insect_phenology_model: insect_phenology

comparison insect_phenology_model.R @ 20:214217142600 draft

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author	greg
date	Thu, 08 Mar 2018 08:06:18 -0500
parents	3c6e94e477cb
children	6349699fc9fa

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-:3c6e94e477cb
+:214217142600
 }
 }
 return(c(unlist(month_labels)));
 }
 get_file_path = function(life_stage, base_name, life_stage_nymph=NULL, life_stage_adult=NULL) {
 if (!is.null(life_stage_nymph)) {
 lsi = get_life_stage_index(life_stage, life_stage_nymph=life_stage_nymph);
 file_name = paste(lsi, tolower(life_stage_nymph), base_name, sep="_");
 } else if (!is.null(life_stage_adult)) {
 }
 } else if (life_stage=="Total") {
 lsi = "09";
 }
 return(lsi);
+}
+get_mean_and_std_error = function(p_replications, f1_replications, f2_replications) {
+# P mean.
+p_m = apply(p_replications, 1, mean);
+# P standard error.
+p_se = apply(p_replications, 1, sd) / sqrt(opt$replications);
+# F1 mean.
+f1_m = apply(f1_replications, 1, mean);
+# F1 standard error.
+f1_se = apply(f1_replications, 1, sd) / sqrt(opt$replications);
+# F2 mean.
+f2_m = apply(f2_replications, 1, mean);
+# F2 standard error.
+f2_se = apply(f2_replications, 1, sd) / sqrt(opt$replications);
+return(list(p_m, p_se, f1_m, f1_se, f2_m, f2_se))
 }
 get_temperature_at_hour = function(latitude, temperature_data_frame, row, num_days) {
 # Base development threshold for Brown Marmorated Stink Bug
 # insect phenology model.
 colnames(temperature_data_frame) = c("LATITUDE","LONGITUDE", "DATE", "DOY", "TMIN", "TMAX", "DAYLEN");
 }
 return(temperature_data_frame);
 }
 render_chart = function(date_labels, chart_type, plot_std_error, insect, location, latitude, start_date, end_date, days, maxval,
 replications, life_stage, group, group_std_error, group2=NULL, group2_std_error=NULL, group3=NULL, group3_std_error=NULL,
 life_stages_adult=NULL, life_stages_nymph=NULL) {
+cat("In render_chart, chart_type: ", chart_type, "\n");
 if (chart_type=="pop_size_by_life_stage") {
 if (life_stage=="Total") {
 title = paste(insect, ": Reps", replications, ":", life_stage, "Pop :", location, ": Lat", latitude, ":", start_date, "-", end_date, sep=" ");
 legend_text = c("Egg", "Nymph", "Adult");
 columns = c(4, 2, 1);
 title_str = paste(":", life_stages_nymph, "Nymph Pop by Gen", ":", sep=" ");
 } else if (life_stage=="Adult") {
 title_str = paste(":", life_stages_adult, "Adult Pop by Gen", ":", sep=" ");
 }
 title = paste(insect, ": Reps", replications, title_str, location, ": Lat", latitude, ":", start_date, "-", end_date, sep=" ");
+cat("In render_chart, title: ", title, "\n");
+cat("In render_chart, group: ", group, "\n");
+cat("In render_chart, group2: ", group2, "\n");
+cat("In render_chart, group3: ", group3, "\n");
 legend_text = c("P", "F1", "F2");
 columns = c(1, 2, 4);
 plot(days, group, main=title, type="l", ylim=c(0, maxval), axes=F, lwd=2, xlab="", ylab="", cex=3, cex.lab=3, cex.axis=3, cex.main=3);
 legend("topleft", legend_text, lty=c(1, 1, 1), col=columns, cex=3);
 lines(days, group2, lwd=2, lty=1, col=2);
 date_labels = get_date_labels(temperature_data_frame, opt$num_days);
 # All latitude values are the same, so get the value for plots from the first row.
 latitude = temperature_data_frame$LATITUDE[1];
 # Get the number of days for plots.
 num_columns = dim(temperature_data_frame)[2];
+# Determine the specified life stages for processing.
