5
+ − 1 #!/usr/bin/env Rscript
+ − 2
+ − 3 suppressPackageStartupMessages(library("optparse"))
+ − 4
+ − 5 option_list <- list(
6
+ − 6 make_option(c("--adult_mortality"), action="store", dest="adult_mortality", type="integer", help="Adjustment rate for adult mortality"),
+ − 7 make_option(c("--adult_accumulation"), action="store", dest="adult_accumulation", type="integer", help="Adjustment of degree-days accumulation (old nymph->adult)"),
+ − 8 make_option(c("--egg_mortality"), action="store", dest="egg_mortality", type="integer", help="Adjustment rate for egg mortality"),
+ − 9 make_option(c("--input"), action="store", dest="input", help="Temperature data for selected location"),
+ − 10 make_option(c("--insect"), action="store", dest="insect", help="Insect name"),
+ − 11 make_option(c("--insects_per_replication"), action="store", dest="insects_per_replication", type="integer", help="Number of insects with which to start each replication"),
10
+ − 12 make_option(c("--life_stages"), action="store", dest="life_stages", help="Selected life stages for plotting"),
+ − 13 make_option(c("--life_stages_adult"), action="store", dest="life_stages_adult", default=NULL, help="Adult life stages for plotting"),
16
+ − 14 make_option(c("--life_stages_nymph"), action="store", dest="life_stages_nymph", default=NULL, help="Nymph life stages for plotting"),
6
+ − 15 make_option(c("--location"), action="store", dest="location", help="Selected location"),
+ − 16 make_option(c("--min_clutch_size"), action="store", dest="min_clutch_size", type="integer", help="Adjustment of minimum clutch size"),
+ − 17 make_option(c("--max_clutch_size"), action="store", dest="max_clutch_size", type="integer", help="Adjustment of maximum clutch size"),
27
+ − 18 make_option(c("--num_days"), action="store", dest="num_days", type="integer", help="Total number of days in the temperature dataset"),
6
+ − 19 make_option(c("--nymph_mortality"), action="store", dest="nymph_mortality", type="integer", help="Adjustment rate for nymph mortality"),
+ − 20 make_option(c("--old_nymph_accumulation"), action="store", dest="old_nymph_accumulation", type="integer", help="Adjustment of degree-days accumulation (young nymph->old nymph)"),
+ − 21 make_option(c("--oviposition"), action="store", dest="oviposition", type="integer", help="Adjustment for oviposition rate"),
+ − 22 make_option(c("--photoperiod"), action="store", dest="photoperiod", type="double", help="Critical photoperiod for diapause induction/termination"),
10
+ − 23 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"),
+ − 24 make_option(c("--plot_std_error"), action="store", dest="plot_std_error", help="Plot Standard error"),
27
+ − 25 make_option(c("--replications"), action="store", dest="replications", type="integer", help="Number of replications"),
6
+ − 26 make_option(c("--young_nymph_accumulation"), action="store", dest="young_nymph_accumulation", type="integer", help="Adjustment of degree-days accumulation (egg->young nymph)")
5
+ − 27 )
+ − 28
8
+ − 29 parser <- OptionParser(usage="%prog [options] file", option_list=option_list);
+ − 30 args <- parse_args(parser, positional_arguments=TRUE);
+ − 31 opt <- args$options;
5
+ − 32
27
+ − 33 add_daylight_length = function(temperature_data_frame, num_rows) {
5
+ − 34 # Return a vector of daylight length (photoperido profile) for
+ − 35 # the number of days specified in the input temperature data
+ − 36 # (from Forsythe 1995).
8
+ − 37 p = 0.8333;
+ − 38 latitude = temperature_data_frame$LATITUDE[1];
+ − 39 daylight_length_vector = NULL;
5
+ − 40 for (i in 1:num_rows) {
+ − 41 # Get the day of the year from the current row
+ − 42 # of the temperature data for computation.
8
+ − 43 doy = temperature_data_frame$DOY[i];
+ − 44 theta = 0.2163108 + 2 * atan(0.9671396 * tan(0.00860 * (doy - 186)));
+ − 45 phi = asin(0.39795 * cos(theta));
5
+ − 46 # Compute the length of daylight for the day of the year.
8
+ − 47 darkness_length = 24 / pi * acos((sin(p * pi / 180) + sin(latitude * pi / 180) * sin(phi)) / (cos(latitude * pi / 180) * cos(phi)));
+ − 48 daylight_length_vector[i] = 24 - darkness_length;
5
+ − 49 }
+ − 50 # Append daylight_length_vector as a new column to temperature_data_frame.
27
+ − 51 temperature_data_frame = append_vector(temperature_data_frame, daylight_length_vector, "DAYLEN");
8
+ − 52 return(temperature_data_frame);
5
+ − 53 }
+ − 54
27
+ − 55 append_vector = function(data_frame, vec, new_column_name) {
+ − 56 num_columns = dim(data_frame)[2];
+ − 57 current_column_names = colnames(data_frame);
+ − 58 # Append vector vec as a new column to data_frame.
+ − 59 data_frame[,num_columns+1] = vec;
+ − 60 # Reset the column names with the additional column for later access.
+ − 61 colnames(data_frame) = append(current_column_names, new_column_name);
+ − 62 return(data_frame);
+ − 63 }
+ − 64
34
+ − 65 get_x_axis_ticks_and_labels = function(temperature_data_frame, num_rows) {
8
+ − 66 # Keep track of the years to see if spanning years.
+ − 67 month_labels = list();
34
+ − 68 ticks = list();
8
+ − 69 current_month_label = NULL;
+ − 70 for (i in 1:num_rows) {
+ − 71 # Get the year and month from the date which
+ − 72 # has the format YYYY-MM-DD.
+ − 73 date = format(temperature_data_frame$DATE[i]);
34
+ − 74 # Get the month label.
8
+ − 75 items = strsplit(date, "-")[[1]];
+ − 76 month = items[2];
+ − 77 month_label = month.abb[as.integer(month)];
+ − 78 if (!identical(current_month_label, month_label)) {
34
+ − 79 # Add an x-axis tick for the month.
+ − 80 ticks[length(ticks)+1] = i;
8
+ − 81 month_labels[length(month_labels)+1] = month_label;
+ − 82 current_month_label = month_label;
+ − 83 }
34
+ − 84 # Get the day.
+ − 85 day = weekdays(as.Date(date));
+ − 86 if (day=="Sunday") {
+ − 87 # Add an x-axis tick if we're on a Sunday.
+ − 88 ticks[length(ticks)+1] = i;
+ − 89 # Add a blank month label so it is not displayed.
+ − 90 month_labels[length(month_labels)+1] = "";
+ − 91 }
8
+ − 92 }
34
+ − 93 return(list(ticks, month_labels));
6
+ − 94 }
+ − 95
19
+ − 96 get_file_path = function(life_stage, base_name, life_stage_nymph=NULL, life_stage_adult=NULL) {
+ − 97 if (!is.null(life_stage_nymph)) {
+ − 98 lsi = get_life_stage_index(life_stage, life_stage_nymph=life_stage_nymph);
+ − 99 file_name = paste(lsi, tolower(life_stage_nymph), base_name, sep="_");
+ − 100 } else if (!is.null(life_stage_adult)) {
+ − 101 lsi = get_life_stage_index(life_stage, life_stage_adult=life_stage_adult);
+ − 102 file_name = paste(lsi, tolower(life_stage_adult), base_name, sep="_");
+ − 103 } else {
+ − 104 lsi = get_life_stage_index(life_stage);
+ − 105 file_name = paste(lsi, base_name, sep="_");
+ − 106 }
34
+ − 107 file_path = paste("output_plots_dir", file_name, sep="/");
19
+ − 108 return(file_path);
+ − 109 }
+ − 110
18
+ − 111 get_life_stage_index = function(life_stage, life_stage_nymph=NULL, life_stage_adult=NULL) {
+ − 112 # Name collection elements so that they
+ − 113 # are displayed in logical order.
+ − 114 if (life_stage=="Egg") {
+ − 115 lsi = "01";
+ − 116 } else if (life_stage=="Nymph") {
+ − 117 if (life_stage_nymph=="Young") {
+ − 118 lsi = "02";
+ − 119 } else if (life_stage_nymph=="Old") {
+ − 120 lsi = "03";
+ − 121 } else if (life_stage_nymph=="Total") {
+ − 122 lsi="04";
+ − 123 }
+ − 124 } else if (life_stage=="Adult") {
+ − 125 if (life_stage_adult=="Pre-vittelogenic") {
+ − 126 lsi = "05";
+ − 127 } else if (life_stage_adult=="Vittelogenic") {
+ − 128 lsi = "06";
+ − 129 } else if (life_stage_adult=="Diapausing") {
+ − 130 lsi = "07";
+ − 131 } else if (life_stage_adult=="Total") {
+ − 132 lsi = "08";
+ − 133 }
+ − 134 } else if (life_stage=="Total") {
+ − 135 lsi = "09";
+ − 136 }
+ − 137 return(lsi);
+ − 138 }
+ − 139
20
+ − 140 get_mean_and_std_error = function(p_replications, f1_replications, f2_replications) {
+ − 141 # P mean.
+ − 142 p_m = apply(p_replications, 1, mean);
+ − 143 # P standard error.
+ − 144 p_se = apply(p_replications, 1, sd) / sqrt(opt$replications);
+ − 145 # F1 mean.
+ − 146 f1_m = apply(f1_replications, 1, mean);
+ − 147 # F1 standard error.
+ − 148 f1_se = apply(f1_replications, 1, sd) / sqrt(opt$replications);
+ − 149 # F2 mean.
+ − 150 f2_m = apply(f2_replications, 1, mean);
+ − 151 # F2 standard error.
+ − 152 f2_se = apply(f2_replications, 1, sd) / sqrt(opt$replications);
+ − 153 return(list(p_m, p_se, f1_m, f1_se, f2_m, f2_se))
+ − 154 }
+ − 155
5
+ − 156 get_temperature_at_hour = function(latitude, temperature_data_frame, row, num_days) {
8
+ − 157 # Base development threshold for Brown Marmorated Stink Bug
5
+ − 158 # insect phenology model.
8
+ − 159 threshold = 14.17;
5
+ − 160 # Minimum temperature for current row.
8
+ − 161 curr_min_temp = temperature_data_frame$TMIN[row];
5
+ − 162 # Maximum temperature for current row.
8
+ − 163 curr_max_temp = temperature_data_frame$TMAX[row];
5
+ − 164 # Mean temperature for current row.
8
+ − 165 curr_mean_temp = 0.5 * (curr_min_temp + curr_max_temp);
5
+ − 166 # Initialize degree day accumulation
8
+ − 167 averages = 0;
6
+ − 168 if (curr_max_temp < threshold) {
8
+ − 169 averages = 0;
5
+ − 170 }
+ − 171 else {
+ − 172 # Initialize hourly temperature.
8
+ − 173 T = NULL;
5
+ − 174 # Initialize degree hour vector.
8
+ − 175 dh = NULL;
5
+ − 176 # Daylight length for current row.
8
+ − 177 y = temperature_data_frame$DAYLEN[row];
5
+ − 178 # Darkness length.
8
+ − 179 z = 24 - y;
5
+ − 180 # Lag coefficient.
8
+ − 181 a = 1.86;
5
+ − 182 # Darkness coefficient.
8
+ − 183 b = 2.20;
5
+ − 184 # Sunrise time.
8
+ − 185 risetime = 12 - y / 2;
5
+ − 186 # Sunset time.
8
+ − 187 settime = 12 + y / 2;
+ − 188 ts = (curr_max_temp - curr_min_temp) * sin(pi * (settime - 5) / (y + 2 * a)) + curr_min_temp;
5
+ − 189 for (i in 1:24) {
+ − 190 if (i > risetime && i < settime) {
+ − 191 # Number of hours after Tmin until sunset.
