# HG changeset patch
# User greg
# Date 1527598825 14400
# Node ID bcb12b7e8563ed0735d9699bfdd2b25065d2e86e
# Parent  37ac68b6ff107a4b010fd636666a4ca947e64016
Uploaded

diff -r 37ac68b6ff10 -r bcb12b7e8563 insect_phenology_model.R
--- a/insect_phenology_model.R	Tue Feb 13 13:47:32 2018 -0500
+++ b/insect_phenology_model.R	Tue May 29 09:00:25 2018 -0400
@@ -6,20 +6,24 @@
     make_option(c("--adult_mortality"), action="store", dest="adult_mortality", type="integer", help="Adjustment rate for adult mortality"),
     make_option(c("--adult_accumulation"), action="store", dest="adult_accumulation", type="integer", help="Adjustment of degree-days accumulation (old nymph->adult)"),
     make_option(c("--egg_mortality"), action="store", dest="egg_mortality", type="integer", help="Adjustment rate for egg mortality"),
-    make_option(c("--input"), action="store", dest="input", help="Temperature data for selected location"),
+    make_option(c("--input_norm"), action="store", dest="input_norm", help="30 year normals temperature data for selected station"),
+    make_option(c("--input_ytd"), action="store", dest="input_ytd", default=NULL, help="Year-to-date 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("--location"), action="store", dest="location", help="Selected location"),
+    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", default=NULL, 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("--num_days_ytd"), action="store", dest="num_days_ytd", default=NULL, type="integer", help="Total number of days in the year-to-date 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("--num_days"), action="store", dest="num_days", type="integer", help="Total number of days in the temperature dataset"),
-    make_option(c("--output"), action="store", dest="output", help="Output dataset"),
     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"),
-    make_option(c("--std_error_plot"), action="store", dest="std_error_plot", help="Plot Standard error"),
     make_option(c("--young_nymph_accumulation"), action="store", dest="young_nymph_accumulation", type="integer", help="Adjustment of degree-days accumulation (egg->young nymph)")
 )
 
@@ -27,9 +31,9 @@
 args <- parse_args(parser, positional_arguments=TRUE);
 opt <- args$options;
 
-add_daylight_length = function(temperature_data_frame, num_columns, num_rows) {
+add_daylight_length = function(temperature_data_frame, num_rows) {
     # Return a vector of daylight length (photoperido profile) for
-    # the number of days specified in the input temperature data
+    # the number of days specified in the input_ytd temperature data
     # (from Forsythe 1995).
     p = 0.8333;
     latitude = temperature_data_frame$LATITUDE[1];
@@ -45,52 +49,98 @@
         daylight_length_vector[i] = 24 - darkness_length;
     }
     # Append daylight_length_vector as a new column to temperature_data_frame.
-    temperature_data_frame[, num_columns+1] = daylight_length_vector;
+    temperature_data_frame = append_vector(temperature_data_frame, daylight_length_vector, "DAYLEN");
     return(temperature_data_frame);
 }
 
-dev.egg = function(temperature) {
-    dev.rate = -0.9843 * temperature + 33.438;
-    return(dev.rate);
+append_vector = function(data_frame, vec, new_column_name) {
+    num_columns = dim(data_frame)[2];
+    current_column_names = colnames(data_frame);
+    # Append vector vec as a new column to data_frame.
+    data_frame[,num_columns+1] = vec;
+    # Reset the column names with the additional column for later access.
+    colnames(data_frame) = append(current_column_names, new_column_name);
+    return(data_frame);
 }
 
-dev.emerg = function(temperature) {
-    emerg.rate = -0.5332 * temperature + 24.147;
-    return(emerg.rate);
-}
-
-dev.old = function(temperature) {
-    n34 = -0.6119 * temperature + 17.602;
-    n45 = -0.4408 * temperature + 19.036;
-    dev.rate = mean(n34 + n45);
-    return(dev.rate);
+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_plots_dir", file_name, sep="/");
+    return(file_path);
 }
 
-dev.young = function(temperature) {
-    n12 = -0.3728 * temperature + 14.68;
-    n23 = -0.6119 * temperature + 25.249;
-    dev.rate = mean(n12 + n23);
-    return(dev.rate);
+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.
+    if (life_stage=="Egg") {
+        lsi = "01";
+    } else if (life_stage=="Nymph") {
+        if (life_stage_nymph=="Young") {
+            lsi = "02";
+        } else if (life_stage_nymph=="Old") {
+            lsi = "03";
+        } else if (life_stage_nymph=="Total") {
+            lsi="04";
+        }
+    } else if (life_stage=="Adult") {
+        if (life_stage_adult=="Pre-vittelogenic") {
+            lsi = "05";
+        } else if (life_stage_adult=="Vittelogenic") {
+            lsi = "06";
+        } else if (life_stage_adult=="Diapausing") {
+            lsi = "07";
+        } else if (life_stage_adult=="Total") {
+            lsi = "08";
+        }
+    } else if (life_stage=="Total") {
+        lsi = "09";
+    }
+    return(lsi);
 }
 
+get_mean_and_std_error = function(p_replications, f1_replications, f2_replications) {
+    # P mean.
+    p_m = apply(p_replications, 1, mean);
+    # P standard error.
+    p_se = apply(p_replications, 1, sd) / sqrt(opt$replications);
+    # F1 mean.
+    f1_m = apply(f1_replications, 1, mean);
+    # F1 standard error.
+    f1_se = apply(f1_replications, 1, sd) / sqrt(opt$replications);
+    # F2 mean.
+    f2_m = apply(f2_replications, 1, mean);
+    # F2 standard error.
+    f2_se = apply(f2_replications, 1, sd) / sqrt(opt$replications);
+    return(list(p_m, p_se, f1_m, f1_se, f2_m, f2_se))
+}
 
-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;
-        }
+get_next_normals_row = function(norm_data_frame, year, is_leap_year, index) {
+    # Return the next 30 year normals row formatted
+    # appropriately for the year-to-date data.
+    latitude = norm_data_frame[index,"LATITUDE"][1];
+    longitude = norm_data_frame[index,"LONGITUDE"][1];
+    # Format the date.
+    mmdd = norm_data_frame[index,"MMDD"][1];
+    date_str = paste(year, mmdd, sep="-");
+    doy = norm_data_frame[index,"DOY"][1];
+    if (!is_leap_year) {
+        # Since all normals data includes Feb 29, we have to
+        # subtract 1 from DOY if we're not in a leap year since
+        # we removed the Feb 29 row from the data frame above.
+        doy = as.integer(doy) - 1;
     }
-    return(c(unlist(month_labels)));
+    tmin = norm_data_frame[index,"TMIN"][1];
+    tmax = norm_data_frame[index,"TMAX"][1];
+    return(list(latitude, longitude, date_str, doy, tmin, tmax));
 }
 
 get_temperature_at_hour = function(latitude, temperature_data_frame, row, num_days) {
@@ -164,6 +214,112 @@
     return(c(curr_mean_temp, averages))
 }
 
+get_tick_index = function(index, last_tick, ticks, month_labels) {
+    # The R code tries hard not to draw overlapping tick labels, and so
+    # will omit labels where they would abut or overlap previously drawn
+    # labels. This can result in, for example, every other tick being
+    # labelled.  We'll keep track of the last tick to make sure all of
+    # the month labels are displayed, and missing ticks are restricted
+    # to Sundays which have no labels anyway.
+    if (last_tick==0) {
+        return(length(ticks)+1);
+    }
+    last_saved_tick = ticks[[length(ticks)]];
+    if (index-last_saved_tick<3) {
+        last_saved_month = month_labels[[length(month_labels)]];
+        if (last_saved_month=="") {
+            # We're safe overwriting a tick
+            # with no label (i.e., a Sunday tick).
+            return(length(ticks));
+        } else {
+            # Don't eliminate a Month label.
+            return(NULL);
+        }
+    }
+    return(length(ticks)+1);
+}
+
+get_total_days = function(is_leap_year) {
+    # Get the total number of days in the current year.
+    if (is_leap_year) {
+        return(366);
+    } else {
+        return(365);
+    }
+}
+
+get_x_axis_ticks_and_labels = function(temperature_data_frame, num_rows, start_doy_ytd, end_doy_ytd) {
+    # Keep track of the years to see if spanning years.
+    month_labels = list();
+    ticks = list();
+    current_month_label = NULL;
+    last_tick = 0;
+    for (i in 1:num_rows) {
+        if (start_doy_ytd > 1 & i==start_doy_ytd-1) {
+            # Add a tick for the end of the 30 year normnals data
+            # that was prepended to the year-to-date data.
+            tick_index = get_tick_index(i, last_tick, ticks, month_labels)
+            ticks[tick_index] = i;
+            month_labels[tick_index] = "End prepended 30 year normals";
+            last_tick = i;
+        } else  if (end_doy_ytd > 0 & i==end_doy_ytd+1) {
+            # Add a tick for the start of the 30 year normnals data
+            # that was appended to the year-to-date data.
+            tick_index = get_tick_index(i, last_tick, ticks, month_labels)
+            ticks[tick_index] = i;
+            month_labels[tick_index] = "Start appended 30 year normals";
+            last_tick = i;
+        } else if (i==num_rows) {
+            # Add a tick for the last day of the year.
+            tick_index = get_tick_index(i, last_tick, ticks, month_labels)
+            ticks[tick_index] = i;
+            month_labels[tick_index] = "";
+            last_tick = i;
+        } else {
+            # 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.
+                tick_index = get_tick_index(i, last_tick, ticks, month_labels)
+                ticks[tick_index] = i;
+                month_labels[tick_index] = month_label;
+                current_month_label = month_label;
+                last_tick = i;
+            }
+            tick_index = get_tick_index(i, last_tick, ticks, month_labels)
+            if (!is.null(tick_index)) {
+                # Get the day.
+                day = weekdays(as.Date(date));
+                if (day=="Sunday") {
+                    # Add an x-axis tick if we're on a Sunday.
+                    ticks[tick_index] = i;
+                    # Add a blank month label so it is not displayed.
+                    month_labels[tick_index] = "";
+                    last_tick = i;
+                }
+            }
+        }
+    }
+    return(list(ticks, month_labels));
+}
+
+is_leap_year = function(date_str) {
+    # Extract the year from the date_str.
+    date = format(date_str);
+    items = strsplit(date, "-")[[1]];
+    year = as.integer(items[1]);
+    if (((year %% 4 == 0) & (year %% 100 != 0)) | (year %% 400 == 0)) {
+        return(TRUE);
+    } else {
+        return(FALSE);
+    }
+}
+
 mortality.adult = function(temperature) {
     if (temperature < 12.7) {
         mortality.probability = 0.002;
@@ -197,125 +353,432 @@
     return(mortality.probability);
 }
 
-parse_input_data = function(input_file, num_rows) {
-    # Read in the input temperature datafile into a data frame.
-    temperature_data_frame = read.csv(file=input_file, header=T, strip.white=TRUE, sep=",");
-    num_columns = dim(temperature_data_frame)[2];
-    if (num_columns == 6) {
-        # The input data has the following 6 columns:
+parse_input_data = function(input_ytd, input_norm, num_days_ytd, location) {
+    if (is.null(input_ytd)) {
+        # We're analysing only the 30 year normals data, so create an empty
+        # data frame for containing temperature data after it is converted
+        # from the 30 year normals format to the year-to-date format.
+        temperature_data_frame = data.frame(matrix(ncol=6, nrow=0));
+        colnames(temperature_data_frame) = c("LATITUDE", "LONGITUDE", "DATE", "DOY", "TMIN", "TMAX");
+        # Base all dates on the current date since 30 year
+        # normals data does not include any dates.
+        year = format(Sys.Date(), "%Y");
+        start_date = paste(year, "01", "01", sep="-");
+        end_date = paste(year, "12", "31", sep="-");
+        # Set invalid start and end DOY.
+        start_doy_ytd = 0;
+        end_doy_ytd = 0;
+    } else {
+        # Read the input_ytd temperature datafile into a data frame.
+        # The input_ytd data has the following 6 columns:
         # LATITUDE, LONGITUDE, DATE, DOY, TMIN, TMAX
-        # Set the column names for access when adding daylight length..
-        colnames(temperature_data_frame) = c("LATITUDE","LONGITUDE", "DATE", "DOY", "TMIN", "TMAX");
-        # Add a column containing the daylight length for each day.
-        temperature_data_frame = add_daylight_length(temperature_data_frame, num_columns, num_rows);
-        # Reset the column names with the additional column for later access.
-        colnames(temperature_data_frame) = c("LATITUDE","LONGITUDE", "DATE", "DOY", "TMIN", "TMAX", "DAYLEN");
+        temperature_data_frame = read.csv(file=input_ytd, header=T, strip.white=TRUE, stringsAsFactors=FALSE, sep=",");
+        # Set the temperature_data_frame column names for access.
+        colnames(temperature_data_frame) = c("LATITUDE", "LONGITUDE", "DATE", "DOY", "TMIN", "TMAX");
+        # Get the start date.
+        start_date = temperature_data_frame$DATE[1];
+        end_date = temperature_data_frame$DATE[num_days_ytd];
+        # Extract the year from the start date.
+        date_str = format(start_date);
+        date_str_items = strsplit(date_str, "-")[[1]];
+        year = date_str_items[1];
+        # Save the first DOY to later check if start_date is Jan 1.
+        start_doy_ytd = as.integer(temperature_data_frame$DOY[1]);
+        end_doy_ytd = as.integer(temperature_data_frame$DOY[num_days_ytd]);
+    }
+    # See if we're in a leap year.
+    is_leap_year = is_leap_year(start_date);
+    # Get the number of days in the year.
+    total_days = get_total_days(is_leap_year);
+    # Read the input_norm temperature datafile into a data frame.
+    # The input_norm data has the following 10 columns:
+    # STATIONID, LATITUDE, LONGITUDE, ELEV_M, NAME, ST, MMDD, DOY, TMIN, TMAX
+    norm_data_frame = read.csv(file=input_norm, header=T, strip.white=TRUE, stringsAsFactors=FALSE, sep=",");
+    # Set the norm_data_frame column names for access.
+    colnames(norm_data_frame) = c("STATIONID", "LATITUDE","LONGITUDE", "ELEV_M", "NAME", "ST", "MMDD", "DOY", "TMIN", "TMAX");
+    # All normals data includes Feb 29 which is row 60 in
+    # the data, so delete that row if we're not in a leap year.
+    if (!is_leap_year) {
+        norm_data_frame = norm_data_frame[-c(60),];
     }
-    return(temperature_data_frame);
+    # Set the location to be the station name if the user elected no to enter it.
+    if (is.null(location) | length(location)==0) {
+        location = norm_data_frame$NAME[1];
+    }
+    if (is.null(input_ytd)) {
+        # Convert the 30 year normals data to the year-to-date format.
+        for (i in 1:total_days) {
+            temperature_data_frame[i,] = get_next_normals_row(norm_data_frame, year, is_leap_year, i);
+        }
+    } else {
+        # Merge the year-to-date data with the 30 year normals data.
+        if (start_doy_ytd > 1) {
+            # The year-to-date data starts after Jan 1, so create a
+            # temporary data frame to contain the 30 year normals data
+            # from Jan 1 to the date immediately prior to start_date.
+            tmp_data_frame = temperature_data_frame[FALSE,];
+            for (i in 1:start_doy_ytd-1) {
+                tmp_data_frame[i,] = get_next_normals_row(norm_data_frame, year, is_leap_year, i);
+            }
+            # Next merge the temporary data frame with the year-to-date data frame.
+            temperature_data_frame = rbind(tmp_data_frame, temperature_data_frame);
+        }
+        # Define the next row for the year-to-date data from the 30 year normals data.
+        first_normals_append_row = end_doy_ytd + 1;
+        # Append the 30 year normals data to the year-to-date data.
+        for (i in first_normals_append_row:total_days) {
+            temperature_data_frame[i,] = get_next_normals_row(norm_data_frame, year, is_leap_year, i);
+        }
+    }
+    # Add a column containing the daylight length for each day.
+    temperature_data_frame = add_daylight_length(temperature_data_frame, total_days);
+    return(list(temperature_data_frame, start_date, end_date, start_doy_ytd, end_doy_ytd, is_leap_year, total_days, location));
 }
 
