comparison insect_phenology_model.R @ 31:ef6aa8c21729 draft

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30:0e49e1d1c5a1

    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"), action="store", dest="output", help="Dataset containing analyzed data"),
    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"),

} 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];
# Determine the specified life stages for processing.

    F2.std_error = m_se[[6]];
    if (process_eggs) {
        m_se = get_mean_and_std_error(P_eggs.replications, F1_eggs.replications, F2_eggs.replications);
        P_eggs = m_se[[1]];
        P_eggs.std_error = m_se[[2]];
        F1_eggs = m_se[[3]];
        F1_eggs.std_error = m_se[[4]];
        F2_eggs = m_se[[5]];
        F2_eggs.std_error = m_se[[6]];
    }
    if (process_young_nymphs) {
        m_se = get_mean_and_std_error(P_young_nymphs.replications, F1_young_nymphs.replications, F2_young_nymphs.replications);
        P_young_nymphs = m_se[[1]];
        P_young_nymphs.std_error = m_se[[2]];
        F1_young_nymphs = m_se[[3]];
        F1_young_nymphs.std_error = m_se[[4]];
        F2_young_nymphs = m_se[[5]];
        F2_young_nymphs.std_error = m_se[[6]];
    }
    if (process_old_nymphs) {
        m_se = get_mean_and_std_error(P_old_nymphs.replications, F1_old_nymphs.replications, F2_old_nymphs.replications);
        P_old_nymphs = m_se[[1]];
        P_old_nymphs.std_error = m_se[[2]];
        F1_old_nymphs = m_se[[3]];
        F1_old_nymphs.std_error = m_se[[4]];
        F2_old_nymphs = m_se[[5]];
        F2_old_nymphs.std_error = m_se[[6]];
    }
    if (process_total_nymphs) {
        m_se = get_mean_and_std_error(P_total_nymphs.replications, F1_total_nymphs.replications, F2_total_nymphs.replications);
        P_total_nymphs = m_se[[1]];
        P_total_nymphs.std_error = m_se[[2]];
        F1_total_nymphs = m_se[[3]];
        F1_total_nymphs.std_error = m_se[[4]];
        F2_total_nymphs = m_se[[5]];
        F2_total_nymphs.std_error = m_se[[6]];
    }
    if (process_previttelogenic_adults) {
        m_se = get_mean_and_std_error(P_previttelogenic_adults.replications, F1_previttelogenic_adults.replications, F2_previttelogenic_adults.replications);
        P_previttelogenic_adults = m_se[[1]];
        P_previttelogenic_adults.std_error = m_se[[2]];
        F1_previttelogenic_adults = m_se[[3]];
        F1_previttelogenic_adults.std_error = m_se[[4]];
        F2_previttelogenic_adults = m_se[[5]];
        F2_previttelogenic_adults.std_error = m_se[[6]];
    }
    if (process_vittelogenic_adults) {
        m_se = get_mean_and_std_error(P_vittelogenic_adults.replications, F1_vittelogenic_adults.replications, F2_vittelogenic_adults.replications);
        P_vittelogenic_adults = m_se[[1]];
        P_vittelogenic_adults.std_error = m_se[[2]];
        F1_vittelogenic_adults = m_se[[3]];
        F1_vittelogenic_adults.std_error = m_se[[4]];
        F2_vittelogenic_adults = m_se[[5]];
        F2_vittelogenic_adults.std_error = m_se[[6]];
    }
    if (process_diapausing_adults) {
        m_se = get_mean_and_std_error(P_diapausing_adults.replications, F1_diapausing_adults.replications, F2_diapausing_adults.replications);
        P_diapausing_adults = m_se[[1]];
        P_diapausing_adults.std_error = m_se[[2]];
        F1_diapausing_adults = m_se[[3]];
        F1_diapausing_adults.std_error = m_se[[4]];
        F2_diapausing_adults = m_se[[5]];
        F2_diapausing_adults.std_error = m_se[[6]];
    }
    if (process_total_adults) {
        m_se = get_mean_and_std_error(P_total_adults.replications, F1_total_adults.replications, F2_total_adults.replications);
        P_total_adults = m_se[[1]];
        P_total_adults.std_error = m_se[[2]];
        F1_total_adults = m_se[[3]];
        F1_total_adults.std_error = m_se[[4]];
        F2_total_adults = m_se[[5]];
        F2_total_adults.std_error = m_se[[6]];
    }
}

