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"),
+ − 18 make_option(c("--nymph_mortality"), action="store", dest="nymph_mortality", type="integer", help="Adjustment rate for nymph mortality"),
+ − 19 make_option(c("--old_nymph_accumulation"), action="store", dest="old_nymph_accumulation", type="integer", help="Adjustment of degree-days accumulation (young nymph->old nymph)"),
+ − 20 make_option(c("--num_days"), action="store", dest="num_days", type="integer", help="Total number of days in the temperature dataset"),
+ − 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"),
+ − 23 make_option(c("--replications"), action="store", dest="replications", type="integer", help="Number of replications"),
10
+ − 24 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"),
+ − 25 make_option(c("--plot_std_error"), action="store", dest="plot_std_error", help="Plot Standard error"),
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$options;
5
+ − 32
+ − 33 add_daylight_length = function(temperature_data_frame, num_columns, num_rows) {
+ − 34 # Return a vector of daylight length (photoperido profile) for
+ − 35 # the number of days specified in the input temperature data
+ − 36 # (from Forsythe 1995).
8
+ − 37 p = 0.8333;
+ − 38 latitude = temperature_data_frame$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$DOY[i];
+ − 44 theta = 0.2163108 + 2 * atan(0.9671396 * tan(0.00860 * (doy - 186)));
+ − 45 phi = asin(0.39795 * cos(theta));
5
+ − 46 # Compute the length of daylight for the day of the year.
8
+ − 47 darkness_length = 24 / pi * acos((sin(p * pi / 180) + sin(latitude * pi / 180) * sin(phi)) / (cos(latitude * pi / 180) * cos(phi)));
+ − 48 daylight_length_vector[i] = 24 - darkness_length;
5
+ − 49 }
+ − 50 # Append daylight_length_vector as a new column to temperature_data_frame.
8
+ − 51 temperature_data_frame[, num_columns+1] = daylight_length_vector;
+ − 52 return(temperature_data_frame);
5
+ − 53 }
+ − 54
8
+ − 55 get_date_labels = function(temperature_data_frame, num_rows) {
+ − 56 # Keep track of the years to see if spanning years.
+ − 57 month_labels = list();
+ − 58 current_month_label = NULL;
+ − 59 for (i in 1:num_rows) {
+ − 60 # Get the year and month from the date which
+ − 61 # has the format YYYY-MM-DD.
+ − 62 date = format(temperature_data_frame$DATE[i]);
+ − 63 items = strsplit(date, "-")[[1]];
+ − 64 month = items[2];
+ − 65 month_label = month.abb[as.integer(month)];
+ − 66 if (!identical(current_month_label, month_label)) {
+ − 67 month_labels[length(month_labels)+1] = month_label;
+ − 68 current_month_label = month_label;
+ − 69 }
+ − 70 }
+ − 71 return(c(unlist(month_labels)));
6
+ − 72 }
+ − 73
19
+ − 74
+ − 75 get_file_path = function(life_stage, base_name, life_stage_nymph=NULL, life_stage_adult=NULL) {
+ − 76 if (!is.null(life_stage_nymph)) {
+ − 77 lsi = get_life_stage_index(life_stage, life_stage_nymph=life_stage_nymph);
+ − 78 file_name = paste(lsi, tolower(life_stage_nymph), base_name, sep="_");
+ − 79 } else if (!is.null(life_stage_adult)) {
+ − 80 lsi = get_life_stage_index(life_stage, life_stage_adult=life_stage_adult);
+ − 81 file_name = paste(lsi, tolower(life_stage_adult), base_name, sep="_");
+ − 82 } else {
+ − 83 lsi = get_life_stage_index(life_stage);
+ − 84 file_name = paste(lsi, base_name, sep="_");
+ − 85 }
+ − 86 file_path = paste("output_dir", file_name, sep="/");
+ − 87 return(file_path);
+ − 88 }
+ − 89
18
+ − 90 get_life_stage_index = function(life_stage, life_stage_nymph=NULL, life_stage_adult=NULL) {
+ − 91 # Name collection elements so that they
+ − 92 # are displayed in logical order.
+ − 93 if (life_stage=="Egg") {
+ − 94 lsi = "01";
+ − 95 } else if (life_stage=="Nymph") {
+ − 96 if (life_stage_nymph=="Young") {
+ − 97 lsi = "02";
+ − 98 } else if (life_stage_nymph=="Old") {
+ − 99 lsi = "03";
+ − 100 } else if (life_stage_nymph=="Total") {
+ − 101 lsi="04";
+ − 102 }
+ − 103 } else if (life_stage=="Adult") {
+ − 104 if (life_stage_adult=="Pre-vittelogenic") {
+ − 105 lsi = "05";
+ − 106 } else if (life_stage_adult=="Vittelogenic") {
+ − 107 lsi = "06";
+ − 108 } else if (life_stage_adult=="Diapausing") {
+ − 109 lsi = "07";
+ − 110 } else if (life_stage_adult=="Total") {
+ − 111 lsi = "08";
+ − 112 }
+ − 113 } else if (life_stage=="Total") {
+ − 114 lsi = "09";
+ − 115 }
+ − 116 return(lsi);
+ − 117 }
+ − 118
5
+ − 119 get_temperature_at_hour = function(latitude, temperature_data_frame, row, num_days) {
8
+ − 120 # Base development threshold for Brown Marmorated Stink Bug
5
+ − 121 # insect phenology model.
8
+ − 122 threshold = 14.17;
5
+ − 123 # Minimum temperature for current row.
8
+ − 124 curr_min_temp = temperature_data_frame$TMIN[row];
5
+ − 125 # Maximum temperature for current row.
8
+ − 126 curr_max_temp = temperature_data_frame$TMAX[row];
5
+ − 127 # Mean temperature for current row.
8
+ − 128 curr_mean_temp = 0.5 * (curr_min_temp + curr_max_temp);
5
+ − 129 # Initialize degree day accumulation
8
+ − 130 averages = 0;
6
+ − 131 if (curr_max_temp < threshold) {
8
+ − 132 averages = 0;
5
+ − 133 }
+ − 134 else {
+ − 135 # Initialize hourly temperature.
8
+ − 136 T = NULL;
5
+ − 137 # Initialize degree hour vector.
