insect_phenology_model: insect_phenology

comparison insect_phenology_model.R @ 23:36d7bb034285 draft

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author	greg
date	Thu, 08 Mar 2018 13:29:02 -0500
parents	6349699fc9fa
children	b90f9b781a77

comparison

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-:58255c06d24b
+:36d7bb034285
 process_nymphs = FALSE;
 process_young_nymphs = FALSE;
 process_old_nymphs = FALSE;
 process_total_nymphs = FALSE;
 process_adults = FALSE;
-process_previtellogenic_adults = FALSE;
+process_previttelogenic_adults = FALSE;
-process_vitellogenic_adults = FALSE;
+process_vittelogenic_adults = FALSE;
 process_diapausing_adults = FALSE;
 process_total_adults = FALSE;
 for (life_stage in life_stages) {
 if (life_stage=="Total") {
 process_eggs = 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) {
+for (life_stage_nymph in 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") {
 }
 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) {
+for (life_stage_adult in life_stages_adult) {
-if (life_stage_adult=="Previtellogenic") {
+if (life_stage_adult=="Pre-vittelogenic") {
-process_previtellogenic_adults = TRUE;
+process_previttelogenic_adults = TRUE;
-} else if (life_stage_adult=="Vitellogenic") {
+} else if (life_stage_adult=="Vitelogenic") {
-process_vitellogenic_adults = TRUE;
+process_vittelogenic_adults = TRUE;
 } else if (life_stage_adult=="Diapausing") {
 process_diapausing_adults = TRUE;
 } else if (life_stage_adult=="Total") {
 process_total_adults = TRUE;
 }
 }
 }
 # Initialize matrices.
 if (process_eggs) {
 Eggs.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
 }
-if (process_young_nymphs==TRUE | process_total_nymphs==TRUE) {
+if (process_young_nymphs | process_total_nymphs) {
 YoungNymphs.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
 }
-if (process_old_nymphs==TRUE | process_total_nymphs==TRUE) {
+if (process_old_nymphs | process_total_nymphs) {
 OldNymphs.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
 }
-if (process_adults) {
+if (process_previttelogenic_adults | process_total_adults) {
-Previtellogenic.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
+Previttelogenic.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_vittelogenic_adults | process_total_adults) {
+Vitelogenic.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
+}
+if (process_diapausing_adults | process_total_adults) {
 Diapausing.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
 }
 newborn.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
 adult.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
 death.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) {
+if (process_previttelogenic_adults) {
-P_adults.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
+P_previttelogenic_adults.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
-F1_adults.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
+F1_previttelogenic_adults.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
-F2_adults.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
+F2_previttelogenic_adults.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
+}
+if (process_vittelogenic_adults) {
+P_vittelogenic_adults.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
+F1_vittelogenic_adults = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
+F2_vittelogenic_adults.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
+}
+if (process_diapausing_adults) {
+P_diapausing_adults.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
+F1_diapausing_adults.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
+F2_diapausing_adults.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
+}
+if (process_total_adults) {
+P_total_adults.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
+F1_total_adults.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
+F2_total_adults.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
 }
 }
 # Total population.
 population.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
 vector.matrix = base::t(matrix(vector.matrix, nrow=5));