8
+ − 192 m = i - 5;
+ − 193 T[i] = (curr_max_temp - curr_min_temp) * sin(pi * m / (y + 2 * a)) + curr_min_temp;
5
+ − 194 if (T[i] < 8.4) {
8
+ − 195 dh[i] = 0;
5
+ − 196 }
+ − 197 else {
8
+ − 198 dh[i] = T[i] - 8.4;
5
+ − 199 }
+ − 200 }
6
+ − 201 else if (i > settime) {
8
+ − 202 n = i - settime;
+ − 203 T[i] = curr_min_temp + (ts - curr_min_temp) * exp( - b * n / z);
5
+ − 204 if (T[i] < 8.4) {
8
+ − 205 dh[i] = 0;
5
+ − 206 }
+ − 207 else {
8
+ − 208 dh[i] = T[i] - 8.4;
5
+ − 209 }
+ − 210 }
+ − 211 else {
8
+ − 212 n = i + 24 - settime;
+ − 213 T[i] = curr_min_temp + (ts - curr_min_temp) * exp( - b * n / z);
5
+ − 214 if (T[i] < 8.4) {
8
+ − 215 dh[i] = 0;
5
+ − 216 }
+ − 217 else {
8
+ − 218 dh[i] = T[i] - 8.4;
5
+ − 219 }
+ − 220 }
+ − 221 }
8
+ − 222 averages = sum(dh) / 24;
5
+ − 223 }
6
+ − 224 return(c(curr_mean_temp, averages))
5
+ − 225 }
+ − 226
6
+ − 227 mortality.adult = function(temperature) {
+ − 228 if (temperature < 12.7) {
8
+ − 229 mortality.probability = 0.002;
6
+ − 230 }
+ − 231 else {
8
+ − 232 mortality.probability = temperature * 0.0005 + 0.02;
6
+ − 233 }
+ − 234 return(mortality.probability)
5
+ − 235 }
+ − 236
+ − 237 mortality.egg = function(temperature) {
+ − 238 if (temperature < 12.7) {
8
+ − 239 mortality.probability = 0.8;
5
+ − 240 }
+ − 241 else {
8
+ − 242 mortality.probability = 0.8 - temperature / 40.0;
6
+ − 243 if (mortality.probability < 0) {
8
+ − 244 mortality.probability = 0.01;
5
+ − 245 }
+ − 246 }
6
+ − 247 return(mortality.probability)
5
+ − 248 }
+ − 249
+ − 250 mortality.nymph = function(temperature) {
+ − 251 if (temperature < 12.7) {
8
+ − 252 mortality.probability = 0.03;
5
+ − 253 }
+ − 254 else {
8
+ − 255 mortality.probability = temperature * 0.0008 + 0.03;
5
+ − 256 }
8
+ − 257 return(mortality.probability);
6
+ − 258 }
+ − 259
+ − 260 parse_input_data = function(input_file, num_rows) {
+ − 261 # Read in the input temperature datafile into a data frame.
8
+ − 262 temperature_data_frame = read.csv(file=input_file, header=T, strip.white=TRUE, sep=",");
+ − 263 num_columns = dim(temperature_data_frame)[2];
6
+ − 264 if (num_columns == 6) {
+ − 265 # The input data has the following 6 columns:
+ − 266 # LATITUDE, LONGITUDE, DATE, DOY, TMIN, TMAX
+ − 267 # Set the column names for access when adding daylight length..
8
+ − 268 colnames(temperature_data_frame) = c("LATITUDE","LONGITUDE", "DATE", "DOY", "TMIN", "TMAX");
27
+ − 269 current_column_names = colnames(temperature_data_frame);
6
+ − 270 # Add a column containing the daylight length for each day.
27
+ − 271 temperature_data_frame = add_daylight_length(temperature_data_frame, num_rows);
6
+ − 272 }
8
+ − 273 return(temperature_data_frame);
5
+ − 274 }
+ − 275
34
+ − 276 render_chart = function(ticks, date_labels, chart_type, plot_std_error, insect, location, latitude, start_date, end_date, days, maxval,
20
+ − 277 replications, life_stage, group, group_std_error, group2=NULL, group2_std_error=NULL, group3=NULL, group3_std_error=NULL,
+ − 278 life_stages_adult=NULL, life_stages_nymph=NULL) {
10
+ − 279 if (chart_type=="pop_size_by_life_stage") {
+ − 280 if (life_stage=="Total") {
+ − 281 title = paste(insect, ": Reps", replications, ":", life_stage, "Pop :", location, ": Lat", latitude, ":", start_date, "-", end_date, sep=" ");
+ − 282 legend_text = c("Egg", "Nymph", "Adult");
+ − 283 columns = c(4, 2, 1);
+ − 284 plot(days, group, main=title, type="l", ylim=c(0, maxval), axes=F, lwd=2, xlab="", ylab="", cex=3, cex.lab=3, cex.axis=3, cex.main=3);
+ − 285 legend("topleft", legend_text, lty=c(1, 1, 1), col=columns, cex=3);
+ − 286 lines(days, group2, lwd=2, lty=1, col=2);
+ − 287 lines(days, group3, lwd=2, lty=1, col=4);
34
+ − 288 axis(side=1, at=ticks, labels=date_labels);
+ − 289 axis(side=2);
10
+ − 290 if (plot_std_error=="yes") {
+ − 291 # Standard error for group.
+ − 292 lines(days, group+group_std_error, lty=2);
+ − 293 lines(days, group-group_std_error, lty=2);
+ − 294 # Standard error for group2.
+ − 295 lines(days, group2+group2_std_error, col=2, lty=2);
+ − 296 lines(days, group2-group2_std_error, col=2, lty=2);
+ − 297 # Standard error for group3.
+ − 298 lines(days, group3+group3_std_error, col=4, lty=2);
+ − 299 lines(days, group3-group3_std_error, col=4, lty=2);
+ − 300 }
+ − 301 } else {
+ − 302 if (life_stage=="Egg") {
+ − 303 title = paste(insect, ": Reps", replications, ":", life_stage, "Pop :", location, ": Lat", latitude, ":", start_date, "-", end_date, sep=" ");
+ − 304 legend_text = c(life_stage);
15
+ − 305 columns = c(4);
10
+ − 306 } else if (life_stage=="Nymph") {
16
+ − 307 stage = paste(life_stages_nymph, "Nymph Pop :", sep=" ");
10
+ − 308 title = paste(insect, ": Reps", replications, ":", stage, location, ": Lat", latitude, ":", start_date, "-", end_date, sep=" ");
16
+ − 309 legend_text = c(paste(life_stages_nymph, life_stage, sep=" "));
10
+ − 310 columns = c(2);
+ − 311 } else if (life_stage=="Adult") {
+ − 312 stage = paste(life_stages_adult, "Adult Pop", sep=" ");
+ − 313 title = paste(insect, ": Reps", replications, ":", stage, location, ": Lat", latitude, ":", start_date, "-", end_date, sep=" ");
+ − 314 legend_text = c(paste(life_stages_adult, life_stage, sep=" "));
+ − 315 columns = c(1);
+ − 316 }
+ − 317 plot(days, group, main=title, type="l", ylim=c(0, maxval), axes=F, lwd=2, xlab="", ylab="", cex=3, cex.lab=3, cex.axis=3, cex.main=3);
+ − 318 legend("topleft", legend_text, lty=c(1), col="black", cex=3);
34
+ − 319 axis(side=1, at=ticks, labels=date_labels);
+ − 320 axis(side=2);
10
+ − 321 if (plot_std_error=="yes") {
+ − 322 # Standard error for group.
+ − 323 lines(days, group+group_std_error, lty=2);
+ − 324 lines(days, group-group_std_error, lty=2);
+ − 325 }
+ − 326 }
+ − 327 } else if (chart_type=="pop_size_by_generation") {
+ − 328 if (life_stage=="Total") {
+ − 329 title_str = ": Total Pop by Gen :";
+ − 330 } else if (life_stage=="Egg") {
+ − 331 title_str = ": Egg Pop by Gen :";
+ − 332 } else if (life_stage=="Nymph") {
16
+ − 333 title_str = paste(":", life_stages_nymph, "Nymph Pop by Gen", ":", sep=" ");
10
+ − 334 } else if (life_stage=="Adult") {
+ − 335 title_str = paste(":", life_stages_adult, "Adult Pop by Gen", ":", sep=" ");
+ − 336 }
+ − 337 title = paste(insect, ": Reps", replications, title_str, location, ": Lat", latitude, ":", start_date, "-", end_date, sep=" ");
8
+ − 338 legend_text = c("P", "F1", "F2");
+ − 339 columns = c(1, 2, 4);
10
+ − 340 plot(days, group, main=title, type="l", ylim=c(0, maxval), axes=F, lwd=2, xlab="", ylab="", cex=3, cex.lab=3, cex.axis=3, cex.main=3);
+ − 341 legend("topleft", legend_text, lty=c(1, 1, 1), col=columns, cex=3);
+ − 342 lines(days, group2, lwd=2, lty=1, col=2);
+ − 343 lines(days, group3, lwd=2, lty=1, col=4);
34
+ − 344 axis(side=1, at=ticks, labels=date_labels);
+ − 345 axis(side=2);
10
+ − 346 if (plot_std_error=="yes") {
+ − 347 # Standard error for group.
+ − 348 lines(days, group+group_std_error, lty=2);
+ − 349 lines(days, group-group_std_error, lty=2);
+ − 350 # Standard error for group2.
+ − 351 lines(days, group2+group2_std_error, col=2, lty=2);
+ − 352 lines(days, group2-group2_std_error, col=2, lty=2);
+ − 353 # Standard error for group3.
+ − 354 lines(days, group3+group3_std_error, col=4, lty=2);
+ − 355 lines(days, group3-group3_std_error, col=4, lty=2);
+ − 356 }
5
+ − 357 }
+ − 358 }
+ − 359
10
+ − 360 # Determine if we're plotting generations separately.
+ − 361 if (opt$plot_generations_separately=="yes") {
+ − 362 plot_generations_separately = TRUE;
+ − 363 } else {
+ − 364 plot_generations_separately = FALSE;
+ − 365 }
+ − 366 # Read the temperature data into a data frame.
8
+ − 367 temperature_data_frame = parse_input_data(opt$input, opt$num_days);
31
+ − 368 # Create copies of the temperature data for generations P, F1 and F2 if we're plotting generations separately.
+ − 369 if (plot_generations_separately) {
+ − 370 temperature_data_frame_P = data.frame(temperature_data_frame);
+ − 371 temperature_data_frame_F1 = data.frame(temperature_data_frame);
+ − 372 temperature_data_frame_F2 = data.frame(temperature_data_frame);
+ − 373 }
10
+ − 374 # Get the date labels for plots.
34
+ − 375 ticks_and_labels = get_x_axis_ticks_and_labels(temperature_data_frame, opt$num_days);
+ − 376 ticks = c(unlist(ticks_and_labels[1]));
+ − 377 date_labels = c(unlist(ticks_and_labels[2]));
10
+ − 378 # All latitude values are the same, so get the value for plots from the first row.
8
+ − 379 latitude = temperature_data_frame$LATITUDE[1];
20
+ − 380 # Determine the specified life stages for processing.
10
+ − 381 # Split life_stages into a list of strings for plots.
+ − 382 life_stages_str = as.character(opt$life_stages);
+ − 383 life_stages = strsplit(life_stages_str, ",")[[1]];
+ − 384 # Determine the data we need to generate for plotting.
+ − 385 process_eggs = FALSE;
+ − 386 process_nymphs = FALSE;
20
+ − 387 process_young_nymphs = FALSE;
+ − 388 process_old_nymphs = FALSE;
+ − 389 process_total_nymphs = FALSE;
10
+ − 390 process_adults = FALSE;
23
+ − 391 process_previttelogenic_adults = FALSE;
+ − 392 process_vittelogenic_adults = FALSE;
20
+ − 393 process_diapausing_adults = FALSE;
+ − 394 process_total_adults = FALSE;
10
+ − 395 for (life_stage in life_stages) {
+ − 396 if (life_stage=="Total") {
+ − 397 process_eggs = TRUE;
+ − 398 process_nymphs = TRUE;
+ − 399 process_adults = TRUE;
+ − 400 } else if (life_stage=="Egg") {
+ − 401 process_eggs = TRUE;
+ − 402 } else if (life_stage=="Nymph") {
+ − 403 process_nymphs = TRUE;
+ − 404 } else if (life_stage=="Adult") {
+ − 405 process_adults = TRUE;
+ − 406 }
+ − 407 }
20
+ − 408 if (process_nymphs) {
+ − 409 # Split life_stages_nymph into a list of strings for plots.
