comparison insect_phenology_model.R @ 34:7aa848b0e55c draft

Uploaded

33:ef5add7dea47

    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("--num_days"), action="store", dest="num_days", type="integer", help="Total number of days in the temperature dataset"),
    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)"),
    make_option(c("--output_combined"), action="store", dest="output_combined", help="Dataset containing analyzed data for combined generations"),
    make_option(c("--output_f1"), action="store", dest="output_f1", default=NULL, help="Dataset containing analyzed data for generation F1"),
    make_option(c("--output_f2"), action="store", dest="output_f2", default=NULL, help="Dataset containing analyzed data for generation F2"),
    make_option(c("--output_p"), action="store", dest="output_p", default=NULL, help="Dataset containing analyzed data for generation P"),
    make_option(c("--oviposition"), action="store", dest="oviposition", type="integer", help="Adjustment for oviposition rate"),
    make_option(c("--photoperiod"), action="store", dest="photoperiod", type="double", help="Critical photoperiod for diapause induction/termination"),
    make_option(c("--plot_generations_separately"), action="store", dest="plot_generations_separately", help="Plot Plot P, F1 and F2 as separate lines or pool across them"),
    make_option(c("--plot_std_error"), action="store", dest="plot_std_error", help="Plot Standard error"),
    make_option(c("--replications"), action="store", dest="replications", type="integer", help="Number of replications"),

    # Reset the column names with the additional column for later access.
    colnames(data_frame) = append(current_column_names, new_column_name);
    return(data_frame);
}

get_date_labels = function(temperature_data_frame, num_rows) {
    # Keep track of the years to see if spanning years.
    month_labels = list();
    current_month_label = NULL;
    for (i in 1:num_rows) {
        # Get the year and month from the date which
        # has the format YYYY-MM-DD.
        date = format(temperature_data_frame$DATE[i]);
        items = strsplit(date, "-")[[1]];
        month = items[2];
        month_label = month.abb[as.integer(month)];
        if (!identical(current_month_label, month_label)) {
            month_labels[length(month_labels)+1] = month_label;
            current_month_label = month_label;
        }
    }
    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_adult), base_name, sep="_");
    } else {
        lsi = get_life_stage_index(life_stage);
        file_name = paste(lsi, base_name, sep="_");
    }
    file_path = paste("output_dir", file_name, sep="/");
    return(file_path);
}

get_life_stage_index = function(life_stage, life_stage_nymph=NULL, life_stage_adult=NULL) {
    # Name collection elements so that they

        temperature_data_frame = add_daylight_length(temperature_data_frame, num_rows);
    }
    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=" ");

            columns = c(4, 2, 1);
            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);
            lines(days, group3, lwd=2, lty=1, col=4);
            axis(1, at=c(1:length(date_labels)) * 30 - 15, cex.axis=3, labels=date_labels);
            axis(2, cex.axis=3);
            if (plot_std_error=="yes") {
                # Standard error for group.
                lines(days, group+group_std_error, lty=2);
                lines(days, group-group_std_error, lty=2);
                # Standard error for group2.

                legend_text = c(paste(life_stages_adult, life_stage, sep=" "));
                columns = c(1);
            }
            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), col="black", cex=3);
            axis(1, at=c(1:length(date_labels)) * 30 - 15, cex.axis=3, labels=date_labels);
            axis(2, cex.axis=3);
            if (plot_std_error=="yes") {
                # Standard error for group.
                lines(days, group+group_std_error, lty=2);
                lines(days, group-group_std_error, lty=2);
            }

        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);
        lines(days, group3, lwd=2, lty=1, col=4);
        axis(1, at=c(1:length(date_labels)) * 30 - 15, cex.axis=3, labels=date_labels);
        axis(2, cex.axis=3);
        if (plot_std_error=="yes") {
            # Standard error for group.
            lines(days, group+group_std_error, lty=2);
            lines(days, group-group_std_error, lty=2);
            # Standard error for group2.

    temperature_data_frame_P = data.frame(temperature_data_frame);
    temperature_data_frame_F1 = data.frame(temperature_data_frame);
    temperature_data_frame_F2 = data.frame(temperature_data_frame);
}
# Get the date labels for plots.
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];
# 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);

        temperature_data_frame_F2 = append_vector(temperature_data_frame_F2, F2_total_adults.std_error, "TOTALADULT-F2-SE");
    }
}