 # Time series of population size.
 if (process_eggs) {
 Eggs = rep(0, opt$num_days);
 }
-if (process_nymphs) {
+if (process_young_nymphs | process_total_nymphs) {
 YoungNymphs = rep(0, opt$num_days);
+}
+if (process_old_nymphs | process_total_nymphs) {
 OldNymphs = rep(0, opt$num_days);
 }
-if (process_adults) {
+if (process_previttelogenic_adults | process_total_adults) {
-Previtellogenic = rep(0, opt$num_days);
+Previttelogenic = rep(0, opt$num_days);
-Vitellogenic = rep(0, opt$num_days);
+}
+if (process_vittelogenic_adults | process_total_adults) {
+Vitelogenic = rep(0, opt$num_days);
+}
+if (process_diapausing_adults | process_total_adults) {
 Diapausing = rep(0, opt$num_days);
 }
 N.newborn = rep(0, opt$num_days);
 N.adult = rep(0, opt$num_days);
 N.death = 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) {
+if (process_previttelogenic_adults) {
-P.adult = rep(0, opt$num_days);
+P.previttelogenic_adult = rep(0, opt$num_days);
-F1.adult = rep(0, opt$num_days);
+F1.previttelogenic_adult = rep(0, opt$num_days);
-F2.adult = rep(0, opt$num_days);
+F2.previttelogenic_adult = rep(0, opt$num_days);
+}
+if (process_vittelogenic_adults) {
+P.vittelogenic_adult = rep(0, opt$num_days);
+F1.vittelogenic_adult = rep(0, opt$num_days);
+F2.vittelogenic_adult = rep(0, opt$num_days);
+}
+if (process_diapausing_adults) {
+P.diapausing_adult = rep(0, opt$num_days);
+F1.diapausing_adult = rep(0, opt$num_days);
+F2.diapausing_adult = rep(0, opt$num_days);
+}
+if (process_total_adults) {
+P.total_adult = rep(0, opt$num_days);
+F1.total_adult = rep(0, opt$num_days);
+F2.total_adult = rep(0, opt$num_days);
 }
 }
 total.population = NULL;
 averages.day = rep(0, opt$num_days);
 # All the days included in the input temperature dataset.
 # 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_young_nymphs) {
+if (process_young_nymphs | process_total_nymphs) {
 # For young nymph population size, column 2 (Stage) must be 1.
 YoungNymphs[row] = sum(vector.matrix[,2]==1);
 }
-if (process_old_nymphs) {
+if (process_old_nymphs | process_total_nymphs) {
 # For old nymph population size, column 2 (Stage) must be 2.
 OldNymphs[row] = sum(vector.matrix[,2]==2);
 }
-if (process_adults) {
+if (process_previttelogenic_adults | process_total_adults) {
-# For pre-vitellogenic population size, column 2 (Stage) must be 3.
+# For pre-vittelogenic population size, column 2 (Stage) must be 3.
-Previtellogenic[row] = sum(vector.matrix[,2]==3);
+Previttelogenic[row] = sum(vector.matrix[,2]==3);
-# For vitellogenic population size, column 2 (Stage) must be 4.
+}
-Vitellogenic[row] = sum(vector.matrix[,2]==4);
+if (process_vittelogenic_adults | process_total_adults) {
+# For vittelogenic population size, column 2 (Stage) must be 4.
+Vitelogenic[row] = sum(vector.matrix[,2]==4);
+}
+if (process_diapausing_adults | process_total_adults) {
 # For diapausing population size, column 2 (Stage) must be 5.
 Diapausing[row] = sum(vector.matrix[,2]==5);
 }
 # Newborn population size.
 # 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.total_nymph[row] = sum((vector.matrix[,1]==2 & vector.matrix[,2]==1) | (vector.matrix[,1]==2 & vector.matrix[,2]==2));
 }
-if (process_adults) {
+if (process_previttelogenic_adults) {
-# For adult life stage of generation P population
+# For previttelogenic adult life stage of generation P population
+# size, the following combination is required:
+# - column 1 (Generation) is 0 and column 2 (Stage) is 3 (Pre-vittelogenic)
+P.previttelogenic_adult[row] = sum(vector.matrix[,1]==0 & vector.matrix[,2]==3);
+# For previttelogenic adult life stage of generation F1 population
+# size, the following combination is required:
+# - column 1 (Generation) is 1 and column 2 (Stage) is 3 (Pre-vittelogenic)
+F1.previttelogenic_adult[row] = sum(vector.matrix[,1]==1 & vector.matrix[,2]==3);
+# For previttelogenic adult life stage of generation F2 population
+# size, the following combination is required:
+# - column 1 (Generation) is 2 and column 2 (Stage) is 3 (Pre-vittelogenic)
+F2.previttelogenic_adult[row] = sum(vector.matrix[,1]==2 & vector.matrix[,2]==3);
+}
+if (process_vittelogenic_adults) {
