insect_phenology_model: insect_phenology

comparison insect_phenology_model.R @ 18:f5ecff4800f2 draft

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author	greg
date	Tue, 06 Mar 2018 13:39:14 -0500
parents	309954bbe999
children	3c6e94e477cb

comparison

equal deleted inserted replaced

-:6f31ade9a0f4
+:f5ecff4800f2
 temperature_data_frame[, num_columns+1] = daylight_length_vector;
 return(temperature_data_frame);
 }
 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);
 return(dev.rate);
 }
 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);
 return(dev.rate);
 }
 month_labels[length(month_labels)+1] = month_label;
 current_month_label = month_label;
 }
 }
 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.
 return(temperature_data_frame);
 }
 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) {
 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=" ");
 legend_text = c("Egg", "Nymph", "Adult");
 columns = c(4, 2, 1);
 }
 # Total population.
 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.
 vector.ini = c(0, 3, 0, 0, 0);
 # Replicate to create a matrix where the columns are
 if (vector.individual[2] == 0) {
 # Egg.
 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) {
 # Adult.
 if (doy < day.kill) {
 # size, column 1 (Generation) must be 2.
 second_generation.population[row] = sum(vector.matrix[,1]==2);
 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,
 # column 1 (generation) is 1 and column 2 (Stage) is 0.
 F1.egg[row] = sum(vector.matrix[,1]==1 & vector.matrix[,2]==0);
 # For egg life stage of generation F2 population size,
 # column 1 (generation) is 2 and column 2 (Stage) is 0.
 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)
 P.nymph[row] = sum((vector.matrix[,1]==0 & vector.matrix[,2]==1) | (vector.matrix[,1]==0 & vector.matrix[,2]==2));
 # For nymph life stage of generation F1 population
 averages.cum = cumsum(averages.day);
 # 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;
+YoungNymphs.replications[,current_replication] = YoungNymphs;
-OldNymphs.replications[,N.replications] = OldNymphs;
+OldNymphs.replications[,current_replication] = OldNymphs;
 }
 if (process_adults) {
-Previtellogenic.replications[,N.replications] = Previtellogenic;
+Previtellogenic.replications[,current_replication] = Previtellogenic;
-Vitellogenic.replications[,N.replications] = Vitellogenic;
+Vitellogenic.replications[,current_replication] = Vitellogenic;
-Diapausing.replications[,N.replications] = Diapausing;
+Diapausing.replications[,current_replication] = Diapausing;
 }
-newborn.replications[,N.replications] = N.newborn;
+newborn.replications[,current_replication] = N.newborn;
-adult.replications[,N.replications] = N.adult;
+adult.replications[,current_replication] = N.adult;
-death.replications[,N.replications] = N.death;
+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;
+P_eggs.replications[,current_replication] = P.egg;
-F1_eggs.replications[,N.replications] = F1.egg;
+F1_eggs.replications[,current_replication] = F1.egg;
-F2_eggs.replications[,N.replications] = F2.egg;
+F2_eggs.replications[,current_replication] = F2.egg;
 }
 if (process_nymphs) {
-P_nymphs.replications[,N.replications] = P.nymph;
+P_nymphs.replications[,current_replication] = P.nymph;
-F1_nymphs.replications[,N.replications] = F1.nymph;
+F1_nymphs.replications[,current_replication] = F1.nymph;
-F2_nymphs.replications[,N.replications] = F2.nymph;
+F2_nymphs.replications[,current_replication] = F2.nymph;
 }
 if (process_adults) {
-P_adults.replications[,N.replications] = P.adult;
+P_adults.replications[,current_replication] = P.adult;
-F1_adults.replications[,N.replications] = F1.adult;
+F1_adults.replications[,current_replication] = F1.adult;
-F2_adults.replications[,N.replications] = F2.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) {
 # Mean value for eggs.
 eggs = apply(Eggs.replications, 1, mean);
 eggs.std_error = apply(Eggs.replications, 1, sd) / sqrt(opt$replications);
 }
 if (process_nymphs) {
 # Calculate nymph populations for selected life stage.
 for (life_stage_nymph in life_stages_nymph) {
-if (life_stages_nymph=="Total") {
+if (life_stage_nymph=="Total") {
 # Mean value for all nymphs.
 total_nymphs = apply((YoungNymphs.replications+OldNymphs.replications), 1, mean);
 # Standard error for all nymphs.
 total_nymphs.std_error = apply((YoungNymphs.replications+OldNymphs.replications) / sqrt(opt$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$replications), 1, sd);
-} else if (life_stages_nymph=="Old") {
+} else if (life_stage_nymph=="Old") {
 # Mean value for old nymphs.
 old_nymphs = apply(OldNymphs.replications, 1, mean);
 # Standard error for old nymphs.
 old_nymphs.std_error = apply(OldNymphs.replications / sqrt(opt$replications), 1, sd);
 }
 }
 }
 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$replications);
-} else if (life_stages_adult == "Diapausing") {
+} else if (life_stage_adult == "Diapausing") {
 # Mean value for vitellogenic adults.
 diapausing_adults = apply(Diapausing.replications, 1, mean);
 # Standard error for vitellogenic adults.
 diapausing_adults.std_error = apply(Diapausing.replications, 1, sd) / sqrt(opt$replications);
 }
 if (plot_generations_separately) {
 for (life_stage in life_stages) {
 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);
 # Turn off device driver to flush output.
 dev.off();
 } else if (life_stage == "Nymph") {
 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);
 # Turn off device driver to flush output.
 dev.off();
 }
 } else if (life_stage == "Adult") {
 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);
 # Turn off device driver to flush output.
 dev.off();
 }
 } 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.
 dev.off();
 }
 } else {
 for (life_stage in life_stages) {
 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.
 dev.off();
 } else if (life_stage == "Nymph") {
 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));
 if (life_stage_nymph=="Total") {
 # Total nymph population size.
 } else if (life_stage_nymph=="Old") {
 # Old nymph population size.
 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.
 dev.off();
 }
 } else if (life_stage == "Adult") {
 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));
 if (life_stage_adult=="Total") {
 # Total adult population size.
 } else if (life_stage_adult=="Diapausing") {
 # Diapausing adult population size.
 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.
 dev.off();
 }
 } 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);
 # Turn off device driver to flush output.
 dev.off();

Mercurial > repos > greg > insect_phenology_model

comparison insect_phenology_model.R @ 18:f5ecff4800f2 draft