8
+ − 138 dh = NULL;
5
+ − 139 # Daylight length for current row.
8
+ − 140 y = temperature_data_frame$DAYLEN[row];
5
+ − 141 # Darkness length.
8
+ − 142 z = 24 - y;
5
+ − 143 # Lag coefficient.
8
+ − 144 a = 1.86;
5
+ − 145 # Darkness coefficient.
8
+ − 146 b = 2.20;
5
+ − 147 # Sunrise time.
8
+ − 148 risetime = 12 - y / 2;
5
+ − 149 # Sunset time.
8
+ − 150 settime = 12 + y / 2;
+ − 151 ts = (curr_max_temp - curr_min_temp) * sin(pi * (settime - 5) / (y + 2 * a)) + curr_min_temp;
5
+ − 152 for (i in 1:24) {
+ − 153 if (i > risetime && i < settime) {
+ − 154 # Number of hours after Tmin until sunset.
8
+ − 155 m = i - 5;
+ − 156 T[i] = (curr_max_temp - curr_min_temp) * sin(pi * m / (y + 2 * a)) + curr_min_temp;
5
+ − 157 if (T[i] < 8.4) {
8
+ − 158 dh[i] = 0;
5
+ − 159 }
+ − 160 else {
8
+ − 161 dh[i] = T[i] - 8.4;
5
+ − 162 }
+ − 163 }
6
+ − 164 else if (i > settime) {
8
+ − 165 n = i - settime;
+ − 166 T[i] = curr_min_temp + (ts - curr_min_temp) * exp( - b * n / z);
5
+ − 167 if (T[i] < 8.4) {
8
+ − 168 dh[i] = 0;
5
+ − 169 }
+ − 170 else {
8
+ − 171 dh[i] = T[i] - 8.4;
5
+ − 172 }
+ − 173 }
+ − 174 else {
8
+ − 175 n = i + 24 - settime;
+ − 176 T[i] = curr_min_temp + (ts - curr_min_temp) * exp( - b * n / z);
5
+ − 177 if (T[i] < 8.4) {
8
+ − 178 dh[i] = 0;
5
+ − 179 }
+ − 180 else {
8
+ − 181 dh[i] = T[i] - 8.4;
5
+ − 182 }
+ − 183 }
+ − 184 }
8
+ − 185 averages = sum(dh) / 24;
5
+ − 186 }
6
+ − 187 return(c(curr_mean_temp, averages))
5
+ − 188 }
+ − 189
6
+ − 190 mortality.adult = function(temperature) {
+ − 191 if (temperature < 12.7) {
8
+ − 192 mortality.probability = 0.002;
6
+ − 193 }
+ − 194 else {
8
+ − 195 mortality.probability = temperature * 0.0005 + 0.02;
6
+ − 196 }
+ − 197 return(mortality.probability)
5
+ − 198 }
+ − 199
+ − 200 mortality.egg = function(temperature) {
+ − 201 if (temperature < 12.7) {
8
+ − 202 mortality.probability = 0.8;
5
+ − 203 }
+ − 204 else {
8
+ − 205 mortality.probability = 0.8 - temperature / 40.0;
6
+ − 206 if (mortality.probability < 0) {
8
+ − 207 mortality.probability = 0.01;
5
+ − 208 }
+ − 209 }
6
+ − 210 return(mortality.probability)
5
+ − 211 }
+ − 212
+ − 213 mortality.nymph = function(temperature) {
+ − 214 if (temperature < 12.7) {
8
+ − 215 mortality.probability = 0.03;
5
+ − 216 }
+ − 217 else {
8
+ − 218 mortality.probability = temperature * 0.0008 + 0.03;
5
+ − 219 }
8
+ − 220 return(mortality.probability);
6
+ − 221 }
+ − 222
+ − 223 parse_input_data = function(input_file, num_rows) {
+ − 224 # Read in the input temperature datafile into a data frame.
8
+ − 225 temperature_data_frame = read.csv(file=input_file, header=T, strip.white=TRUE, sep=",");
+ − 226 num_columns = dim(temperature_data_frame)[2];
6
+ − 227 if (num_columns == 6) {
+ − 228 # The input data has the following 6 columns:
+ − 229 # LATITUDE, LONGITUDE, DATE, DOY, TMIN, TMAX
+ − 230 # Set the column names for access when adding daylight length..
8
+ − 231 colnames(temperature_data_frame) = c("LATITUDE","LONGITUDE", "DATE", "DOY", "TMIN", "TMAX");
6
+ − 232 # Add a column containing the daylight length for each day.
8
+ − 233 temperature_data_frame = add_daylight_length(temperature_data_frame, num_columns, num_rows);
6
+ − 234 # Reset the column names with the additional column for later access.
8
+ − 235 colnames(temperature_data_frame) = c("LATITUDE","LONGITUDE", "DATE", "DOY", "TMIN", "TMAX", "DAYLEN");
6
+ − 236 }
8
+ − 237 return(temperature_data_frame);
5
+ − 238 }
+ − 239
8
+ − 240
10
+ − 241 render_chart = function(date_labels, chart_type, plot_std_error, insect, location, latitude, start_date, end_date, days, maxval,
18
+ − 242 replications, life_stage, group, group_std_error, group2=NULL, group2_std_error=NULL, group3=NULL, group3_std_error=NULL,
+ − 243 life_stages_adult=NULL, life_stages_nymph=NULL) {
10
+ − 244 if (chart_type=="pop_size_by_life_stage") {
+ − 245 if (life_stage=="Total") {
+ − 246 title = paste(insect, ": Reps", replications, ":", life_stage, "Pop :", location, ": Lat", latitude, ":", start_date, "-", end_date, sep=" ");
+ − 247 legend_text = c("Egg", "Nymph", "Adult");
+ − 248 columns = c(4, 2, 1);
+ − 249 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);
+ − 250 legend("topleft", legend_text, lty=c(1, 1, 1), col=columns, cex=3);
+ − 251 lines(days, group2, lwd=2, lty=1, col=2);
+ − 252 lines(days, group3, lwd=2, lty=1, col=4);
+ − 253 axis(1, at=c(1:length(date_labels)) * 30 - 15, cex.axis=3, labels=date_labels);
+ − 254 axis(2, cex.axis=3);
+ − 255 if (plot_std_error=="yes") {
+ − 256 # Standard error for group.