+ − 410 life_stages_nymph_str = as.character(opt$life_stages_nymph);
+ − 411 life_stages_nymph = strsplit(life_stages_nymph_str, ",")[[1]];
23
+ − 412 for (life_stage_nymph in life_stages_nymph) {
20
+ − 413 if (life_stage_nymph=="Young") {
+ − 414 process_young_nymphs = TRUE;
+ − 415 } else if (life_stage_nymph=="Old") {
+ − 416 process_old_nymphs = TRUE;
+ − 417 } else if (life_stage_nymph=="Total") {
+ − 418 process_total_nymphs = TRUE;
+ − 419 }
+ − 420 }
+ − 421 }
16
+ − 422 if (process_adults) {
+ − 423 # Split life_stages_adult into a list of strings for plots.
+ − 424 life_stages_adult_str = as.character(opt$life_stages_adult);
+ − 425 life_stages_adult = strsplit(life_stages_adult_str, ",")[[1]];
23
+ − 426 for (life_stage_adult in life_stages_adult) {
+ − 427 if (life_stage_adult=="Pre-vittelogenic") {
+ − 428 process_previttelogenic_adults = TRUE;
24
+ − 429 } else if (life_stage_adult=="Vittelogenic") {
23
+ − 430 process_vittelogenic_adults = TRUE;
20
+ − 431 } else if (life_stage_adult=="Diapausing") {
+ − 432 process_diapausing_adults = TRUE;
+ − 433 } else if (life_stage_adult=="Total") {
+ − 434 process_total_adults = TRUE;
+ − 435 }
+ − 436 }
16
+ − 437 }
6
+ − 438 # Initialize matrices.
10
+ − 439 if (process_eggs) {
+ − 440 Eggs.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
+ − 441 }
23
+ − 442 if (process_young_nymphs | process_total_nymphs) {
10
+ − 443 YoungNymphs.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
20
+ − 444 }
23
+ − 445 if (process_old_nymphs | process_total_nymphs) {
10
+ − 446 OldNymphs.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
+ − 447 }
23
+ − 448 if (process_previttelogenic_adults | process_total_adults) {
+ − 449 Previttelogenic.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
+ − 450 }
+ − 451 if (process_vittelogenic_adults | process_total_adults) {
24
+ − 452 Vittelogenic.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
23
+ − 453 }
+ − 454 if (process_diapausing_adults | process_total_adults) {
10
+ − 455 Diapausing.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
+ − 456 }
8
+ − 457 newborn.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
+ − 458 adult.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
+ − 459 death.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
10
+ − 460 if (plot_generations_separately) {
+ − 461 # P is Parental, or overwintered adults.
+ − 462 P.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
+ − 463 # F1 is the first field-produced generation.
+ − 464 F1.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
+ − 465 # F2 is the second field-produced generation.
+ − 466 F2.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
+ − 467 if (process_eggs) {
+ − 468 P_eggs.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
+ − 469 F1_eggs.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
+ − 470 F2_eggs.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
+ − 471 }
20
+ − 472 if (process_young_nymphs) {
+ − 473 P_young_nymphs.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
+ − 474 F1_young_nymphs.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
+ − 475 F2_young_nymphs.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
+ − 476 }
+ − 477 if (process_old_nymphs) {
+ − 478 P_old_nymphs.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
+ − 479 F1_old_nymphs.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
+ − 480 F2_old_nymphs.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
+ − 481 }
+ − 482 if (process_total_nymphs) {
+ − 483 P_total_nymphs.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
+ − 484 F1_total_nymphs.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
+ − 485 F2_total_nymphs.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
10
+ − 486 }
23
+ − 487 if (process_previttelogenic_adults) {
+ − 488 P_previttelogenic_adults.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
+ − 489 F1_previttelogenic_adults.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
+ − 490 F2_previttelogenic_adults.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
+ − 491 }
+ − 492 if (process_vittelogenic_adults) {
+ − 493 P_vittelogenic_adults.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
25
+ − 494 F1_vittelogenic_adults.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
23
+ − 495 F2_vittelogenic_adults.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
+ − 496 }
+ − 497 if (process_diapausing_adults) {
+ − 498 P_diapausing_adults.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
+ − 499 F1_diapausing_adults.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
+ − 500 F2_diapausing_adults.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
+ − 501 }
+ − 502 if (process_total_adults) {
+ − 503 P_total_adults.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
+ − 504 F1_total_adults.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
+ − 505 F2_total_adults.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
10
+ − 506 }
+ − 507 }
+ − 508 # Total population.
8
+ − 509 population.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
5
+ − 510
6
+ − 511 # Process replications.
18
+ − 512 for (current_replication in 1:opt$replications) {
6
+ − 513 # Start with the user-defined number of insects per replication.
8
+ − 514 num_insects = opt$insects_per_replication;
6
+ − 515 # Generation, Stage, degree-days, T, Diapause.
8
+ − 516 vector.ini = c(0, 3, 0, 0, 0);
10
+ − 517 # Replicate to create a matrix where the columns are
+ − 518 # Generation, Stage, degree-days, T, Diapause and the
+ − 519 # rows are the initial number of insects per replication.
8
+ − 520 vector.matrix = rep(vector.ini, num_insects);
10
+ − 521 # Complete transposed matrix for the population, so now
+ − 522 # the rows are Generation, Stage, degree-days, T, Diapause
8
+ − 523 vector.matrix = base::t(matrix(vector.matrix, nrow=5));
5
+ − 524 # Time series of population size.
10
+ − 525 if (process_eggs) {
+ − 526 Eggs = rep(0, opt$num_days);
+ − 527 }
23
+ − 528 if (process_young_nymphs | process_total_nymphs) {
10
+ − 529 YoungNymphs = rep(0, opt$num_days);
23
+ − 530 }
+ − 531 if (process_old_nymphs | process_total_nymphs) {
10
+ − 532 OldNymphs = rep(0, opt$num_days);
+ − 533 }
23
+ − 534 if (process_previttelogenic_adults | process_total_adults) {
+ − 535 Previttelogenic = rep(0, opt$num_days);
+ − 536 }
+ − 537 if (process_vittelogenic_adults | process_total_adults) {
24
+ − 538 Vittelogenic = rep(0, opt$num_days);
23
+ − 539 }
+ − 540 if (process_diapausing_adults | process_total_adults) {
10
+ − 541 Diapausing = rep(0, opt$num_days);
+ − 542 }
8
+ − 543 N.newborn = rep(0, opt$num_days);
+ − 544 N.adult = rep(0, opt$num_days);
+ − 545 N.death = rep(0, opt$num_days);
+ − 546 overwintering_adult.population = rep(0, opt$num_days);
+ − 547 first_generation.population = rep(0, opt$num_days);
+ − 548 second_generation.population = rep(0, opt$num_days);
10
+ − 549 if (plot_generations_separately) {
+ − 550 # P is Parental, or overwintered adults.
+ − 551 # F1 is the first field-produced generation.
+ − 552 # F2 is the second field-produced generation.
+ − 553 if (process_eggs) {
+ − 554 P.egg = rep(0, opt$num_days);
+ − 555 F1.egg = rep(0, opt$num_days);
+ − 556 F2.egg = rep(0, opt$num_days);
+ − 557 }
20
+ − 558 if (process_young_nymphs) {
+ − 559 P.young_nymph = rep(0, opt$num_days);
+ − 560 F1.young_nymph = rep(0, opt$num_days);
+ − 561 F2.young_nymph = rep(0, opt$num_days);
+ − 562 }
+ − 563 if (process_old_nymphs) {
+ − 564 P.old_nymph = rep(0, opt$num_days);
+ − 565 F1.old_nymph = rep(0, opt$num_days);
+ − 566 F2.old_nymph = rep(0, opt$num_days);
+ − 567 }
+ − 568 if (process_total_nymphs) {
+ − 569 P.total_nymph = rep(0, opt$num_days);
+ − 570 F1.total_nymph = rep(0, opt$num_days);
+ − 571 F2.total_nymph = rep(0, opt$num_days);
10
+ − 572 }
23
+ − 573 if (process_previttelogenic_adults) {
+ − 574 P.previttelogenic_adult = rep(0, opt$num_days);
+ − 575 F1.previttelogenic_adult = rep(0, opt$num_days);
+ − 576 F2.previttelogenic_adult = rep(0, opt$num_days);
+ − 577 }
+ − 578 if (process_vittelogenic_adults) {
+ − 579 P.vittelogenic_adult = rep(0, opt$num_days);
+ − 580 F1.vittelogenic_adult = rep(0, opt$num_days);
+ − 581 F2.vittelogenic_adult = rep(0, opt$num_days);
+ − 582 }
+ − 583 if (process_diapausing_adults) {
+ − 584 P.diapausing_adult = rep(0, opt$num_days);
+ − 585 F1.diapausing_adult = rep(0, opt$num_days);
+ − 586 F2.diapausing_adult = rep(0, opt$num_days);
+ − 587 }
+ − 588 if (process_total_adults) {
+ − 589 P.total_adult = rep(0, opt$num_days);
+ − 590 F1.total_adult = rep(0, opt$num_days);
+ − 591 F2.total_adult = rep(0, opt$num_days);
10
+ − 592 }
+ − 593 }
8
+ − 594 total.population = NULL;
+ − 595 averages.day = rep(0, opt$num_days);
5
+ − 596 # All the days included in the input temperature dataset.
+ − 597 for (row in 1:opt$num_days) {
+ − 598 # Get the integer day of the year for the current row.
8
+ − 599 doy = temperature_data_frame$DOY[row];
5
+ − 600 # Photoperiod in the day.
8
+ − 601 photoperiod = temperature_data_frame$DAYLEN[row];
+ − 602 temp.profile = get_temperature_at_hour(latitude, temperature_data_frame, row, opt$num_days);
+ − 603 mean.temp = temp.profile[1];
+ − 604 averages.temp = temp.profile[2];
+ − 605 averages.day[row] = averages.temp;
5
+ − 606 # Trash bin for death.
8
+ − 607 death.vector = NULL;
5
+ − 608 # Newborn.
8
+ − 609 birth.vector = NULL;
5
+ − 610 # All individuals.
6
+ − 611 for (i in 1:num_insects) {
+ − 612 # Individual record.
8
+ − 613 vector.individual = vector.matrix[i,];
6
+ − 614 # Adjustment for late season mortality rate (still alive?).
5
+ − 615 if (latitude < 40.0) {
8
+ − 616 post.mortality = 1;
+ − 617 day.kill = 300;
5
+ − 618 }
+ − 619 else {
8
+ − 620 post.mortality = 2;
+ − 621 day.kill = 250;
5
+ − 622 }
6
+ − 623 if (vector.individual[2] == 0) {
5
+ − 624 # Egg.
8
+ − 625 death.probability = opt$egg_mortality * mortality.egg(mean.temp);
5
+ − 626 }
6
+ − 627 else if (vector.individual[2] == 1 | vector.individual[2] == 2) {
18
+ − 628 # Nymph.
8
+ − 629 death.probability = opt$nymph_mortality * mortality.nymph(mean.temp);
5
+ − 630 }
6
+ − 631 else if (vector.individual[2] == 3 | vector.individual[2] == 4 | vector.individual[2] == 5) {
+ − 632 # Adult.
5
+ − 633 if (doy < day.kill) {
8
+ − 634 death.probability = opt$adult_mortality * mortality.adult(mean.temp);
5
+ − 635 }
+ − 636 else {
+ − 637 # Increase adult mortality after fall equinox.
8
+ − 638 death.probability = opt$adult_mortality * post.mortality * mortality.adult(mean.temp);
5
+ − 639 }
+ − 640 }
6
+ − 641 # Dependent on temperature and life stage?
8
+ − 642 u.d = runif(1);
6
+ − 643 if (u.d < death.probability) {
8
+ − 644 death.vector = c(death.vector, i);
6
+ − 645 }
5
+ − 646 else {
6
+ − 647 # End of diapause.
+ − 648 if (vector.individual[1] == 0 && vector.individual[2] == 3) {
27
+ − 649 # Overwintering adult (pre-vittelogenic).
6
+ − 650 if (photoperiod > opt$photoperiod && vector.individual[3] > 68 && doy < 180) {
5
+ − 651 # Add 68C to become fully reproductively matured.
+ − 652 # Transfer to vittelogenic.
