comparison insect_phenology_model.R @ 18:f5ecff4800f2 draft

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17:6f31ade9a0f4

    temperature_data_frame[, num_columns+1] = daylight_length_vector;
    return(temperature_data_frame);
}

dev.egg = function(temperature) {
    dev.rate = -0.9843 * temperature + 33.438;
    return(dev.rate);
}

dev.emerg = function(temperature) {
    emerg.rate = -0.5332 * temperature + 24.147;
    return(emerg.rate);
}

dev.old = function(temperature) {
    n34 = -0.6119 * temperature + 17.602;
    n45 = -0.4408 * temperature + 19.036;
    dev.rate = mean(n34 + n45);
    return(dev.rate);
}

dev.young = function(temperature) {
    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_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$replications) {
    # Start with the user-defined number of insects per replication.
    num_insects = opt$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$egg_mortality * mortality.egg(mean.temp);
            }
            else if (vector.individual[2] == 1 | vector.individual[2] == 2) {
                death.probability = opt$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,
                # 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
                # 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;
    }
    if (process_nymphs) {
        YoungNymphs.replications[,N.replications] = YoungNymphs;
        OldNymphs.replications[,N.replications] = OldNymphs;
    }
    if (process_adults) {
        Previtellogenic.replications[,N.replications] = Previtellogenic;
        Vitellogenic.replications[,N.replications] = Vitellogenic;
        Diapausing.replications[,N.replications] = Diapausing;
    }
    newborn.replications[,N.replications] = N.newborn;
    adult.replications[,N.replications] = N.adult;
    death.replications[,N.replications] = N.death;
    if (plot_generations_separately) {
        # P is Parental, or overwintered adults.
        P.replications[,N.replications] = overwintering_adult.population;
        # F1 is the first field-produced generation.
        F1.replications[,N.replications] = first_generation.population;
        # F2 is the second field-produced generation.
        F2.replications[,N.replications] = 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;
        }
        if (process_nymphs) {
            P_nymphs.replications[,N.replications] = P.nymph;
            F1_nymphs.replications[,N.replications] = F1.nymph;
            F2_nymphs.replications[,N.replications] = 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;
        }
    }
    population.replications[,N.replications] = total.population;
}

if (process_eggs) {
    # Mean value for eggs.
    eggs = apply(Eggs.replications, 1, mean);

    eggs.std_error = apply(Eggs.replications, 1, sd) / sqrt(opt$replications);
}
if (process_nymphs) {
    # Calculate nymph populations for selected life stage.
    for (life_stage_nymph in life_stages_nymph) {
        if (life_stages_nymph=="Total") {
            # Mean value for all nymphs.
            total_nymphs = apply((YoungNymphs.replications+OldNymphs.replications), 1, mean);
            # Standard error for all nymphs.
            total_nymphs.std_error = apply((YoungNymphs.replications+OldNymphs.replications) / sqrt(opt$replications), 1, sd);
        } else if (life_stages_nymph=="Young") {
            # 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$replications), 1, sd);
        } else if (life_stages_nymph=="Old") {
            # Mean value for old nymphs.
            old_nymphs = apply(OldNymphs.replications, 1, mean);
            # Standard error for old nymphs.
            old_nymphs.std_error = apply(OldNymphs.replications / sqrt(opt$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") {
            # 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$replications);
        } else if (life_stages_adult == "Pre-vittelogenic") {
            # Mean value for previtellogenic adults.
            previttelogenic_adults = apply(Previtellogenic.replications, 1, mean);
            # Standard error for previtellogenic adults.
            previttelogenic_adults.std_error = apply(Previtellogenic.replications, 1, sd) / sqrt(opt$replications);
        } else if (life_stages_adult == "Vittelogenic") {
            # 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$replications);
        } else if (life_stages_adult == "Diapausing") {
            # Mean value for vitellogenic adults.
            diapausing_adults = apply(Diapausing.replications, 1, mean);
            # Standard error for vitellogenic adults.
            diapausing_adults.std_error = apply(Diapausing.replications, 1, sd) / sqrt(opt$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="/");
            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;
            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="_");
                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;
                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="_");
                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;
                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.
            dev.new(width=20, height=30);
            file_path = paste(output_dir, "total_pop_by_generation.pdf", 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);
            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="/");
            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);
            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="_");
                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);
                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="_");
                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);
                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="/");
            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);
            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();

18: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 (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 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 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[,current_replication] = Eggs;
    }
    if (process_nymphs) {
        YoungNymphs.replications[,current_replication] = YoungNymphs;
        OldNymphs.replications[,current_replication] = OldNymphs;
    }
    if (process_adults) {
        Previtellogenic.replications[,current_replication] = Previtellogenic;
        Vitellogenic.replications[,current_replication] = Vitellogenic;
        Diapausing.replications[,current_replication] = Diapausing;
    }
    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[,current_replication] = overwintering_adult.population;
        # F1 is the first field-produced generation.
        F1.replications[,current_replication] = first_generation.population;
        # F2 is the second field-produced generation.
        F2.replications[,current_replication] = second_generation.population;
        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) {
            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[,current_replication] = P.adult;
            F1_adults.replications[,current_replication] = F1.adult;
            F2_adults.replications[,current_replication] = F2.adult;
        }
    }
    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$replications);
}
if (process_nymphs) {
    # Calculate nymph populations for selected life stage.
    for (life_stage_nymph in life_stages_nymph) {
        if (life_stage_nymph=="Total") {
            # Mean value for all nymphs.
            total_nymphs = apply((YoungNymphs.replications+OldNymphs.replications), 1, mean);
            # Standard error for all nymphs.
            total_nymphs.std_error = apply((YoungNymphs.replications+OldNymphs.replications) / sqrt(opt$replications), 1, sd);
        } else if (life_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$replications), 1, sd);
        } else if (life_stage_nymph=="Old") {
            # Mean value for old nymphs.
            old_nymphs = apply(OldNymphs.replications, 1, mean);
            # Standard error for old nymphs.
            old_nymphs.std_error = apply(OldNymphs.replications / sqrt(opt$replications), 1, sd);
        }
    }
}
if (process_adults) {
    # Calculate adult populations for selected life stage.
    for (life_stage_adult in life_stages_adult) {
        if (life_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$replications);
        } else if (life_stage_adult == "Pre-vittelogenic") {
            # Mean value for previtellogenic adults.
            previttelogenic_adults = apply(Previtellogenic.replications, 1, mean);
            # Standard error for previtellogenic adults.
            previttelogenic_adults.std_error = apply(Previtellogenic.replications, 1, sd) / sqrt(opt$replications);
        } else if (life_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$replications);
        } else if (life_stage_adult == "Diapausing") {
            # Mean value for vitellogenic adults.
            diapausing_adults = apply(Diapausing.replications, 1, mean);
            # Standard error for vitellogenic adults.
            diapausing_adults.std_error = apply(Diapausing.replications, 1, sd) / sqrt(opt$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);
            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(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);
                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(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);
                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(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);
            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(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);
            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) + 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);
                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) + 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);
                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) + 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);
            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, 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();