+ − 257 lines(days, group+group_std_error, lty=2);
+ − 258 lines(days, group-group_std_error, lty=2);
+ − 259 # Standard error for group2.
+ − 260 lines(days, group2+group2_std_error, col=2, lty=2);
+ − 261 lines(days, group2-group2_std_error, col=2, lty=2);
+ − 262 # Standard error for group3.
+ − 263 lines(days, group3+group3_std_error, col=4, lty=2);
+ − 264 lines(days, group3-group3_std_error, col=4, lty=2);
+ − 265 }
+ − 266 } else {
+ − 267 if (life_stage=="Egg") {
+ − 268 title = paste(insect, ": Reps", replications, ":", life_stage, "Pop :", location, ": Lat", latitude, ":", start_date, "-", end_date, sep=" ");
+ − 269 legend_text = c(life_stage);
15
+ − 270 columns = c(4);
10
+ − 271 } else if (life_stage=="Nymph") {
16
+ − 272 stage = paste(life_stages_nymph, "Nymph Pop :", sep=" ");
10
+ − 273 title = paste(insect, ": Reps", replications, ":", stage, location, ": Lat", latitude, ":", start_date, "-", end_date, sep=" ");
16
+ − 274 legend_text = c(paste(life_stages_nymph, life_stage, sep=" "));
10
+ − 275 columns = c(2);
+ − 276 } else if (life_stage=="Adult") {
+ − 277 stage = paste(life_stages_adult, "Adult Pop", sep=" ");
+ − 278 title = paste(insect, ": Reps", replications, ":", stage, location, ": Lat", latitude, ":", start_date, "-", end_date, sep=" ");
+ − 279 legend_text = c(paste(life_stages_adult, life_stage, sep=" "));
+ − 280 columns = c(1);
+ − 281 }
+ − 282 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);
+ − 283 legend("topleft", legend_text, lty=c(1), col="black", cex=3);
+ − 284 axis(1, at=c(1:length(date_labels)) * 30 - 15, cex.axis=3, labels=date_labels);
+ − 285 axis(2, cex.axis=3);
+ − 286 if (plot_std_error=="yes") {
+ − 287 # Standard error for group.
+ − 288 lines(days, group+group_std_error, lty=2);
+ − 289 lines(days, group-group_std_error, lty=2);
+ − 290 }
+ − 291 }
+ − 292 } else if (chart_type=="pop_size_by_generation") {
+ − 293 if (life_stage=="Total") {
+ − 294 title_str = ": Total Pop by Gen :";
+ − 295 } else if (life_stage=="Egg") {
+ − 296 title_str = ": Egg Pop by Gen :";
+ − 297 } else if (life_stage=="Nymph") {
16
+ − 298 title_str = paste(":", life_stages_nymph, "Nymph Pop by Gen", ":", sep=" ");
10
+ − 299 } else if (life_stage=="Adult") {
+ − 300 title_str = paste(":", life_stages_adult, "Adult Pop by Gen", ":", sep=" ");
+ − 301 }
+ − 302 title = paste(insect, ": Reps", replications, title_str, location, ": Lat", latitude, ":", start_date, "-", end_date, sep=" ");
8
+ − 303 legend_text = c("P", "F1", "F2");
+ − 304 columns = c(1, 2, 4);
10
+ − 305 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);
+ − 306 legend("topleft", legend_text, lty=c(1, 1, 1), col=columns, cex=3);
+ − 307 lines(days, group2, lwd=2, lty=1, col=2);
+ − 308 lines(days, group3, lwd=2, lty=1, col=4);
+ − 309 axis(1, at=c(1:length(date_labels)) * 30 - 15, cex.axis=3, labels=date_labels);
+ − 310 axis(2, cex.axis=3);
+ − 311 if (plot_std_error=="yes") {
+ − 312 # Standard error for group.
+ − 313 lines(days, group+group_std_error, lty=2);
+ − 314 lines(days, group-group_std_error, lty=2);
+ − 315 # Standard error for group2.
+ − 316 lines(days, group2+group2_std_error, col=2, lty=2);
+ − 317 lines(days, group2-group2_std_error, col=2, lty=2);
+ − 318 # Standard error for group3.
+ − 319 lines(days, group3+group3_std_error, col=4, lty=2);
+ − 320 lines(days, group3-group3_std_error, col=4, lty=2);
+ − 321 }
5
+ − 322 }
+ − 323 }
+ − 324
10
+ − 325 # Determine if we're plotting generations separately.
+ − 326 if (opt$plot_generations_separately=="yes") {
+ − 327 plot_generations_separately = TRUE;
+ − 328 } else {
+ − 329 plot_generations_separately = FALSE;
+ − 330 }
+ − 331 # Read the temperature data into a data frame.
8
+ − 332 temperature_data_frame = parse_input_data(opt$input, opt$num_days);
10
+ − 333 # Get the date labels for plots.
+ − 334 date_labels = get_date_labels(temperature_data_frame, opt$num_days);
+ − 335 # All latitude values are the same, so get the value for plots from the first row.
8
+ − 336 latitude = temperature_data_frame$LATITUDE[1];
10
+ − 337 # Get the number of days for plots.
8
+ − 338 num_columns = dim(temperature_data_frame)[2];
10
+ − 339 # Split life_stages into a list of strings for plots.
+ − 340 life_stages_str = as.character(opt$life_stages);
+ − 341 life_stages = strsplit(life_stages_str, ",")[[1]];
+ − 342 # Determine the data we need to generate for plotting.
+ − 343 process_eggs = FALSE;
+ − 344 process_nymphs = FALSE;
+ − 345 process_adults = FALSE;
+ − 346 for (life_stage in life_stages) {
+ − 347 if (life_stage=="Total") {
+ − 348 process_eggs = TRUE;
+ − 349 process_nymphs = TRUE;
+ − 350 process_adults = TRUE;
+ − 351 } else if (life_stage=="Egg") {
+ − 352 process_eggs = TRUE;
+ − 353 } else if (life_stage=="Nymph") {
+ − 354 process_nymphs = TRUE;
+ − 355 } else if (life_stage=="Adult") {
+ − 356 process_adults = TRUE;
+ − 357 }
+ − 358 }
16
+ − 359 if (process_adults) {
+ − 360 # Split life_stages_adult into a list of strings for plots.