 # Split life_stages into a list of strings for plots.
 life_stages_str = as.character(opt$life_stages);
 life_stages = strsplit(life_stages_str, ",")[[1]];
 # Determine the data we need to generate for plotting.
 process_eggs = FALSE;
 process_nymphs = FALSE;
+process_young_nymphs = FALSE;
+process_old_nymphs = FALSE;
+process_total_nymphs = FALSE;
 process_adults = FALSE;
+process_previtellogenic_adults = FALSE;
+process_vitellogenic_adults = FALSE;
+process_diapausing_adults = FALSE;
+process_total_adults = FALSE;
 for (life_stage in life_stages) {
 if (life_stage=="Total") {
 process_eggs = TRUE;
 process_nymphs = TRUE;
 process_adults = TRUE;
 process_nymphs = TRUE;
 } else if (life_stage=="Adult") {
 process_adults = TRUE;
 }
 }
+if (process_nymphs) {
+# Split life_stages_nymph into a list of strings for plots.
+life_stages_nymph_str = as.character(opt$life_stages_nymph);
+life_stages_nymph = strsplit(life_stages_nymph_str, ",")[[1]];
+for (life_stage_nymph in opt$life_stages_nymph) {
+if (life_stage_nymph=="Young") {
+process_young_nymphs = TRUE;
+} else if (life_stage_nymph=="Old") {
+process_old_nymphs = TRUE;
+} else if (life_stage_nymph=="Total") {
+process_total_nymphs = TRUE;
+}
+}
+}
 if (process_adults) {
 # Split life_stages_adult into a list of strings for plots.
 life_stages_adult_str = as.character(opt$life_stages_adult);
 life_stages_adult = strsplit(life_stages_adult_str, ",")[[1]];
-}
+for (life_stage_adult in opt$life_stages_adult) {
-if (process_nymphs) {
+if (life_stage_adult=="Previtellogenic") {
-# Split life_stages_nymph into a list of strings for plots.
+process_previtellogenic_adults = TRUE;
-life_stages_nymph_str = as.character(opt$life_stages_nymph);
+} else if (life_stage_adult=="Vitellogenic") {
-life_stages_nymph = strsplit(life_stages_nymph_str, ",")[[1]];
+process_vitellogenic_adults = TRUE;
-}
+} else if (life_stage_adult=="Diapausing") {
+process_diapausing_adults = TRUE;
+} else if (life_stage_adult=="Total") {
+process_total_adults = TRUE;
+}
+}
+}
+cat("process_eggs: ", process_eggs, "\n");
+cat("process_nymphs: ", process_nymphs, "\n");
+cat("process_young_nymphs: ", process_young_nymphs, "\n");
+cat("process_old_nymphs: ", process_old_nymphs, "\n");
+cat("process_total_nymphs: ", process_total_nymphs, "\n");
+cat("process_adults: ", process_adults, "\n");
+cat("process_previtellogenic_adults: ", process_previtellogenic_adults, "\n");
+cat("process_vitellogenic_adults: ", process_vitellogenic_adults, "\n");
+cat("process_diapausing_adults: ", process_diapausing_adults, "\n");
+cat("process_total_adults: ", process_total_adults, "\n");
+cat("life_stages: ", life_stages, "\n");
+cat("life_stages_nymph: ", life_stages_nymph, "\n");
+cat("life_stages_adult: ", life_stages_adult, "\n");