# Save the analyzed data.
write.csv(temperature_data_frame, file=opt$output, row.names=F);
# Display the total number of days in the Galaxy history item blurb.
cat("Number of days: ", opt$num_days, "\n");
# Information needed for plots plots.
days = c(1:opt$num_days);
start_date = temperature_data_frame$DATE[1];

31:ef6aa8c21729

    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"),

} else {
    plot_generations_separately = FALSE;
}
# Read the temperature data into a data frame.
temperature_data_frame = parse_input_data(opt$input, opt$num_days);
# Create copies of the temperature data for generations P, F1 and F2 if we're plotting generations separately.
if (plot_generations_separately) {
    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.

    F2.std_error = m_se[[6]];
    if (process_eggs) {
        m_se = get_mean_and_std_error(P_eggs.replications, F1_eggs.replications, F2_eggs.replications);
        P_eggs = m_se[[1]];
        P_eggs.std_error = m_se[[2]];
        temperature_data_frame_P = append_vector(temperature_data_frame_P, P_eggs, "EGG-P");
        temperature_data_frame_P = append_vector(temperature_data_frame_P, P_eggs.std_error, "EGG-P-SE");
        F1_eggs = m_se[[3]];
        F1_eggs.std_error = m_se[[4]];
        temperature_data_frame_F1 = append_vector(temperature_data_frame_F1, F1_eggs, "EGG-F1");
        temperature_data_frame_F1 = append_vector(temperature_data_frame_F1, F1_eggs.std_error, "EGG-F1-SE");
        F2_eggs = m_se[[5]];
        F2_eggs.std_error = m_se[[6]];
        temperature_data_frame_F2 = append_vector(temperature_data_frame_F2, F2_eggs, "EGG-F2");
        temperature_data_frame_F2 = append_vector(temperature_data_frame_F2, F2_eggs.std_error, "EGG-F2-SE");
    }
    if (process_young_nymphs) {
        m_se = get_mean_and_std_error(P_young_nymphs.replications, F1_young_nymphs.replications, F2_young_nymphs.replications);
        P_young_nymphs = m_se[[1]];
        P_young_nymphs.std_error = m_se[[2]];
        temperature_data_frame_P = append_vector(temperature_data_frame_P, P_young_nymphs, "YOUNGNYMPH-P");
        temperature_data_frame_P = append_vector(temperature_data_frame_P, P_young_nymphs.std_error, "YOUNGNYMPH-P-SE");
        F1_young_nymphs = m_se[[3]];
        F1_young_nymphs.std_error = m_se[[4]];
        temperature_data_frame_F1 = append_vector(temperature_data_frame_F1, F1_young_nymphs, "YOUNGNYMPH-F1");
        temperature_data_frame_F1 = append_vector(temperature_data_frame_F1, F1_young_nymphs.std_error, "YOUNGNYMPH-F1-SE");
        F2_young_nymphs = m_se[[5]];
        F2_young_nymphs.std_error = m_se[[6]];
        temperature_data_frame_F2 = append_vector(temperature_data_frame_F2, F2_young_nymphs, "YOUNGNYMPH-F2");
        temperature_data_frame_F2 = append_vector(temperature_data_frame_F2, F2_young_nymphs.std_error, "YOUNGNYMPH-F2-SE");
    }
    if (process_old_nymphs) {
        m_se = get_mean_and_std_error(P_old_nymphs.replications, F1_old_nymphs.replications, F2_old_nymphs.replications);
        P_old_nymphs = m_se[[1]];
        P_old_nymphs.std_error = m_se[[2]];
        temperature_data_frame_P = append_vector(temperature_data_frame_P, P_old_nymphs, "OLDNYMPH-P");
        temperature_data_frame_P = append_vector(temperature_data_frame_P, P_old_nymphs.std_error, "OLDNYMPH-P-SE");