8
+ − 653 vector.individual = c(0, 4, 0, 0, 0);
+ − 654 vector.matrix[i,] = vector.individual;
5
+ − 655 }
+ − 656 else {
27
+ − 657 # Add average temperature for current day.
8
+ − 658 vector.individual[3] = vector.individual[3] + averages.temp;
5
+ − 659 # Add 1 day in current stage.
8
+ − 660 vector.individual[4] = vector.individual[4] + 1;
+ − 661 vector.matrix[i,] = vector.individual;
5
+ − 662 }
+ − 663 }
6
+ − 664 if (vector.individual[1] != 0 && vector.individual[2] == 3) {
27
+ − 665 # Not overwintering adult (pre-vittelogenic).
8
+ − 666 current.gen = vector.individual[1];
6
+ − 667 if (vector.individual[3] > 68) {
5
+ − 668 # Add 68C to become fully reproductively matured.
+ − 669 # Transfer to vittelogenic.
8
+ − 670 vector.individual = c(current.gen, 4, 0, 0, 0);
+ − 671 vector.matrix[i,] = vector.individual;
5
+ − 672 }
+ − 673 else {
6
+ − 674 # Add average temperature for current day.
8
+ − 675 vector.individual[3] = vector.individual[3] + averages.temp;
5
+ − 676 # Add 1 day in current stage.
8
+ − 677 vector.individual[4] = vector.individual[4] + 1;
+ − 678 vector.matrix[i,] = vector.individual;
5
+ − 679 }
+ − 680 }
6
+ − 681 # Oviposition -- where population dynamics comes from.
+ − 682 if (vector.individual[2] == 4 && vector.individual[1] == 0 && mean.temp > 10) {
5
+ − 683 # Vittelogenic stage, overwintering generation.
6
+ − 684 if (vector.individual[4] == 0) {
5
+ − 685 # Just turned in vittelogenic stage.
8
+ − 686 num_insects.birth = round(runif(1, 2 + opt$min_clutch_size, 8 + opt$max_clutch_size));
5
+ − 687 }
+ − 688 else {
+ − 689 # Daily probability of birth.
8
+ − 690 p.birth = opt$oviposition * 0.01;
+ − 691 u1 = runif(1);
5
+ − 692 if (u1 < p.birth) {
8
+ − 693 num_insects.birth = round(runif(1, 2, 8));
5
+ − 694 }
+ − 695 }
6
+ − 696 # Add average temperature for current day.
8
+ − 697 vector.individual[3] = vector.individual[3] + averages.temp;
5
+ − 698 # Add 1 day in current stage.
8
+ − 699 vector.individual[4] = vector.individual[4] + 1;
+ − 700 vector.matrix[i,] = vector.individual;
6
+ − 701 if (num_insects.birth > 0) {
5
+ − 702 # Add new birth -- might be in different generations.
8
+ − 703 new.gen = vector.individual[1] + 1;
5
+ − 704 # Egg profile.
8
+ − 705 new.individual = c(new.gen, 0, 0, 0, 0);
+ − 706 new.vector = rep(new.individual, num_insects.birth);
5
+ − 707 # Update batch of egg profile.
8
+ − 708 new.vector = t(matrix(new.vector, nrow=5));
5
+ − 709 # Group with total eggs laid in that day.
8
+ − 710 birth.vector = rbind(birth.vector, new.vector);
5
+ − 711 }
+ − 712 }
6
+ − 713 # Oviposition -- for generation 1.
+ − 714 if (vector.individual[2] == 4 && vector.individual[1] == 1 && mean.temp > 12.5 && doy < 222) {
5
+ − 715 # Vittelogenic stage, 1st generation
6
+ − 716 if (vector.individual[4] == 0) {
5
+ − 717 # Just turned in vittelogenic stage.
8
+ − 718 num_insects.birth = round(runif(1, 2+opt$min_clutch_size, 8+opt$max_clutch_size));
5
+ − 719 }
+ − 720 else {
+ − 721 # Daily probability of birth.
8
+ − 722 p.birth = opt$oviposition * 0.01;
+ − 723 u1 = runif(1);
5
+ − 724 if (u1 < p.birth) {
8
+ − 725 num_insects.birth = round(runif(1, 2, 8));
5
+ − 726 }
+ − 727 }
6
+ − 728 # Add average temperature for current day.
8
+ − 729 vector.individual[3] = vector.individual[3] + averages.temp;
5
+ − 730 # Add 1 day in current stage.
8
+ − 731 vector.individual[4] = vector.individual[4] + 1;
+ − 732 vector.matrix[i,] = vector.individual;
6
+ − 733 if (num_insects.birth > 0) {
5
+ − 734 # Add new birth -- might be in different generations.
8
+ − 735 new.gen = vector.individual[1] + 1;
5
+ − 736 # Egg profile.
8
+ − 737 new.individual = c(new.gen, 0, 0, 0, 0);
+ − 738 new.vector = rep(new.individual, num_insects.birth);
5
+ − 739 # Update batch of egg profile.
8
+ − 740 new.vector = t(matrix(new.vector, nrow=5));
5
+ − 741 # Group with total eggs laid in that day.
8
+ − 742 birth.vector = rbind(birth.vector, new.vector);
5
+ − 743 }
+ − 744 }
6
+ − 745 # Egg to young nymph.
+ − 746 if (vector.individual[2] == 0) {
+ − 747 # Add average temperature for current day.
8
+ − 748 vector.individual[3] = vector.individual[3] + averages.temp;
6
+ − 749 if (vector.individual[3] >= (68+opt$young_nymph_accumulation)) {
+ − 750 # From egg to young nymph, degree-days requirement met.
8
+ − 751 current.gen = vector.individual[1];
5
+ − 752 # Transfer to young nymph stage.
8
+ − 753 vector.individual = c(current.gen, 1, 0, 0, 0);
5
+ − 754 }
+ − 755 else {
+ − 756 # Add 1 day in current stage.
8
+ − 757 vector.individual[4] = vector.individual[4] + 1;
5
+ − 758 }
8
+ − 759 vector.matrix[i,] = vector.individual;
5
+ − 760 }
6
+ − 761 # Young nymph to old nymph.
+ − 762 if (vector.individual[2] == 1) {
+ − 763 # Add average temperature for current day.
8
+ − 764 vector.individual[3] = vector.individual[3] + averages.temp;
6
+ − 765 if (vector.individual[3] >= (250+opt$old_nymph_accumulation)) {
+ − 766 # From young to old nymph, degree_days requirement met.
8
+ − 767 current.gen = vector.individual[1];
5
+ − 768 # Transfer to old nym stage.
8
+ − 769 vector.individual = c(current.gen, 2, 0, 0, 0);
5
+ − 770 if (photoperiod < opt$photoperiod && doy > 180) {
8
+ − 771 vector.individual[5] = 1;
5
+ − 772 } # Prepare for diapausing.
+ − 773 }
+ − 774 else {
+ − 775 # Add 1 day in current stage.
8
+ − 776 vector.individual[4] = vector.individual[4] + 1;
5
+ − 777 }
8
+ − 778 vector.matrix[i,] = vector.individual;
6
+ − 779 }
27
+ − 780 # Old nymph to adult: pre-vittelogenic or diapausing?
6
+ − 781 if (vector.individual[2] == 2) {
+ − 782 # Add average temperature for current day.
8
+ − 783 vector.individual[3] = vector.individual[3] + averages.temp;
6
+ − 784 if (vector.individual[3] >= (200+opt$adult_accumulation)) {
+ − 785 # From old to adult, degree_days requirement met.
8
+ − 786 current.gen = vector.individual[1];
6
+ − 787 if (vector.individual[5] == 0) {
+ − 788 # Previttelogenic.
8
+ − 789 vector.individual = c(current.gen, 3, 0, 0, 0);
5
+ − 790 }
+ − 791 else {
+ − 792 # Diapausing.
8
+ − 793 vector.individual = c(current.gen, 5, 0, 0, 1);
5
+ − 794 }
+ − 795 }
+ − 796 else {
+ − 797 # Add 1 day in current stage.
8
+ − 798 vector.individual[4] = vector.individual[4] + 1;
5
+ − 799 }
8
+ − 800 vector.matrix[i,] = vector.individual;
5
+ − 801 }
6
+ − 802 # Growing of diapausing adult (unimportant, but still necessary).
+ − 803 if (vector.individual[2] == 5) {
8
+ − 804 vector.individual[3] = vector.individual[3] + averages.temp;
+ − 805 vector.individual[4] = vector.individual[4] + 1;
+ − 806 vector.matrix[i,] = vector.individual;
5
+ − 807 }
+ − 808 } # Else if it is still alive.
+ − 809 } # End of the individual bug loop.
6
+ − 810
+ − 811 # Number of deaths.
8
+ − 812 num_insects.death = length(death.vector);
6
+ − 813 if (num_insects.death > 0) {
+ − 814 # Remove record of dead.
8
+ − 815 vector.matrix = vector.matrix[-death.vector,];
5
+ − 816 }
6
+ − 817 # Number of births.
8
+ − 818 num_insects.newborn = length(birth.vector[,1]);
+ − 819 vector.matrix = rbind(vector.matrix, birth.vector);
5
+ − 820 # Update population size for the next day.
8
+ − 821 num_insects = num_insects - num_insects.death + num_insects.newborn;
5
+ − 822
10
+ − 823 # Aggregate results by day. Due to multiple transpose calls
+ − 824 # on vector.matrix above, the columns of vector.matrix
+ − 825 # are now Generation, Stage, degree-days, T, Diapause,
+ − 826 if (process_eggs) {
+ − 827 # For egg population size, column 2 (Stage), must be 0.
+ − 828 Eggs[row] = sum(vector.matrix[,2]==0);
+ − 829 }
23
+ − 830 if (process_young_nymphs | process_total_nymphs) {
10
+ − 831 # For young nymph population size, column 2 (Stage) must be 1.
+ − 832 YoungNymphs[row] = sum(vector.matrix[,2]==1);
20
+ − 833 }
23
+ − 834 if (process_old_nymphs | process_total_nymphs) {
10
+ − 835 # For old nymph population size, column 2 (Stage) must be 2.
+ − 836 OldNymphs[row] = sum(vector.matrix[,2]==2);
+ − 837 }
23
+ − 838 if (process_previttelogenic_adults | process_total_adults) {
+ − 839 # For pre-vittelogenic population size, column 2 (Stage) must be 3.
+ − 840 Previttelogenic[row] = sum(vector.matrix[,2]==3);
+ − 841 }
+ − 842 if (process_vittelogenic_adults | process_total_adults) {
+ − 843 # For vittelogenic population size, column 2 (Stage) must be 4.
24
+ − 844 Vittelogenic[row] = sum(vector.matrix[,2]==4);
23
+ − 845 }
+ − 846 if (process_diapausing_adults | process_total_adults) {
10
+ − 847 # For diapausing population size, column 2 (Stage) must be 5.
+ − 848 Diapausing[row] = sum(vector.matrix[,2]==5);
+ − 849 }
5
+ − 850
6
+ − 851 # Newborn population size.
8
+ − 852 N.newborn[row] = num_insects.newborn;
6
+ − 853 # Adult population size.
8
+ − 854 N.adult[row] = sum(vector.matrix[,2]==3) + sum(vector.matrix[,2]==4) + sum(vector.matrix[,2]==5);
6
+ − 855 # Dead population size.
8
+ − 856 N.death[row] = num_insects.death;
6
+ − 857
8
+ − 858 total.population = c(total.population, num_insects);
6
+ − 859
10
+ − 860 # For overwintering adult (P) population
+ − 861 # size, column 1 (Generation) must be 0.
8
+ − 862 overwintering_adult.population[row] = sum(vector.matrix[,1]==0);
10
+ − 863 # For first field generation (F1) population
+ − 864 # size, column 1 (Generation) must be 1.
8
+ − 865 first_generation.population[row] = sum(vector.matrix[,1]==1);
10
+ − 866 # For second field generation (F2) population
+ − 867 # size, column 1 (Generation) must be 2.
8
+ − 868 second_generation.population[row] = sum(vector.matrix[,1]==2);
5
+ − 869
10
+ − 870 if (plot_generations_separately) {
+ − 871 if (process_eggs) {
18
+ − 872 # For egg life stage of generation P population size,
10
+ − 873 # column 1 (generation) is 0 and column 2 (Stage) is 0.