-
-render_chart = function(chart_type, insect, location, latitude, start_date, end_date, days, maxval, plot_std_error,
-                        group1, group2, group3, group1_std_error, group2_std_error, group3_std_error, date_labels) {
-    if (chart_type == "pop_size_by_life_stage") {
-        title = paste(insect, ": Total pop. by life stage :", location, ": Lat:", latitude, ":", start_date, "-", end_date, sep=" ");
-        legend_text = c("Egg", "Nymph", "Adult");
-        columns = c(4, 2, 1);
-    } else if (chart_type == "pop_size_by_generation") {
-        title = paste(insect, ": Total pop. by generation :", location, ": Lat:", latitude, ":", start_date, "-", end_date, sep=" ");
-        legend_text = c("P", "F1", "F2");
-        columns = c(1, 2, 4);
-    } else if (chart_type == "adult_pop_size_by_generation") {
-        title = paste(insect, ": Adult pop. by generation :", location, ": Lat:", latitude, ":", start_date, "-", end_date, sep=" ");
+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=" ");
+            legend_text = c("Egg", "Nymph", "Adult");
+            columns = c(4, 2, 1);
+            plot(days, group, main=title, type="l", ylim=c(0, maxval), axes=FALSE, 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, las=2, font.axis=3, xpd=TRUE, cex=3, cex.lab=3, cex.axis=3, cex.main=3);
+            axis(side=2, font.axis=3, xpd=TRUE, cex=3, cex.lab=3, cex.axis=3, cex.main=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.
+                lines(days, group2+group2_std_error, col=2, lty=2);
+                lines(days, group2-group2_std_error, col=2, lty=2);
+                # Standard error for group3.
+                lines(days, group3+group3_std_error, col=4, lty=2);
+                lines(days, group3-group3_std_error, col=4, lty=2);
+            }
+        } else {
+            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=" "));
+                columns = c(1);
+            }
+            plot(days, group, main=title, type="l", ylim=c(0, maxval), axes=FALSE, 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, las=2, font.axis=3, xpd=TRUE, cex=3, cex.lab=3, cex.axis=3, cex.main=3);
+            axis(side=2, font.axis=3, xpd=TRUE, cex=3, cex.lab=3, cex.axis=3, cex.main=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);
+            }
+        }
+    } else if (chart_type=="pop_size_by_generation") {
+        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");
         columns = c(1, 2, 4);
-    }
-    plot(days, group1, 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==1) {
-        # Standard error for group1.
-        lines(days, group1+group1_std_error, lty=2);
-        lines(days, group1-group1_std_error, lty=2);
-        # Standard error for group2.
-        lines(days, group2+group2_std_error, col=2, lty=2);
-        lines(days, group2-group2_std_error, col=2, lty=2);
-        # Standard error for group3.
-        lines(days, group3+group3_std_error, col=4, lty=2);
-        lines(days, group3-group3_std_error, col=4, lty=2);
+        plot(days, group, main=title, type="l", ylim=c(0, maxval), axes=FALSE, 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, las=2, font.axis=3, xpd=TRUE, cex=3, cex.lab=3, cex.axis=3, cex.main=3);
+        axis(side=2, font.axis=3, xpd=TRUE, cex=3, cex.lab=3, cex.axis=3, cex.main=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.
+            lines(days, group2+group2_std_error, col=2, lty=2);
+            lines(days, group2-group2_std_error, col=2, lty=2);
+            # Standard error for group3.
+            lines(days, group3+group3_std_error, col=4, lty=2);
+            lines(days, group3-group3_std_error, col=4, lty=2);
+        }
     }
 }
 
-temperature_data_frame = parse_input_data(opt$input, opt$num_days);
-# All latitude values are the same, so get the value from the first row.
+# Determine if we're plotting generations separately.
+if (opt$plot_generations_separately=="yes") {
+    plot_generations_separately = TRUE;
+} else {
+    plot_generations_separately = FALSE;
+}
+# Display the total number of days in the Galaxy history item blurb.
+cat("Year-to-date number of days: ", opt$num_days_ytd, "\n");
+
+# Parse the inputs.
+data_list = parse_input_data(opt$input_ytd, opt$input_norm, opt$num_days_ytd, opt$location);
+temperature_data_frame = data_list[[1]];
+# Information needed for plots.
+start_date = data_list[[2]];
+end_date = data_list[[3]];
+start_doy_ytd = data_list[[4]];
+end_doy_ytd = data_list[[5]];
+is_leap_year = data_list[[6]];
+total_days = data_list[[7]];
+total_days_vector = c(1:total_days);
+location =  data_list[[8]];
+
+# 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 ticks date labels for plots.
+ticks_and_labels = get_x_axis_ticks_and_labels(temperature_data_frame, total_days, start_doy_ytd, end_doy_ytd);
+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$LATITUDE[1];
-num_columns = dim(temperature_data_frame)[2];
-date_labels = get_date_labels(temperature_data_frame, opt$num_days);
+
+# 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);
+life_stages = strsplit(life_stages_str, ",")[[1]];
 
+# Determine the data we need to generate for plotting.
+process_eggs = FALSE;
+process_nymphs = FALSE;
+process_young_nymphs = FALSE;
+process_old_nymphs = FALSE;
+process_total_nymphs = FALSE;
+process_adults = FALSE;
+process_previttelogenic_adults = FALSE;
+process_vittelogenic_adults = FALSE;
+process_diapausing_adults = FALSE;
+process_total_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_nymphs) {
+    # Split life_stages_nymph into a list of strings for plots.
+    life_stages_nymph_str = as.character(opt$life_stages_nymph);
+    life_stages_nymph = strsplit(life_stages_nymph_str, ",")[[1]];
+    for (life_stage_nymph in life_stages_nymph) {
+        if (life_stage_nymph=="Young") {
+            process_young_nymphs = TRUE;
+        } else if (life_stage_nymph=="Old") {
+            process_old_nymphs = TRUE;
+        } else if (life_stage_nymph=="Total") {
+            process_total_nymphs = TRUE;
+        }
+    }
+}
+if (process_adults) {
+    # Split life_stages_adult into a list of strings for plots.
+    life_stages_adult_str = as.character(opt$life_stages_adult);
+    life_stages_adult = strsplit(life_stages_adult_str, ",")[[1]];
+    for (life_stage_adult in life_stages_adult) {
+        if (life_stage_adult=="Pre-vittelogenic") {
+            process_previttelogenic_adults = TRUE;
+        } else if (life_stage_adult=="Vittelogenic") {
+            process_vittelogenic_adults = TRUE;
+        } else if (life_stage_adult=="Diapausing") {
+            process_diapausing_adults = TRUE;
+        } else if (life_stage_adult=="Total") {
+            process_total_adults = TRUE;
+        }
+    }
+}
 # Initialize matrices.
-Eggs.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
-YoungNymphs.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
-OldNymphs.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
-Previtellogenic.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
-Vitellogenic.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
-Diapausing.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
-
-newborn.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
-adult.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
-death.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
-
-P.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
-P_adults.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
-F1.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
-F1_adults.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
-F2.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
-F2_adults.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
-
-population.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
+if (process_eggs) {
+    Eggs.replications = matrix(rep(0, total_days*opt$replications), ncol=opt$replications);
+}
+if (process_young_nymphs | process_total_nymphs) {
+    YoungNymphs.replications = matrix(rep(0, total_days*opt$replications), ncol=opt$replications);
+}
+if (process_old_nymphs | process_total_nymphs) {
+    OldNymphs.replications = matrix(rep(0, total_days*opt$replications), ncol=opt$replications);
+}
+if (process_previttelogenic_adults | process_total_adults) {
+    Previttelogenic.replications = matrix(rep(0, total_days*opt$replications), ncol=opt$replications);
+}
+if (process_vittelogenic_adults | process_total_adults) {
+    Vittelogenic.replications = matrix(rep(0, total_days*opt$replications), ncol=opt$replications);
+}
+if (process_diapausing_adults | process_total_adults) {
+    Diapausing.replications = matrix(rep(0, total_days*opt$replications), ncol=opt$replications);
+}
+newborn.replications = matrix(rep(0, total_days*opt$replications), ncol=opt$replications);
+adult.replications = matrix(rep(0, total_days*opt$replications), ncol=opt$replications);
+death.replications = matrix(rep(0, total_days*opt$replications), ncol=opt$replications);
+if (plot_generations_separately) {
+    # P is Parental, or overwintered adults.
+    P.replications = matrix(rep(0, total_days*opt$replications), ncol=opt$replications);
+    # F1 is the first field-produced generation.
+    F1.replications = matrix(rep(0, total_days*opt$replications), ncol=opt$replications);
+    # F2 is the second field-produced generation.
+    F2.replications = matrix(rep(0, total_days*opt$replications), ncol=opt$replications);
+    if (process_eggs) {
+        P_eggs.replications = matrix(rep(0, total_days*opt$replications), ncol=opt$replications);
+        F1_eggs.replications = matrix(rep(0, total_days*opt$replications), ncol=opt$replications);
+        F2_eggs.replications = matrix(rep(0, total_days*opt$replications), ncol=opt$replications);
+    }
+    if (process_young_nymphs) {
+        P_young_nymphs.replications = matrix(rep(0, total_days*opt$replications), ncol=opt$replications);
+        F1_young_nymphs.replications = matrix(rep(0, total_days*opt$replications), ncol=opt$replications);
+        F2_young_nymphs.replications = matrix(rep(0, total_days*opt$replications), ncol=opt$replications);
+    }
+    if (process_old_nymphs) {
+        P_old_nymphs.replications = matrix(rep(0, total_days*opt$replications), ncol=opt$replications);
+        F1_old_nymphs.replications = matrix(rep(0, total_days*opt$replications), ncol=opt$replications);
+        F2_old_nymphs.replications = matrix(rep(0, total_days*opt$replications), ncol=opt$replications);
+    }
+    if (process_total_nymphs) {
+        P_total_nymphs.replications = matrix(rep(0, total_days*opt$replications), ncol=opt$replications);
+        F1_total_nymphs.replications = matrix(rep(0, total_days*opt$replications), ncol=opt$replications);
+        F2_total_nymphs.replications = matrix(rep(0, total_days*opt$replications), ncol=opt$replications);
+    }
+    if (process_previttelogenic_adults) {
+        P_previttelogenic_adults.replications = matrix(rep(0, total_days*opt$replications), ncol=opt$replications);
+        F1_previttelogenic_adults.replications = matrix(rep(0, total_days*opt$replications), ncol=opt$replications);
+        F2_previttelogenic_adults.replications = matrix(rep(0, total_days*opt$replications), ncol=opt$replications);
+    }
+    if (process_vittelogenic_adults) {
+        P_vittelogenic_adults.replications = matrix(rep(0, total_days*opt$replications), ncol=opt$replications);
+        F1_vittelogenic_adults.replications = matrix(rep(0, total_days*opt$replications), ncol=opt$replications);
+        F2_vittelogenic_adults.replications = matrix(rep(0, total_days*opt$replications), ncol=opt$replications);
+    }
+    if (process_diapausing_adults) {
+        P_diapausing_adults.replications = matrix(rep(0, total_days*opt$replications), ncol=opt$replications);
+        F1_diapausing_adults.replications = matrix(rep(0, total_days*opt$replications), ncol=opt$replications);
+        F2_diapausing_adults.replications = matrix(rep(0, total_days*opt$replications), ncol=opt$replications);
+    }
+    if (process_total_adults) {
+        P_total_adults.replications = matrix(rep(0, total_days*opt$replications), ncol=opt$replications);
+        F1_total_adults.replications = matrix(rep(0, total_days*opt$replications), ncol=opt$replications);
+        F2_total_adults.replications = matrix(rep(0, total_days*opt$replications), ncol=opt$replications);
+    }
+}
+# Total population.
+population.replications = matrix(rep(0, total_days*opt$replications), ncol=opt$replications);
 