 # Initialize matrices.
 if (process_eggs) {
 Eggs.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
 }
-if (process_nymphs) {
+cat("process_young_nymphs==TRUE: ", process_young_nymphs==TRUE, "\n");
+cat("process_total_nymphs==TRUE: ", process_total_nymphs==TRUE, "\n");
+if (process_young_nymphs==TRUE | process_total_nymphs==TRUE) {
 YoungNymphs.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
+}
+if (process_old_nymphs==TRUE | process_total_nymphs==TRUE) {
 OldNymphs.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
 }
 if (process_adults) {
 Previtellogenic.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
 Vitellogenic.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
 if (process_eggs) {
 P_eggs.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
 F1_eggs.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
 F2_eggs.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
 }
-if (process_nymphs) {
+if (process_young_nymphs) {
-P_nymphs.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
+P_young_nymphs.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
-F1_nymphs.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
+F1_young_nymphs.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
-F2_nymphs.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
+F2_young_nymphs.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
+}
+if (process_old_nymphs) {
+P_old_nymphs.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
+F1_old_nymphs.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
+F2_old_nymphs.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
+}
+if (process_total_nymphs) {
+P_total_nymphs.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
+F1_total_nymphs.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
+F2_total_nymphs.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
 }
 if (process_adults) {
 P_adults.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
 F1_adults.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
 F2_adults.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
 if (process_eggs) {
 P.egg = rep(0, opt$num_days);
 F1.egg = rep(0, opt$num_days);
 F2.egg = rep(0, opt$num_days);
 }
-if (process_nymphs) {
+if (process_young_nymphs) {
-P.nymph = rep(0, opt$num_days);
+P.young_nymph = rep(0, opt$num_days);
-F1.nymph = rep(0, opt$num_days);
+F1.young_nymph = rep(0, opt$num_days);
-F2.nymph = rep(0, opt$num_days);
+F2.young_nymph = rep(0, opt$num_days);
+}
+if (process_old_nymphs) {
+P.old_nymph = rep(0, opt$num_days);
+F1.old_nymph = rep(0, opt$num_days);
+F2.old_nymph = rep(0, opt$num_days);
+}
+if (process_total_nymphs) {
+P.total_nymph = rep(0, opt$num_days);
+F1.total_nymph = rep(0, opt$num_days);
+F2.total_nymph = rep(0, opt$num_days);
 }
 if (process_adults) {
 P.adult = rep(0, opt$num_days);
 F1.adult = rep(0, opt$num_days);
 F2.adult = rep(0, opt$num_days);
 # are now Generation, Stage, degree-days, T, Diapause,
 if (process_eggs) {
 # For egg population size, column 2 (Stage), must be 0.
 Eggs[row] = sum(vector.matrix[,2]==0);
 }
-if (process_nymphs) {
+if (process_young_nymphs) {
 # For young nymph population size, column 2 (Stage) must be 1.
 YoungNymphs[row] = sum(vector.matrix[,2]==1);
+}
+if (process_old_nymphs) {
 # For old nymph population size, column 2 (Stage) must be 2.
 OldNymphs[row] = sum(vector.matrix[,2]==2);
 }
 if (process_adults) {
 # For pre-vitellogenic population size, column 2 (Stage) must be 3.
 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) {
+if (process_young_nymphs) {
-# For nymph life stage of generation P population
+# For young nymph life stage of generation P population
+# size, the following combination is required:
+# - column 1 (Generation) is 0 and column 2 (Stage) is 1 (Young nymph)
+P.young_nymph[row] = sum(vector.matrix[,1]==0 & vector.matrix[,2]==1);
+# For young nymph life stage of generation F1 population
+# size, the following combination is required:
+# - column 1 (Generation) is 1 and column 2 (Stage) is 1 (Young nymph)
+F1.young_nymph[row] = sum(vector.matrix[,1]==1 & vector.matrix[,2]==1);
+# For young nymph life stage of generation F2 population
+# size, the following combination is required:
+# - column 1 (Generation) is 2 and column 2 (Stage) is 1 (Young nymph)
+F2.young_nymph[row] = sum(vector.matrix[,1]==2 & vector.matrix[,2]==1);
+}
+if (process_old_nymphs) {
+# For old nymph life stage of generation P population