# Save the analyzed data for combined generations.
write.csv(temperature_data_frame, file=opt$output_combined, row.names=F);
if (plot_generations_separately) {
    # Save the analyzed data for generation P.
    write.csv(temperature_data_frame_P, file=opt$output_p, row.names=F);
    # Save the analyzed data for generation F1.
    write.csv(temperature_data_frame_F1, file=opt$output_f1, row.names=F);
    # Save the analyzed data for generation F2.
    write.csv(temperature_data_frame_F2, file=opt$output_f2, row.names=F);
}
# Display the total number of days in the Galaxy history item blurb.
cat("Number of days: ", opt$num_days, "\n");
# Information needed for plots plots.
days = c(1:opt$num_days);

            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;
            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") {

                    group2 = F1_total_nymphs;
                    group2_std_error = F1_total_nymphs.std_error;
                    group3 = F2_total_nymphs;
                    group3_std_error = F2_total_nymphs.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=group, group_std_error=group_std_error, group2=group2, group2_std_error=group2_std_error,
                    group3=group3, group3_std_error=group3_std_error, life_stages_nymph=life_stage_nymph);
                # Turn off device driver to flush output.
                dev.off();
            }

                    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=group, group_std_error=group_std_error, group2=group2, group2_std_error=group2_std_error,
                    group3=group3, group3_std_error=group3_std_error, life_stages_adult=life_stage_adult);
                # Turn off device driver to flush output.
                dev.off();
            }

            file_path = get_file_path(life_stage, "total_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));
            # 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();
        }
    }

            file_path = get_file_path(life_stage, "egg_pop.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.
            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) {

                    # 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") {

                    # 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") {

            file_path = get_file_path(life_stage, "total_pop.pdf")
            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();
        }

34:7aa848b0e55c

    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("--num_days"), action="store", dest="num_days", type="integer", help="Total number of days in the temperature dataset"),
    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)"),
    make_option(c("--oviposition"), action="store", dest="oviposition", type="integer", help="Adjustment for oviposition rate"),
    make_option(c("--photoperiod"), action="store", dest="photoperiod", type="double", help="Critical photoperiod for diapause induction/termination"),
    make_option(c("--plot_generations_separately"), action="store", dest="plot_generations_separately", help="Plot Plot P, F1 and F2 as separate lines or pool across them"),
    make_option(c("--plot_std_error"), action="store", dest="plot_std_error", help="Plot Standard error"),
    make_option(c("--replications"), action="store", dest="replications", type="integer", help="Number of replications"),

    # Reset the column names with the additional column for later access.
    colnames(data_frame) = append(current_column_names, new_column_name);
    return(data_frame);
}

get_x_axis_ticks_and_labels = function(temperature_data_frame, num_rows) {
    # Keep track of the years to see if spanning years.
    month_labels = list();
    ticks = list();
    current_month_label = NULL;
    for (i in 1:num_rows) {
        # Get the year and month from the date which
        # has the format YYYY-MM-DD.
        date = format(temperature_data_frame$DATE[i]);
        # Get the month label.
        items = strsplit(date, "-")[[1]];
        month = items[2];
        month_label = month.abb[as.integer(month)];
        if (!identical(current_month_label, month_label)) {
            # Add an x-axis tick for the month.
            ticks[length(ticks)+1] = i;
            month_labels[length(month_labels)+1] = month_label;
            current_month_label = month_label;
        }
        # Get the day.
        day = weekdays(as.Date(date));
        if (day=="Sunday") {
            # Add an x-axis tick if we're on a Sunday.
            ticks[length(ticks)+1] = i;
            # Add a blank month label so it is not displayed.
            month_labels[length(month_labels)+1] = "";
        }
    }
    return(list(ticks, 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_adult), base_name, sep="_");
    } else {
        lsi = get_life_stage_index(life_stage);
        file_name = paste(lsi, base_name, sep="_");
    }
    file_path = paste("output_plots_dir", file_name, sep="/");
    return(file_path);
}

get_life_stage_index = function(life_stage, life_stage_nymph=NULL, life_stage_adult=NULL) {
    # Name collection elements so that they

        temperature_data_frame = add_daylight_length(temperature_data_frame, num_rows);
    }
    return(temperature_data_frame);
}

render_chart = function(ticks, 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=" ");

            columns = c(4, 2, 1);
            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);
            lines(days, group3, lwd=2, lty=1, col=4);
            axis(side=1, at=ticks, labels=date_labels);
            axis(side=2);
            if (plot_std_error=="yes") {
                # Standard error for group.
                lines(days, group+group_std_error, lty=2);
                lines(days, group-group_std_error, lty=2);
                # Standard error for group2.