        F1_old_nymphs = m_se[[3]];
        F1_old_nymphs.std_error = m_se[[4]];
        temperature_data_frame_F1 = append_vector(temperature_data_frame_F1, F1_old_nymphs, "OLDNYMPH-F1");
        temperature_data_frame_F1 = append_vector(temperature_data_frame_F1, F1_old_nymphs.std_error, "OLDNYMPH-F1-SE");
        F2_old_nymphs = m_se[[5]];
        F2_old_nymphs.std_error = m_se[[6]];
        temperature_data_frame_F2 = append_vector(temperature_data_frame_F2, F2_old_nymphs, "OLDNYMPH-F2");
        temperature_data_frame_F2 = append_vector(temperature_data_frame_F2, F2_old_nymphs.std_error, "OLDNYMPH-F2-SE");
    }
    if (process_total_nymphs) {
        m_se = get_mean_and_std_error(P_total_nymphs.replications, F1_total_nymphs.replications, F2_total_nymphs.replications);
        P_total_nymphs = m_se[[1]];
        P_total_nymphs.std_error = m_se[[2]];
        temperature_data_frame_P = append_vector(temperature_data_frame_P, P_total_nymphs, "TOTALNYMPH-P");
        temperature_data_frame_P = append_vector(temperature_data_frame_P, P_total_nymphs.std_error, "TOTALNYMPH-P-SE");
        F1_total_nymphs = m_se[[3]];
        F1_total_nymphs.std_error = m_se[[4]];
        temperature_data_frame_F1 = append_vector(temperature_data_frame_F1, F1_total_nymphs, "TOTALNYMPH-F1");
        temperature_data_frame_F1 = append_vector(temperature_data_frame_F1, F1_total_nymphs.std_error, "TOTALNYMPH-F1-SE");
        F2_total_nymphs = m_se[[5]];
        F2_total_nymphs.std_error = m_se[[6]];
        temperature_data_frame_F2 = append_vector(temperature_data_frame_F2, F2_total_nymphs, "TOTALNYMPH-F2");
        temperature_data_frame_F2 = append_vector(temperature_data_frame_F2, F2_total_nymphs.std_error, "TOTALNYMPH-F2-SE");
    }
    if (process_previttelogenic_adults) {
        m_se = get_mean_and_std_error(P_previttelogenic_adults.replications, F1_previttelogenic_adults.replications, F2_previttelogenic_adults.replications);
        P_previttelogenic_adults = m_se[[1]];
        P_previttelogenic_adults.std_error = m_se[[2]];
        temperature_data_frame_P = append_vector(temperature_data_frame_P, P_previttelogenic_adults, "PRE-VITADULT-P");
        temperature_data_frame_P = append_vector(temperature_data_frame_P, P_previttelogenic_adults.std_error, "PRE-VITADULT-P-SE");
        F1_previttelogenic_adults = m_se[[3]];
        F1_previttelogenic_adults.std_error = m_se[[4]];
        temperature_data_frame_F1 = append_vector(temperature_data_frame_F1, F1_previttelogenic_adults, "PRE-VITADULT-F1");
        temperature_data_frame_F1 = append_vector(temperature_data_frame_F1, F1_previttelogenic_adults.std_error, "PRE-VITADULT-F1-SE");
        F2_previttelogenic_adults = m_se[[5]];
        F2_previttelogenic_adults.std_error = m_se[[6]];
        temperature_data_frame_F2 = append_vector(temperature_data_frame_F2, F2_previttelogenic_adults, "PRE-VITADULT-F2");
        temperature_data_frame_F2 = append_vector(temperature_data_frame_F2, F2_previttelogenic_adults.std_error, "PRE-VITADULT-F2-SE");
    }
    if (process_vittelogenic_adults) {
        m_se = get_mean_and_std_error(P_vittelogenic_adults.replications, F1_vittelogenic_adults.replications, F2_vittelogenic_adults.replications);
        P_vittelogenic_adults = m_se[[1]];