+# For vittelogenic adult life stage of generation P population
+# size, the following combination is required:
+# - column 1 (Generation) is 0 and column 2 (Stage) is 4 (Vitelogenic)
+P.vittelogenic_adult[row] = sum(vector.matrix[,1]==0 & vector.matrix[,2]==4);
+# For vittelogenic adult life stage of generation F1 population
+# size, the following combination is required:
+# - column 1 (Generation) is 1 and column 2 (Stage) is 4 (Vitelogenic)
+F1.vittelogenic_adult[row] = sum(vector.matrix[,1]==1 & vector.matrix[,2]==4);
+# For vittelogenic adult life stage of generation F2 population
+# size, the following combination is required:
+# - column 1 (Generation) is 2 and column 2 (Stage) is 4 (Vitelogenic)
+F2.vittelogenic_adult[row] = sum(vector.matrix[,1]==2 & vector.matrix[,2]==4);
+}
+if (process_diapausing_adults) {
+# For diapausing adult life stage of generation P population
+# size, the following combination is required:
+# - column 1 (Generation) is 0 and column 2 (Stage) is 5 (Diapausing)
+P.diapausing_adult[row] = sum(vector.matrix[,1]==0 & vector.matrix[,2]==5);
+# For diapausing adult life stage of generation F1 population
+# size, the following combination is required:
+# - column 1 (Generation) is 1 and column 2 (Stage) is 5 (Diapausing)
+F1.diapausing_adult[row] = sum(vector.matrix[,1]==1 & vector.matrix[,2]==5);
+# For diapausing adult life stage of generation F2 population
+# size, the following combination is required:
+# - column 1 (Generation) is 2 and column 2 (Stage) is 5 (Diapausing)
+F2.diapausing_adult[row] = sum(vector.matrix[,1]==2 & vector.matrix[,2]==5);
+}
+if (process_total_adults) {
+# For total 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)
+# - column 1 (Generation) is 0 and column 2 (Stage) is 3 (Pre-vittelogenic)
-# - column 1 (Generation) is 0 and column 2 (Stage) is 4 (Vitellogenic)
+# - column 1 (Generation) is 0 and column 2 (Stage) is 4 (Vitelogenic)
 # - column 1 (Generation) is 0 and column 2 (Stage) is 5 (Diapausing)
-P.adult[row] = sum((vector.matrix[,1]==0 & vector.matrix[,2]==3) | (vector.matrix[,1]==0 & vector.matrix[,2]==4) | (vector.matrix[,1]==0 & vector.matrix[,2]==5));
+P.total_adult[row] = sum((vector.matrix[,1]==0 & vector.matrix[,2]==3) | (vector.matrix[,1]==0 & vector.matrix[,2]==4) | (vector.matrix[,1]==0 & vector.matrix[,2]==5));
-# For adult life stage of generation F1 population
+# For total adult life stage of generation F1 population
 # size, one of the following combinations is required:
-# - column 1 (Generation) is 1 and column 2 (Stage) is 3 (Pre-vitellogenic)
+# - column 1 (Generation) is 1 and column 2 (Stage) is 3 (Pre-vittelogenic)
-# - column 1 (Generation) is 1 and column 2 (Stage) is 4 (Vitellogenic)
+# - column 1 (Generation) is 1 and column 2 (Stage) is 4 (Vitelogenic)
 # - column 1 (Generation) is 1 and column 2 (Stage) is 5 (Diapausing)
-F1.adult[row] = sum((vector.matrix[,1]==1 & vector.matrix[,2]==3) | (vector.matrix[,1]==1 & vector.matrix[,2]==4) | (vector.matrix[,1]==1 & vector.matrix[,2]==5));
+F1.total_adult[row] = sum((vector.matrix[,1]==1 & vector.matrix[,2]==3) | (vector.matrix[,1]==1 & vector.matrix[,2]==4) | (vector.matrix[,1]==1 & vector.matrix[,2]==5));
-# For adult life stage of generation F2 population
+# For total adult life stage of generation F2 population
 # size, one of the following combinations is required:
-# - column 1 (Generation) is 2 and column 2 (Stage) is 3 (Pre-vitellogenic)
+# - column 1 (Generation) is 2 and column 2 (Stage) is 3 (Pre-vittelogenic)
-# - column 1 (Generation) is 2 and column 2 (Stage) is 4 (Vitellogenic)
+# - column 1 (Generation) is 2 and column 2 (Stage) is 4 (Vitelogenic)
 # - column 1 (Generation) is 2 and column 2 (Stage) is 5 (Diapausing)
-F2.adult[row] = sum((vector.matrix[,1]==2 & vector.matrix[,2]==3) | (vector.matrix[,1]==2 & vector.matrix[,2]==4) | (vector.matrix[,1]==2 & vector.matrix[,2]==5));
+F2.total_adult[row] = sum((vector.matrix[,1]==2 & vector.matrix[,2]==3) | (vector.matrix[,1]==2 & vector.matrix[,2]==4) | (vector.matrix[,1]==2 & vector.matrix[,2]==5));
 }
 }
 }   # End of days specified in the input temperature data.