+# size, the following combination is required:
+# - column 1 (Generation) is 0 and column 2 (Stage) is 2 (Old nymph)
+P.old_nymph[row] = sum(vector.matrix[,1]==0 & vector.matrix[,2]==2);
+# For old nymph life stage of generation F1 population
+# size, the following combination is required:
+# - column 1 (Generation) is 1 and column 2 (Stage) is 2 (Old nymph)
+F1.old_nymph[row] = sum(vector.matrix[,1]==1 & vector.matrix[,2]==2);
+# For old nymph life stage of generation F2 population
+# size, the following combination is required:
+# - column 1 (Generation) is 2 and column 2 (Stage) is 2 (Old nymph)
+F2.old_nymph[row] = sum(vector.matrix[,1]==2 & vector.matrix[,2]==2);
+}
+if (process_total_nymphs) {
+# For total 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));
+P.total_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
+# For total nymph life stage of generation F1 population
 # size, one of the following combinations is required:
 # - column 1 (Generation) is 1 and column 2 (Stage) is 1 (Young nymph)
 # - column 1 (Generation) is 1 and column 2 (Stage) is 2 (Old nymph)
-F1.nymph[row] = sum((vector.matrix[,1]==1 & vector.matrix[,2]==1) | (vector.matrix[,1]==1 & vector.matrix[,2]==2));
+F1.total_nymph[row] = sum((vector.matrix[,1]==1 & vector.matrix[,2]==1) | (vector.matrix[,1]==1 & vector.matrix[,2]==2));
-# For nymph life stage of generation F2 population
+# For total nymph life stage of generation F2 population
 # size, one of the following combinations is required:
 # - column 1 (Generation) is 2 and column 2 (Stage) is 1 (Young nymph)
 # - column 1 (Generation) is 2 and column 2 (Stage) is 2 (Old nymph)
-F2.nymph[row] = sum((vector.matrix[,1]==2 & vector.matrix[,2]==1) | (vector.matrix[,1]==2 & vector.matrix[,2]==2));
+F2.total_nymph[row] = sum((vector.matrix[,1]==2 & vector.matrix[,2]==1) | (vector.matrix[,1]==2 & vector.matrix[,2]==2));
 }
 if (process_adults) {
 # For adult life stage of generation P population
 # size, one of the following combinations is required:
 # - column 1 (Generation) is 0 and column 2 (Stage) is 3 (Pre-vitellogenic)
 # Define the output values.
 if (process_eggs) {
 Eggs.replications[,current_replication] = Eggs;
 }
-if (process_nymphs) {
+if (process_young_nymphs==TRUE | process_total_nymphs==TRUE) {
 YoungNymphs.replications[,current_replication] = YoungNymphs;
+}
+if (process_old_nymphs==TRUE | process_total_nymphs==TRUE) {
 OldNymphs.replications[,current_replication] = OldNymphs;
 }
 if (process_adults) {
 Previtellogenic.replications[,current_replication] = Previtellogenic;
 Vitellogenic.replications[,current_replication] = Vitellogenic;
 if (process_eggs) {
 P_eggs.replications[,current_replication] = P.egg;
 F1_eggs.replications[,current_replication] = F1.egg;
 F2_eggs.replications[,current_replication] = F2.egg;
 }
-if (process_nymphs) {
+if (process_young_nymphs) {
-P_nymphs.replications[,current_replication] = P.nymph;
+P_young_nymphs.replications[,current_replication] = P.young_nymph;
-F1_nymphs.replications[,current_replication] = F1.nymph;
+F1_young_nymphs.replications[,current_replication] = F1.young_nymph;
-F2_nymphs.replications[,current_replication] = F2.nymph;
+F2_young_nymphs.replications[,current_replication] = F2.young_nymph;
+}
+if (process_old_nymphs) {
+P_old_nymphs.replications[,current_replication] = P.old_nymph;
+F1_old_nymphs.replications[,current_replication] = F1.old_nymph;
+F2_old_nymphs.replications[,current_replication] = F2.old_nymph;
+}
+if (process_total_nymphs) {
+P_total_nymphs.replications[,current_replication] = P.total_nymph;
+F1_total_nymphs.replications[,current_replication] = F1.total_nymph;
+F2_total_nymphs.replications[,current_replication] = F2.total_nymph;
 }
 if (process_adults) {
 P_adults.replications[,current_replication] = P.adult;
 F1_adults.replications[,current_replication] = F1.adult;
 F2_adults.replications[,current_replication] = F2.adult;
 }
 }
 }
 if (plot_generations_separately) {
-# Mean value for P which is Parental, or overwintered adults.
+m_se = get_mean_and_std_error(P.replications, F1.replications, F2.replications);
-P = apply(P.replications, 1, mean);
+P = m_se[[1]];
-# Standard error for P.
+P.std_error = m_se[[2]];
-P.std_error = apply(P.replications, 1, sd) / sqrt(opt$replications);
+F1 = m_se[[3]];
-# Mean value for F1, which is the first field-produced generation.
+F1.std_error = m_se[[4]];
-F1 = apply(F1.replications, 1, mean);
+F2 = m_se[[5]];
-# Standard error for F1.