+ − 361 life_stages_adult_str = as.character(opt$life_stages_adult);
+ − 362 life_stages_adult = strsplit(life_stages_adult_str, ",")[[1]];
+ − 363 }
+ − 364 if (process_nymphs) {
+ − 365 # Split life_stages_nymph into a list of strings for plots.
+ − 366 life_stages_nymph_str = as.character(opt$life_stages_nymph);
+ − 367 life_stages_nymph = strsplit(life_stages_nymph_str, ",")[[1]];
+ − 368 }
6
+ − 369 # Initialize matrices.
10
+ − 370 if (process_eggs) {
+ − 371 Eggs.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
+ − 372 }
+ − 373 if (process_nymphs) {
+ − 374 YoungNymphs.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
+ − 375 OldNymphs.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
+ − 376 }
+ − 377 if (process_adults) {
+ − 378 Previtellogenic.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
+ − 379 Vitellogenic.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
+ − 380 Diapausing.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
+ − 381 }
8
+ − 382 newborn.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
+ − 383 adult.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
+ − 384 death.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
10
+ − 385 if (plot_generations_separately) {
+ − 386 # P is Parental, or overwintered adults.
+ − 387 P.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
+ − 388 # F1 is the first field-produced generation.
+ − 389 F1.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
+ − 390 # F2 is the second field-produced generation.
+ − 391 F2.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
+ − 392 if (process_eggs) {
+ − 393 P_eggs.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
+ − 394 F1_eggs.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
+ − 395 F2_eggs.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
+ − 396 }
+ − 397 if (process_nymphs) {
+ − 398 P_nymphs.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
+ − 399 F1_nymphs.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
+ − 400 F2_nymphs.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
+ − 401 }
+ − 402 if (process_adults) {
+ − 403 P_adults.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
+ − 404 F1_adults.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
+ − 405 F2_adults.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
+ − 406 }
+ − 407 }
+ − 408 # Total population.
8
+ − 409 population.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
5
+ − 410
6
+ − 411 # Process replications.
18
+ − 412 for (current_replication in 1:opt$replications) {
6
+ − 413 # Start with the user-defined number of insects per replication.
8
+ − 414 num_insects = opt$insects_per_replication;
6
+ − 415 # Generation, Stage, degree-days, T, Diapause.
8
+ − 416 vector.ini = c(0, 3, 0, 0, 0);
10
+ − 417 # Replicate to create a matrix where the columns are
+ − 418 # Generation, Stage, degree-days, T, Diapause and the
+ − 419 # rows are the initial number of insects per replication.
8
+ − 420 vector.matrix = rep(vector.ini, num_insects);
10
+ − 421 # Complete transposed matrix for the population, so now
+ − 422 # the rows are Generation, Stage, degree-days, T, Diapause
8
+ − 423 vector.matrix = base::t(matrix(vector.matrix, nrow=5));
5
+ − 424 # Time series of population size.
10
+ − 425 if (process_eggs) {
+ − 426 Eggs = rep(0, opt$num_days);
+ − 427 }
+ − 428 if (process_nymphs) {
+ − 429 YoungNymphs = rep(0, opt$num_days);
+ − 430 OldNymphs = rep(0, opt$num_days);
+ − 431 }
+ − 432 if (process_adults) {
+ − 433 Previtellogenic = rep(0, opt$num_days);
+ − 434 Vitellogenic = rep(0, opt$num_days);
+ − 435 Diapausing = rep(0, opt$num_days);
+ − 436 }
8
+ − 437 N.newborn = rep(0, opt$num_days);
+ − 438 N.adult = rep(0, opt$num_days);
+ − 439 N.death = rep(0, opt$num_days);
+ − 440 overwintering_adult.population = rep(0, opt$num_days);
+ − 441 first_generation.population = rep(0, opt$num_days);
+ − 442 second_generation.population = rep(0, opt$num_days);
10
+ − 443 if (plot_generations_separately) {
+ − 444 # P is Parental, or overwintered adults.
+ − 445 # F1 is the first field-produced generation.
+ − 446 # F2 is the second field-produced generation.
+ − 447 if (process_eggs) {
+ − 448 P.egg = rep(0, opt$num_days);
+ − 449 F1.egg = rep(0, opt$num_days);
+ − 450 F2.egg = rep(0, opt$num_days);
+ − 451 }
+ − 452 if (process_nymphs) {
+ − 453 P.nymph = rep(0, opt$num_days);
+ − 454 F1.nymph = rep(0, opt$num_days);
+ − 455 F2.nymph = rep(0, opt$num_days);
+ − 456 }
+ − 457 if (process_adults) {
+ − 458 P.adult = rep(0, opt$num_days);
+ − 459 F1.adult = rep(0, opt$num_days);
+ − 460 F2.adult = rep(0, opt$num_days);
+ − 461 }
+ − 462 }
8
+ − 463 total.population = NULL;
+ − 464 averages.day = rep(0, opt$num_days);
5
+ − 465 # All the days included in the input temperature dataset.
+ − 466 for (row in 1:opt$num_days) {
+ − 467 # Get the integer day of the year for the current row.
8
+ − 468 doy = temperature_data_frame$DOY[row];
5
+ − 469 # Photoperiod in the day.
8
+ − 470 photoperiod = temperature_data_frame$DAYLEN[row];
+ − 471 temp.profile = get_temperature_at_hour(latitude, temperature_data_frame, row, opt$num_days);
+ − 472 mean.temp = temp.profile[1];
+ − 473 averages.temp = temp.profile[2];
+ − 474 averages.day[row] = averages.temp;
5
+ − 475 # Trash bin for death.
8
+ − 476 death.vector = NULL;
5
+ − 477 # Newborn.
8
+ − 478 birth.vector = NULL;
5
+ − 479 # All individuals.
6
+ − 480 for (i in 1:num_insects) {
+ − 481 # Individual record.
8
+ − 482 vector.individual = vector.matrix[i,];
6
+ − 483 # Adjustment for late season mortality rate (still alive?).
5
+ − 484 if (latitude < 40.0) {
8
+ − 485 post.mortality = 1;
+ − 486 day.kill = 300;
5
+ − 487 }
+ − 488 else {
8
+ − 489 post.mortality = 2;
+ − 490 day.kill = 250;
5
+ − 491 }
6
+ − 492 if (vector.individual[2] == 0) {
5
+ − 493 # Egg.