+ − 874 P.egg[row] = sum(vector.matrix[,1]==0 & vector.matrix[,2]==0);
+ − 875 # For egg life stage of generation F1 population size,
+ − 876 # column 1 (generation) is 1 and column 2 (Stage) is 0.
+ − 877 F1.egg[row] = sum(vector.matrix[,1]==1 & vector.matrix[,2]==0);
+ − 878 # For egg life stage of generation F2 population size,
+ − 879 # column 1 (generation) is 2 and column 2 (Stage) is 0.
+ − 880 F2.egg[row] = sum(vector.matrix[,1]==2 & vector.matrix[,2]==0);
+ − 881 }
20
+ − 882 if (process_young_nymphs) {
+ − 883 # For young nymph life stage of generation P population
+ − 884 # size, the following combination is required:
+ − 885 # - column 1 (Generation) is 0 and column 2 (Stage) is 1 (Young nymph)
+ − 886 P.young_nymph[row] = sum(vector.matrix[,1]==0 & vector.matrix[,2]==1);
+ − 887 # For young nymph life stage of generation F1 population
+ − 888 # size, the following combination is required:
+ − 889 # - column 1 (Generation) is 1 and column 2 (Stage) is 1 (Young nymph)
+ − 890 F1.young_nymph[row] = sum(vector.matrix[,1]==1 & vector.matrix[,2]==1);
+ − 891 # For young nymph life stage of generation F2 population
+ − 892 # size, the following combination is required:
+ − 893 # - column 1 (Generation) is 2 and column 2 (Stage) is 1 (Young nymph)
+ − 894 F2.young_nymph[row] = sum(vector.matrix[,1]==2 & vector.matrix[,2]==1);
+ − 895 }
+ − 896 if (process_old_nymphs) {
+ − 897 # For old nymph life stage of generation P population
+ − 898 # size, the following combination is required:
+ − 899 # - column 1 (Generation) is 0 and column 2 (Stage) is 2 (Old nymph)
+ − 900 P.old_nymph[row] = sum(vector.matrix[,1]==0 & vector.matrix[,2]==2);
+ − 901 # For old nymph life stage of generation F1 population
+ − 902 # size, the following combination is required:
+ − 903 # - column 1 (Generation) is 1 and column 2 (Stage) is 2 (Old nymph)
+ − 904 F1.old_nymph[row] = sum(vector.matrix[,1]==1 & vector.matrix[,2]==2);
+ − 905 # For old nymph life stage of generation F2 population
+ − 906 # size, the following combination is required:
+ − 907 # - column 1 (Generation) is 2 and column 2 (Stage) is 2 (Old nymph)
+ − 908 F2.old_nymph[row] = sum(vector.matrix[,1]==2 & vector.matrix[,2]==2);
+ − 909 }
+ − 910 if (process_total_nymphs) {
+ − 911 # For total nymph life stage of generation P population
10
+ − 912 # size, one of the following combinations is required:
+ − 913 # - column 1 (Generation) is 0 and column 2 (Stage) is 1 (Young nymph)
+ − 914 # - column 1 (Generation) is 0 and column 2 (Stage) is 2 (Old nymph)
20
+ − 915 P.total_nymph[row] = sum((vector.matrix[,1]==0 & vector.matrix[,2]==1) | (vector.matrix[,1]==0 & vector.matrix[,2]==2));
+ − 916 # For total nymph life stage of generation F1 population
10
+ − 917 # size, one of the following combinations is required:
+ − 918 # - column 1 (Generation) is 1 and column 2 (Stage) is 1 (Young nymph)
+ − 919 # - column 1 (Generation) is 1 and column 2 (Stage) is 2 (Old nymph)
20
+ − 920 F1.total_nymph[row] = sum((vector.matrix[,1]==1 & vector.matrix[,2]==1) | (vector.matrix[,1]==1 & vector.matrix[,2]==2));
+ − 921 # For total nymph life stage of generation F2 population
10
+ − 922 # size, one of the following combinations is required:
+ − 923 # - column 1 (Generation) is 2 and column 2 (Stage) is 1 (Young nymph)
+ − 924 # - column 1 (Generation) is 2 and column 2 (Stage) is 2 (Old nymph)
20
+ − 925 F2.total_nymph[row] = sum((vector.matrix[,1]==2 & vector.matrix[,2]==1) | (vector.matrix[,1]==2 & vector.matrix[,2]==2));
10
+ − 926 }
23
+ − 927 if (process_previttelogenic_adults) {
+ − 928 # For previttelogenic adult life stage of generation P population
+ − 929 # size, the following combination is required:
+ − 930 # - column 1 (Generation) is 0 and column 2 (Stage) is 3 (Pre-vittelogenic)
+ − 931 P.previttelogenic_adult[row] = sum(vector.matrix[,1]==0 & vector.matrix[,2]==3);
+ − 932 # For previttelogenic adult life stage of generation F1 population
+ − 933 # size, the following combination is required:
+ − 934 # - column 1 (Generation) is 1 and column 2 (Stage) is 3 (Pre-vittelogenic)
+ − 935 F1.previttelogenic_adult[row] = sum(vector.matrix[,1]==1 & vector.matrix[,2]==3);
+ − 936 # For previttelogenic adult life stage of generation F2 population
+ − 937 # size, the following combination is required:
+ − 938 # - column 1 (Generation) is 2 and column 2 (Stage) is 3 (Pre-vittelogenic)
+ − 939 F2.previttelogenic_adult[row] = sum(vector.matrix[,1]==2 & vector.matrix[,2]==3);
+ − 940 }
+ − 941 if (process_vittelogenic_adults) {
+ − 942 # For vittelogenic adult life stage of generation P population
+ − 943 # size, the following combination is required:
24
+ − 944 # - column 1 (Generation) is 0 and column 2 (Stage) is 4 (Vittelogenic)
23
+ − 945 P.vittelogenic_adult[row] = sum(vector.matrix[,1]==0 & vector.matrix[,2]==4);
+ − 946 # For vittelogenic adult life stage of generation F1 population
+ − 947 # size, the following combination is required:
24
+ − 948 # - column 1 (Generation) is 1 and column 2 (Stage) is 4 (Vittelogenic)
23
+ − 949 F1.vittelogenic_adult[row] = sum(vector.matrix[,1]==1 & vector.matrix[,2]==4);
+ − 950 # For vittelogenic adult life stage of generation F2 population
+ − 951 # size, the following combination is required:
24
+ − 952 # - column 1 (Generation) is 2 and column 2 (Stage) is 4 (Vittelogenic)
23
+ − 953 F2.vittelogenic_adult[row] = sum(vector.matrix[,1]==2 & vector.matrix[,2]==4);
+ − 954 }
+ − 955 if (process_diapausing_adults) {
+ − 956 # For diapausing adult life stage of generation P population
+ − 957 # size, the following combination is required:
10
+ − 958 # - column 1 (Generation) is 0 and column 2 (Stage) is 5 (Diapausing)
23
+ − 959 P.diapausing_adult[row] = sum(vector.matrix[,1]==0 & vector.matrix[,2]==5);
+ − 960 # For diapausing adult life stage of generation F1 population
+ − 961 # size, the following combination is required:
+ − 962 # - column 1 (Generation) is 1 and column 2 (Stage) is 5 (Diapausing)
+ − 963 F1.diapausing_adult[row] = sum(vector.matrix[,1]==1 & vector.matrix[,2]==5);
+ − 964 # For diapausing adult life stage of generation F2 population
+ − 965 # size, the following combination is required:
+ − 966 # - column 1 (Generation) is 2 and column 2 (Stage) is 5 (Diapausing)
+ − 967 F2.diapausing_adult[row] = sum(vector.matrix[,1]==2 & vector.matrix[,2]==5);
+ − 968 }
+ − 969 if (process_total_adults) {
+ − 970 # For total adult life stage of generation P population
10
+ − 971 # size, one of the following combinations is required:
23
+ − 972 # - column 1 (Generation) is 0 and column 2 (Stage) is 3 (Pre-vittelogenic)
24
+ − 973 # - column 1 (Generation) is 0 and column 2 (Stage) is 4 (Vittelogenic)
23
+ − 974 # - column 1 (Generation) is 0 and column 2 (Stage) is 5 (Diapausing)
+ − 975 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));
+ − 976 # For total adult life stage of generation F1 population
+ − 977 # size, one of the following combinations is required:
+ − 978 # - column 1 (Generation) is 1 and column 2 (Stage) is 3 (Pre-vittelogenic)
24
+ − 979 # - column 1 (Generation) is 1 and column 2 (Stage) is 4 (Vittelogenic)
10
+ − 980 # - column 1 (Generation) is 1 and column 2 (Stage) is 5 (Diapausing)
23
+ − 981 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));
+ − 982 # For total adult life stage of generation F2 population
10
+ − 983 # size, one of the following combinations is required:
23
+ − 984 # - column 1 (Generation) is 2 and column 2 (Stage) is 3 (Pre-vittelogenic)
24
+ − 985 # - column 1 (Generation) is 2 and column 2 (Stage) is 4 (Vittelogenic)
10
+ − 986 # - column 1 (Generation) is 2 and column 2 (Stage) is 5 (Diapausing)
23
+ − 987 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));
10
+ − 988 }
+ − 989 }
6
+ − 990 } # End of days specified in the input temperature data.
5
+ − 991
8
+ − 992 averages.cum = cumsum(averages.day);
5
+ − 993
6
+ − 994 # Define the output values.
10
+ − 995 if (process_eggs) {
18
+ − 996 Eggs.replications[,current_replication] = Eggs;
10
+ − 997 }
23
+ − 998 if (process_young_nymphs | process_total_nymphs) {
18
+ − 999 YoungNymphs.replications[,current_replication] = YoungNymphs;
20
+ − 1000 }
23
+ − 1001 if (process_old_nymphs | process_total_nymphs) {
18
+ − 1002 OldNymphs.replications[,current_replication] = OldNymphs;
10
+ − 1003 }
23
+ − 1004 if (process_previttelogenic_adults | process_total_adults) {
+ − 1005 Previttelogenic.replications[,current_replication] = Previttelogenic;
+ − 1006 }
+ − 1007 if (process_vittelogenic_adults | process_total_adults) {
24
+ − 1008 Vittelogenic.replications[,current_replication] = Vittelogenic;
23
+ − 1009 }
+ − 1010 if (process_diapausing_adults | process_total_adults) {
18
+ − 1011 Diapausing.replications[,current_replication] = Diapausing;
10
+ − 1012 }
18
+ − 1013 newborn.replications[,current_replication] = N.newborn;
+ − 1014 adult.replications[,current_replication] = N.adult;
+ − 1015 death.replications[,current_replication] = N.death;
10
+ − 1016 if (plot_generations_separately) {
+ − 1017 # P is Parental, or overwintered adults.
18
+ − 1018 P.replications[,current_replication] = overwintering_adult.population;
10
+ − 1019 # F1 is the first field-produced generation.
18
+ − 1020 F1.replications[,current_replication] = first_generation.population;
10
+ − 1021 # F2 is the second field-produced generation.