 # Process replications.
-for (N.replications in 1:opt$replications) {
+for (current_replication in 1:opt$replications) {
     # Start with the user-defined number of insects per replication.
     num_insects = opt$insects_per_replication;
     # Generation, Stage, degree-days, T, Diapause.
     vector.ini = c(0, 3, 0, 0, 0);
-    # Overwintering, previttelogenic, degree-days=0, T=0, no-diapause.
+    # Replicate to create a matrix where the columns are
+    # Generation, Stage, degree-days, T, Diapause and the
+    # rows are the initial number of insects per replication.
     vector.matrix = rep(vector.ini, num_insects);
-    # Complete matrix for the population.
+    # Complete transposed matrix for the population, so now
+    # the rows are Generation, Stage, degree-days, T, Diapause
     vector.matrix = base::t(matrix(vector.matrix, nrow=5));
     # Time series of population size.
-    Eggs = rep(0, opt$num_days);
-    YoungNymphs = rep(0, opt$num_days);
-    OldNymphs = rep(0, opt$num_days);
-    Previtellogenic = rep(0, opt$num_days);
-    Vitellogenic = rep(0, opt$num_days);
-    Diapausing = rep(0, opt$num_days);
-
-    N.newborn = rep(0, opt$num_days);
-    N.adult = rep(0, opt$num_days);
-    N.death = rep(0, opt$num_days);
-
-    overwintering_adult.population = rep(0, opt$num_days);
-    first_generation.population = rep(0, opt$num_days);
-    second_generation.population = rep(0, opt$num_days);
-
-    P.adult = rep(0, opt$num_days);
-    F1.adult = rep(0, opt$num_days);
-    F2.adult = rep(0, opt$num_days);
-
+    if (process_eggs) {
+        Eggs = rep(0, total_days);
+    }
+    if (process_young_nymphs | process_total_nymphs) {
+        YoungNymphs = rep(0, total_days);
+    }
+    if (process_old_nymphs | process_total_nymphs) {
+        OldNymphs = rep(0, total_days);
+    }
+    if (process_previttelogenic_adults | process_total_adults) {
+        Previttelogenic = rep(0, total_days);
+    }
+    if (process_vittelogenic_adults | process_total_adults) {
+        Vittelogenic = rep(0, total_days);
+    }
+    if (process_diapausing_adults | process_total_adults) {
+        Diapausing = rep(0, total_days);
+    }
+    N.newborn = rep(0, total_days);
+    N.adult = rep(0, total_days);
+    N.death = rep(0, total_days);
+    overwintering_adult.population = rep(0, total_days);
+    first_generation.population = rep(0, total_days);
+    second_generation.population = rep(0, total_days);
+    if (plot_generations_separately) {
+        # P is Parental, or overwintered adults.
+        # F1 is the first field-produced generation.
+        # F2 is the second field-produced generation.
+        if (process_eggs) {
+            P.egg = rep(0, total_days);
+            F1.egg = rep(0, total_days);
+            F2.egg = rep(0, total_days);
+        }
+        if (process_young_nymphs) {
+            P.young_nymph = rep(0, total_days);
+            F1.young_nymph = rep(0, total_days);
+            F2.young_nymph = rep(0, total_days);
+        }
+        if (process_old_nymphs) {
+            P.old_nymph = rep(0, total_days);
+            F1.old_nymph = rep(0, total_days);
+            F2.old_nymph = rep(0, total_days);
+        }
+        if (process_total_nymphs) {
+            P.total_nymph = rep(0, total_days);
+            F1.total_nymph = rep(0, total_days);
+            F2.total_nymph = rep(0, total_days);
+        }
+        if (process_previttelogenic_adults) {
+            P.previttelogenic_adult = rep(0, total_days);
+            F1.previttelogenic_adult = rep(0, total_days);
+            F2.previttelogenic_adult = rep(0, total_days);
+        }
+        if (process_vittelogenic_adults) {
+            P.vittelogenic_adult = rep(0, total_days);
+            F1.vittelogenic_adult = rep(0, total_days);
+            F2.vittelogenic_adult = rep(0, total_days);
+        }
+        if (process_diapausing_adults) {
+            P.diapausing_adult = rep(0, total_days);
+            F1.diapausing_adult = rep(0, total_days);
+            F2.diapausing_adult = rep(0, total_days);
+        }
+        if (process_total_adults) {
+            P.total_adult = rep(0, total_days);
+            F1.total_adult = rep(0, total_days);
+            F2.total_adult = rep(0, total_days);
+        }
+    }
     total.population = NULL;
-
-    averages.day = rep(0, opt$num_days);
-    # All the days included in the input temperature dataset.
-    for (row in 1:opt$num_days) {
+    averages.day = rep(0, total_days);
+    # All the days included in the input_ytd temperature dataset.
+    for (row in 1:total_days) {
         # Get the integer day of the year for the current row.
         doy = temperature_data_frame$DOY[row];
         # Photoperiod in the day.
         photoperiod = temperature_data_frame$DAYLEN[row];
-        temp.profile = get_temperature_at_hour(latitude, temperature_data_frame, row, opt$num_days);
+        temp.profile = get_temperature_at_hour(latitude, temperature_data_frame, row, total_days);
         mean.temp = temp.profile[1];
         averages.temp = temp.profile[2];
         averages.day[row] = averages.temp;
@@ -341,6 +804,7 @@
                 death.probability = opt$egg_mortality * mortality.egg(mean.temp);
             }
             else if (vector.individual[2] == 1 | vector.individual[2] == 2) {
+                # Nymph.
                 death.probability = opt$nymph_mortality * mortality.nymph(mean.temp);
             }
             else if (vector.individual[2] == 3 | vector.individual[2] == 4 | vector.individual[2] == 5) {
@@ -361,7 +825,7 @@
             else {
                 # End of diapause.
                 if (vector.individual[1] == 0 && vector.individual[2] == 3) {
-                    # Overwintering adult (previttelogenic).
+                    # Overwintering adult (pre-vittelogenic).
                     if (photoperiod > opt$photoperiod && vector.individual[3] > 68 && doy < 180) {
                         # Add 68C to become fully reproductively matured.
                         # Transfer to vittelogenic.
@@ -369,7 +833,7 @@
                         vector.matrix[i,] = vector.individual;
                     }
                     else {
-                        # Add to # Add average temperature for current day.
+                        # Add average temperature for current day.
                         vector.individual[3] = vector.individual[3] + averages.temp;
                         # Add 1 day in current stage.
                         vector.individual[4] = vector.individual[4] + 1;
@@ -377,7 +841,7 @@
                     }
                 }
                 if (vector.individual[1] != 0 && vector.individual[2] == 3) {
-                    # Not overwintering adult (previttelogenic).
+                    # Not overwintering adult (pre-vittelogenic).
                     current.gen = vector.individual[1];
                     if (vector.individual[3] > 68) {
                         # Add 68C to become fully reproductively matured.
@@ -492,7 +956,7 @@
                     }
                     vector.matrix[i,] = vector.individual;
                 }
-                # Old nymph to adult: previttelogenic or diapausing?
+                # Old nymph to adult: pre-vittelogenic or diapausing?
                 if (vector.individual[2] == 2) {
                     # Add average temperature for current day.
                     vector.individual[3] = vector.individual[3] + averages.temp;
@@ -535,19 +999,33 @@
         # Update population size for the next day.
         num_insects = num_insects - num_insects.death + num_insects.newborn;
 
-        # Aggregate results by day.
-        # Egg population size.
-        Eggs[row] = sum(vector.matrix[,2]==0);
-        # Young nymph population size.
-        YoungNymphs[row] = sum(vector.matrix[,2]==1);
-        # Old nymph population size.
-        OldNymphs[row] = sum(vector.matrix[,2]==2);
-        # Previtellogenic population size.
-        Previtellogenic[row] = sum(vector.matrix[,2]==3);
-        # Vitellogenic population size.
-        Vitellogenic[row] = sum(vector.matrix[,2]==4);
-        # Diapausing population size.
-        Diapausing[row] = sum(vector.matrix[,2]==5);
+        # Aggregate results by day.  Due to multiple transpose calls
+        # on vector.matrix above, the columns of vector.matrix
+        # are now Generation, Stage, degree-days, T, Diapause,
+        if (process_eggs) {
+            # For egg population size, column 2 (Stage), must be 0.
+            Eggs[row] = sum(vector.matrix[,2]==0);
+        }
+        if (process_young_nymphs | process_total_nymphs) {
+            # For young nymph population size, column 2 (Stage) must be 1.
+            YoungNymphs[row] = sum(vector.matrix[,2]==1);
+        }
+        if (process_old_nymphs | process_total_nymphs) {
+            # For old nymph population size, column 2 (Stage) must be 2.
+            OldNymphs[row] = sum(vector.matrix[,2]==2);
+        }
+        if (process_previttelogenic_adults | process_total_adults) {
+            # For pre-vittelogenic population size, column 2 (Stage) must be 3.
+            Previttelogenic[row] = sum(vector.matrix[,2]==3);
+        }
+        if (process_vittelogenic_adults | process_total_adults) {
+            # For vittelogenic population size, column 2 (Stage) must be 4.
+            Vittelogenic[row] = sum(vector.matrix[,2]==4);
+        }
+        if (process_diapausing_adults | process_total_adults) {
+            # For diapausing population size, column 2 (Stage) must be 5.
+            Diapausing[row] = sum(vector.matrix[,2]==5);
+        }
 
         # Newborn population size.
         N.newborn[row] = num_insects.newborn;
@@ -558,117 +1036,637 @@
 
         total.population = c(total.population, num_insects);
 
-        # Overwintering adult population size.
+        # For overwintering adult (P) population
+        # size, column 1 (Generation) must be 0.
         overwintering_adult.population[row] = sum(vector.matrix[,1]==0);
-        # First generation population size.
+        # For first field generation (F1) population
+        # size, column 1 (Generation) must be 1.
         first_generation.population[row] = sum(vector.matrix[,1]==1);
-        # Second generation population size.
+        # For second field generation (F2) population
+        # size, column 1 (Generation) must be 2.
         second_generation.population[row] = sum(vector.matrix[,1]==2);
 