8
+ − 494 death.probability = opt$egg_mortality * mortality.egg(mean.temp);
5
+ − 495 }
6
+ − 496 else if (vector.individual[2] == 1 | vector.individual[2] == 2) {
18
+ − 497 # Nymph.
8
+ − 498 death.probability = opt$nymph_mortality * mortality.nymph(mean.temp);
5
+ − 499 }
6
+ − 500 else if (vector.individual[2] == 3 | vector.individual[2] == 4 | vector.individual[2] == 5) {
+ − 501 # Adult.
5
+ − 502 if (doy < day.kill) {
8
+ − 503 death.probability = opt$adult_mortality * mortality.adult(mean.temp);
5
+ − 504 }
+ − 505 else {
+ − 506 # Increase adult mortality after fall equinox.
8
+ − 507 death.probability = opt$adult_mortality * post.mortality * mortality.adult(mean.temp);
5
+ − 508 }
+ − 509 }
6
+ − 510 # Dependent on temperature and life stage?
8
+ − 511 u.d = runif(1);
6
+ − 512 if (u.d < death.probability) {
8
+ − 513 death.vector = c(death.vector, i);
6
+ − 514 }
5
+ − 515 else {
6
+ − 516 # End of diapause.
+ − 517 if (vector.individual[1] == 0 && vector.individual[2] == 3) {
5
+ − 518 # Overwintering adult (previttelogenic).
6
+ − 519 if (photoperiod > opt$photoperiod && vector.individual[3] > 68 && doy < 180) {
5
+ − 520 # Add 68C to become fully reproductively matured.
+ − 521 # Transfer to vittelogenic.
8
+ − 522 vector.individual = c(0, 4, 0, 0, 0);
+ − 523 vector.matrix[i,] = vector.individual;
5
+ − 524 }
+ − 525 else {
6
+ − 526 # Add to # Add average temperature for current day.
8
+ − 527 vector.individual[3] = vector.individual[3] + averages.temp;
5
+ − 528 # Add 1 day in current stage.
8
+ − 529 vector.individual[4] = vector.individual[4] + 1;
+ − 530 vector.matrix[i,] = vector.individual;
5
+ − 531 }
+ − 532 }
6
+ − 533 if (vector.individual[1] != 0 && vector.individual[2] == 3) {
5
+ − 534 # Not overwintering adult (previttelogenic).
8
+ − 535 current.gen = vector.individual[1];
6
+ − 536 if (vector.individual[3] > 68) {
5
+ − 537 # Add 68C to become fully reproductively matured.
+ − 538 # Transfer to vittelogenic.
8
+ − 539 vector.individual = c(current.gen, 4, 0, 0, 0);
+ − 540 vector.matrix[i,] = vector.individual;
5
+ − 541 }
+ − 542 else {
6
+ − 543 # Add average temperature for current day.
8
+ − 544 vector.individual[3] = vector.individual[3] + averages.temp;
5
+ − 545 # Add 1 day in current stage.
8
+ − 546 vector.individual[4] = vector.individual[4] + 1;
+ − 547 vector.matrix[i,] = vector.individual;
5
+ − 548 }
+ − 549 }
6
+ − 550 # Oviposition -- where population dynamics comes from.
+ − 551 if (vector.individual[2] == 4 && vector.individual[1] == 0 && mean.temp > 10) {
5
+ − 552 # Vittelogenic stage, overwintering generation.
6
+ − 553 if (vector.individual[4] == 0) {
5
+ − 554 # Just turned in vittelogenic stage.
8
+ − 555 num_insects.birth = round(runif(1, 2 + opt$min_clutch_size, 8 + opt$max_clutch_size));
5
+ − 556 }
+ − 557 else {
+ − 558 # Daily probability of birth.
8
+ − 559 p.birth = opt$oviposition * 0.01;
+ − 560 u1 = runif(1);
5
+ − 561 if (u1 < p.birth) {
8
+ − 562 num_insects.birth = round(runif(1, 2, 8));
5
+ − 563 }
+ − 564 }
6
+ − 565 # Add average temperature for current day.
8
+ − 566 vector.individual[3] = vector.individual[3] + averages.temp;
5
+ − 567 # Add 1 day in current stage.
8
+ − 568 vector.individual[4] = vector.individual[4] + 1;
+ − 569 vector.matrix[i,] = vector.individual;
6
+ − 570 if (num_insects.birth > 0) {
5
+ − 571 # Add new birth -- might be in different generations.
8
+ − 572 new.gen = vector.individual[1] + 1;
5
+ − 573 # Egg profile.
8
+ − 574 new.individual = c(new.gen, 0, 0, 0, 0);
+ − 575 new.vector = rep(new.individual, num_insects.birth);
5
+ − 576 # Update batch of egg profile.
8
+ − 577 new.vector = t(matrix(new.vector, nrow=5));
5
+ − 578 # Group with total eggs laid in that day.
8
+ − 579 birth.vector = rbind(birth.vector, new.vector);
5
+ − 580 }
+ − 581 }
6
+ − 582 # Oviposition -- for generation 1.
+ − 583 if (vector.individual[2] == 4 && vector.individual[1] == 1 && mean.temp > 12.5 && doy < 222) {
5
+ − 584 # Vittelogenic stage, 1st generation
6
+ − 585 if (vector.individual[4] == 0) {
5
+ − 586 # Just turned in vittelogenic stage.
8
+ − 587 num_insects.birth = round(runif(1, 2+opt$min_clutch_size, 8+opt$max_clutch_size));
5
+ − 588 }
+ − 589 else {
+ − 590 # Daily probability of birth.
8
+ − 591 p.birth = opt$oviposition * 0.01;
+ − 592 u1 = runif(1);
5
+ − 593 if (u1 < p.birth) {
8
+ − 594 num_insects.birth = round(runif(1, 2, 8));
5
+ − 595 }
+ − 596 }
6
+ − 597 # Add average temperature for current day.
8
+ − 598 vector.individual[3] = vector.individual[3] + averages.temp;
5
+ − 599 # Add 1 day in current stage.