18
+ − 1022 F2.replications[,current_replication] = second_generation.population;
10
+ − 1023 if (process_eggs) {
18
+ − 1024 P_eggs.replications[,current_replication] = P.egg;
+ − 1025 F1_eggs.replications[,current_replication] = F1.egg;
+ − 1026 F2_eggs.replications[,current_replication] = F2.egg;
10
+ − 1027 }
20
+ − 1028 if (process_young_nymphs) {
+ − 1029 P_young_nymphs.replications[,current_replication] = P.young_nymph;
+ − 1030 F1_young_nymphs.replications[,current_replication] = F1.young_nymph;
+ − 1031 F2_young_nymphs.replications[,current_replication] = F2.young_nymph;
+ − 1032 }
+ − 1033 if (process_old_nymphs) {
+ − 1034 P_old_nymphs.replications[,current_replication] = P.old_nymph;
+ − 1035 F1_old_nymphs.replications[,current_replication] = F1.old_nymph;
+ − 1036 F2_old_nymphs.replications[,current_replication] = F2.old_nymph;
+ − 1037 }
+ − 1038 if (process_total_nymphs) {
+ − 1039 P_total_nymphs.replications[,current_replication] = P.total_nymph;
+ − 1040 F1_total_nymphs.replications[,current_replication] = F1.total_nymph;
+ − 1041 F2_total_nymphs.replications[,current_replication] = F2.total_nymph;
10
+ − 1042 }
23
+ − 1043 if (process_previttelogenic_adults) {
+ − 1044 P_previttelogenic_adults.replications[,current_replication] = P.previttelogenic_adult;
+ − 1045 F1_previttelogenic_adults.replications[,current_replication] = F1.previttelogenic_adult;
+ − 1046 F2_previttelogenic_adults.replications[,current_replication] = F2.previttelogenic_adult;
+ − 1047 }
+ − 1048 if (process_vittelogenic_adults) {
+ − 1049 P_vittelogenic_adults.replications[,current_replication] = P.vittelogenic_adult;
+ − 1050 F1_vittelogenic_adults.replications[,current_replication] = F1.vittelogenic_adult;
+ − 1051 F2_vittelogenic_adults.replications[,current_replication] = F2.vittelogenic_adult;
+ − 1052 }
+ − 1053 if (process_diapausing_adults) {
+ − 1054 P_diapausing_adults.replications[,current_replication] = P.diapausing_adult;
+ − 1055 F1_diapausing_adults.replications[,current_replication] = F1.diapausing_adult;
+ − 1056 F2_diapausing_adults.replications[,current_replication] = F2.diapausing_adult;
+ − 1057 }
+ − 1058 if (process_total_adults) {
+ − 1059 P_total_adults.replications[,current_replication] = P.total_adult;
+ − 1060 F1_total_adults.replications[,current_replication] = F1.total_adult;
+ − 1061 F2_total_adults.replications[,current_replication] = F2.total_adult;
10
+ − 1062 }
+ − 1063 }
18
+ − 1064 population.replications[,current_replication] = total.population;
+ − 1065 # End processing replications.
5
+ − 1066 }
+ − 1067
10
+ − 1068 if (process_eggs) {
+ − 1069 # Mean value for eggs.
+ − 1070 eggs = apply(Eggs.replications, 1, mean);
27
+ − 1071 temperature_data_frame = append_vector(temperature_data_frame, eggs, "EGG");
10
+ − 1072 # Standard error for eggs.
+ − 1073 eggs.std_error = apply(Eggs.replications, 1, sd) / sqrt(opt$replications);
27
+ − 1074 temperature_data_frame = append_vector(temperature_data_frame, eggs.std_error, "EGGSE");
10
+ − 1075 }
+ − 1076 if (process_nymphs) {
+ − 1077 # Calculate nymph populations for selected life stage.
16
+ − 1078 for (life_stage_nymph in life_stages_nymph) {
28
+ − 1079 if (life_stage_nymph=="Young") {
16
+ − 1080 # Mean value for young nymphs.
+ − 1081 young_nymphs = apply(YoungNymphs.replications, 1, mean);
27
+ − 1082 temperature_data_frame = append_vector(temperature_data_frame, young_nymphs, "YOUNGNYMPH");
16
+ − 1083 # Standard error for young nymphs.
+ − 1084 young_nymphs.std_error = apply(YoungNymphs.replications / sqrt(opt$replications), 1, sd);
27
+ − 1085 temperature_data_frame = append_vector(temperature_data_frame, young_nymphs.std_error, "YOUNGNYMPHSE");
18
+ − 1086 } else if (life_stage_nymph=="Old") {
16
+ − 1087 # Mean value for old nymphs.
+ − 1088 old_nymphs = apply(OldNymphs.replications, 1, mean);
27
+ − 1089 temperature_data_frame = append_vector(temperature_data_frame, old_nymphs, "OLDNYMPH");
16
+ − 1090 # Standard error for old nymphs.
+ − 1091 old_nymphs.std_error = apply(OldNymphs.replications / sqrt(opt$replications), 1, sd);
27
+ − 1092 temperature_data_frame = append_vector(temperature_data_frame, old_nymphs.std_error, "OLDNYMPHSE");
28
+ − 1093 } else if (life_stage_nymph=="Total") {
+ − 1094 # Mean value for all nymphs.
+ − 1095 total_nymphs = apply((YoungNymphs.replications+OldNymphs.replications), 1, mean);
+ − 1096 temperature_data_frame = append_vector(temperature_data_frame, total_nymphs, "TOTALNYMPH");
+ − 1097 # Standard error for all nymphs.
+ − 1098 total_nymphs.std_error = apply((YoungNymphs.replications+OldNymphs.replications) / sqrt(opt$replications), 1, sd);
+ − 1099 temperature_data_frame = append_vector(temperature_data_frame, total_nymphs.std_error, "TOTALNYMPHSE");
16
+ − 1100 }
10
+ − 1101 }
+ − 1102 }
+ − 1103 if (process_adults) {
+ − 1104 # Calculate adult populations for selected life stage.
16
+ − 1105 for (life_stage_adult in life_stages_adult) {
28
+ − 1106 if (life_stage_adult == "Pre-vittelogenic") {
23
+ − 1107 # Mean value for previttelogenic adults.
+ − 1108 previttelogenic_adults = apply(Previttelogenic.replications, 1, mean);
27
+ − 1109 temperature_data_frame = append_vector(temperature_data_frame, previttelogenic_adults, "PRE-VITADULT");
23
+ − 1110 # Standard error for previttelogenic adults.
+ − 1111 previttelogenic_adults.std_error = apply(Previttelogenic.replications, 1, sd) / sqrt(opt$replications);
27
+ − 1112 temperature_data_frame = append_vector(temperature_data_frame, previttelogenic_adults.std_error, "PRE-VITADULTSE");
18
+ − 1113 } else if (life_stage_adult == "Vittelogenic") {
23
+ − 1114 # Mean value for vittelogenic adults.
24
+ − 1115 vittelogenic_adults = apply(Vittelogenic.replications, 1, mean);
27
+ − 1116 temperature_data_frame = append_vector(temperature_data_frame, vittelogenic_adults, "VITADULT");
23
+ − 1117 # Standard error for vittelogenic adults.
24
+ − 1118 vittelogenic_adults.std_error = apply(Vittelogenic.replications, 1, sd) / sqrt(opt$replications);
27
+ − 1119 temperature_data_frame = append_vector(temperature_data_frame, vittelogenic_adults.std_error, "VITADULTSE");
18
+ − 1120 } else if (life_stage_adult == "Diapausing") {
23
+ − 1121 # Mean value for vittelogenic adults.
16
+ − 1122 diapausing_adults = apply(Diapausing.replications, 1, mean);
27
+ − 1123 temperature_data_frame = append_vector(temperature_data_frame, diapausing_adults, "DIAPAUSINGADULT");
23
+ − 1124 # Standard error for vittelogenic adults.
16
+ − 1125 diapausing_adults.std_error = apply(Diapausing.replications, 1, sd) / sqrt(opt$replications);
27
+ − 1126 temperature_data_frame = append_vector(temperature_data_frame, diapausing_adults.std_error, "DIAPAUSINGADULTSE");
28
+ − 1127 } else if (life_stage_adult=="Total") {
+ − 1128 # Mean value for all adults.
+ − 1129 total_adults = apply((Previttelogenic.replications+Vittelogenic.replications+Diapausing.replications), 1, mean);
+ − 1130 temperature_data_frame = append_vector(temperature_data_frame, total_adults, "TOTALADULT");
+ − 1131 # Standard error for all adults.
+ − 1132 total_adults.std_error = apply((Previttelogenic.replications+Vittelogenic.replications+Diapausing.replications), 1, sd) / sqrt(opt$replications);
+ − 1133 temperature_data_frame = append_vector(temperature_data_frame, total_adults.std_error, "TOTALADULTSE");
16
+ − 1134 }
10
+ − 1135 }
+ − 1136 }
5
+ − 1137
10
+ − 1138 if (plot_generations_separately) {
20
+ − 1139 m_se = get_mean_and_std_error(P.replications, F1.replications, F2.replications);
+ − 1140 P = m_se[[1]];
+ − 1141 P.std_error = m_se[[2]];
+ − 1142 F1 = m_se[[3]];
+ − 1143 F1.std_error = m_se[[4]];
+ − 1144 F2 = m_se[[5]];
+ − 1145 F2.std_error = m_se[[6]];
10
+ − 1146 if (process_eggs) {
20
+ − 1147 m_se = get_mean_and_std_error(P_eggs.replications, F1_eggs.replications, F2_eggs.replications);
+ − 1148 P_eggs = m_se[[1]];
+ − 1149 P_eggs.std_error = m_se[[2]];
31
+ − 1150 temperature_data_frame_P = append_vector(temperature_data_frame_P, P_eggs, "EGG-P");
+ − 1151 temperature_data_frame_P = append_vector(temperature_data_frame_P, P_eggs.std_error, "EGG-P-SE");
20
+ − 1152 F1_eggs = m_se[[3]];
+ − 1153 F1_eggs.std_error = m_se[[4]];
31
+ − 1154 temperature_data_frame_F1 = append_vector(temperature_data_frame_F1, F1_eggs, "EGG-F1");
+ − 1155 temperature_data_frame_F1 = append_vector(temperature_data_frame_F1, F1_eggs.std_error, "EGG-F1-SE");
20
+ − 1156 F2_eggs = m_se[[5]];
+ − 1157 F2_eggs.std_error = m_se[[6]];
31
+ − 1158 temperature_data_frame_F2 = append_vector(temperature_data_frame_F2, F2_eggs, "EGG-F2");
+ − 1159 temperature_data_frame_F2 = append_vector(temperature_data_frame_F2, F2_eggs.std_error, "EGG-F2-SE");
20
+ − 1160 }
+ − 1161 if (process_young_nymphs) {
+ − 1162 m_se = get_mean_and_std_error(P_young_nymphs.replications, F1_young_nymphs.replications, F2_young_nymphs.replications);
+ − 1163 P_young_nymphs = m_se[[1]];
+ − 1164 P_young_nymphs.std_error = m_se[[2]];
31
+ − 1165 temperature_data_frame_P = append_vector(temperature_data_frame_P, P_young_nymphs, "YOUNGNYMPH-P");
+ − 1166 temperature_data_frame_P = append_vector(temperature_data_frame_P, P_young_nymphs.std_error, "YOUNGNYMPH-P-SE");
20
+ − 1167 F1_young_nymphs = m_se[[3]];
+ − 1168 F1_young_nymphs.std_error = m_se[[4]];
31
+ − 1169 temperature_data_frame_F1 = append_vector(temperature_data_frame_F1, F1_young_nymphs, "YOUNGNYMPH-F1");
+ − 1170 temperature_data_frame_F1 = append_vector(temperature_data_frame_F1, F1_young_nymphs.std_error, "YOUNGNYMPH-F1-SE");
20
+ − 1171 F2_young_nymphs = m_se[[5]];
+ − 1172 F2_young_nymphs.std_error = m_se[[6]];
31
+ − 1173 temperature_data_frame_F2 = append_vector(temperature_data_frame_F2, F2_young_nymphs, "YOUNGNYMPH-F2");
+ − 1174 temperature_data_frame_F2 = append_vector(temperature_data_frame_F2, F2_young_nymphs.std_error, "YOUNGNYMPH-F2-SE");
10
+ − 1175 }
20
+ − 1176 if (process_old_nymphs) {