-        # P adult population size.
-        P.adult[row] = sum(vector.matrix[,1]==0);
-        # F1 adult population size.
-        F1.adult[row] = sum((vector.matrix[,1]==1 & vector.matrix[,2]==3) | (vector.matrix[,1]==1 & vector.matrix[,2]==4) | (vector.matrix[,1]==1 & vector.matrix[,2]==5));
-        # F2 adult population size
-        F2.adult[row] = sum((vector.matrix[,1]==2 & vector.matrix[,2]==3) | (vector.matrix[,1]==2 & vector.matrix[,2]==4) | (vector.matrix[,1]==2 & vector.matrix[,2]==5));
-    }   # End of days specified in the input temperature data.
+        if (plot_generations_separately) {
+            if (process_eggs) {
+                # For egg life stage of generation P population size,
+                # column 1 (generation) is 0 and column 2 (Stage) is 0.
+                P.egg[row] = sum(vector.matrix[,1]==0 & vector.matrix[,2]==0);
+                # For egg life stage of generation F1 population size,
+                # column 1 (generation) is 1 and column 2 (Stage) is 0.
+                F1.egg[row] = sum(vector.matrix[,1]==1 & vector.matrix[,2]==0);
+                # For egg life stage of generation F2 population size,
+                # column 1 (generation) is 2 and column 2 (Stage) is 0.
+                F2.egg[row] = sum(vector.matrix[,1]==2 & vector.matrix[,2]==0);
+            }
+            if (process_young_nymphs) {
+                # For young nymph life stage of generation P population
+                # size, the following combination is required:
+                # - column 1 (Generation) is 0 and column 2 (Stage) is 1 (Young nymph)
+                P.young_nymph[row] = sum(vector.matrix[,1]==0 & vector.matrix[,2]==1);
+                # For young nymph life stage of generation F1 population
+                # size, the following combination is required:
+                # - column 1 (Generation) is 1 and column 2 (Stage) is 1 (Young nymph)
+                F1.young_nymph[row] = sum(vector.matrix[,1]==1 & vector.matrix[,2]==1);
+                # For young nymph life stage of generation F2 population
+                # size, the following combination is required:
+                # - column 1 (Generation) is 2 and column 2 (Stage) is 1 (Young nymph)
+                F2.young_nymph[row] = sum(vector.matrix[,1]==2 & vector.matrix[,2]==1);
+            }
+            if (process_old_nymphs) {
+                # For old nymph life stage of generation P population
+                # size, the following combination is required:
+                # - column 1 (Generation) is 0 and column 2 (Stage) is 2 (Old nymph)
+                P.old_nymph[row] = sum(vector.matrix[,1]==0 & vector.matrix[,2]==2);
+                # For old nymph life stage of generation F1 population
+                # size, the following combination is required:
+                # - column 1 (Generation) is 1 and column 2 (Stage) is 2 (Old nymph)
+                F1.old_nymph[row] = sum(vector.matrix[,1]==1 & vector.matrix[,2]==2);
+                # For old nymph life stage of generation F2 population
+                # size, the following combination is required:
+                # - column 1 (Generation) is 2 and column 2 (Stage) is 2 (Old nymph)
+                F2.old_nymph[row] = sum(vector.matrix[,1]==2 & vector.matrix[,2]==2);
+            }
+            if (process_total_nymphs) {
+                # For total nymph life stage of generation P population
+                # size, one of the following combinations is required:
+                # - column 1 (Generation) is 0 and column 2 (Stage) is 1 (Young nymph)
+                # - column 1 (Generation) is 0 and column 2 (Stage) is 2 (Old nymph)
+                P.total_nymph[row] = sum((vector.matrix[,1]==0 & vector.matrix[,2]==1) | (vector.matrix[,1]==0 & vector.matrix[,2]==2));
+                # For total nymph life stage of generation F1 population
+                # size, one of the following combinations is required:
+                # - column 1 (Generation) is 1 and column 2 (Stage) is 1 (Young nymph)
+                # - column 1 (Generation) is 1 and column 2 (Stage) is 2 (Old nymph)
+                F1.total_nymph[row] = sum((vector.matrix[,1]==1 & vector.matrix[,2]==1) | (vector.matrix[,1]==1 & vector.matrix[,2]==2));
+                # For total nymph life stage of generation F2 population
+                # size, one of the following combinations is required:
+                # - column 1 (Generation) is 2 and column 2 (Stage) is 1 (Young nymph)
+                # - column 1 (Generation) is 2 and column 2 (Stage) is 2 (Old nymph)
+                F2.total_nymph[row] = sum((vector.matrix[,1]==2 & vector.matrix[,2]==1) | (vector.matrix[,1]==2 & vector.matrix[,2]==2));
+            }
+            if (process_previttelogenic_adults) {
+                # For previttelogenic adult life stage of generation P population
+                # size, the following combination is required:
+                # - column 1 (Generation) is 0 and column 2 (Stage) is 3 (Pre-vittelogenic)
+                P.previttelogenic_adult[row] = sum(vector.matrix[,1]==0 & vector.matrix[,2]==3);
+                # For previttelogenic adult life stage of generation F1 population
+                # size, the following combination is required:
+                # - column 1 (Generation) is 1 and column 2 (Stage) is 3 (Pre-vittelogenic)
+                F1.previttelogenic_adult[row] = sum(vector.matrix[,1]==1 & vector.matrix[,2]==3);
+                # For previttelogenic adult life stage of generation F2 population
+                # size, the following combination is required:
+                # - column 1 (Generation) is 2 and column 2 (Stage) is 3 (Pre-vittelogenic)
+                F2.previttelogenic_adult[row] = sum(vector.matrix[,1]==2 & vector.matrix[,2]==3);
+            }
+            if (process_vittelogenic_adults) {
+                # For vittelogenic adult life stage of generation P population
+                # size, the following combination is required:
+                # - column 1 (Generation) is 0 and column 2 (Stage) is 4 (Vittelogenic)
+                P.vittelogenic_adult[row] = sum(vector.matrix[,1]==0 & vector.matrix[,2]==4);
+                # For vittelogenic adult life stage of generation F1 population
+                # size, the following combination is required:
+                # - column 1 (Generation) is 1 and column 2 (Stage) is 4 (Vittelogenic)
+                F1.vittelogenic_adult[row] = sum(vector.matrix[,1]==1 & vector.matrix[,2]==4);
+                # For vittelogenic adult life stage of generation F2 population
+                # size, the following combination is required:
+                # - column 1 (Generation) is 2 and column 2 (Stage) is 4 (Vittelogenic)
+                F2.vittelogenic_adult[row] = sum(vector.matrix[,1]==2 & vector.matrix[,2]==4);
+            }
+            if (process_diapausing_adults) {
+                # For diapausing adult life stage of generation P population
+                # size, the following combination is required:
+                # - column 1 (Generation) is 0 and column 2 (Stage) is 5 (Diapausing)
+                P.diapausing_adult[row] = sum(vector.matrix[,1]==0 & vector.matrix[,2]==5);
+                # For diapausing adult life stage of generation F1 population
+                # size, the following combination is required:
+                # - column 1 (Generation) is 1 and column 2 (Stage) is 5 (Diapausing)
+                F1.diapausing_adult[row] = sum(vector.matrix[,1]==1 & vector.matrix[,2]==5);
+                # For diapausing adult life stage of generation F2 population
+                # size, the following combination is required:
+                # - column 1 (Generation) is 2 and column 2 (Stage) is 5 (Diapausing)
+                F2.diapausing_adult[row] = sum(vector.matrix[,1]==2 & vector.matrix[,2]==5);
+            }
+            if (process_total_adults) {
+                # For total adult life stage of generation P population
+                # size, one of the following combinations is required:
+                # - column 1 (Generation) is 0 and column 2 (Stage) is 3 (Pre-vittelogenic)
+                # - column 1 (Generation) is 0 and column 2 (Stage) is 4 (Vittelogenic)
+                # - column 1 (Generation) is 0 and column 2 (Stage) is 5 (Diapausing)
+                P.total_adult[row] = sum((vector.matrix[,1]==0 & vector.matrix[,2]==3) | (vector.matrix[,1]==0 & vector.matrix[,2]==4) | (vector.matrix[,1]==0 & vector.matrix[,2]==5));
+                # For total adult life stage of generation F1 population
+                # size, one of the following combinations is required:
+                # - column 1 (Generation) is 1 and column 2 (Stage) is 3 (Pre-vittelogenic)
+                # - column 1 (Generation) is 1 and column 2 (Stage) is 4 (Vittelogenic)
+                # - column 1 (Generation) is 1 and column 2 (Stage) is 5 (Diapausing)
+                F1.total_adult[row] = sum((vector.matrix[,1]==1 & vector.matrix[,2]==3) | (vector.matrix[,1]==1 & vector.matrix[,2]==4) | (vector.matrix[,1]==1 & vector.matrix[,2]==5));
+                # For total adult life stage of generation F2 population
+                # size, one of the following combinations is required:
+                # - column 1 (Generation) is 2 and column 2 (Stage) is 3 (Pre-vittelogenic)
+                # - column 1 (Generation) is 2 and column 2 (Stage) is 4 (Vittelogenic)
+                # - column 1 (Generation) is 2 and column 2 (Stage) is 5 (Diapausing)
+                F2.total_adult[row] = sum((vector.matrix[,1]==2 & vector.matrix[,2]==3) | (vector.matrix[,1]==2 & vector.matrix[,2]==4) | (vector.matrix[,1]==2 & vector.matrix[,2]==5));
+            }
+        }
+    }   # End of days specified in the input_ytd temperature data.
 
     averages.cum = cumsum(averages.day);
 
     # Define the output values.
-    Eggs.replications[,N.replications] = Eggs;
-    YoungNymphs.replications[,N.replications] = YoungNymphs;
-    OldNymphs.replications[,N.replications] = OldNymphs;
-    Previtellogenic.replications[,N.replications] = Previtellogenic;
-    Vitellogenic.replications[,N.replications] = Vitellogenic;
-    Diapausing.replications[,N.replications] = Diapausing;
+    if (process_eggs) {
+        Eggs.replications[,current_replication] = Eggs;
+    }
+    if (process_young_nymphs | process_total_nymphs) {
+        YoungNymphs.replications[,current_replication] = YoungNymphs;
+    }
+    if (process_old_nymphs | process_total_nymphs) {
+        OldNymphs.replications[,current_replication] = OldNymphs;
+    }
+    if (process_previttelogenic_adults | process_total_adults) {
+        Previttelogenic.replications[,current_replication] = Previttelogenic;
+    }
+    if (process_vittelogenic_adults | process_total_adults) {
+        Vittelogenic.replications[,current_replication] = Vittelogenic;
+    }
+    if (process_diapausing_adults | process_total_adults) {
+        Diapausing.replications[,current_replication] = Diapausing;
+    }
+    newborn.replications[,current_replication] = N.newborn;
+    adult.replications[,current_replication] = N.adult;
+    death.replications[,current_replication] = N.death;
+    if (plot_generations_separately) {
+        # P is Parental, or overwintered adults.
+        P.replications[,current_replication] = overwintering_adult.population;
+        # F1 is the first field-produced generation.
+        F1.replications[,current_replication] = first_generation.population;
+        # F2 is the second field-produced generation.
+        F2.replications[,current_replication] = second_generation.population;
+        if (process_eggs) {
+            P_eggs.replications[,current_replication] = P.egg;
+            F1_eggs.replications[,current_replication] = F1.egg;
+            F2_eggs.replications[,current_replication] = F2.egg;
+        }
+        if (process_young_nymphs) {
+            P_young_nymphs.replications[,current_replication] = P.young_nymph;
+            F1_young_nymphs.replications[,current_replication] = F1.young_nymph;
+            F2_young_nymphs.replications[,current_replication] = F2.young_nymph;
+        }
+        if (process_old_nymphs) {
+            P_old_nymphs.replications[,current_replication] = P.old_nymph;
+            F1_old_nymphs.replications[,current_replication] = F1.old_nymph;
+            F2_old_nymphs.replications[,current_replication] = F2.old_nymph;
+        }
+        if (process_total_nymphs) {
+            P_total_nymphs.replications[,current_replication] = P.total_nymph;
+            F1_total_nymphs.replications[,current_replication] = F1.total_nymph;
+            F2_total_nymphs.replications[,current_replication] = F2.total_nymph;
+        }
+        if (process_previttelogenic_adults) {
+            P_previttelogenic_adults.replications[,current_replication] = P.previttelogenic_adult;
+            F1_previttelogenic_adults.replications[,current_replication] = F1.previttelogenic_adult;
+            F2_previttelogenic_adults.replications[,current_replication] = F2.previttelogenic_adult;
+        }
+        if (process_vittelogenic_adults) {
+            P_vittelogenic_adults.replications[,current_replication] = P.vittelogenic_adult;
+            F1_vittelogenic_adults.replications[,current_replication] = F1.vittelogenic_adult;
+            F2_vittelogenic_adults.replications[,current_replication] = F2.vittelogenic_adult;
+        }
+        if (process_diapausing_adults) {
+            P_diapausing_adults.replications[,current_replication] = P.diapausing_adult;
+            F1_diapausing_adults.replications[,current_replication] = F1.diapausing_adult;
+            F2_diapausing_adults.replications[,current_replication] = F2.diapausing_adult;
+        }
+        if (process_total_adults) {
+            P_total_adults.replications[,current_replication] = P.total_adult;
+            F1_total_adults.replications[,current_replication] = F1.total_adult;
+            F2_total_adults.replications[,current_replication] = F2.total_adult;
+        }
+    }
+    population.replications[,current_replication] = total.population;
+    # End processing replications.
+}
 
-    newborn.replications[,N.replications] = N.newborn;
-    adult.replications[,N.replications] = N.adult;
-    death.replications[,N.replications] = N.death;
-
-    P.replications[,N.replications] = overwintering_adult.population;
-    P_adults.replications[,N.replications] = P.adult;
-    F1.replications[,N.replications] = first_generation.population;
-    F1_adults.replications[,N.replications] = F1.adult;
-    F2.replications[,N.replications] = second_generation.population;
-    F2_adults.replications[,N.replications] = F2.adult;
-
-    population.replications[,N.replications] = total.population;
+if (process_eggs) {
+    # Mean value for eggs.
+    eggs = apply(Eggs.replications, 1, mean);
+    temperature_data_frame = append_vector(temperature_data_frame, eggs, "EGG");
+    # Standard error for eggs.
+    eggs.std_error = apply(Eggs.replications, 1, sd) / sqrt(opt$replications);
+    temperature_data_frame = append_vector(temperature_data_frame, eggs.std_error, "EGGSE");
+}
+if (process_nymphs) {
+    # Calculate nymph populations for selected life stage.
+    for (life_stage_nymph in life_stages_nymph) {
+        if (life_stage_nymph=="Young") {
+            # Mean value for young nymphs.
+            young_nymphs = apply(YoungNymphs.replications, 1, mean);
+            temperature_data_frame = append_vector(temperature_data_frame, young_nymphs, "YOUNGNYMPH");
+            # Standard error for young nymphs.
+            young_nymphs.std_error = apply(YoungNymphs.replications / sqrt(opt$replications), 1, sd);
+            temperature_data_frame = append_vector(temperature_data_frame, young_nymphs.std_error, "YOUNGNYMPHSE");
+        } else if (life_stage_nymph=="Old") {
+            # Mean value for old nymphs.
+            old_nymphs = apply(OldNymphs.replications, 1, mean);
+            temperature_data_frame = append_vector(temperature_data_frame, old_nymphs, "OLDNYMPH");
+            # Standard error for old nymphs.
+            old_nymphs.std_error = apply(OldNymphs.replications / sqrt(opt$replications), 1, sd);
+            temperature_data_frame = append_vector(temperature_data_frame, old_nymphs.std_error, "OLDNYMPHSE");
+        } else if (life_stage_nymph=="Total") {
+            # Mean value for all nymphs.
+            total_nymphs = apply((YoungNymphs.replications+OldNymphs.replications), 1, mean);
+            temperature_data_frame = append_vector(temperature_data_frame, total_nymphs, "TOTALNYMPH");
+            # Standard error for all nymphs.
+            total_nymphs.std_error = apply((YoungNymphs.replications+OldNymphs.replications) / sqrt(opt$replications), 1, sd);
+            temperature_data_frame = append_vector(temperature_data_frame, total_nymphs.std_error, "TOTALNYMPHSE");
+        }
+    }
+}
+if (process_adults) {
+    # Calculate adult populations for selected life stage.
+    for (life_stage_adult in life_stages_adult) {
+        if (life_stage_adult == "Pre-vittelogenic") {
+            # Mean value for previttelogenic adults.
+            previttelogenic_adults = apply(Previttelogenic.replications, 1, mean);
+            temperature_data_frame = append_vector(temperature_data_frame, previttelogenic_adults, "PRE-VITADULT");
+            # Standard error for previttelogenic adults.
+            previttelogenic_adults.std_error = apply(Previttelogenic.replications, 1, sd) / sqrt(opt$replications);
+            temperature_data_frame = append_vector(temperature_data_frame, previttelogenic_adults.std_error, "PRE-VITADULTSE");
+        } else if (life_stage_adult == "Vittelogenic") {
+            # Mean value for vittelogenic adults.
+            vittelogenic_adults = apply(Vittelogenic.replications, 1, mean);
+            temperature_data_frame = append_vector(temperature_data_frame, vittelogenic_adults, "VITADULT");
+            # Standard error for vittelogenic adults.
+            vittelogenic_adults.std_error = apply(Vittelogenic.replications, 1, sd) / sqrt(opt$replications);
+            temperature_data_frame = append_vector(temperature_data_frame, vittelogenic_adults.std_error, "VITADULTSE");
+        } else if (life_stage_adult == "Diapausing") {
+            # Mean value for vittelogenic adults.
+            diapausing_adults = apply(Diapausing.replications, 1, mean);
+            temperature_data_frame = append_vector(temperature_data_frame, diapausing_adults, "DIAPAUSINGADULT");
+            # Standard error for vittelogenic adults.
+            diapausing_adults.std_error = apply(Diapausing.replications, 1, sd) / sqrt(opt$replications);
+            temperature_data_frame = append_vector(temperature_data_frame, diapausing_adults.std_error, "DIAPAUSINGADULTSE");
+        } else if (life_stage_adult=="Total") {
+            # Mean value for all adults.
+            total_adults = apply((Previttelogenic.replications+Vittelogenic.replications+Diapausing.replications), 1, mean);
+            temperature_data_frame = append_vector(temperature_data_frame, total_adults, "TOTALADULT");
+            # Standard error for all adults.
+            total_adults.std_error = apply((Previttelogenic.replications+Vittelogenic.replications+Diapausing.replications), 1, sd) / sqrt(opt$replications);
+            temperature_data_frame = append_vector(temperature_data_frame, total_adults.std_error, "TOTALADULTSE");
+        }
+    }
 }
 