 averages.cum = cumsum(averages.day);
 # Define the output values.
 if (process_eggs) {
 Eggs.replications[,current_replication] = Eggs;
 }
-if (process_young_nymphs==TRUE | process_total_nymphs==TRUE) {
+if (process_young_nymphs | process_total_nymphs) {
 YoungNymphs.replications[,current_replication] = YoungNymphs;
 }
-if (process_old_nymphs==TRUE | process_total_nymphs==TRUE) {
+if (process_old_nymphs | process_total_nymphs) {
 OldNymphs.replications[,current_replication] = OldNymphs;
 }
-if (process_adults) {
+if (process_previttelogenic_adults | process_total_adults) {
-Previtellogenic.replications[,current_replication] = Previtellogenic;
+Previttelogenic.replications[,current_replication] = Previttelogenic;
-Vitellogenic.replications[,current_replication] = Vitellogenic;
+}
+if (process_vittelogenic_adults | process_total_adults) {
+Vitelogenic.replications[,current_replication] = Vitelogenic;
+}
+if (process_diapausing_adults | process_total_adults) {
 Diapausing.replications[,current_replication] = Diapausing;
 }
 newborn.replications[,current_replication] = N.newborn;
 adult.replications[,current_replication] = N.adult;
 death.replications[,current_replication] = N.death;
 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) {
+if (process_previttelogenic_adults) {
-P_adults.replications[,current_replication] = P.adult;
+P_previttelogenic_adults.replications[,current_replication] = P.previttelogenic_adult;
-F1_adults.replications[,current_replication] = F1.adult;
+F1_previttelogenic_adults.replications[,current_replication] = F1.previttelogenic_adult;
-F2_adults.replications[,current_replication] = F2.adult;
+F2_previttelogenic_adults.replications[,current_replication] = F2.previttelogenic_adult;
+}
+if (process_vittelogenic_adults) {
+P_vittelogenic_adults.replications[,current_replication] = P.vittelogenic_adult;
+F1_vittelogenic_adults.replications[,current_replication] = F1.vittelogenic_adult;
+F2_vittelogenic_adults.replications[,current_replication] = F2.vittelogenic_adult;
+}
+if (process_diapausing_adults) {
+P_diapausing_adults.replications[,current_replication] = P.diapausing_adult;
+F1_diapausing_adults.replications[,current_replication] = F1.diapausing_adult;
+F2_diapausing_adults.replications[,current_replication] = F2.diapausing_adult;
+}
+if (process_total_adults) {
+P_total_adults.replications[,current_replication] = P.total_adult;
+F1_total_adults.replications[,current_replication] = F1.total_adult;
+F2_total_adults.replications[,current_replication] = F2.total_adult;
 }
 }
 population.replications[,current_replication] = total.population;
 # End processing replications.
 }
 if (process_adults) {
 # Calculate adult populations for selected life stage.
 for (life_stage_adult in life_stages_adult) {
 if (life_stage_adult=="Total") {
 # Mean value for all adults.
-total_adults = apply((Previtellogenic.replications+Vitellogenic.replications+Diapausing.replications), 1, mean);
+total_adults = apply((Previttelogenic.replications+Vitelogenic.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$replications);
+total_adults.std_error = apply((Previttelogenic.replications+Vitelogenic.replications+Diapausing.replications), 1, sd) / sqrt(opt$replications);
 } else if (life_stage_adult == "Pre-vittelogenic") {
-# Mean value for previtellogenic adults.