8
+ − 600 vector.individual[4] = vector.individual[4] + 1;
+ − 601 vector.matrix[i,] = vector.individual;
6
+ − 602 if (num_insects.birth > 0) {
5
+ − 603 # Add new birth -- might be in different generations.
8
+ − 604 new.gen = vector.individual[1] + 1;
5
+ − 605 # Egg profile.
8
+ − 606 new.individual = c(new.gen, 0, 0, 0, 0);
+ − 607 new.vector = rep(new.individual, num_insects.birth);
5
+ − 608 # Update batch of egg profile.
8
+ − 609 new.vector = t(matrix(new.vector, nrow=5));
5
+ − 610 # Group with total eggs laid in that day.
8
+ − 611 birth.vector = rbind(birth.vector, new.vector);
5
+ − 612 }
+ − 613 }
6
+ − 614 # Egg to young nymph.
+ − 615 if (vector.individual[2] == 0) {
+ − 616 # Add average temperature for current day.
8
+ − 617 vector.individual[3] = vector.individual[3] + averages.temp;
6
+ − 618 if (vector.individual[3] >= (68+opt$young_nymph_accumulation)) {
+ − 619 # From egg to young nymph, degree-days requirement met.
8
+ − 620 current.gen = vector.individual[1];
5
+ − 621 # Transfer to young nymph stage.
8
+ − 622 vector.individual = c(current.gen, 1, 0, 0, 0);
5
+ − 623 }
+ − 624 else {
+ − 625 # Add 1 day in current stage.
8
+ − 626 vector.individual[4] = vector.individual[4] + 1;
5
+ − 627 }
8
+ − 628 vector.matrix[i,] = vector.individual;
5
+ − 629 }
6
+ − 630 # Young nymph to old nymph.
+ − 631 if (vector.individual[2] == 1) {
+ − 632 # Add average temperature for current day.
8
+ − 633 vector.individual[3] = vector.individual[3] + averages.temp;
6
+ − 634 if (vector.individual[3] >= (250+opt$old_nymph_accumulation)) {
+ − 635 # From young to old nymph, degree_days requirement met.
8
+ − 636 current.gen = vector.individual[1];
5
+ − 637 # Transfer to old nym stage.
8
+ − 638 vector.individual = c(current.gen, 2, 0, 0, 0);
5
+ − 639 if (photoperiod < opt$photoperiod && doy > 180) {
8
+ − 640 vector.individual[5] = 1;
5
+ − 641 } # Prepare for diapausing.
+ − 642 }
+ − 643 else {
+ − 644 # Add 1 day in current stage.
8
+ − 645 vector.individual[4] = vector.individual[4] + 1;
5
+ − 646 }
8
+ − 647 vector.matrix[i,] = vector.individual;
6
+ − 648 }
+ − 649 # Old nymph to adult: previttelogenic or diapausing?
+ − 650 if (vector.individual[2] == 2) {
+ − 651 # Add average temperature for current day.
8
+ − 652 vector.individual[3] = vector.individual[3] + averages.temp;
6
+ − 653 if (vector.individual[3] >= (200+opt$adult_accumulation)) {
+ − 654 # From old to adult, degree_days requirement met.
8
+ − 655 current.gen = vector.individual[1];
6
+ − 656 if (vector.individual[5] == 0) {
+ − 657 # Previttelogenic.
8
+ − 658 vector.individual = c(current.gen, 3, 0, 0, 0);
5
+ − 659 }
+ − 660 else {
+ − 661 # Diapausing.
8
+ − 662 vector.individual = c(current.gen, 5, 0, 0, 1);
5
+ − 663 }
+ − 664 }
+ − 665 else {
+ − 666 # Add 1 day in current stage.
8
+ − 667 vector.individual[4] = vector.individual[4] + 1;
5
+ − 668 }
8
+ − 669 vector.matrix[i,] = vector.individual;
5
+ − 670 }
6
+ − 671 # Growing of diapausing adult (unimportant, but still necessary).
+ − 672 if (vector.individual[2] == 5) {
8
+ − 673 vector.individual[3] = vector.individual[3] + averages.temp;
+ − 674 vector.individual[4] = vector.individual[4] + 1;
+ − 675 vector.matrix[i,] = vector.individual;
5
+ − 676 }
+ − 677 } # Else if it is still alive.
+ − 678 } # End of the individual bug loop.
6
+ − 679
+ − 680 # Number of deaths.
8
+ − 681 num_insects.death = length(death.vector);
6
+ − 682 if (num_insects.death > 0) {
+ − 683 # Remove record of dead.
8
+ − 684 vector.matrix = vector.matrix[-death.vector,];
5
+ − 685 }
6
+ − 686 # Number of births.
8
+ − 687 num_insects.newborn = length(birth.vector[,1]);
+ − 688 vector.matrix = rbind(vector.matrix, birth.vector);
5
+ − 689 # Update population size for the next day.
8
+ − 690 num_insects = num_insects - num_insects.death + num_insects.newborn;
5
+ − 691
10
+ − 692 # Aggregate results by day. Due to multiple transpose calls
+ − 693 # on vector.matrix above, the columns of vector.matrix
+ − 694 # are now Generation, Stage, degree-days, T, Diapause,
+ − 695 if (process_eggs) {
+ − 696 # For egg population size, column 2 (Stage), must be 0.
+ − 697 Eggs[row] = sum(vector.matrix[,2]==0);
+ − 698 }
+ − 699 if (process_nymphs) {
+ − 700 # For young nymph population size, column 2 (Stage) must be 1.
+ − 701 YoungNymphs[row] = sum(vector.matrix[,2]==1);
+ − 702 # For old nymph population size, column 2 (Stage) must be 2.
+ − 703 OldNymphs[row] = sum(vector.matrix[,2]==2);
+ − 704 }
+ − 705 if (process_adults) {
+ − 706 # For pre-vitellogenic population size, column 2 (Stage) must be 3.
+ − 707 Previtellogenic[row] = sum(vector.matrix[,2]==3);
+ − 708 # For vitellogenic population size, column 2 (Stage) must be 4.
+ − 709 Vitellogenic[row] = sum(vector.matrix[,2]==4);
+ − 710 # For diapausing population size, column 2 (Stage) must be 5.
+ − 711 Diapausing[row] = sum(vector.matrix[,2]==5);
+ − 712 }
5
+ − 713
6
+ − 714 # Newborn population size.