-# Mean value for eggs.
-eggs = apply(Eggs.replications, 1, mean);
-# Standard error for eggs.
-eggs.std_error = apply(Eggs.replications, 1, sd) / sqrt(opt$replications);
-
-# Mean value for nymphs.
-nymphs = apply((YoungNymphs.replications+OldNymphs.replications), 1, mean);
-# Standard error for nymphs.
-nymphs.std_error = apply((YoungNymphs.replications+OldNymphs.replications) / sqrt(opt$replications), 1, sd);
-
-# Mean value for adults.
-adults = apply((Previtellogenic.replications+Vitellogenic.replications+Diapausing.replications), 1, mean);
-# Standard error for adults.
-adults.std_error = apply((Previtellogenic.replications+Vitellogenic.replications+Diapausing.replications), 1, sd) / sqrt(opt$replications);
+if (plot_generations_separately) {
+    m_se = get_mean_and_std_error(P.replications, F1.replications, F2.replications);
+    P = m_se[[1]];
+    P.std_error = m_se[[2]];
+    F1 = m_se[[3]];
+    F1.std_error = m_se[[4]];
+    F2 = m_se[[5]];
+    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");
+    }
+}
 
-# Mean value for P.
-P = apply(P.replications, 1, mean);
-# Standard error for P.
-P.std_error = apply(P.replications, 1, sd) / sqrt(opt$replications);
-
-# Mean value for P adults.
-P_adults = apply(P_adults.replications, 1, mean);
-# Standard error for P_adult.
-P_adults.std_error = apply(P_adults.replications, 1, sd) / sqrt(opt$replications);
-
-# Mean value for F1.
-F1 = apply(F1.replications, 1, mean);
-# Standard error for F1.
-F1.std_error = apply(F1.replications, 1, sd) / sqrt(opt$replications);
-
-# Mean value for F1 adults.
-F1_adults = apply(F1_adults.replications, 1, mean);
-# Standard error for F1 adult.
-F1_adults.std_error = apply(F1_adults.replications, 1, sd) / sqrt(opt$replications);
+# 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);
+}
 
