comparison insect_phenology_model.R @ 16:309954bbe999 draft

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15:dd86ee185113

    make_option(c("--input"), action="store", dest="input", help="Temperature data for selected location"),
    make_option(c("--insect"), action="store", dest="insect", help="Insect name"),
    make_option(c("--insects_per_replication"), action="store", dest="insects_per_replication", type="integer", help="Number of insects with which to start each replication"),
    make_option(c("--life_stages"), action="store", dest="life_stages", help="Selected life stages for plotting"),
    make_option(c("--life_stages_adult"), action="store", dest="life_stages_adult", default=NULL, help="Adult life stages for plotting"),
    make_option(c("--life_stage_nymph"), action="store", dest="life_stage_nymph", default=NULL, help="Nymph life stages for plotting"),
    make_option(c("--location"), action="store", dest="location", help="Selected location"),
    make_option(c("--min_clutch_size"), action="store", dest="min_clutch_size", type="integer", help="Adjustment of minimum clutch size"),
    make_option(c("--max_clutch_size"), action="store", dest="max_clutch_size", type="integer", help="Adjustment of maximum clutch size"),
    make_option(c("--nymph_mortality"), action="store", dest="nymph_mortality", type="integer", help="Adjustment rate for nymph mortality"),
    make_option(c("--old_nymph_accumulation"), action="store", dest="old_nymph_accumulation", type="integer", help="Adjustment of degree-days accumulation (young nymph->old nymph)"),

}


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_stage_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);

            if (life_stage=="Egg") {
                title = paste(insect,  ": Reps", replications, ":", life_stage, "Pop :", location, ": Lat", latitude, ":", start_date, "-", end_date, sep=" ");
                legend_text = c(life_stage);
                columns = c(4);
            } else if (life_stage=="Nymph") {
                stage = paste(life_stage_nymph, "Nymph Pop :", sep=" ");
                title = paste(insect, ": Reps", replications, ":", stage, location, ": Lat", latitude, ":", start_date, "-", end_date, sep=" ");
                legend_text = c(paste(life_stage_nymph, life_stage, sep=" "));
                columns = c(2);
            } else if (life_stage=="Adult") {
                stage = paste(life_stages_adult, "Adult Pop", sep=" ");
                title = paste(insect, ": Reps", replications, ":", stage, location, ": Lat", latitude, ":", start_date, "-", end_date, sep=" ");
                legend_text = c(paste(life_stages_adult, life_stage, sep=" "));

        if (life_stage=="Total") {
            title_str = ": Total Pop by Gen :";
        } else if (life_stage=="Egg") {
            title_str = ": Egg Pop by Gen :";
        } else if (life_stage=="Nymph") {
            title_str = paste(":", life_stage_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=" ");
        legend_text = c("P", "F1", "F2");

process_adults = FALSE;
for (life_stage in life_stages) {
    if (life_stage=="Total") {
        process_eggs = TRUE;
        process_nymphs = TRUE;
        life_stage_nymph = "Total";
        process_adults = TRUE;
        life_stages_adult = "Total";
    } else if (life_stage=="Egg") {
        process_eggs = TRUE;
    } else if (life_stage=="Nymph") {
        process_nymphs = TRUE;
        life_stage_nymph = opt$life_stage_nymph;
    } else if (life_stage=="Adult") {
        process_adults = TRUE;
        life_stages_adult = opt$life_stages_adult;
    }
}

# Initialize matrices.
if (process_eggs) {
    Eggs.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
}
if (process_nymphs) {

