausing_adults;
                     group_std_error = diapausing_adults.std_error
                 }
-                maxval = max(group+group_std_error);
+                maxval = max(group+group_std_error) + 100;
                 render_chart(date_labels, "pop_size_by_life_stage", opt$plot_std_error, opt$insect, opt$location, latitude, start_date, end_date, days, maxval,
                     opt$replications, life_stage, group=group, group_std_error=group_std_error, life_stages_adult=life_stage_adult);
                 # Turn off device driver to flush output.
@@ -1060,11 +1111,13 @@
         } else if (life_stage == "Total") {
             # Start PDF device driver.
             dev.new(width=20, height=30);
-            file_path = paste(output_dir, "total_pop.pdf", sep="/");
+            lsi = get_life_stage_index(life_stage);
+            file_name = paste(lsi, "total_pop.pdf", sep="_");
+            file_path = paste(output_dir, file_name, sep="/");
             pdf(file=file_path, width=20, height=30, bg="white");
             par(mar=c(5, 6, 4, 4), mfrow=c(3, 1));
             # Total population size.
-            maxval = max(eggs+eggs.std_error, nymphs+nymphs.std_error, adults+adults.std_error);
+            maxval = max(eggs+eggs.std_error, total_nymphs+total_nymphs.std_error, total_adults+total_adults.std_error) + 100;
             render_chart(date_labels, "pop_size_by_life_stage", opt$plot_std_error, opt$insect, opt$location, latitude, start_date, end_date, days, maxval,
                 opt$replications, life_stage, group=total_adults, group_std_error=total_adults.std_error, group2=total_nymphs, group2_std_error=total_nymphs.std_error, group3=eggs,
                 group3_std_error=eggs.std_error);
diff -r 6f31ade9a0f4 -r f5ecff4800f2 insect_phenology_model.xml
--- a/insect_phenology_model.xml	Tue Mar 06 08:26:50 2018 -0500
+++ b/insect_phenology_model.xml	Tue Mar 06 13:39:14 2018 -0500
@@ -118,7 +118,10 @@
             <param name="location" value="State College PA" />
             <param name="replications" value="2" />
             <output_collection name="output_collection" type="list">
-                <element name="total_pop_by_generation.pdf" file="total_pop_by_generation.pdf" ftype="pdf" compare="contains"/>
+                <element name="01_egg_pop_by_generation.pdf" file="pop_by_generation.pdf" ftype="pdf" compare="contains"/>
+                <element name="04_total_nymph_pop_by_generation.pdf" file="pop_by_generation.pdf" ftype="pdf" compare="contains"/>
+                <element name="08_total_adult_pop_by_generation.pdf" file="pop_by_generation.pdf" ftype="pdf" compare="contains"/>
+                <element name="09_total_pop_by_generation.pdf" file="pop_by_generation.pdf" ftype="pdf" compare="contains"/>
             </output_collection>
         </test>
     </tests>
diff -r 6f31ade9a0f4 -r f5ecff4800f2 test-data/pop_by_generation.pdf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pop_by_generation.pdf	Tue Mar 06 13:39:14 2018 -0500
@@ -0,0 +1,52 @@
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diff -r 6f31ade9a0f4 -r f5ecff4800f2 test-data/total_pop_by_generation.pdf
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