+F2.std_error = m_se[[6]];
-F1.std_error = apply(F1.replications, 1, sd) / sqrt(opt$replications);
-# Mean value for F2, which is the second field-produced generation.
-F2 = apply(F2.replications, 1, mean);
-# Standard error for F2.
-F2.std_error = apply(F2.replications, 1, sd) / sqrt(opt$replications);
 if (process_eggs) {
-# Mean value for P eggs.
+m_se = get_mean_and_std_error(P_eggs.replications, F1_eggs.replications, F2_eggs.replications);
-P_eggs = apply(P_eggs.replications, 1, mean);
+P_eggs = m_se[[1]];
-# Standard error for P_eggs.
+P_eggs.std_error = m_se[[2]];
-P_eggs.std_error = apply(P_eggs.replications, 1, sd) / sqrt(opt$replications);
+F1_eggs = m_se[[3]];
-# Mean value for F1 eggs.
+F1_eggs.std_error = m_se[[4]];
-F1_eggs = apply(F1_eggs.replications, 1, mean);
+F2_eggs = m_se[[5]];
-# Standard error for F1 eggs.
+F2_eggs.std_error = m_se[[6]];
-F1_eggs.std_error = apply(F1_eggs.replications, 1, sd) / sqrt(opt$replications);
+}
-# Mean value for F2 eggs.
+if (process_young_nymphs) {
-F2_eggs = apply(F2_eggs.replications, 1, mean);
+m_se = get_mean_and_std_error(P_young_nymphs.replications, F1_young_nymphs.replications, F2_young_nymphs.replications);
-# Standard error for F2 eggs.
+P_young_nymphs = m_se[[1]];
-F2_eggs.std_error = apply(F2_eggs.replications, 1, sd) / sqrt(opt$replications);
+P_young_nymphs.std_error = m_se[[2]];
-}
+F1_young_nymphs = m_se[[3]];
-if (process_nymphs) {
+F1_young_nymphs.std_error = m_se[[4]];
-# Mean value for P nymphs.
+F2_young_nymphs = m_se[[5]];
-P_nymphs = apply(P_nymphs.replications, 1, mean);
+F2_young_nymphs.std_error = m_se[[6]];
-# Standard error for P_nymphs.
+}
-P_nymphs.std_error = apply(P_nymphs.replications, 1, sd) / sqrt(opt$replications);
+if (process_old_nymphs) {
-# Mean value for F1 nymphs.
+m_se = get_mean_and_std_error(P_old_nymphs.replications, F1_old_nymphs.replications, F2_old_nymphs.replications);
-F1_nymphs = apply(F1_nymphs.replications, 1, mean);
+P_old_nymphs = m_se[[1]];
-# Standard error for F1 nymphs.
+P_old_nymphs.std_error = m_se[[2]];
-F1_nymphs.std_error = apply(F1_nymphs.replications, 1, sd) / sqrt(opt$replications);
+F1_old_nymphs = m_se[[3]];
-# Mean value for F2 nymphs.
+F1_old_nymphs.std_error = m_se[[4]];
-F2_nymphs = apply(F2_nymphs.replications, 1, mean);
+F2_old_nymphs = m_se[[5]];
-# Standard error for F2 eggs.
+F2_old_nymphs.std_error = m_se[[6]];
-F2_nymphs.std_error = apply(F2_nymphs.replications, 1, sd) / sqrt(opt$replications);
+}
+if (process_total_nymphs) {
+m_se = get_mean_and_std_error(P_total_nymphs.replications, F1_total_nymphs.replications, F2_total_nymphs.replications);
+P_total_nymphs = m_se[[1]];
+P_total_nymphs.std_error = m_se[[2]];
+F1_total_nymphs = m_se[[3]];
+F1_total_nymphs.std_error = m_se[[4]];
+F2_total_nymphs = m_se[[5]];
+F2_total_nymphs.std_error = m_se[[6]];
 }
 if (process_adults) {
-# Mean value for P adults.
+# Mean value for P_adults.
 P_adults = apply(P_adults.replications, 1, mean);
 # Standard error for P_adults.
 P_adults.std_error = apply(P_adults.replications, 1, sd) / sqrt(opt$replications);
 # Mean value for F1 adults.
 F1_adults = apply(F1_adults.replications, 1, mean);
-# Standard error for F1 adults.