    # Standard error for eggs.
    eggs.std_error = apply(Eggs.replications, 1, sd) / sqrt(opt$replications);
}
if (process_nymphs) {
    # Calculate nymph populations for selected life stage.
    if (life_stage_nymph=="Total") {
        # Mean value for all nymphs.
        nymphs = apply((YoungNymphs.replications+OldNymphs.replications), 1, mean);
        # Standard error for all nymphs.
        nymphs.std_error = apply((YoungNymphs.replications+OldNymphs.replications) / sqrt(opt$replications), 1, sd);
    } else if (life_stage_nymph=="Young") {
        # Mean value for young nymphs.
        nymphs = apply(YoungNymphs.replications, 1, mean);
        # Standard error for young nymphs.
        nymphs.std_error = apply(YoungNymphs.replications / sqrt(opt$replications), 1, sd);
    } else if (life_stage_nymph=="Old") {
        # Mean value for old nymphs.
        nymphs = apply(OldNymphs.replications, 1, mean);
        # Standard error for old nymphs.
        nymphs.std_error = apply(OldNymphs.replications / sqrt(opt$replications), 1, sd);
    }
}
if (process_adults) {
    # Calculate adult populations for selected life stage.
    if (life_stages_adult=="Total") {
        # Mean value for all adults.
        adults = apply((Previtellogenic.replications+Vitellogenic.replications+Diapausing.replications), 1, mean);
        # Standard error for all adults.
        adults.std_error = apply((Previtellogenic.replications+Vitellogenic.replications+Diapausing.replications), 1, sd) / sqrt(opt$replications);
    } else if (life_stages_adult == "Pre-vittelogenic") {
        # Mean value for previtellogenic adults.
        adults = apply(Previtellogenic.replications, 1, mean);
        # Standard error for previtellogenic adults.
        adults.std_error = apply(Previtellogenic.replications, 1, sd) / sqrt(opt$replications);
    } else if (life_stages_adult == "Vittelogenic") {
        # Mean value for vitellogenic adults.
        adults = apply(Vitellogenic.replications, 1, mean);
        # Standard error for vitellogenic adults.
        adults.std_error = apply(Vitellogenic.replications, 1, sd) / sqrt(opt$replications);
    } else if (life_stages_adult == "Diapausing") {
        # Mean value for vitellogenic adults.
        adults = apply(Diapausing.replications, 1, mean);
        # Standard error for vitellogenic adults.
        adults.std_error = apply(Diapausing.replications, 1, sd) / sqrt(opt$replications);
    }
}

if (plot_generations_separately) {
    # Mean value for P which is Parental, or overwintered adults.

                opt$replications, life_stage, group=P_eggs, group_std_error=P_eggs.std_error, group2=F1_eggs, group2_std_error=F1_eggs.std_error, group3=F2_eggs,
                group3_std_error=F2_eggs.std_error);
            # Turn off device driver to flush output.
            dev.off();
        } else if (life_stage == "Nymph") {
            # Start PDF device driver.
            dev.new(width=20, height=30);
            file_name = paste(tolower(life_stage_nymph), "nymph_pop_by_generation.pdf", sep="_");
            file_path = paste(output_dir, file_name, sep="/");
            pdf(file=file_path, width=20, height=30, bg="white");
            par(mar=c(5, 6, 4, 4), mfrow=c(3, 1));
            # Nymph population size by generation.
            maxval = max(F2_nymphs) + 100;
            render_chart(date_labels, "pop_size_by_generation", opt$plot_std_error, opt$insect, opt$location, latitude, start_date, end_date, days, maxval,
                opt$replications, life_stage, group=P_nymphs, group_std_error=P_nymphs.std_error, group2=F1_nymphs, group2_std_error=F1_nymphs.std_error,
                group3=F2_nymphs, group3_std_error=F2_nymphs.std_error, life_stage_nymph=life_stage_nymph);
            # Turn off device driver to flush output.
            dev.off();
        } else if (life_stage == "Adult") {
            # Start PDF device driver.
            dev.new(width=20, height=30);
            file_name = paste(tolower(life_stages_adult), "adult_pop_by_generation.pdf", sep="_");
            file_path = paste(output_dir, file_name, sep="/");
            pdf(file=file_path, width=20, height=30, bg="white");
            par(mar=c(5, 6, 4, 4), mfrow=c(3, 1));
            # Adult population size by generation.
            maxval = max(F2_adults) + 100;
            render_chart(date_labels, "pop_size_by_generation", opt$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_stages_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");

            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") {
            # 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));
            # Nymph population size.
            maxval = max(nymphs+nymphs.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=nymphs, group_std_error=nymphs.std_error, life_stage_nymph=life_stage_nymph);
            # Turn off device driver to flush output.
            dev.off();
        } else if (life_stage == "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));
            # Adult population size.
            maxval = max(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=adults, group_std_error=adults.std_error, life_stages_adult=life_stages_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=adults, group_std_error=adults.std_error, group2=nymphs, group2_std_error=nymphs.std_error, group3=eggs,
                group3_std_error=eggs.std_error);
            # Turn off device driver to flush output.
            dev.off();
        }
    }