8
+ − 715 N.newborn[row] = num_insects.newborn;
6
+ − 716 # Adult population size.
8
+ − 717 N.adult[row] = sum(vector.matrix[,2]==3) + sum(vector.matrix[,2]==4) + sum(vector.matrix[,2]==5);
6
+ − 718 # Dead population size.
8
+ − 719 N.death[row] = num_insects.death;
6
+ − 720
8
+ − 721 total.population = c(total.population, num_insects);
6
+ − 722
10
+ − 723 # For overwintering adult (P) population
+ − 724 # size, column 1 (Generation) must be 0.
8
+ − 725 overwintering_adult.population[row] = sum(vector.matrix[,1]==0);
10
+ − 726 # For first field generation (F1) population
+ − 727 # size, column 1 (Generation) must be 1.
8
+ − 728 first_generation.population[row] = sum(vector.matrix[,1]==1);
10
+ − 729 # For second field generation (F2) population
+ − 730 # size, column 1 (Generation) must be 2.
8
+ − 731 second_generation.population[row] = sum(vector.matrix[,1]==2);
5
+ − 732
10
+ − 733 if (plot_generations_separately) {
+ − 734 if (process_eggs) {
18
+ − 735 # For egg life stage of generation P population size,
10
+ − 736 # column 1 (generation) is 0 and column 2 (Stage) is 0.
+ − 737 P.egg[row] = sum(vector.matrix[,1]==0 & vector.matrix[,2]==0);
+ − 738 # For egg life stage of generation F1 population size,
+ − 739 # column 1 (generation) is 1 and column 2 (Stage) is 0.
+ − 740 F1.egg[row] = sum(vector.matrix[,1]==1 & vector.matrix[,2]==0);
+ − 741 # For egg life stage of generation F2 population size,
+ − 742 # column 1 (generation) is 2 and column 2 (Stage) is 0.
+ − 743 F2.egg[row] = sum(vector.matrix[,1]==2 & vector.matrix[,2]==0);
+ − 744 }
+ − 745 if (process_nymphs) {
18
+ − 746 # For nymph life stage of generation P population
10
+ − 747 # size, one of the following combinations is required:
+ − 748 # - column 1 (Generation) is 0 and column 2 (Stage) is 1 (Young nymph)
+ − 749 # - column 1 (Generation) is 0 and column 2 (Stage) is 2 (Old nymph)
+ − 750 P.nymph[row] = sum((vector.matrix[,1]==0 & vector.matrix[,2]==1) | (vector.matrix[,1]==0 & vector.matrix[,2]==2));
+ − 751 # For nymph life stage of generation F1 population
+ − 752 # size, one of the following combinations is required:
+ − 753 # - column 1 (Generation) is 1 and column 2 (Stage) is 1 (Young nymph)
+ − 754 # - column 1 (Generation) is 1 and column 2 (Stage) is 2 (Old nymph)
+ − 755 F1.nymph[row] = sum((vector.matrix[,1]==1 & vector.matrix[,2]==1) | (vector.matrix[,1]==1 & vector.matrix[,2]==2));
+ − 756 # For nymph life stage of generation F2 population
+ − 757 # size, one of the following combinations is required:
+ − 758 # - column 1 (Generation) is 2 and column 2 (Stage) is 1 (Young nymph)
+ − 759 # - column 1 (Generation) is 2 and column 2 (Stage) is 2 (Old nymph)
+ − 760 F2.nymph[row] = sum((vector.matrix[,1]==2 & vector.matrix[,2]==1) | (vector.matrix[,1]==2 & vector.matrix[,2]==2));
+ − 761 }
+ − 762 if (process_adults) {
+ − 763 # For adult life stage of generation P population
+ − 764 # size, one of the following combinations is required:
+ − 765 # - column 1 (Generation) is 0 and column 2 (Stage) is 3 (Pre-vitellogenic)
+ − 766 # - column 1 (Generation) is 0 and column 2 (Stage) is 4 (Vitellogenic)
+ − 767 # - column 1 (Generation) is 0 and column 2 (Stage) is 5 (Diapausing)
+ − 768 P.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));
+ − 769 # For adult life stage of generation F1 population
+ − 770 # size, one of the following combinations is required:
+ − 771 # - column 1 (Generation) is 1 and column 2 (Stage) is 3 (Pre-vitellogenic)
+ − 772 # - column 1 (Generation) is 1 and column 2 (Stage) is 4 (Vitellogenic)
+ − 773 # - column 1 (Generation) is 1 and column 2 (Stage) is 5 (Diapausing)
+ − 774 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));
+ − 775 # For adult life stage of generation F2 population
+ − 776 # size, one of the following combinations is required:
+ − 777 # - column 1 (Generation) is 2 and column 2 (Stage) is 3 (Pre-vitellogenic)
+ − 778 # - column 1 (Generation) is 2 and column 2 (Stage) is 4 (Vitellogenic)
+ − 779 # - column 1 (Generation) is 2 and column 2 (Stage) is 5 (Diapausing)
+ − 780 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));
+ − 781 }
+ − 782 }
6
+ − 783 } # End of days specified in the input temperature data.
5
+ − 784
8
+ − 785 averages.cum = cumsum(averages.day);
5
+ − 786
6
+ − 787 # Define the output values.
10
+ − 788 if (process_eggs) {
18
+ − 789 Eggs.replications[,current_replication] = Eggs;
10
+ − 790 }
+ − 791 if (process_nymphs) {
18
+ − 792 YoungNymphs.replications[,current_replication] = YoungNymphs;
+ − 793 OldNymphs.replications[,current_replication] = OldNymphs;
10
+ − 794 }
+ − 795 if (process_adults) {
18
+ − 796 Previtellogenic.replications[,current_replication] = Previtellogenic;
+ − 797 Vitellogenic.replications[,current_replication] = Vitellogenic;
+ − 798 Diapausing.replications[,current_replication] = Diapausing;
10
+ − 799 }
18
+ − 800 newborn.replications[,current_replication] = N.newborn;
+ − 801 adult.replications[,current_replication] = N.adult;
+ − 802 death.replications[,current_replication] = N.death;
10
+ − 803 if (plot_generations_separately) {
+ − 804 # P is Parental, or overwintered adults.