+# Standard error for F1_adults.
 F1_adults.std_error = apply(F1_adults.replications, 1, sd) / sqrt(opt$replications);
-# Mean value for F2 adults.
+# Mean value for F2_adults.
 F2_adults = apply(F2_adults.replications, 1, mean);
-# Standard error for F2 adults.
+# Standard error for F2_adults.
 F2_adults.std_error = apply(F2_adults.replications, 1, sd) / sqrt(opt$replications);
 }
 }
 # Display the total number of days in the Galaxy history item blurb.
 # Information needed for plots plots.
 days = c(1:opt$num_days);
 start_date = temperature_data_frame$DATE[1];
 end_date = temperature_data_frame$DATE[opt$num_days];
+cat("life_stages: ", toString(life_stages), "\n");
+cat("plot_generations_separately: ", plot_generations_separately, "\n");
 if (plot_generations_separately) {
 for (life_stage in life_stages) {
+cat("life_stage: ", life_stage, "\n");
 if (life_stage == "Egg") {
 # Start PDF device driver.
 dev.new(width=20, height=30);
 file_path = get_file_path(life_stage, "egg_pop_by_generation.pdf")
 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(P_eggs+F1_eggs+F2_eggs) + 100;
+cat("maxval: ", maxval, "\n");
+cat("P_eggs: ", toString(P_eggs), "\n");
+cat("is.vector(P_eggs): ", is.vector(P_eggs), "\n");
+cat("length(P_eggs): ", length(P_eggs), "\n");
+cat("P_eggs.std_error: ", toString(P_eggs.std_error), "\n");
+cat("F1_eggs: ", toString(F1_eggs), "\n");
+cat("F1_eggs.std_error: ", toString(F1_eggs.std_error), "\n");
+cat("F2_eggs: ", toString(F2_eggs), "\n");
+cat("F2_eggs.std_error: ", toString(F2_eggs.std_error), "\n");
 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) {
+cat("life_stage_nymph: ", life_stage_nymph, "\n");
 # Start PDF device driver.
 dev.new(width=20, height=30);
 file_path = get_file_path(life_stage, "nymph_pop_by_generation.pdf", life_stage_nymph=life_stage_nymph)
 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.
+if (life_stage_nymph=="Young") {
-maxval = max(P_nymphs+F1_nymphs+F2_nymphs) + 100;
+# Young nymph population size by generation.
+maxval = max(P_young_nymphs+F1_young_nymphs+F2_young_nymphs) + 100;
+group = P_young_nymphs;
+group_std_error = P_young_nymphs.std_error;
+group2 = F1_young_nymphs;
+group2_std_error = F1_young_nymphs.std_error;
+group3 = F2_young_nymphs;
+group3_std_error = F2_young_nymphs.std_error;
+} else if (life_stage_nymph=="Old") {
+# Total nymph population size by generation.
+maxval = max(P_old_nymphs+F1_old_nymphs+F2_old_nymphs) + 100;
+group = P_old_nymphs;
+group_std_error = P_old_nymphs.std_error;
+group2 = F1_old_nymphs;
+group2_std_error = F1_old_nymphs.std_error;
+group3 = F2_old_nymphs;
+group3_std_error = F2_old_nymphs.std_error;
+} else if (life_stage_nymph=="Total") {
+# Total nymph population size by generation.
+maxval = max(P_total_nymphs+F1_total_nymphs+F2_total_nymphs) + 100;
+group = P_total_nymphs;
+group_std_error = P_total_nymphs.std_error;
+group2 = F1_total_nymphs;
+group2_std_error = F1_total_nymphs.std_error;
+group3 = F2_total_nymphs;
+group3_std_error = F2_total_nymphs.std_error;
+}
+cat("XXX group: ", group, "\n");
 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,
+opt$replications, life_stage, group=group, group_std_error=group_std_error, group2=group2, group2_std_error=group2_std_error,
-group3=F2_nymphs, group3_std_error=F2_nymphs.std_error, life_stages_nymph=life_stage_nymph);
+group3=group3, group3_std_error=group3_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) {

Mercurial > repos > greg > insect_phenology_model

comparison insect_phenology_model.R @ 20:214217142600 draft