comparison extract_ipm_date_interval.R @ 11:2a438187d051 draft

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10:c2eb16ef23c0

            P_total_adults = temperature_data_frame$TOTALADULT.P;
            if (plot_std_error) {
                P_total_adults.std_error = temperature_data_frame$TOTALADULT.P.SE;
            }
        }
    } else if (file_name == "02_generation_F1.csv") {
        if (process_eggs) {
            F1_eggs = temperature_data_frame$EGG.F1;
            if (plot_std_error) {
                F1_eggs.std_error = temperature_data_frame$EGG.F1.SE;

            F1_total_adults = temperature_data_frame$TOTALADULT.F1;
            if (plot_std_error) {
                F1_total_adults.std_error = temperature_data_frame$TOTALADULT.F1.SE;
            }
        }
    } else if (file_name == "03_generation_F2.csv") {
        if (process_eggs) {
            F2_eggs = temperature_data_frame$EGG.F2;
            if (plot_std_error) {
                F2_eggs.std_error = temperature_data_frame$EGG.F2.SE;

        }
        if (process_total_adults) {
            F2_total_adults = temperature_data_frame$TOTALADULT.F2;
            if (plot_std_error) {
                F2_total_adults.std_error = temperature_data_frame$TOTALADULT.F2.SE;
            }
        }
    }
}

    if (process_total) {
        life_stage = "Total";
        # Total population size for egg, nymph and adult by generation.
        file_path = get_file_path(life_stage, "total_pop_by_generation.pdf")
        maxval = max(total_adults+eggs+total_nymphs) + 100;
        # P == total_adults
        # P.std_error == total_adults.std_error
        # F1 == eggs
        # F1.std_error == eggs.std_error
        # F2 == ???
        # F2.std_error == ???
        # FIXME: testing demonstrates that P and F1 are properly assigned
        # above, but F2 cannot be determined.  F2 should undoubtedly be
        # total_nymphs, but the data is not the same bewteen the output
        # from the insect_phenology_model tool and the date interval from
        # this tool.  We won't plot the total until we get time to figure
        # this out.
        #prepare_plot(life_stage, file_path, maxval, ticks, date_labels, chart_type, params_hash$plot_std_error,
        #    params_hash$insect, params_hash$location, latitude, start_date, end_date, total_days_vector,
        #    params_hash$replications, group=total_adults, group_std_error=total_adults.std_error, group2=eggs,
        #    group2_std_error=eggs.std_error, group3=total_nymphs, group3_std_error=total_nymphs.std_error);
    }
} else {
    chart_type = "pop_size_by_life_stage";
    if (process_eggs) {
        # Egg population size.

11:2a438187d051

            P_total_adults = temperature_data_frame$TOTALADULT.P;
            if (plot_std_error) {
                P_total_adults.std_error = temperature_data_frame$TOTALADULT.P.SE;
            }
        }
        if (process_total) {
            P_all_total = temperature_data_frame$ALL.TOTAL.P;
            if (plot_std_error) {
                P_all_total.std_error = temperature_data_frame$ALL.TOTAL.P.SE;
            }
        }
    } else if (file_name == "02_generation_F1.csv") {
        if (process_eggs) {
            F1_eggs = temperature_data_frame$EGG.F1;
            if (plot_std_error) {
                F1_eggs.std_error = temperature_data_frame$EGG.F1.SE;

            F1_total_adults = temperature_data_frame$TOTALADULT.F1;
            if (plot_std_error) {
                F1_total_adults.std_error = temperature_data_frame$TOTALADULT.F1.SE;
            }
        }
        if (process_total) {
            F1_all_total = temperature_data_frame$ALL.TOTAL.F1;
            if (plot_std_error) {
                F1_all_total.std_error = temperature_data_frame$ALL.TOTAL.F1.SE;
            }
        }
    } else if (file_name == "03_generation_F2.csv") {
        if (process_eggs) {
            F2_eggs = temperature_data_frame$EGG.F2;
            if (plot_std_error) {
                F2_eggs.std_error = temperature_data_frame$EGG.F2.SE;

        }
        if (process_total_adults) {
            F2_total_adults = temperature_data_frame$TOTALADULT.F2;
            if (plot_std_error) {
                F2_total_adults.std_error = temperature_data_frame$TOTALADULT.F2.SE;
            }
        }
        if (process_total) {
            F2_all_total = temperature_data_frame$ALL.TOTAL.F2;
            if (plot_std_error) {
                F2_all_total.std_error = temperature_data_frame$ALL.TOTAL.F2.SE;
            }
        }
    }
}

    if (process_total) {
        life_stage = "Total";
        # Total population size for egg, nymph and adult by generation.
        file_path = get_file_path(life_stage, "total_pop_by_generation.pdf")
        maxval = max(total_adults+eggs+total_nymphs) + 100;
        prepare_plot(life_stage, file_path, maxval, ticks, date_labels, chart_type, params_hash$plot_std_error,
            params_hash$insect, params_hash$location, latitude, start_date, end_date, total_days_vector,
            params_hash$replications, group=P_all_total, group_std_error=P_all_total.std_error, group2=F1_all_total,
            group2_std_error=F1_all_total.std_error, group3=F2_all_total, group3_std_error=F2_all_total.std_error);
    }
} else {
    chart_type = "pop_size_by_life_stage";
    if (process_eggs) {
        # Egg population size.