        P_vittelogenic_adults.std_error = m_se[[2]];
        temperature_data_frame_P = append_vector(temperature_data_frame_P, P_vittelogenic_adults, "VITADULT-P");
        temperature_data_frame_P = append_vector(temperature_data_frame_P, P_vittelogenic_adults.std_error, "VITADULT-P-SE");
        F1_vittelogenic_adults = m_se[[3]];
        F1_vittelogenic_adults.std_error = m_se[[4]];
        temperature_data_frame_F1 = append_vector(temperature_data_frame_F1, F1_vittelogenic_adults, "VITADULT-F1");
        temperature_data_frame_F1 = append_vector(temperature_data_frame_F1, F1_vittelogenic_adults.std_error, "VITADULT-F1-SE");
        F2_vittelogenic_adults = m_se[[5]];
        F2_vittelogenic_adults.std_error = m_se[[6]];
        temperature_data_frame_F2 = append_vector(temperature_data_frame_F2, F2_vittelogenic_adults, "VITADULT-F2");
        temperature_data_frame_F2 = append_vector(temperature_data_frame_F2, F2_vittelogenic_adults.std_error, "VITADULT-F2-SE");
    }
    if (process_diapausing_adults) {
        m_se = get_mean_and_std_error(P_diapausing_adults.replications, F1_diapausing_adults.replications, F2_diapausing_adults.replications);
        P_diapausing_adults = m_se[[1]];
        P_diapausing_adults.std_error = m_se[[2]];
        temperature_data_frame_P = append_vector(temperature_data_frame_P, P_diapausing_adults, "DIAPAUSINGADULT-P");
        temperature_data_frame_P = append_vector(temperature_data_frame_P, P_diapausing_adults.std_error, "DIAPAUSINGADULT-P-SE");
        F1_diapausing_adults = m_se[[3]];
        F1_diapausing_adults.std_error = m_se[[4]];
        temperature_data_frame_F1 = append_vector(temperature_data_frame_F1, F1_diapausing_adults, "DIAPAUSINGADULT-F1");
        temperature_data_frame_F1 = append_vector(temperature_data_frame_F1, F1_diapausing_adults.std_error, "DIAPAUSINGADULT-F1-SE");
        F2_diapausing_adults = m_se[[5]];
        F2_diapausing_adults.std_error = m_se[[6]];
        temperature_data_frame_F2 = append_vector(temperature_data_frame_F2, F2_diapausing_adults, "DIAPAUSINGADULT-F2");
        temperature_data_frame_F2 = append_vector(temperature_data_frame_F2, F2_diapausing_adults.std_error, "DIAPAUSINGADULT-F2-SE");
    }
    if (process_total_adults) {
        m_se = get_mean_and_std_error(P_total_adults.replications, F1_total_adults.replications, F2_total_adults.replications);
        P_total_adults = m_se[[1]];
        P_total_adults.std_error = m_se[[2]];
        temperature_data_frame_P = append_vector(temperature_data_frame_P, P_total_adults, "TOTALADULT-P");
        temperature_data_frame_P = append_vector(temperature_data_frame_P, P_total_adults.std_error, "TOTALADULT-P-SE");
        F1_total_adults = m_se[[3]];
        F1_total_adults.std_error = m_se[[4]];
        temperature_data_frame_F1 = append_vector(temperature_data_frame_F1, F1_total_adults, "TOTALADULT-F1");
        temperature_data_frame_F1 = append_vector(temperature_data_frame_F1, F1_total_adults.std_error, "TOTALADULT-F1-SE");
        F2_total_adults = m_se[[5]];
        F2_total_adults.std_error = m_se[[6]];
        temperature_data_frame_F2 = append_vector(temperature_data_frame_F2, F2_total_adults, "TOTALADULT-F2");
        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);
start_date = temperature_data_frame$DATE[1];