+ − 1177 m_se = get_mean_and_std_error(P_old_nymphs.replications, F1_old_nymphs.replications, F2_old_nymphs.replications);
+ − 1178 P_old_nymphs = m_se[[1]];
+ − 1179 P_old_nymphs.std_error = m_se[[2]];
31
+ − 1180 temperature_data_frame_P = append_vector(temperature_data_frame_P, P_old_nymphs, "OLDNYMPH-P");
+ − 1181 temperature_data_frame_P = append_vector(temperature_data_frame_P, P_old_nymphs.std_error, "OLDNYMPH-P-SE");
20
+ − 1182 F1_old_nymphs = m_se[[3]];
+ − 1183 F1_old_nymphs.std_error = m_se[[4]];
31
+ − 1184 temperature_data_frame_F1 = append_vector(temperature_data_frame_F1, F1_old_nymphs, "OLDNYMPH-F1");
+ − 1185 temperature_data_frame_F1 = append_vector(temperature_data_frame_F1, F1_old_nymphs.std_error, "OLDNYMPH-F1-SE");
20
+ − 1186 F2_old_nymphs = m_se[[5]];
+ − 1187 F2_old_nymphs.std_error = m_se[[6]];
31
+ − 1188 temperature_data_frame_F2 = append_vector(temperature_data_frame_F2, F2_old_nymphs, "OLDNYMPH-F2");
+ − 1189 temperature_data_frame_F2 = append_vector(temperature_data_frame_F2, F2_old_nymphs.std_error, "OLDNYMPH-F2-SE");
20
+ − 1190 }
+ − 1191 if (process_total_nymphs) {
+ − 1192 m_se = get_mean_and_std_error(P_total_nymphs.replications, F1_total_nymphs.replications, F2_total_nymphs.replications);
+ − 1193 P_total_nymphs = m_se[[1]];
+ − 1194 P_total_nymphs.std_error = m_se[[2]];
31
+ − 1195 temperature_data_frame_P = append_vector(temperature_data_frame_P, P_total_nymphs, "TOTALNYMPH-P");
+ − 1196 temperature_data_frame_P = append_vector(temperature_data_frame_P, P_total_nymphs.std_error, "TOTALNYMPH-P-SE");
20
+ − 1197 F1_total_nymphs = m_se[[3]];
+ − 1198 F1_total_nymphs.std_error = m_se[[4]];
31
+ − 1199 temperature_data_frame_F1 = append_vector(temperature_data_frame_F1, F1_total_nymphs, "TOTALNYMPH-F1");
+ − 1200 temperature_data_frame_F1 = append_vector(temperature_data_frame_F1, F1_total_nymphs.std_error, "TOTALNYMPH-F1-SE");
20
+ − 1201 F2_total_nymphs = m_se[[5]];
+ − 1202 F2_total_nymphs.std_error = m_se[[6]];
31
+ − 1203 temperature_data_frame_F2 = append_vector(temperature_data_frame_F2, F2_total_nymphs, "TOTALNYMPH-F2");
+ − 1204 temperature_data_frame_F2 = append_vector(temperature_data_frame_F2, F2_total_nymphs.std_error, "TOTALNYMPH-F2-SE");
10
+ − 1205 }
23
+ − 1206 if (process_previttelogenic_adults) {
+ − 1207 m_se = get_mean_and_std_error(P_previttelogenic_adults.replications, F1_previttelogenic_adults.replications, F2_previttelogenic_adults.replications);
+ − 1208 P_previttelogenic_adults = m_se[[1]];
+ − 1209 P_previttelogenic_adults.std_error = m_se[[2]];
31
+ − 1210 temperature_data_frame_P = append_vector(temperature_data_frame_P, P_previttelogenic_adults, "PRE-VITADULT-P");
+ − 1211 temperature_data_frame_P = append_vector(temperature_data_frame_P, P_previttelogenic_adults.std_error, "PRE-VITADULT-P-SE");
23
+ − 1212 F1_previttelogenic_adults = m_se[[3]];
+ − 1213 F1_previttelogenic_adults.std_error = m_se[[4]];
31
+ − 1214 temperature_data_frame_F1 = append_vector(temperature_data_frame_F1, F1_previttelogenic_adults, "PRE-VITADULT-F1");
+ − 1215 temperature_data_frame_F1 = append_vector(temperature_data_frame_F1, F1_previttelogenic_adults.std_error, "PRE-VITADULT-F1-SE");
23
+ − 1216 F2_previttelogenic_adults = m_se[[5]];
+ − 1217 F2_previttelogenic_adults.std_error = m_se[[6]];
31
+ − 1218 temperature_data_frame_F2 = append_vector(temperature_data_frame_F2, F2_previttelogenic_adults, "PRE-VITADULT-F2");
+ − 1219 temperature_data_frame_F2 = append_vector(temperature_data_frame_F2, F2_previttelogenic_adults.std_error, "PRE-VITADULT-F2-SE");
23
+ − 1220 }
+ − 1221 if (process_vittelogenic_adults) {
+ − 1222 m_se = get_mean_and_std_error(P_vittelogenic_adults.replications, F1_vittelogenic_adults.replications, F2_vittelogenic_adults.replications);
+ − 1223 P_vittelogenic_adults = m_se[[1]];
+ − 1224 P_vittelogenic_adults.std_error = m_se[[2]];
31
+ − 1225 temperature_data_frame_P = append_vector(temperature_data_frame_P, P_vittelogenic_adults, "VITADULT-P");
+ − 1226 temperature_data_frame_P = append_vector(temperature_data_frame_P, P_vittelogenic_adults.std_error, "VITADULT-P-SE");
23
+ − 1227 F1_vittelogenic_adults = m_se[[3]];
+ − 1228 F1_vittelogenic_adults.std_error = m_se[[4]];
31
+ − 1229 temperature_data_frame_F1 = append_vector(temperature_data_frame_F1, F1_vittelogenic_adults, "VITADULT-F1");
+ − 1230 temperature_data_frame_F1 = append_vector(temperature_data_frame_F1, F1_vittelogenic_adults.std_error, "VITADULT-F1-SE");
23
+ − 1231 F2_vittelogenic_adults = m_se[[5]];
+ − 1232 F2_vittelogenic_adults.std_error = m_se[[6]];
31
+ − 1233 temperature_data_frame_F2 = append_vector(temperature_data_frame_F2, F2_vittelogenic_adults, "VITADULT-F2");
+ − 1234 temperature_data_frame_F2 = append_vector(temperature_data_frame_F2, F2_vittelogenic_adults.std_error, "VITADULT-F2-SE");
23
+ − 1235 }
+ − 1236 if (process_diapausing_adults) {
+ − 1237 m_se = get_mean_and_std_error(P_diapausing_adults.replications, F1_diapausing_adults.replications, F2_diapausing_adults.replications);
+ − 1238 P_diapausing_adults = m_se[[1]];
+ − 1239 P_diapausing_adults.std_error = m_se[[2]];
31
+ − 1240 temperature_data_frame_P = append_vector(temperature_data_frame_P, P_diapausing_adults, "DIAPAUSINGADULT-P");
+ − 1241 temperature_data_frame_P = append_vector(temperature_data_frame_P, P_diapausing_adults.std_error, "DIAPAUSINGADULT-P-SE");
23
+ − 1242 F1_diapausing_adults = m_se[[3]];
+ − 1243 F1_diapausing_adults.std_error = m_se[[4]];
31
+ − 1244 temperature_data_frame_F1 = append_vector(temperature_data_frame_F1, F1_diapausing_adults, "DIAPAUSINGADULT-F1");
+ − 1245 temperature_data_frame_F1 = append_vector(temperature_data_frame_F1, F1_diapausing_adults.std_error, "DIAPAUSINGADULT-F1-SE");
23
+ − 1246 F2_diapausing_adults = m_se[[5]];
+ − 1247 F2_diapausing_adults.std_error = m_se[[6]];
31
+ − 1248 temperature_data_frame_F2 = append_vector(temperature_data_frame_F2, F2_diapausing_adults, "DIAPAUSINGADULT-F2");
+ − 1249 temperature_data_frame_F2 = append_vector(temperature_data_frame_F2, F2_diapausing_adults.std_error, "DIAPAUSINGADULT-F2-SE");
23
+ − 1250 }
+ − 1251 if (process_total_adults) {
+ − 1252 m_se = get_mean_and_std_error(P_total_adults.replications, F1_total_adults.replications, F2_total_adults.replications);
+ − 1253 P_total_adults = m_se[[1]];
+ − 1254 P_total_adults.std_error = m_se[[2]];
31
+ − 1255 temperature_data_frame_P = append_vector(temperature_data_frame_P, P_total_adults, "TOTALADULT-P");
+ − 1256 temperature_data_frame_P = append_vector(temperature_data_frame_P, P_total_adults.std_error, "TOTALADULT-P-SE");
23
+ − 1257 F1_total_adults = m_se[[3]];
+ − 1258 F1_total_adults.std_error = m_se[[4]];
31
+ − 1259 temperature_data_frame_F1 = append_vector(temperature_data_frame_F1, F1_total_adults, "TOTALADULT-F1");
+ − 1260 temperature_data_frame_F1 = append_vector(temperature_data_frame_F1, F1_total_adults.std_error, "TOTALADULT-F1-SE");
23
+ − 1261 F2_total_adults = m_se[[5]];
+ − 1262 F2_total_adults.std_error = m_se[[6]];
31
+ − 1263 temperature_data_frame_F2 = append_vector(temperature_data_frame_F2, F2_total_adults, "TOTALADULT-F2");
+ − 1264 temperature_data_frame_F2 = append_vector(temperature_data_frame_F2, F2_total_adults.std_error, "TOTALADULT-F2-SE");
10
+ − 1265 }
+ − 1266 }
6
+ − 1267
31
+ − 1268 # Save the analyzed data for combined generations.
34
+ − 1269 file_path = paste("output_data_dir", "04_combined_generations.csv", sep="/");
+ − 1270 write.csv(temperature_data_frame, file=file_path, row.names=F);
31
+ − 1271 if (plot_generations_separately) {
+ − 1272 # Save the analyzed data for generation P.
34
+ − 1273 file_path = paste("output_data_dir", "01_generation_P.csv", sep="/");
+ − 1274 write.csv(temperature_data_frame_P, file=file_path, row.names=F);
31
+ − 1275 # Save the analyzed data for generation F1.
34
+ − 1276 file_path = paste("output_data_dir", "02_generation_F1.csv", sep="/");
+ − 1277 write.csv(temperature_data_frame_F1, file=file_path, row.names=F);
31
+ − 1278 # Save the analyzed data for generation F2.
34
+ − 1279 file_path = paste("output_data_dir", "03_generation_F2.csv", sep="/");
+ − 1280 write.csv(temperature_data_frame_F2, file=file_path, row.names=F);
31
+ − 1281 }
6
+ − 1282 # Display the total number of days in the Galaxy history item blurb.
8
+ − 1283 cat("Number of days: ", opt$num_days, "\n");
10
+ − 1284 # Information needed for plots plots.
8
+ − 1285 days = c(1:opt$num_days);
+ − 1286 start_date = temperature_data_frame$DATE[1];
+ − 1287 end_date = temperature_data_frame$DATE[opt$num_days];
5
+ − 1288
10
+ − 1289 if (plot_generations_separately) {
15
+ − 1290 for (life_stage in life_stages) {
10
+ − 1291 if (life_stage == "Egg") {
+ − 1292 # Start PDF device driver.
+ − 1293 dev.new(width=20, height=30);
19
+ − 1294 file_path = get_file_path(life_stage, "egg_pop_by_generation.pdf")
10
+ − 1295 pdf(file=file_path, width=20, height=30, bg="white");
+ − 1296 par(mar=c(5, 6, 4, 4), mfrow=c(3, 1));
+ − 1297 # Egg population size by generation.
18
+ − 1298 maxval = max(P_eggs+F1_eggs+F2_eggs) + 100;
34
+ − 1299 render_chart(ticks, date_labels, "pop_size_by_generation", opt$plot_std_error, opt$insect, opt$location, latitude, start_date, end_date, days, maxval,
10
+ − 1300 opt$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,
+ − 1301 group3_std_error=F2_eggs.std_error);
+ − 1302 # Turn off device driver to flush output.
+ − 1303 dev.off();
+ − 1304 } else if (life_stage == "Nymph") {
16
+ − 1305 for (life_stage_nymph in life_stages_nymph) {
+ − 1306 # Start PDF device driver.
+ − 1307 dev.new(width=20, height=30);
19
+ − 1308 file_path = get_file_path(life_stage, "nymph_pop_by_generation.pdf", life_stage_nymph=life_stage_nymph)
16
+ − 1309 pdf(file=file_path, width=20, height=30, bg="white");
+ − 1310 par(mar=c(5, 6, 4, 4), mfrow=c(3, 1));
20
+ − 1311 if (life_stage_nymph=="Young") {
+ − 1312 # Young nymph population size by generation.