                legend_text = c(paste(life_stages_adult, life_stage, sep=" "));
                columns = c(1);
            }
            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), col="black", cex=3);
            axis(side=1, at=ticks, labels=date_labels);
            axis(side=2);
            if (plot_std_error=="yes") {
                # Standard error for group.
                lines(days, group+group_std_error, lty=2);
                lines(days, group-group_std_error, lty=2);
            }

        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);
        lines(days, group3, lwd=2, lty=1, col=4);
        axis(side=1, at=ticks, labels=date_labels);
        axis(side=2);
        if (plot_std_error=="yes") {
            # Standard error for group.
            lines(days, group+group_std_error, lty=2);
            lines(days, group-group_std_error, lty=2);
            # Standard error for group2.

    temperature_data_frame_P = data.frame(temperature_data_frame);
    temperature_data_frame_F1 = data.frame(temperature_data_frame);
    temperature_data_frame_F2 = data.frame(temperature_data_frame);
}
# Get the date labels for plots.
ticks_and_labels = get_x_axis_ticks_and_labels(temperature_data_frame, opt$num_days);
ticks = c(unlist(ticks_and_labels[1]));
date_labels = c(unlist(ticks_and_labels[2]));
# All latitude values are the same, so get the value for plots from the first row.
latitude = temperature_data_frame$LATITUDE[1];
# 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);

        temperature_data_frame_F2 = append_vector(temperature_data_frame_F2, F2_total_adults.std_error, "TOTALADULT-F2-SE");
    }
}

# Save the analyzed data for combined generations.
file_path = paste("output_data_dir", "04_combined_generations.csv", sep="/");
write.csv(temperature_data_frame, file=file_path, row.names=F);
if (plot_generations_separately) {
    # Save the analyzed data for generation P.
    file_path = paste("output_data_dir", "01_generation_P.csv", sep="/");
    write.csv(temperature_data_frame_P, file=file_path, row.names=F);
    # Save the analyzed data for generation F1.
    file_path = paste("output_data_dir", "02_generation_F1.csv", sep="/");
    write.csv(temperature_data_frame_F1, file=file_path, row.names=F);
    # Save the analyzed data for generation F2.
    file_path = paste("output_data_dir", "03_generation_F2.csv", sep="/");
    write.csv(temperature_data_frame_F2, file=file_path, row.names=F);
}
# Display the total number of days in the Galaxy history item blurb.
cat("Number of days: ", opt$num_days, "\n");
# Information needed for plots plots.
days = c(1:opt$num_days);

            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;
            render_chart(ticks, 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") {

                    group2 = F1_total_nymphs;
                    group2_std_error = F1_total_nymphs.std_error;
                    group3 = F2_total_nymphs;
                    group3_std_error = F2_total_nymphs.std_error;
                }
                render_chart(ticks, 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=group, group_std_error=group_std_error, group2=group2, group2_std_error=group2_std_error,
                    group3=group3, group3_std_error=group3_std_error, life_stages_nymph=life_stage_nymph);
                # Turn off device driver to flush output.
                dev.off();
            }

                    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(ticks, 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=group, group_std_error=group_std_error, group2=group2, group2_std_error=group2_std_error,
                    group3=group3, group3_std_error=group3_std_error, life_stages_adult=life_stage_adult);
                # Turn off device driver to flush output.
                dev.off();
            }

            file_path = get_file_path(life_stage, "total_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));
            # Total population size by generation.
            maxval = max(P+F1+F2) + 100;
            render_chart(ticks, 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();
        }
    }

            file_path = get_file_path(life_stage, "egg_pop.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.
            maxval = max(eggs+eggs.std_error) + 100;
            render_chart(ticks, 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) {

                    # Old nymph population size.
                    group = old_nymphs;
                    group_std_error = old_nymphs.std_error;
                }
                maxval = max(group+group_std_error) + 100;
                render_chart(ticks, 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") {

                    # Diapausing adult population size.
                    group = diapausing_adults;
                    group_std_error = diapausing_adults.std_error
                }
                maxval = max(group+group_std_error) + 100;
                render_chart(ticks, 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") {

            file_path = get_file_path(life_stage, "total_pop.pdf")
            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(ticks, 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();
        }