comparison insect_phenology_model.R @ 19:3c6e94e477cb draft

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18:f5ecff4800f2

    # Append daylight_length_vector as a new column to temperature_data_frame.
    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);
}

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) {

            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.

} else {
    plot_generations_separately = FALSE;
}
# Read the temperature data into a data frame.
temperature_data_frame = parse_input_data(opt$input, opt$num_days);
output_dir = "output_dir";
# 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];
# Get the number of days for plots.

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,

            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,

        } 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,

} 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,

            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.
                    group = total_nymphs;

            }
        } 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.
                    group = total_adults;

                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,

19:3c6e94e477cb

    # Append daylight_length_vector as a new column to temperature_data_frame.
    temperature_data_frame[, num_columns+1] = daylight_length_vector;
    return(temperature_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) {

            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_nymph), base_name, sep="_");
    } else if (!is.null(life_stage_adult)) {
        lsi = get_life_stage_index(life_stage, life_stage_adult=life_stage_adult);
        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
    # are displayed in logical order.

} else {
    plot_generations_separately = FALSE;
}
# Read the temperature data into a data frame.
temperature_data_frame = parse_input_data(opt$input, opt$num_days);
# 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];
# Get the number of days for plots.

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 = 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,

            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_path = get_file_path(life_stage, "nymph_pop_by_generation.pdf", life_stage_nymph=life_stage_nymph)
                pdf(file=file_path, width=20, height=30, bg="white");
                par(mar=c(5, 6, 4, 4), mfrow=c(3, 1));
                # Nymph population size by generation.
                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);
                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.
                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,

        } 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);
            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,

} else {
    for (life_stage in life_stages) {
        if (life_stage == "Egg") {
            # Start PDF device driver.
            dev.new(width=20, height=30);
            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,

            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_path = get_file_path(life_stage, "nymph_pop.pdf", life_stage_nymph=life_stage_nymph)
                pdf(file=file_path, width=20, height=30, bg="white");
                par(mar=c(5, 6, 4, 4), mfrow=c(3, 1));
                if (life_stage_nymph=="Total") {
                    # Total nymph population size.
                    group = total_nymphs;

            }
        } else if (life_stage == "Adult") {
            for (life_stage_adult in life_stages_adult) {
                # Start PDF device driver.
                dev.new(width=20, height=30);
                file_path = get_file_path(life_stage, "adult_pop.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));
                if (life_stage_adult=="Total") {
                    # Total adult population size.
                    group = total_adults;

                dev.off();
            }
        } else if (life_stage == "Total") {
            # Start PDF device driver.
            dev.new(width=20, height=30);
            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,