-# Mean value for F2.
-F2 = apply(F2.replications, 1, mean);
-# Standard error for F2.
-F2.std_error = apply(F2.replications, 1, sd) / sqrt(opt$replications);
-
-# Mean value for F2 adults.
-F2_adults = apply(F2_adults.replications, 1, mean);
-# Standard error for F2 adult.
-F2_adults.std_error = apply(F2_adults.replications, 1, sd) / sqrt(opt$replications);
-
-# Display the total number of days in the Galaxy history item blurb.
-cat("Number of days: ", opt$num_days, "\n");
-
-dev.new(width=20, height=30);
-
-# Start PDF device driver to save charts to output.
-pdf(file=opt$output, width=20, height=30, bg="white");
-par(mar=c(5, 6, 4, 4), mfrow=c(3, 1));
-
-# Data analysis and visualization plots only within a single calendar year.
-days = c(1:opt$num_days);
-start_date = temperature_data_frame$DATE[1];
-end_date = temperature_data_frame$DATE[opt$num_days];
-
-# Subfigure 1: population size by life stage.
-maxval = max(eggs+eggs.std_error, nymphs+nymphs.std_error, adults+adults.std_error);
-render_chart("pop_size_by_life_stage", opt$insect, opt$location, latitude, start_date, end_date, days, maxval,
-             opt$std_error_plot, adults, nymphs, eggs, adults.std_error, nymphs.std_error, eggs.std_error, date_labels);
-# Subfigure 2: population size by generation.
-maxval = max(F2);
-render_chart("pop_size_by_generation", opt$insect, opt$location, latitude, start_date, end_date, days, maxval,
-             opt$std_error_plot, P, F1, F2, P.std_error, F1.std_error, F2.std_error, date_labels);
-# Subfigure 3: adult population size by generation.
-maxval = max(F2_adults) + 100;
-render_chart("adult_pop_size_by_generation", opt$insect, opt$location, latitude, start_date, end_date, days, maxval,
-             opt$std_error_plot, P_adults, F1_adults, F2_adults, P_adults.std_error, F1_adults.std_error, F2_adults.std_error,
-             date_labels);
-
-# Turn off device driver to flush output.
-dev.off();
+if (plot_generations_separately) {
+    for (life_stage in life_stages) {
+        if (life_stage == "Egg") {
+            # Start PDF device driver.
+            dev.new(width=20, height=30);
+            file_path = get_file_path(life_stage, "egg_pop_by_generation.pdf")
+            pdf(file=file_path, width=20, height=30, bg="white");
+            par(mar=c(5, 6, 4, 4), mfrow=c(3, 1));
+            # Egg population size by generation.
+            maxval = max(P_eggs+F1_eggs+F2_eggs) + 100;
+            render_chart(ticks, date_labels, "pop_size_by_generation", opt$plot_std_error, opt$insect, location, latitude,
+                start_date, end_date, total_days_vector, maxval, opt$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") {
+            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));
+                if (life_stage_nymph=="Young") {
+                    # Young nymph population size by generation.
+                    maxval = max(P_young_nymphs+F1_young_nymphs+F2_young_nymphs) + 100;
+                    group = P_young_nymphs;
+                    group_std_error = P_young_nymphs.std_error;
+                    group2 = F1_young_nymphs;
+                    group2_std_error = F1_young_nymphs.std_error;
+                    group3 = F2_young_nymphs;
+                    group3_std_error = F2_young_nymphs.std_error;
+                } else if (life_stage_nymph=="Old") {
+                    # Total nymph population size by generation.
+                    maxval = max(P_old_nymphs+F1_old_nymphs+F2_old_nymphs) + 100;
+                    group = P_old_nymphs;
+                    group_std_error = P_old_nymphs.std_error;
+                    group2 = F1_old_nymphs;
+                    group2_std_error = F1_old_nymphs.std_error;
+                    group3 = F2_old_nymphs;
+                    group3_std_error = F2_old_nymphs.std_error;
+                } else if (life_stage_nymph=="Total") {
+                    # Total nymph population size by generation.
+                    maxval = max(P_total_nymphs+F1_total_nymphs+F2_total_nymphs) + 100;
+                    group = P_total_nymphs;
+                    group_std_error = P_total_nymphs.std_error;
+                    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, location, latitude,
+                    start_date, end_date, total_days_vector, 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();
+            }
+        } 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));
+                if (life_stage_adult=="Pre-vittelogenic") {
+                    # Pre-vittelogenic adult population size by generation.
+                    maxval = max(P_previttelogenic_adults+F1_previttelogenic_adults+F2_previttelogenic_adults) + 100;
+                    group = P_previttelogenic_adults;
+                    group_std_error = P_previttelogenic_adults.std_error;
+                    group2 = F1_previttelogenic_adults;
+                    group2_std_error = F1_previttelogenic_adults.std_error;
+                    group3 = F2_previttelogenic_adults;
+                    group3_std_error = F2_previttelogenic_adults.std_error;
+                } else if (life_stage_adult=="Vittelogenic") {
+                    # Vittelogenic adult population size by generation.
+                    maxval = max(P_vittelogenic_adults+F1_vittelogenic_adults+F2_vittelogenic_adults) + 100;
+                    group = P_vittelogenic_adults;
+                    group_std_error = P_vittelogenic_adults.std_error;
+                    group2 = F1_vittelogenic_adults;
+                    group2_std_error = F1_vittelogenic_adults.std_error;
+                    group3 = F2_vittelogenic_adults;
+                    group3_std_error = F2_vittelogenic_adults.std_error;
+                } else if (life_stage_adult=="Diapausing") {
+                    # Diapausing adult population size by generation.
+                    maxval = max(P_diapausing_adults+F1_diapausing_adults+F2_diapausing_adults) + 100;
+                    group = P_diapausing_adults;
+                    group_std_error = P_diapausing_adults.std_error;
+                    group2 = F1_diapausing_adults;
+                    group2_std_error = F1_diapausing_adults.std_error;
+                    group3 = F2_diapausing_adults;
+                    group3_std_error = F2_diapausing_adults.std_error;
+                } else if (life_stage_adult=="Total") {
+                    # Total adult population size by generation.
+                    maxval = max(P_total_adults+F1_total_adults+F2_total_adults) + 100;
+                    group = P_total_adults;
+                    group_std_error = P_total_adults.std_error;
+                    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$insect, location, latitude,
+                    start_date, end_date, total_days_vector, maxval, opt$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();
+            }
+        } 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(ticks, date_labels, "pop_size_by_generation", opt$plot_std_error, opt$insect, location, latitude,
+                start_date, end_date, total_days_vector, maxval, opt$replications, life_stage, group=P, group_std_error=P.std_error,
+                group2=F1, group2_std_error=F1.std_error, group3=F2, group3_std_error=F2.std_error);
+            # Turn off device driver to flush output.
+            dev.off();
+        }
+    }
+} else {
+    for (life_stage in life_stages) {
+        if (life_stage == "Egg") {
+            # Start PDF device driver.
+            dev.new(width=20, height=30);
+            file_path = get_file_path(life_stage, "egg_pop.pdf")
+            pdf(file=file_path, width=20, height=30, bg="white");
+            par(mar=c(5, 6, 4, 4), mfrow=c(3, 1));
+            # Egg population size.
+            maxval = max(eggs+eggs.std_error) + 100;
+            render_chart(ticks, date_labels, "pop_size_by_life_stage", opt$plot_std_error, opt$insect, location, latitude,
+                start_date, end_date, total_days_vector, maxval, opt$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_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;
+                    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) + 100;
+                render_chart(ticks, date_labels, "pop_size_by_life_stage", opt$plot_std_error, opt$insect, location, latitude,
+                    start_date, end_date, total_days_vector, maxval, opt$replications, life_stage, group=group, group_std_error=group_std_error,
+                    life_stages_nymph=life_stage_nymph);
+                # Turn off device driver to flush output.
+                dev.off();
+            }
+        } else if (life_stage == "Adult") {
+            for (life_stage_adult in life_stages_adult) {
+                # Start PDF device driver.
+                dev.new(width=20, height=30);
+                file_path = get_file_path(life_stage, "adult_pop.pdf", life_stage_adult=life_stage_adult)
+                pdf(file=file_path, width=20, height=30, bg="white");
+                par(mar=c(5, 6, 4, 4), mfrow=c(3, 1));
+                if (life_stage_adult=="Total") {
+                    # Total adult population size.
+                    group = total_adults;
+                    group_std_error = total_adults.std_error
+                } else if (life_stage_adult=="Pre-vittelogenic") {
+                    # Pre-vittelogenic adult population size.
+                    group = previttelogenic_adults;
+                    group_std_error = previttelogenic_adults.std_error
+                } else if (life_stage_adult=="Vittelogenic") {
+                    # Vittelogenic adult population size.
+                    group = vittelogenic_adults;
+                    group_std_error = vittelogenic_adults.std_error
+                } else if (life_stage_adult=="Diapausing") {
+                    # Diapausing adult population size.
+                    group = diapausing_adults;
+                    group_std_error = diapausing_adults.std_error
+                }
+                maxval = max(group+group_std_error) + 100;
+                render_chart(ticks, date_labels, "pop_size_by_life_stage", opt$plot_std_error, opt$insect, location, latitude,
+                    start_date, end_date, total_days_vector, maxval, opt$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 = 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, location, latitude,
+                start_date, end_date, total_days_vector, 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();
+        }
+    }
+}
diff -r 37ac68b6ff10 -r bcb12b7e8563 insect_phenology_model.xml
--- a/insect_phenology_model.xml	Tue Feb 13 13:47:32 2018 -0500
+++ b/insect_phenology_model.xml	Tue May 29 09:00:25 2018 -0400
@@ -4,57 +4,229 @@
         <requirement type="package" version="1.4.4">r-optparse</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
+#import os
+#set output_data_dir = "output_data_dir"
+#set output_plots_dir = "output_plots_dir"
+#set error_file = $os.path.join($output_data_dir, "04_combined_generations.csv")
+#set life_stages = list()
+#set plot_adult_life_stage = $plot_adult_life_stage_cond.plot_adult_life_stage
+#set plot_nymph_life_stage = $plot_nymph_life_stage_cond.plot_nymph_life_stage
+#if str($plot_egg_life_stage) == "yes":
+    $life_stages.append("Egg")
+#end if
+#if str($plot_nymph_life_stage) == "yes":
+    $life_stages.append("Nymph")
+#end if
+#if str($plot_adult_life_stage) == "yes":
+    $life_stages.append("Adult")
+#end if
+#if str($plot_egg_life_stage) == "yes" and str($plot_nymph_life_stage) == "yes" and str($plot_adult_life_stage) == "yes":
+    $life_stages.append("Total")
+#end if
+#set life_stages = ",".join($life_stages)
+mkdir output_data_dir &&
+mkdir output_plots_dir &&
 Rscript '$__tool_directory__/insect_phenology_model.R'
 --adult_mortality $adult_mortality
 --adult_accumulation $adult_accumulation
 --egg_mortality $egg_mortality
---input '$input'
+#if str($merge_ytd_temperature_data_cond.merge_ytd_temperature_data) == "yes":
+    --input_ytd '$merge_ytd_temperature_data_cond.input_ytd'
+    --location '$merge_ytd_temperature_data_cond.location'
+    --num_days_ytd $merge_ytd_temperature_data_cond.input_ytd.metadata.data_lines
+#end if
+--input_norm '$input_norm'
 --insect '$insect'
 --insects_per_replication $insects_per_replication
---location '$location'
+--life_stages '$life_stages'
+#if str($plot_adult_life_stage) == "yes":
+    --life_stages_adult '$plot_adult_life_stage_cond.life_stages_adult'
+#end if
+#if str($plot_nymph_life_stage) == "yes":
+    --life_stages_nymph '$plot_nymph_life_stage_cond.life_stages_nymph'
+#end if
 --max_clutch_size $max_clutch_size
 --min_clutch_size $min_clutch_size
 --nymph_mortality $nymph_mortality
---num_days $input.metadata.data_lines
 --old_nymph_accumulation $old_nymph_accumulation
---output '$output'
 --oviposition $oviposition
 --photoperiod $photoperiod
 --replications $replications
---std_error_plot $std_error_plot
---young_nymph_accumulation $young_nymph_accumulation]]></command>
+--plot_generations_separately $plot_generations_separately
+--plot_std_error $plot_std_error
+--young_nymph_accumulation $young_nymph_accumulation
+&>ipm_log.txt;
+if [[ $? -ne 0 ]]; then
+    cp ipm_log.txt '$error_file';
+    exit 1;
+fi]]></command>
     <inputs>
-        <param name="input" type="data" format="csv" label="Temperature data" />
-        <param name="location" type="text" value="" optional="false" label="Location" />
+        <param name="input_norm" type="data" format="csv" label="30 year normals temperature data">
+            <validator type="expression" message="30 year normals temperature data must have 10 columns and 366 rows">value is not None and value.metadata.columns==10 and value.metadata.data_lines==366</validator>
+        </param>
+        <conditional name="merge_ytd_temperature_data_cond">
+            <param name="merge_ytd_temperature_data" type="select" label="Merge year-to-date temperature data with 30 year normals temperature data?">
+                <option value="yes" selected="true">Yes</option>
+                <option value="no">No</option>
+            </param>
+            <when value="yes">
+                <param name="input_ytd" type="data" format="csv" label="Year-to-date temperature data">
+                    <validator type="expression" message="Year-to-date temperature data must have 6 columns">value is not None and value.metadata.columns==6</validator>
+                </param>
+                <param name="location" type="text" value="" optional="true" label="Location" help="Enter the location or leave blank to use the station name from 30 year normals data."/>
+            </when>
+            <when value="no"/>
+        </conditional>
         <param name="insect" type="select" label="Select insect">
-            <option value="Brown Marmorated Stink Bug" selected="True">Brown Marmorated Stink Bug</option>
+            <option value="BMSB" selected="True">Brown Marmorated Stink Bug</option>
         </param>
-        <param name="replications" type="integer" value="10" min="1" label="Number of replications" />
-        <param name="insects_per_replication" type="integer" value="1000" min="1" label="Number of insects with which to start each replication" />
-        <param name="photoperiod" type="float" value="13.5" min="0" label="Critical photoperiod for diapause induction/termination" />
-        <param name="egg_mortality" type="integer" value="1" min="0" label="Adjustment rate for egg mortality" />
-        <param name="nymph_mortality" type="integer" value="1" min="0" label="Adjustment rate for nymph mortality" />
-        <param name="adult_mortality" type="integer" value="1" min="0" label="Adjustment rate for adult mortality" />
-        <param name="oviposition" type="integer" value="1" min="0" label="Adjustment oviposition rate" />
-        <param name="min_clutch_size" type="integer" value="0" min="0" label="Adjustment of minimum clutch size" />
-        <param name="max_clutch_size" type="integer" value="0" min="0" label="Adjustment of maximum clutch size" />
-        <param name="young_nymph_accumulation" type="integer" value="0" min="0" label="Adjustment of degree-days accumulation (egg->young nymph)" />
-        <param name="old_nymph_accumulation" type="integer" value="0" min="0" label="Adjustment of degree-days accumulation (young nymph->old nymph)" />
-        <param name="adult_accumulation" type="integer" value="0" min="0" label="Adjustment of degree-days accumulation (old nymph->adult)" />
-        <param name="std_error_plot" type="select" label="Plot standard error?">
-            <option value="1" selected="True">Yes</option>
-            <option value="0">No</option>
+        <param name="replications" type="integer" value="10" min="2" label="Number of replications"/>
+        <param name="insects_per_replication" type="integer" value="1000" min="1" label="Number of insects with which to start each replication"/>
+        <param name="photoperiod" type="float" value="13.5" min="0" label="Critical photoperiod for diapause induction/termination"/>
+        <param name="egg_mortality" type="integer" value="1" min="0" label="Adjustment rate for egg mortality"/>
+        <param name="nymph_mortality" type="integer" value="1" min="0" label="Adjustment rate for nymph mortality"/>
+        <param name="adult_mortality" type="integer" value="1" min="0" label="Adjustment rate for adult mortality"/>
+        <param name="oviposition" type="integer" value="1" min="0" label="Adjustment oviposition rate"/>
+        <param name="min_clutch_size" type="integer" value="0" min="0" label="Adjustment of minimum clutch size"/>
+        <param name="max_clutch_size" type="integer" value="0" min="0" label="Adjustment of maximum clutch size"/>
+        <param name="young_nymph_accumulation" type="integer" value="0" min="0" label="Adjustment of degree-days accumulation (egg->young nymph)"/>
+        <param name="old_nymph_accumulation" type="integer" value="0" min="0" label="Adjustment of degree-days accumulation (young nymph->old nymph)"/>
+        <param name="adult_accumulation" type="integer" value="0" min="0" label="Adjustment of degree-days accumulation (old nymph->adult)"/>
+        <param name="plot_generations_separately" type="select" label="Plot generations separately?">
+            <option value="yes" selected="True">Yes</option>
+            <option value="no">No</option>
+        </param>
+        <param name="plot_egg_life_stage" type="select" label="Plot egg life stage?">
+            <option value="yes" selected="true">Yes</option>
+            <option value="no">No</option>
+        </param>
+        <conditional name="plot_nymph_life_stage_cond">
+            <param name="plot_nymph_life_stage" type="select" label="Plot nymph life stage?">
+                <option value="yes" selected="true">Yes</option>
+                <option value="no">No</option>
+            </param>
+            <when value="yes">
+                <param name="life_stages_nymph" type="select" multiple="true" label="Select nymph life stage">
+                    <option value="Total" selected="true">All</option>
+                    <option value="Young">Young</option>
+                    <option value="Old">Old</option>
+                </param>
+            </when>
+            <when value="no"/>
+        </conditional>
+        <conditional name="plot_adult_life_stage_cond">
+            <param name="plot_adult_life_stage" type="select" label="Plot adult life stage?">
+                <option value="yes" selected="true">Yes</option>
+                <option value="no">No</option>
+            </param>
+            <when value="yes">
+                <param name="life_stages_adult" type="select" multiple="true" label="Select adult life stage">
+                    <option value="Total" selected="true">All</option>
+                    <option value="Pre-vittelogenic">Pre-vittelogenic</option>
+                    <option value="Vittelogenic">Vittelogenic</option>
+                    <option value="Diapausing">Diapausing</option>
+                </param>
+            </when>
+            <when value="no"/>
+        </conditional>
+        <param name="plot_std_error" type="select" label="Plot standard error?">
+            <option value="yes" selected="True">Yes</option>
+            <option value="no">No</option>
         </param>
     </inputs>
     <outputs>
-        <data name="output" format="pdf" label="${tool.name} ${location}, on ${on_string}" />
+        <collection name="output_data_collection" type="list" label="${tool.name} (data), on ${on_string}">
+            <discover_datasets pattern="__name__" directory="output_data_dir" format="csv"/>
+        </collection>
+        <collection name="output_plots_collection" type="list" label="${tool.name} (plots), on ${on_string}">
+            <discover_datasets pattern="__name__" directory="output_plots_dir" format="pdf"/>
+        </collection>
     </outputs>
     <tests>
         <test>
-            <param name="input" value="state_college.csv" ftype="csv" />
-            <param name="location" value="State College PA" />
-            <param name="replications" value="10" />
-            <output name="output" file="output.pdf" ftype="pdf" compare="contains" />
+            <param name="input_norm" value="30_year_normals.csv" ftype="csv"/>
+            <param name="merge_ytd_temperature_data" value="no"/>
+            <param name="replications" value="2"/>
+            <param name="plot_generations_separately" value="no"/>
+            <param name="plot_egg_life_stage" value="no"/>
+            <param name="life_stages_nymph" value="Young"/>
+            <param name="life_stages_adult" value="Pre-vittelogenic"/>
+            <output_collection name="output_data_collection" type="list">
+                <element name="04_combined_generations.csv" file="output_combined1.csv" ftype="csv" compare="contains"/>
+            </output_collection>
+            <output_collection name="output_plots_collection" type="list">
+                <element name="02_young_nymph_pop.pdf" file="plot.pdf" ftype="pdf" compare="contains"/>
+                <element name="05_pre-vittelogenic_adult_pop.pdf" file="plot.pdf" ftype="pdf" compare="contains"/>
+            </output_collection>
+        </test>
+        <test>
+            <param name="input_norm" value="30_year_normals.csv" ftype="csv"/>
+            <param name="input_ytd" value="state_college_partial.csv" ftype="csv"/>
+            <param name="location" value="State College PA"/>
+            <param name="replications" value="2"/>
+            <param name="plot_generations_separately" value="no"/>
+            <param name="plot_egg_life_stage" value="no"/>
+            <param name="life_stages_nymph" value="Young"/>
+            <param name="life_stages_adult" value="Pre-vittelogenic"/>
+            <output_collection name="output_data_collection" type="list">
+                <element name="04_combined_generations.csv" file="output_combined1.csv" ftype="csv" compare="contains"/>
+            </output_collection>
+            <output_collection name="output_plots_collection" type="list">
+                <element name="02_young_nymph_pop.pdf" file="plot.pdf" ftype="pdf" compare="contains"/>
+                <element name="05_pre-vittelogenic_adult_pop.pdf" file="plot.pdf" ftype="pdf" compare="contains"/>
+            </output_collection>
+        </test>
+        <test>
+            <param name="input_norm" value="30_year_normals.csv" ftype="csv"/>
+            <param name="input_ytd" value="state_college_ytd.csv" ftype="csv"/>
+            <param name="location" value="State College PA"/>
+            <param name="replications" value="2"/>
+            <param name="plot_generations_separately" value="no"/>
+            <output_collection name="output_data_collection" type="list">
+                <element name="04_combined_generations.csv" file="output_combined2.csv" ftype="csv" compare="contains"/>
+            </output_collection>
+            <output_collection name="output_plots_collection" type="list">
+                <element name="01_egg_pop.pdf" file="plot.pdf" ftype="pdf" compare="contains"/>
+                <element name="04_total_nymph_pop.pdf" file="plot.pdf" ftype="pdf" compare="contains"/>
+                <element name="08_total_adult_pop.pdf" file="plot.pdf" ftype="pdf" compare="contains"/>
+                <element name="09_total_pop.pdf" file="plot.pdf" ftype="pdf" compare="contains"/>
+            </output_collection>
+        </test>
+        <test>
+            <param name="input_norm" value="30_year_normals.csv" ftype="csv"/>
+            <param name="input_ytd" value="state_college_partial.csv" ftype="csv"/>
+            <param name="location" value="State College PA"/>
+            <param name="replications" value="2"/>
+            <param name="plot_egg_life_stage" value="no"/>
+            <param name="life_stages_nymph" value="Old"/>
+            <param name="plot_adult_life_stage" value="no"/>
+            <output_collection name="output_data_collection" type="list">
+                <element name="01_generation_P.csv" file="output_p_3.csv" ftype="csv" compare="contains"/>
+                <element name="02_generation_F1.csv" file="output_f1_3.csv" ftype="csv" compare="contains"/>
+                <element name="03_generation_F2.csv" file="output_f2_3.csv" ftype="csv" compare="contains"/>
+                <element name="04_combined_generations.csv" file="output_combined3.csv" ftype="csv" compare="contains"/>
+            </output_collection>
+            <output_collection name="output_plots_collection" type="list">
+                <element name="03_old_nymph_pop_by_generation.pdf" file="plot.pdf" ftype="pdf" compare="contains"/>
+            </output_collection>
+        </test>
+        <test>
+            <param name="input_norm" value="30_year_normals.csv" ftype="csv"/>
+            <param name="input_ytd" value="state_college_ytd.csv" ftype="csv"/>
+            <param name="location" value="State College PA"/>
+            <param name="replications" value="2"/>
+            <output_collection name="output_data_collection" type="list">
+                <element name="01_generation_P.csv" file="output_p_4.csv" ftype="csv" compare="contains"/>
+                <element name="02_generation_F1.csv" file="output_f1_4.csv" ftype="csv" compare="contains"/>
+                <element name="03_generation_F2.csv" file="output_f2_4.csv" ftype="csv" compare="contains"/>
+                <element name="04_combined_generations.csv" file="output_combined4.csv" ftype="csv" compare="contains"/>
+            </output_collection>
+            <output_collection name="output_plots_collection" type="list">
+                <element name="01_egg_pop_by_generation.pdf" file="plot.pdf" ftype="pdf" compare="contains"/>
+                <element name="04_total_nymph_pop_by_generation.pdf" file="plot.pdf" ftype="pdf" compare="contains"/>
+                <element name="08_total_adult_pop_by_generation.pdf" file="plot.pdf" ftype="pdf" compare="contains"/>
+                <element name="09_total_pop_by_generation.pdf" file="plot.pdf" ftype="pdf" compare="contains"/>
+            </output_collection>
         </test>
     </tests>
     <help>
@@ -66,8 +238,12 @@
 