+# Mean value for previttelogenic adults.
-previttelogenic_adults = apply(Previtellogenic.replications, 1, mean);
+previttelogenic_adults = apply(Previttelogenic.replications, 1, mean);
-# Standard error for previtellogenic adults.
+# Standard error for previttelogenic adults.
-previttelogenic_adults.std_error = apply(Previtellogenic.replications, 1, sd) / sqrt(opt$replications);
+previttelogenic_adults.std_error = apply(Previttelogenic.replications, 1, sd) / sqrt(opt$replications);
 } else if (life_stage_adult == "Vittelogenic") {
-# Mean value for vitellogenic adults.
+# Mean value for vittelogenic adults.
-vittelogenic_adults = apply(Vitellogenic.replications, 1, mean);
+vittelogenic_adults = apply(Vitelogenic.replications, 1, mean);
-# Standard error for vitellogenic adults.
+# Standard error for vittelogenic adults.
-vittelogenic_adults.std_error = apply(Vitellogenic.replications, 1, sd) / sqrt(opt$replications);
+vittelogenic_adults.std_error = apply(Vitelogenic.replications, 1, sd) / sqrt(opt$replications);
 } else if (life_stage_adult == "Diapausing") {
-# Mean value for vitellogenic adults.
+# Mean value for vittelogenic adults.
 diapausing_adults = apply(Diapausing.replications, 1, mean);
-# Standard error for vitellogenic adults.
+# Standard error for vittelogenic adults.
 diapausing_adults.std_error = apply(Diapausing.replications, 1, sd) / sqrt(opt$replications);
 }
 }
 }
 F1_total_nymphs = m_se[[3]];
 F1_total_nymphs.std_error = m_se[[4]];
 F2_total_nymphs = m_se[[5]];
 F2_total_nymphs.std_error = m_se[[6]];
 }
-if (process_adults) {
+if (process_previttelogenic_adults) {
-# Mean value for P_adults.
+m_se = get_mean_and_std_error(P_previttelogenic_adults.replications, F1_previttelogenic_adults.replications, F2_previttelogenic_adults.replications);
-P_adults = apply(P_adults.replications, 1, mean);
+P_previttelogenic_adults = m_se[[1]];
-# Standard error for P_adults.
+P_previttelogenic_adults.std_error = m_se[[2]];
-P_adults.std_error = apply(P_adults.replications, 1, sd) / sqrt(opt$replications);
+F1_previttelogenic_adults = m_se[[3]];
-# Mean value for F1 adults.
+F1_previttelogenic_adults.std_error = m_se[[4]];
-F1_adults = apply(F1_adults.replications, 1, mean);
+F2_previttelogenic_adults = m_se[[5]];
-# Standard error for F1_adults.
+F2_previttelogenic_adults.std_error = m_se[[6]];
-F1_adults.std_error = apply(F1_adults.replications, 1, sd) / sqrt(opt$replications);
+}
-# Mean value for F2_adults.
+if (process_vittelogenic_adults) {
-F2_adults = apply(F2_adults.replications, 1, mean);
+m_se = get_mean_and_std_error(P_vittelogenic_adults.replications, F1_vittelogenic_adults.replications, F2_vittelogenic_adults.replications);
-# Standard error for F2_adults.