+ − 1313 maxval = max(P_young_nymphs+F1_young_nymphs+F2_young_nymphs) + 100;
+ − 1314 group = P_young_nymphs;
+ − 1315 group_std_error = P_young_nymphs.std_error;
+ − 1316 group2 = F1_young_nymphs;
+ − 1317 group2_std_error = F1_young_nymphs.std_error;
+ − 1318 group3 = F2_young_nymphs;
+ − 1319 group3_std_error = F2_young_nymphs.std_error;
+ − 1320 } else if (life_stage_nymph=="Old") {
+ − 1321 # Total nymph population size by generation.
+ − 1322 maxval = max(P_old_nymphs+F1_old_nymphs+F2_old_nymphs) + 100;
+ − 1323 group = P_old_nymphs;
+ − 1324 group_std_error = P_old_nymphs.std_error;
+ − 1325 group2 = F1_old_nymphs;
+ − 1326 group2_std_error = F1_old_nymphs.std_error;
+ − 1327 group3 = F2_old_nymphs;
+ − 1328 group3_std_error = F2_old_nymphs.std_error;
+ − 1329 } else if (life_stage_nymph=="Total") {
+ − 1330 # Total nymph population size by generation.
+ − 1331 maxval = max(P_total_nymphs+F1_total_nymphs+F2_total_nymphs) + 100;
+ − 1332 group = P_total_nymphs;
+ − 1333 group_std_error = P_total_nymphs.std_error;
+ − 1334 group2 = F1_total_nymphs;
+ − 1335 group2_std_error = F1_total_nymphs.std_error;
+ − 1336 group3 = F2_total_nymphs;
+ − 1337 group3_std_error = F2_total_nymphs.std_error;
+ − 1338 }
34
+ − 1339 render_chart(ticks, date_labels, "pop_size_by_generation", opt$plot_std_error, opt$insect, opt$location, latitude, start_date, end_date, days, maxval,
20
+ − 1340 opt$replications, life_stage, group=group, group_std_error=group_std_error, group2=group2, group2_std_error=group2_std_error,
+ − 1341 group3=group3, group3_std_error=group3_std_error, life_stages_nymph=life_stage_nymph);
16
+ − 1342 # Turn off device driver to flush output.
+ − 1343 dev.off();
+ − 1344 }
10
+ − 1345 } else if (life_stage == "Adult") {
16
+ − 1346 for (life_stage_adult in life_stages_adult) {
+ − 1347 # Start PDF device driver.
+ − 1348 dev.new(width=20, height=30);
19
+ − 1349 file_path = get_file_path(life_stage, "adult_pop_by_generation.pdf", life_stage_adult=life_stage_adult)
16
+ − 1350 pdf(file=file_path, width=20, height=30, bg="white");
+ − 1351 par(mar=c(5, 6, 4, 4), mfrow=c(3, 1));
23
+ − 1352 if (life_stage_adult=="Pre-vittelogenic") {
+ − 1353 # Pre-vittelogenic adult population size by generation.
+ − 1354 maxval = max(P_previttelogenic_adults+F1_previttelogenic_adults+F2_previttelogenic_adults) + 100;
+ − 1355 group = P_previttelogenic_adults;
+ − 1356 group_std_error = P_previttelogenic_adults.std_error;
+ − 1357 group2 = F1_previttelogenic_adults;
+ − 1358 group2_std_error = F1_previttelogenic_adults.std_error;
+ − 1359 group3 = F2_previttelogenic_adults;
+ − 1360 group3_std_error = F2_previttelogenic_adults.std_error;
+ − 1361 } else if (life_stage_adult=="Vittelogenic") {
+ − 1362 # Vittelogenic adult population size by generation.
+ − 1363 maxval = max(P_vittelogenic_adults+F1_vittelogenic_adults+F2_vittelogenic_adults) + 100;
+ − 1364 group = P_vittelogenic_adults;
+ − 1365 group_std_error = P_vittelogenic_adults.std_error;
+ − 1366 group2 = F1_vittelogenic_adults;
+ − 1367 group2_std_error = F1_vittelogenic_adults.std_error;
+ − 1368 group3 = F2_vittelogenic_adults;
+ − 1369 group3_std_error = F2_vittelogenic_adults.std_error;
+ − 1370 } else if (life_stage_adult=="Diapausing") {
+ − 1371 # Diapausing adult population size by generation.
+ − 1372 maxval = max(P_diapausing_adults+F1_diapausing_adults+F2_diapausing_adults) + 100;
+ − 1373 group = P_diapausing_adults;
+ − 1374 group_std_error = P_diapausing_adults.std_error;
+ − 1375 group2 = F1_diapausing_adults;
+ − 1376 group2_std_error = F1_diapausing_adults.std_error;
+ − 1377 group3 = F2_diapausing_adults;
+ − 1378 group3_std_error = F2_diapausing_adults.std_error;
+ − 1379 } else if (life_stage_adult=="Total") {
+ − 1380 # Total adult population size by generation.
+ − 1381 maxval = max(P_total_adults+F1_total_adults+F2_total_adults) + 100;
+ − 1382 group = P_total_adults;
+ − 1383 group_std_error = P_total_adults.std_error;
+ − 1384 group2 = F1_total_adults;
+ − 1385 group2_std_error = F1_total_adults.std_error;
+ − 1386 group3 = F2_total_adults;
+ − 1387 group3_std_error = F2_total_adults.std_error;
+ − 1388 }
34
+ − 1389 render_chart(ticks, date_labels, "pop_size_by_generation", opt$plot_std_error, opt$insect, opt$location, latitude, start_date, end_date, days, maxval,
23
+ − 1390 opt$replications, life_stage, group=group, group_std_error=group_std_error, group2=group2, group2_std_error=group2_std_error,
+ − 1391 group3=group3, group3_std_error=group3_std_error, life_stages_adult=life_stage_adult);
16
+ − 1392 # Turn off device driver to flush output.
+ − 1393 dev.off();
+ − 1394 }
10
+ − 1395 } else if (life_stage == "Total") {
+ − 1396 # Start PDF device driver.
18
+ − 1397 # Name collection elements so that they
+ − 1398 # are displayed in logical order.
10
+ − 1399 dev.new(width=20, height=30);
19
+ − 1400 file_path = get_file_path(life_stage, "total_pop_by_generation.pdf")
10
+ − 1401 pdf(file=file_path, width=20, height=30, bg="white");
+ − 1402 par(mar=c(5, 6, 4, 4), mfrow=c(3, 1));
+ − 1403 # Total population size by generation.
18
+ − 1404 maxval = max(P+F1+F2) + 100;
34
+ − 1405 render_chart(ticks, date_labels, "pop_size_by_generation", opt$plot_std_error, opt$insect, opt$location, latitude, start_date, end_date, days, maxval,
10
+ − 1406 opt$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);
+ − 1407 # Turn off device driver to flush output.
+ − 1408 dev.off();
+ − 1409 }
15
+ − 1410 }
10
+ − 1411 } else {
+ − 1412 for (life_stage in life_stages) {
+ − 1413 if (life_stage == "Egg") {
+ − 1414 # Start PDF device driver.
+ − 1415 dev.new(width=20, height=30);
19
+ − 1416 file_path = get_file_path(life_stage, "egg_pop.pdf")
10
+ − 1417 pdf(file=file_path, width=20, height=30, bg="white");
+ − 1418 par(mar=c(5, 6, 4, 4), mfrow=c(3, 1));
+ − 1419 # Egg population size.
18
+ − 1420 maxval = max(eggs+eggs.std_error) + 100;
34
+ − 1421 render_chart(ticks, date_labels, "pop_size_by_life_stage", opt$plot_std_error, opt$insect, opt$location, latitude, start_date, end_date, days, maxval,
10
+ − 1422 opt$replications, life_stage, group=eggs, group_std_error=eggs.std_error);
+ − 1423 # Turn off device driver to flush output.
+ − 1424 dev.off();
+ − 1425 } else if (life_stage == "Nymph") {
16
+ − 1426 for (life_stage_nymph in life_stages_nymph) {
+ − 1427 # Start PDF device driver.
+ − 1428 dev.new(width=20, height=30);
19
+ − 1429 file_path = get_file_path(life_stage, "nymph_pop.pdf", life_stage_nymph=life_stage_nymph)
16
+ − 1430 pdf(file=file_path, width=20, height=30, bg="white");
+ − 1431 par(mar=c(5, 6, 4, 4), mfrow=c(3, 1));
+ − 1432 if (life_stage_nymph=="Total") {
+ − 1433 # Total nymph population size.
+ − 1434 group = total_nymphs;
+ − 1435 group_std_error = total_nymphs.std_error;
+ − 1436 } else if (life_stage_nymph=="Young") {
+ − 1437 # Young nymph population size.
+ − 1438 group = young_nymphs;
+ − 1439 group_std_error = young_nymphs.std_error;
+ − 1440 } else if (life_stage_nymph=="Old") {
+ − 1441 # Old nymph population size.
+ − 1442 group = old_nymphs;
+ − 1443 group_std_error = old_nymphs.std_error;
+ − 1444 }
18
+ − 1445 maxval = max(group+group_std_error) + 100;
34
+ − 1446 render_chart(ticks, date_labels, "pop_size_by_life_stage", opt$plot_std_error, opt$insect, opt$location, latitude, start_date, end_date, days, maxval,
16
+ − 1447 opt$replications, life_stage, group=group, group_std_error=group_std_error, life_stages_nymph=life_stage_nymph);
+ − 1448 # Turn off device driver to flush output.
+ − 1449 dev.off();
+ − 1450 }
10
+ − 1451 } else if (life_stage == "Adult") {
16
+ − 1452 for (life_stage_adult in life_stages_adult) {
+ − 1453 # Start PDF device driver.
+ − 1454 dev.new(width=20, height=30);
19
+ − 1455 file_path = get_file_path(life_stage, "adult_pop.pdf", life_stage_adult=life_stage_adult)
16
+ − 1456 pdf(file=file_path, width=20, height=30, bg="white");
+ − 1457 par(mar=c(5, 6, 4, 4), mfrow=c(3, 1));
+ − 1458 if (life_stage_adult=="Total") {
+ − 1459 # Total adult population size.
+ − 1460 group = total_adults;
+ − 1461 group_std_error = total_adults.std_error
+ − 1462 } else if (life_stage_adult=="Pre-vittelogenic") {
+ − 1463 # Pre-vittelogenic adult population size.
+ − 1464 group = previttelogenic_adults;
+ − 1465 group_std_error = previttelogenic_adults.std_error
+ − 1466 } else if (life_stage_adult=="Vittelogenic") {
+ − 1467 # Vittelogenic adult population size.
+ − 1468 group = vittelogenic_adults;
+ − 1469 group_std_error = vittelogenic_adults.std_error
+ − 1470 } else if (life_stage_adult=="Diapausing") {
+ − 1471 # Diapausing adult population size.
+ − 1472 group = diapausing_adults;
+ − 1473 group_std_error = diapausing_adults.std_error
+ − 1474 }
18
+ − 1475 maxval = max(group+group_std_error) + 100;
34
+ − 1476 render_chart(ticks, date_labels, "pop_size_by_life_stage", opt$plot_std_error, opt$insect, opt$location, latitude, start_date, end_date, days, maxval,
16
+ − 1477 opt$replications, life_stage, group=group, group_std_error=group_std_error, life_stages_adult=life_stage_adult);
+ − 1478 # Turn off device driver to flush output.
+ − 1479 dev.off();
+ − 1480 }
10
+ − 1481 } else if (life_stage == "Total") {
+ − 1482 # Start PDF device driver.
+ − 1483 dev.new(width=20, height=30);
19
+ − 1484 file_path = get_file_path(life_stage, "total_pop.pdf")
10
+ − 1485 pdf(file=file_path, width=20, height=30, bg="white");
+ − 1486 par(mar=c(5, 6, 4, 4), mfrow=c(3, 1));
+ − 1487 # Total population size.
18
+ − 1488 maxval = max(eggs+eggs.std_error, total_nymphs+total_nymphs.std_error, total_adults+total_adults.std_error) + 100;
34
+ − 1489 render_chart(ticks, date_labels, "pop_size_by_life_stage", opt$plot_std_error, opt$insect, opt$location, latitude, start_date, end_date, days, maxval,
16
+ − 1490 opt$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,
10
+ − 1491 group3_std_error=eggs.std_error);
+ − 1492 # Turn off device driver to flush output.
+ − 1493 dev.off();
+ − 1494 }
+ − 1495 }
+ − 1496 }