 **Required options**
 
+ * **30 year normals temperature data** - the dataset from your history containing the 30-year normals temperature data (available at http://pestwatch.psu.edu/ghcn).
+ * **Merge year-to-date temperature data with 30 year normals temperature data** - select Yes to merge a year-to-date temperature dataset from your history into the selected 30 year normals temperature data.
+
+  * **Year-to-date temperature data** - the dataset from your history containing the year-to-date temperature data (available at http://pestwatch.psu.edu/minmax).
+
  * **Location** - the location associated with the selected temperature data.
- * **Temperature data** - select the dataset from your history containing the temperature data.
  * **Select insect** - currently only the Brown Marmorated Stink Bug can be analyzed.
  * **Number of replications** - number of replications.
  * **Number of insects with which to start each replication** - the analysis for each replication will start with this number of insects.
@@ -81,8 +257,17 @@
  * **Adjustment of degree-days accumulation (egg->young nymph)** - adjustment of degree-days accumulation (egg->young nymph).
  * **Adjustment of degree-days accumulation (young nymph->old nymph)** - adjustment of degree-days accumulation (young nymph->old nymph).
  * **Adjustment of degree-days accumulation (old nymph->adult)** - adjustment of degree-days accumulation (old nymph->adult).
+ * **Plot generations separately** - select "Yes" to plot P, F1 and F2 as separate lines or "no" to pool across generations, resulting in a total for the selected life states.
+ * **Plot egg life stage** - select "Yes" to plot the egg life stage.  If all life stages (egg, nymph and adult) are selected for plotting, one output for the total will be produced.
+ * **Plot nymph life stage** - select "Yes" to plot the nymph life stage.  If all life stages (egg, nymph and adult) are selected for plotting, one output for the total will be produced.
+
+  * **Select nymph life stage** - select the nymph life stage for plotting.
+
+ * **Plot adult life stage** - select "Yes" to plot the adult life stage.  If all life stages (egg, nymph and adult) are selected for plotting, one output for the total will be produced.
+
+  * **Select adult life stage** - select the adult life stage for plotting.
+
  * **Plot standard error** - add standard error lines to plot.
-
     </help>
     <citations>
         <citation type="doi">10.3389/fphys.2016.00165</citation>
diff -r 37ac68b6ff10 -r bcb12b7e8563 test-data/30_year_normals.csv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/30_year_normals.csv	Tue May 29 09:00:25 2018 -0400
@@ -0,0 +1,367 @@
+stationid,latitude,longitude,elev_m,name,st,mmdd,doy,tmin,tmax
+USC00360785,40.3844,-76.0339,106.7,BLUE MARSH LAKE,PA,01-01, 001,-6.8,2.8
+USC00360785,40.3844,-76.0339,106.7,BLUE MARSH LAKE,PA,01-02, 002,-6.8,2.7
+USC00360785,40.3844,-76.0339,106.7,BLUE MARSH LAKE,PA,01-03, 003,-6.9,2.6
+USC00360785,40.3844,-76.0339,106.7,BLUE MARSH LAKE,PA,01-04, 004,-7.0,2.6
+USC00360785,40.3844,-76.0339,106.7,BLUE MARSH LAKE,PA,01-05, 005,-7.1,2.5
+USC00360785,40.3844,-76.0339,106.7,BLUE MARSH LAKE,PA,01-06, 006,-7.1,2.5
+USC00360785,40.3844,-76.0339,106.7,BLUE MARSH LAKE,PA,01-07, 007,-7.2,2.4
+USC00360785,40.3844,-76.0339,106.7,BLUE MARSH LAKE,PA,01-08, 008,-7.2,2.4
+USC00360785,40.3844,-76.0339,106.7,BLUE MARSH LAKE,PA,01-09, 009,-7.3,2.4
+USC00360785,40.3844,-76.0339,106.7,BLUE MARSH LAKE,PA,01-10, 010,-7.3,2.3
+USC00360785,40.3844,-76.0339,106.7,BLUE MARSH LAKE,PA,01-11, 011,-7.4,2.3
+USC00360785,40.3844,-76.0339,106.7,BLUE MARSH LAKE,PA,01-12, 012,-7.4,2.3
+USC00360785,40.3844,-76.0339,106.7,BLUE MARSH LAKE,PA,01-13, 013,-7.4,2.3
+USC00360785,40.3844,-76.0339,106.7,BLUE MARSH LAKE,PA,01-14, 014,-7.5,2.3
+USC00360785,40.3844,-76.0339,106.7,BLUE MARSH LAKE,PA,01-15, 015,-7.5,2.3
+USC00360785,40.3844,-76.0339,106.7,BLUE MARSH LAKE,PA,01-16, 016,-7.5,2.3
+USC00360785,40.3844,-76.0339,106.7,BLUE MARSH LAKE,PA,01-17, 017,-7.6,2.3
+USC00360785,40.3844,-76.0339,106.7,BLUE MARSH LAKE,PA,01-18, 018,-7.6,2.3
+USC00360785,40.3844,-76.0339,106.7,BLUE MARSH LAKE,PA,01-19, 019,-7.6,2.3
+USC00360785,40.3844,-76.0339,106.7,BLUE MARSH LAKE,PA,01-20, 020,-7.6,2.3
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diff -r 37ac68b6ff10 -r bcb12b7e8563 test-data/output_combined1.csv
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+++ b/test-data/output_combined1.csv	Tue May 29 09:00:25 2018 -0400
@@ -0,0 +1,1 @@
+"LATITUDE","LONGITUDE","DATE","DOY","TMIN","TMAX","DAYLEN","YOUNGNYMPH","YOUNGNYMPHSE","PRE-VITADULT","PRE-VITADULTSE"
diff -r 37ac68b6ff10 -r bcb12b7e8563 test-data/output_combined2.csv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output_combined2.csv	Tue May 29 09:00:25 2018 -0400
@@ -0,0 +1,1 @@
+"LATITUDE","LONGITUDE","DATE","DOY","TMIN","TMAX","DAYLEN","EGG","EGGSE","TOTALNYMPH","TOTALNYMPHSE","TOTALADULT","TOTALADULTSE"
diff -r 37ac68b6ff10 -r bcb12b7e8563 test-data/output_combined3.csv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output_combined3.csv	Tue May 29 09:00:25 2018 -0400
@@ -0,0 +1,1 @@
+"LATITUDE","LONGITUDE","DATE","DOY","TMIN","TMAX","DAYLEN","OLDNYMPH","OLDNYMPHSE"
diff -r 37ac68b6ff10 -r bcb12b7e8563 test-data/output_combined4.csv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output_combined4.csv	Tue May 29 09:00:25 2018 -0400
@@ -0,0 +1,1 @@
+"LATITUDE","LONGITUDE","DATE","DOY","TMIN","TMAX","DAYLEN","EGG","EGGSE","TOTALNYMPH","TOTALNYMPHSE","TOTALADULT","TOTALADULTSE"
diff -r 37ac68b6ff10 -r bcb12b7e8563 test-data/output_f1_3.csv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output_f1_3.csv	Tue May 29 09:00:25 2018 -0400
@@ -0,0 +1,1 @@
+"LATITUDE","LONGITUDE","DATE","DOY","TMIN","TMAX","DAYLEN","OLDNYMPH-F1","OLDNYMPH-F1-SE"
diff -r 37ac68b6ff10 -r bcb12b7e8563 test-data/output_f1_4.csv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output_f1_4.csv	Tue May 29 09:00:25 2018 -0400
@@ -0,0 +1,1 @@
+"LATITUDE","LONGITUDE","DATE","DOY","TMIN","TMAX","DAYLEN","EGG-F1","EGG-F1-SE","TOTALNYMPH-F1","TOTALNYMPH-F1-SE","TOTALADULT-F1","TOTALADULT-F1-SE"
diff -r 37ac68b6ff10 -r bcb12b7e8563 test-data/output_f2_3.csv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output_f2_3.csv	Tue May 29 09:00:25 2018 -0400
@@ -0,0 +1,1 @@
+"LATITUDE","LONGITUDE","DATE","DOY","TMIN","TMAX","DAYLEN","OLDNYMPH-F2","OLDNYMPH-F2-SE"
diff -r 37ac68b6ff10 -r bcb12b7e8563 test-data/output_f2_4.csv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output_f2_4.csv	Tue May 29 09:00:25 2018 -0400
@@ -0,0 +1,1 @@
+"LATITUDE","LONGITUDE","DATE","DOY","TMIN","TMAX","DAYLEN","EGG-F2","EGG-F2-SE","TOTALNYMPH-F2","TOTALNYMPH-F2-SE","TOTALADULT-F2","TOTALADULT-F2-SE"
diff -r 37ac68b6ff10 -r bcb12b7e8563 test-data/output_p_3.csv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output_p_3.csv	Tue May 29 09:00:25 2018 -0400
@@ -0,0 +1,1 @@
+"LATITUDE","LONGITUDE","DATE","DOY","TMIN","TMAX","DAYLEN","OLDNYMPH-P","OLDNYMPH-P-SE"
diff -r 37ac68b6ff10 -r bcb12b7e8563 test-data/output_p_4.csv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output_p_4.csv	Tue May 29 09:00:25 2018 -0400
@@ -0,0 +1,1 @@
+"LATITUDE","LONGITUDE","DATE","DOY","TMIN","TMAX","DAYLEN","EGG-P","EGG-P-SE","TOTALNYMPH-P","TOTALNYMPH-P-SE","TOTALADULT-P","TOTALADULT-P-SE"
diff -r 37ac68b6ff10 -r bcb12b7e8563 test-data/plot.pdf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/plot.pdf	Tue May 29 09:00:25 2018 -0400
@@ -0,0 +1,49 @@
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diff -r 37ac68b6ff10 -r bcb12b7e8563 test-data/state_college.csv
--- a/test-data/state_college.csv	Tue Feb 13 13:47:32 2018 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,184 +0,0 @@
-LATITUDE,LONGITUDE,DATE,DOY,TMIN,TMAX
- 40.81849,-77.84637,2017-04-01,091,3.30,7.66
- 40.81849,-77.84637,2017-04-02,092,1.69,15.19
- 40.81849,-77.84637,2017-04-03,093,3.48,18.81
- 40.81849,-77.84637,2017-04-04,094,9.28,18.75
- 40.81849,-77.84637,2017-04-05,095,8.14,19.01
- 40.81849,-77.84637,2017-04-06,096,4.59,12.02
- 40.81849,-77.84637,2017-04-07,097,1.19,3.66
- 40.81849,-77.84637,2017-04-08,098,-0.56,13.85
- 40.81849,-77.84637,2017-04-09,099,-2.32,21.96
- 40.81849,-77.84637,2017-04-10,100,7.90,26.25
- 40.81849,-77.84637,2017-04-11,101,9.25,26.48
- 40.81849,-77.84637,2017-04-12,102,8.95,19.78
- 40.81849,-77.84637,2017-04-13,103,4.00,15.47
- 40.81849,-77.84637,2017-04-14,104,5.09,20.10
- 40.81849,-77.84637,2017-04-15,105,8.44,25.02
- 40.81849,-77.84637,2017-04-16,106,14.13,26.54
- 40.81849,-77.84637,2017-04-17,107,8.23,20.59
- 40.81849,-77.84637,2017-04-18,108,3.27,20.96
- 40.81849,-77.84637,2017-04-19,109,9.76,13.40
- 40.81849,-77.84637,2017-04-20,110,10.70,25.45
- 40.81849,-77.84637,2017-04-21,111,11.74,22.34
- 40.81849,-77.84637,2017-04-22,112,4.90,13.43
- 40.81849,-77.84637,2017-04-23,113,0.43,20.16
- 40.81849,-77.84637,2017-04-24,114,1.21,17.18
- 40.81849,-77.84637,2017-04-25,115,9.93,14.30
- 40.81849,-77.84637,2017-04-26,116,11.38,23.36
- 40.81849,-77.84637,2017-04-27,117,12.42,23.94
- 40.81849,-77.84637,2017-04-28,118,11.79,25.11
- 40.81849,-77.84637,2017-04-29,119,11.14,24.38
- 40.81849,-77.84637,2017-04-30,120,12.08,25.29
- 40.81849,-77.84637,2017-05-01,121,13.37,25.43
- 40.81849,-77.84637,2017-05-02,122,10.78,15.74
- 40.81849,-77.84637,2017-05-03,123,5.09,16.41
- 40.81849,-77.84637,2017-05-04,124,4.07,14.99
- 40.81849,-77.84637,2017-05-05,125,8.04,17.02
- 40.81849,-77.84637,2017-05-06,126,5.92,12.78
- 40.81849,-77.84637,2017-05-07,127,2.90,12.05
- 40.81849,-77.84637,2017-05-08,128,1.22,13.07
- 40.81849,-77.84637,2017-05-09,129,-1.45,17.87
- 40.81849,-77.84637,2017-05-10,130,5.94,19.31