+P_vittelogenic_adults = m_se[[1]];
-F2_adults.std_error = apply(F2_adults.replications, 1, sd) / sqrt(opt$replications);
+P_vittelogenic_adults.std_error = m_se[[2]];
+F1_vittelogenic_adults = m_se[[3]];
+F1_vittelogenic_adults.std_error = m_se[[4]];
+F2_vittelogenic_adults = m_se[[5]];
+F2_vittelogenic_adults.std_error = m_se[[6]];
+}
+if (process_diapausing_adults) {
+m_se = get_mean_and_std_error(P_diapausing_adults.replications, F1_diapausing_adults.replications, F2_diapausing_adults.replications);
+P_diapausing_adults = m_se[[1]];
+P_diapausing_adults.std_error = m_se[[2]];
+F1_diapausing_adults = m_se[[3]];
+F1_diapausing_adults.std_error = m_se[[4]];
+F2_diapausing_adults = m_se[[5]];
+F2_diapausing_adults.std_error = m_se[[6]];
+}
+if (process_total_adults) {
+m_se = get_mean_and_std_error(P_total_adults.replications, F1_total_adults.replications, F2_total_adults.replications);
+P_total_adults = m_se[[1]];
+P_total_adults.std_error = m_se[[2]];
+F1_total_adults = m_se[[3]];
+F1_total_adults.std_error = m_se[[4]];
+F2_total_adults = m_se[[5]];
+F2_total_adults.std_error = m_se[[6]];
 }
 }
 # Display the total number of days in the Galaxy history item blurb.
 cat("Number of days: ", opt$num_days, "\n");
 # Start PDF device driver.
 dev.new(width=20, height=30);
 file_path = get_file_path(life_stage, "adult_pop_by_generation.pdf", life_stage_adult=life_stage_adult)
 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.
+if (life_stage_adult=="Pre-vittelogenic") {
-maxval = max(P_adults+F1_adults+F2_adults) + 100;
+# Pre-vittelogenic adult population size by generation.
+maxval = max(P_previttelogenic_adults+F1_previttelogenic_adults+F2_previttelogenic_adults) + 100;
+group = P_previttelogenic_adults;
+group_std_error = P_previttelogenic_adults.std_error;
+group2 = F1_previttelogenic_adults;
+group2_std_error = F1_previttelogenic_adults.std_error;
+group3 = F2_previttelogenic_adults;
+group3_std_error = F2_previttelogenic_adults.std_error;
+} else if (life_stage_adult=="Vittelogenic") {
+# Vittelogenic adult population size by generation.
+maxval = max(P_vittelogenic_adults+F1_vittelogenic_adults+F2_vittelogenic_adults) + 100;
+group = P_vittelogenic_adults;
+group_std_error = P_vittelogenic_adults.std_error;
+group2 = F1_vittelogenic_adults;
+group2_std_error = F1_vittelogenic_adults.std_error;
+group3 = F2_vittelogenic_adults;
+group3_std_error = F2_vittelogenic_adults.std_error;
+} else if (life_stage_adult=="Diapausing") {
+# Diapausing adult population size by generation.
+maxval = max(P_diapausing_adults+F1_diapausing_adults+F2_diapausing_adults) + 100;
+group = P_diapausing_adults;
+group_std_error = P_diapausing_adults.std_error;
+group2 = F1_diapausing_adults;
+group2_std_error = F1_diapausing_adults.std_error;
+group3 = F2_diapausing_adults;
+group3_std_error = F2_diapausing_adults.std_error;
+} else if (life_stage_adult=="Total") {
+# Total adult population size by generation.
+maxval = max(P_total_adults+F1_total_adults+F2_total_adults) + 100;
+group = P_total_adults;
+group_std_error = P_total_adults.std_error;
+group2 = F1_total_adults;
+group2_std_error = F1_total_adults.std_error;
+group3 = F2_total_adults;
+group3_std_error = F2_total_adults.std_error;
+}
 render_chart(date_labels, "pop_size_by_generation", opt$plot_std_error, opt$insect, opt$location, latitude, start_date, end_date, days, maxval,
-opt$replications, life_stage, group=P_adults, group_std_error=P_adults.std_error, group2=F1_adults, group2_std_error=F1_adults.std_error,
+opt$replications, life_stage, group=group, group_std_error=group_std_error, group2=group2, group2_std_error=group2_std_error,
-group3=F2_adults, group3_std_error=F2_adults.std_error, life_stages_adult=life_stage_adult);
+group3=group3, group3_std_error=group3_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.

Mercurial > repos > greg > insect_phenology_model

comparison insect_phenology_model.R @ 23:36d7bb034285 draft