16:309954bbe999

    make_option(c("--input"), action="store", dest="input", help="Temperature data for selected location"),
    make_option(c("--insect"), action="store", dest="insect", help="Insect name"),
    make_option(c("--insects_per_replication"), action="store", dest="insects_per_replication", type="integer", help="Number of insects with which to start each replication"),
    make_option(c("--life_stages"), action="store", dest="life_stages", help="Selected life stages for plotting"),
    make_option(c("--life_stages_adult"), action="store", dest="life_stages_adult", default=NULL, help="Adult life stages for plotting"),
    make_option(c("--life_stages_nymph"), action="store", dest="life_stages_nymph", default=NULL, help="Nymph life stages for plotting"),
    make_option(c("--location"), action="store", dest="location", help="Selected location"),
    make_option(c("--min_clutch_size"), action="store", dest="min_clutch_size", type="integer", help="Adjustment of minimum clutch size"),
    make_option(c("--max_clutch_size"), action="store", dest="max_clutch_size", type="integer", help="Adjustment of maximum clutch size"),
    make_option(c("--nymph_mortality"), action="store", dest="nymph_mortality", type="integer", help="Adjustment rate for nymph mortality"),
    make_option(c("--old_nymph_accumulation"), action="store", dest="old_nymph_accumulation", type="integer", help="Adjustment of degree-days accumulation (young nymph->old nymph)"),

}


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);

            if (life_stage=="Egg") {
                title = paste(insect,  ": Reps", replications, ":", life_stage, "Pop :", location, ": Lat", latitude, ":", start_date, "-", end_date, sep=" ");
                legend_text = c(life_stage);
                columns = c(4);
            } else if (life_stage=="Nymph") {
                stage = paste(life_stages_nymph, "Nymph Pop :", sep=" ");
                title = paste(insect, ": Reps", replications, ":", stage, location, ": Lat", latitude, ":", start_date, "-", end_date, sep=" ");
                legend_text = c(paste(life_stages_nymph, life_stage, sep=" "));
                columns = c(2);
            } else if (life_stage=="Adult") {
                stage = paste(life_stages_adult, "Adult Pop", sep=" ");
                title = paste(insect, ": Reps", replications, ":", stage, location, ": Lat", latitude, ":", start_date, "-", end_date, sep=" ");
                legend_text = c(paste(life_stages_adult, life_stage, sep=" "));

        if (life_stage=="Total") {
            title_str = ": Total Pop by Gen :";
        } else if (life_stage=="Egg") {
            title_str = ": Egg Pop by Gen :";
        } else if (life_stage=="Nymph") {
            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=" ");
        legend_text = c("P", "F1", "F2");

process_adults = FALSE;
for (life_stage in life_stages) {
    if (life_stage=="Total") {
        process_eggs = TRUE;
        process_nymphs = TRUE;
        process_adults = TRUE;
    } else if (life_stage=="Egg") {
        process_eggs = TRUE;
    } else if (life_stage=="Nymph") {
        process_nymphs = TRUE;
    } else if (life_stage=="Adult") {
        process_adults = TRUE;
    }
}
if (process_adults) {
    # Split life_stages_adult into a list of strings for plots.
    life_stages_adult_str = as.character(opt$life_stages_adult);
    life_stages_adult = strsplit(life_stages_adult_str, ",")[[1]];
}
if (process_nymphs) {
# Split life_stages_nymph into a list of strings for plots.
    life_stages_nymph_str = as.character(opt$life_stages_nymph);
    life_stages_nymph = strsplit(life_stages_nymph_str, ",")[[1]];
}
# Initialize matrices.
if (process_eggs) {
    Eggs.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
}
if (process_nymphs) {

    # Standard error for eggs.
    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) {
    # Mean value for P which is Parental, or overwintered adults.

                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");

            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.
                    group = total_nymphs;
                    group_std_error = total_nymphs.std_error;
                } else if (life_stage_nymph=="Young") {
                    # Young nymph population size.
                    group = young_nymphs;
                    group_std_error = young_nymphs.std_error;
                } 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.
                    group = total_adults;
                    group_std_error = total_adults.std_error
                } else if (life_stage_adult=="Pre-vittelogenic") {
                    # Pre-vittelogenic adult population size.
                    group = previttelogenic_adults;
                    group_std_error = previttelogenic_adults.std_error
                } else if (life_stage_adult=="Vittelogenic") {
                    # Vittelogenic adult population size.
                    group = vittelogenic_adults;
                    group_std_error = vittelogenic_adults.std_error
                } 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();
        }
    }