- 40.81849,-77.84637,2017-05-11,131,7.90,11.11
- 40.81849,-77.84637,2017-05-12,132,8.75,12.95
- 40.81849,-77.84637,2017-05-13,133,5.68,14.39
- 40.81849,-77.84637,2017-05-14,134,5.94,19.81
- 40.81849,-77.84637,2017-05-15,135,7.37,22.14
- 40.81849,-77.84637,2017-05-16,136,5.18,26.96
- 40.81849,-77.84637,2017-05-17,137,11.12,31.63
- 40.81849,-77.84637,2017-05-18,138,15.39,32.05
- 40.81849,-77.84637,2017-05-19,139,13.92,29.51
- 40.81849,-77.84637,2017-05-20,140,9.38,13.55
- 40.81849,-77.84637,2017-05-21,141,12.60,17.19
- 40.81849,-77.84637,2017-05-22,142,10.93,23.45
- 40.81849,-77.84637,2017-05-23,143,6.24,21.30
- 40.81849,-77.84637,2017-05-24,144,10.97,21.61
- 40.81849,-77.84637,2017-05-25,145,11.91,18.55
- 40.81849,-77.84637,2017-05-26,146,13.00,19.09
- 40.81849,-77.84637,2017-05-27,147,9.28,22.35
- 40.81849,-77.84637,2017-05-28,148,13.02,19.25
- 40.81849,-77.84637,2017-05-29,149,15.61,25.52
- 40.81849,-77.84637,2017-05-30,150,14.89,20.32
- 40.81849,-77.84637,2017-05-31,151,12.29,24.32
- 40.81849,-77.84637,2017-06-01,152,9.02,22.91
- 40.81849,-77.84637,2017-06-02,153,10.83,22.70
- 40.81849,-77.84637,2017-06-03,154,10.01,25.36
- 40.81849,-77.84637,2017-06-04,155,8.05,16.85
- 40.81849,-77.84637,2017-06-05,156,14.04,23.52
- 40.81849,-77.84637,2017-06-06,157,13.20,21.63
- 40.81849,-77.84637,2017-06-07,158,9.99,17.12
- 40.81849,-77.84637,2017-06-08,159,9.42,23.51
- 40.81849,-77.84637,2017-06-09,160,10.71,25.54
- 40.81849,-77.84637,2017-06-10,161,15.90,29.01
- 40.81849,-77.84637,2017-06-11,162,15.11,31.46
- 40.81849,-77.84637,2017-06-12,163,15.59,31.82
- 40.81849,-77.84637,2017-06-13,164,18.19,34.21
- 40.81849,-77.84637,2017-06-14,165,19.55,29.87
- 40.81849,-77.84637,2017-06-15,166,17.02,27.22
- 40.81849,-77.84637,2017-06-16,167,17.59,26.76
- 40.81849,-77.84637,2017-06-17,168,17.43,29.03
- 40.81849,-77.84637,2017-06-18,169,20.91,31.44
- 40.81849,-77.84637,2017-06-19,170,17.51,24.38
- 40.81849,-77.84637,2017-06-20,171,14.80,25.74
- 40.81849,-77.84637,2017-06-21,172,13.97,26.99
- 40.81849,-77.84637,2017-06-22,173,12.72,29.78
- 40.81849,-77.84637,2017-06-23,174,19.03,25.44
- 40.81849,-77.84637,2017-06-24,175,15.76,27.33
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- 40.81849,-77.84637,2017-06-27,178,10.84,20.57
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- 40.81849,-77.84637,2017-06-29,180,14.48,29.26
- 40.81849,-77.84637,2017-06-30,181,19.94,30.59
- 40.81849,-77.84637,2017-07-01,182,20.79,29.10
- 40.81849,-77.84637,2017-07-02,183,17.01,29.60
- 40.81849,-77.84637,2017-07-03,184,17.01,29.60
- 40.81849,-77.84637,2017-07-04,185,20.43,23.44
- 40.81849,-77.84637,2017-07-05,186,20.43,23.44
- 40.81849,-77.84637,2017-07-06,187,19.56,22.32
- 40.81849,-77.84637,2017-07-07,188,19.35,28.04
- 40.81849,-77.84637,2017-07-08,189,15.93,25.53
- 40.81849,-77.84637,2017-07-09,190,11.83,26.33
- 40.81849,-77.84637,2017-07-10,191,12.38,27.23
- 40.81849,-77.84637,2017-07-11,192,17.98,28.99
- 40.81849,-77.84637,2017-07-12,193,21.06,29.84
- 40.81849,-77.84637,2017-07-13,194,21.07,28.19
- 40.81849,-77.84637,2017-07-14,195,19.22,28.46
- 40.81849,-77.84637,2017-07-15,196,16.50,24.54
- 40.81849,-77.84637,2017-07-16,197,14.44,28.05
- 40.81849,-77.84637,2017-07-17,198,17.26,30.80
- 40.81849,-77.84637,2017-07-18,199,17.44,31.69
- 40.81849,-77.84637,2017-07-19,200,16.67,32.40
- 40.81849,-77.84637,2017-07-20,201,19.12,32.13
- 40.81849,-77.84637,2017-07-21,202,20.94,31.43
- 40.81849,-77.84637,2017-07-22,203,19.30,28.36
- 40.81849,-77.84637,2017-07-23,204,20.25,30.59
- 40.81849,-77.84637,2017-07-24,205,18.56,28.17
- 40.81849,-77.84637,2017-07-25,206,15.18,22.72
- 40.81849,-77.84637,2017-07-26,207,12.03,26.34
- 40.81849,-77.84637,2017-07-27,208,16.35,29.74
- 40.81849,-77.84637,2017-07-28,209,16.35,26.24
- 40.81849,-77.84637,2017-07-29,210,11.05,23.78
- 40.81849,-77.84637,2017-07-30,211,7.73,28.01
- 40.81849,-77.84637,2017-07-31,212,13.66,30.13
- 40.81849,-77.84637,2017-08-01,213,15.11,30.81
- 40.81849,-77.84637,2017-08-02,214,16.56,30.22
- 40.81849,-77.84637,2017-08-03,215,15.69,28.57
- 40.81849,-77.84637,2017-08-04,216,16.07,30.48
- 40.81849,-77.84637,2017-08-05,217,12.30,23.46
- 40.81849,-77.84637,2017-08-06,218,11.46,23.44
- 40.81849,-77.84637,2017-08-07,219,15.40,18.35
- 40.81849,-77.84637,2017-08-08,220,12.19,25.48
- 40.81849,-77.84637,2017-08-09,221,9.23,26.69
- 40.81849,-77.84637,2017-08-10,222,9.53,25.78
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- 40.81849,-77.84637,2017-08-13,225,14.17,26.51
- 40.81849,-77.84637,2017-08-14,226,13.98,22.43
- 40.81849,-77.84637,2017-08-15,227,17.69,28.88
- 40.81849,-77.84637,2017-08-16,228,14.84,29.43
- 40.81849,-77.84637,2017-08-17,229,13.40,29.96
- 40.81849,-77.84637,2017-08-18,230,19.42,29.00
- 40.81849,-77.84637,2017-08-19,231,14.40,28.28
- 40.81849,-77.84637,2017-08-20,232,12.31,27.77
- 40.81849,-77.84637,2017-08-21,233,14.27,30.25
- 40.81849,-77.84637,2017-08-22,234,18.44,31.05
- 40.81849,-77.84637,2017-08-23,235,14.22,24.64
- 40.81849,-77.84637,2017-08-24,236,10.30,23.00
- 40.81849,-77.84637,2017-08-25,237,12.57,21.39
- 40.81849,-77.84637,2017-08-26,238,10.93,23.29
- 40.81849,-77.84637,2017-08-27,239,9.96,23.45
- 40.81849,-77.84637,2017-08-28,240,9.26,22.38
- 40.81849,-77.84637,2017-08-29,241,13.80,19.09
- 40.81849,-77.84637,2017-08-30,242,10.88,24.45
- 40.81849,-77.84637,2017-08-31,243,13.15,24.42
- 40.81849,-77.84637,2017-09-01,244,7.82,17.91
- 40.81849,-77.84637,2017-09-02,245,6.20,13.16
- 40.81849,-77.84637,2017-09-03,246,12.37,19.35
- 40.81849,-77.84637,2017-09-04,247,10.67,26.97
- 40.81849,-77.84637,2017-09-05,248,15.39,21.54
- 40.81849,-77.84637,2017-09-06,249,13.80,18.10
- 40.81849,-77.84637,2017-09-07,250,9.30,18.45
- 40.81849,-77.84637,2017-09-08,251,8.86,18.11
- 40.81849,-77.84637,2017-09-09,252,8.44,18.21
- 40.81849,-77.84637,2017-09-10,253,3.93,9.19
- 40.81849,-77.84637,2017-09-11,254,4.98,22.12
- 40.81849,-77.84637,2017-09-12,255,8.70,24.06
- 40.81849,-77.84637,2017-09-13,256,12.75,23.14
- 40.81849,-77.84637,2017-09-14,257,16.60,19.18
- 40.81849,-77.84637,2017-09-15,258,14.89,25.28
- 40.81849,-77.84637,2017-09-16,259,14.73,25.42
- 40.81849,-77.84637,2017-09-17,260,14.85,27.42
- 40.81849,-77.84637,2017-09-18,261,16.12,26.18
- 40.81849,-77.84637,2017-09-19,262,13.36,25.46
- 40.81849,-77.84637,2017-09-20,263,10.90,28.76
- 40.81849,-77.84637,2017-09-21,264,11.68,28.44
- 40.81849,-77.84637,2017-09-22,265,13.10,29.03
- 40.81849,-77.84637,2017-09-23,266,10.11,30.51
- 40.81849,-77.84637,2017-09-24,267,12.33,31.11
- 40.81849,-77.84637,2017-09-25,268,15.03,31.81
- 40.81849,-77.84637,2017-09-26,269,16.01,30.96
- 40.81849,-77.84637,2017-09-27,270,15.03,31.27
- 40.81849,-77.84637,2017-09-28,271,9.61,21.39
- 40.81849,-77.84637,2017-09-29,272,6.03,20.71
- 40.81849,-77.84637,2017-09-30,273,2.85,15.23
diff -r 37ac68b6ff10 -r bcb12b7e8563 test-data/state_college_partial.csv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/state_college_partial.csv	Tue May 29 09:00:25 2018 -0400
@@ -0,0 +1,184 @@
+LATITUDE,LONGITUDE,DATE,DOY,TMIN,TMAX
+ 40.81849,-77.84637,2017-04-01,091,3.30,7.66
+ 40.81849,-77.84637,2017-04-02,092,1.69,15.19
+ 40.81849,-77.84637,2017-04-03,093,3.48,18.81
+ 40.81849,-77.84637,2017-04-04,094,9.28,18.75
+ 40.81849,-77.84637,2017-04-05,095,8.14,19.01
+ 40.81849,-77.84637,2017-04-06,096,4.59,12.02
+ 40.81849,-77.84637,2017-04-07,097,1.19,3.66
+ 40.81849,-77.84637,2017-04-08,098,-0.56,13.85
+ 40.81849,-77.84637,2017-04-09,099,-2.32,21.96
+ 40.81849,-77.84637,2017-04-10,100,7.90,26.25
+ 40.81849,-77.84637,2017-04-11,101,9.25,26.48
+ 40.81849,-77.84637,2017-04-12,102,8.95,19.78
+ 40.81849,-77.84637,2017-04-13,103,4.00,15.47
+ 40.81849,-77.84637,2017-04-14,104,5.09,20.10
+ 40.81849,-77.84637,2017-04-15,105,8.44,25.02
+ 40.81849,-77.84637,2017-04-16,106,14.13,26.54
+ 40.81849,-77.84637,2017-04-17,107,8.23,20.59
+ 40.81849,-77.84637,2017-04-18,108,3.27,20.96
+ 40.81849,-77.84637,2017-04-19,109,9.76,13.40
+ 40.81849,-77.84637,2017-04-20,110,10.70,25.45
+ 40.81849,-77.84637,2017-04-21,111,11.74,22.34
+ 40.81849,-77.84637,2017-04-22,112,4.90,13.43
+ 40.81849,-77.84637,2017-04-23,113,0.43,20.16
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+ 40.81849,-77.84637,2017-09-01,244,7.82,17.91
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+ 40.81849,-77.84637,2017-09-06,249,13.80,18.10
+ 40.81849,-77.84637,2017-09-07,250,9.30,18.45
+ 40.81849,-77.84637,2017-09-08,251,8.86,18.11
+ 40.81849,-77.84637,2017-09-09,252,8.44,18.21
+ 40.81849,-77.84637,2017-09-10,253,3.93,9.19
+ 40.81849,-77.84637,2017-09-11,254,4.98,22.12
+ 40.81849,-77.84637,2017-09-12,255,8.70,24.06
+ 40.81849,-77.84637,2017-09-13,256,12.75,23.14
+ 40.81849,-77.84637,2017-09-14,257,16.60,19.18
+ 40.81849,-77.84637,2017-09-15,258,14.89,25.28
+ 40.81849,-77.84637,2017-09-16,259,14.73,25.42
+ 40.81849,-77.84637,2017-09-17,260,14.85,27.42
+ 40.81849,-77.84637,2017-09-18,261,16.12,26.18
+ 40.81849,-77.84637,2017-09-19,262,13.36,25.46
+ 40.81849,-77.84637,2017-09-20,263,10.90,28.76
+ 40.81849,-77.84637,2017-09-21,264,11.68,28.44
+ 40.81849,-77.84637,2017-09-22,265,13.10,29.03
+ 40.81849,-77.84637,2017-09-23,266,10.11,30.51
+ 40.81849,-77.84637,2017-09-24,267,12.33,31.11
+ 40.81849,-77.84637,2017-09-25,268,15.03,31.81
+ 40.81849,-77.84637,2017-09-26,269,16.01,30.96
+ 40.81849,-77.84637,2017-09-27,270,15.03,31.27
+ 40.81849,-77.84637,2017-09-28,271,9.61,21.39
+ 40.81849,-77.84637,2017-09-29,272,6.03,20.71
+ 40.81849,-77.84637,2017-09-30,273,2.85,15.23
diff -r 37ac68b6ff10 -r bcb12b7e8563 test-data/state_college_ytd.csv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/state_college_ytd.csv	Tue May 29 09:00:25 2018 -0400
@@ -0,0 +1,100 @@
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