18
+ − 805 P.replications[,current_replication] = overwintering_adult.population;
10
+ − 806 # F1 is the first field-produced generation.
18
+ − 807 F1.replications[,current_replication] = first_generation.population;
10
+ − 808 # F2 is the second field-produced generation.
18
+ − 809 F2.replications[,current_replication] = second_generation.population;
10
+ − 810 if (process_eggs) {
18
+ − 811 P_eggs.replications[,current_replication] = P.egg;
+ − 812 F1_eggs.replications[,current_replication] = F1.egg;
+ − 813 F2_eggs.replications[,current_replication] = F2.egg;
10
+ − 814 }
+ − 815 if (process_nymphs) {
18
+ − 816 P_nymphs.replications[,current_replication] = P.nymph;
+ − 817 F1_nymphs.replications[,current_replication] = F1.nymph;
+ − 818 F2_nymphs.replications[,current_replication] = F2.nymph;
10
+ − 819 }
+ − 820 if (process_adults) {
18
+ − 821 P_adults.replications[,current_replication] = P.adult;
+ − 822 F1_adults.replications[,current_replication] = F1.adult;
+ − 823 F2_adults.replications[,current_replication] = F2.adult;
10
+ − 824 }
+ − 825 }
18
+ − 826 population.replications[,current_replication] = total.population;
+ − 827 # End processing replications.
5
+ − 828 }
+ − 829
10
+ − 830 if (process_eggs) {
+ − 831 # Mean value for eggs.
+ − 832 eggs = apply(Eggs.replications, 1, mean);
+ − 833 # Standard error for eggs.
+ − 834 eggs.std_error = apply(Eggs.replications, 1, sd) / sqrt(opt$replications);
+ − 835 }
+ − 836 if (process_nymphs) {
+ − 837 # Calculate nymph populations for selected life stage.
16
+ − 838 for (life_stage_nymph in life_stages_nymph) {
18
+ − 839 if (life_stage_nymph=="Total") {
16
+ − 840 # Mean value for all nymphs.
+ − 841 total_nymphs = apply((YoungNymphs.replications+OldNymphs.replications), 1, mean);
+ − 842 # Standard error for all nymphs.
+ − 843 total_nymphs.std_error = apply((YoungNymphs.replications+OldNymphs.replications) / sqrt(opt$replications), 1, sd);
18
+ − 844 } else if (life_stage_nymph=="Young") {
16
+ − 845 # Mean value for young nymphs.
+ − 846 young_nymphs = apply(YoungNymphs.replications, 1, mean);
+ − 847 # Standard error for young nymphs.
+ − 848 young_nymphs.std_error = apply(YoungNymphs.replications / sqrt(opt$replications), 1, sd);
18
+ − 849 } else if (life_stage_nymph=="Old") {
16
+ − 850 # Mean value for old nymphs.
+ − 851 old_nymphs = apply(OldNymphs.replications, 1, mean);
+ − 852 # Standard error for old nymphs.
+ − 853 old_nymphs.std_error = apply(OldNymphs.replications / sqrt(opt$replications), 1, sd);
+ − 854 }
10
+ − 855 }
+ − 856 }
+ − 857 if (process_adults) {
+ − 858 # Calculate adult populations for selected life stage.
16
+ − 859 for (life_stage_adult in life_stages_adult) {
18
+ − 860 if (life_stage_adult=="Total") {
16
+ − 861 # Mean value for all adults.
+ − 862 total_adults = apply((Previtellogenic.replications+Vitellogenic.replications+Diapausing.replications), 1, mean);
+ − 863 # Standard error for all adults.
+ − 864 total_adults.std_error = apply((Previtellogenic.replications+Vitellogenic.replications+Diapausing.replications), 1, sd) / sqrt(opt$replications);
18
+ − 865 } else if (life_stage_adult == "Pre-vittelogenic") {
16
+ − 866 # Mean value for previtellogenic adults.
+ − 867 previttelogenic_adults = apply(Previtellogenic.replications, 1, mean);
+ − 868 # Standard error for previtellogenic adults.
+ − 869 previttelogenic_adults.std_error = apply(Previtellogenic.replications, 1, sd) / sqrt(opt$replications);
18
+ − 870 } else if (life_stage_adult == "Vittelogenic") {
16
+ − 871 # Mean value for vitellogenic adults.
+ − 872 vittelogenic_adults = apply(Vitellogenic.replications, 1, mean);
+ − 873 # Standard error for vitellogenic adults.
+ − 874 vittelogenic_adults.std_error = apply(Vitellogenic.replications, 1, sd) / sqrt(opt$replications);
18
+ − 875 } else if (life_stage_adult == "Diapausing") {
16
+ − 876 # Mean value for vitellogenic adults.
+ − 877 diapausing_adults = apply(Diapausing.replications, 1, mean);
+ − 878 # Standard error for vitellogenic adults.
+ − 879 diapausing_adults.std_error = apply(Diapausing.replications, 1, sd) / sqrt(opt$replications);
+ − 880 }
10
+ − 881 }
+ − 882 }
5
+ − 883
10
+ − 884 if (plot_generations_separately) {
+ − 885 # Mean value for P which is Parental, or overwintered adults.
+ − 886 P = apply(P.replications, 1, mean);
+ − 887 # Standard error for P.
+ − 888 P.std_error = apply(P.replications, 1, sd) / sqrt(opt$replications);
+ − 889 # Mean value for F1, which is the first field-produced generation.
+ − 890 F1 = apply(F1.replications, 1, mean);
+ − 891 # Standard error for F1.
+ − 892 F1.std_error = apply(F1.replications, 1, sd) / sqrt(opt$replications);
+ − 893 # Mean value for F2, which is the second field-produced generation.
+ − 894 F2 = apply(F2.replications, 1, mean);
+ − 895 # Standard error for F2.
+ − 896 F2.std_error = apply(F2.replications, 1, sd) / sqrt(opt$replications);
+ − 897 if (process_eggs) {
+ − 898 # Mean value for P eggs.
+ − 899 P_eggs = apply(P_eggs.replications, 1, mean);
+ − 900 # Standard error for P_eggs.
+ − 901 P_eggs.std_error = apply(P_eggs.replications, 1, sd) / sqrt(opt$replications);
+ − 902 # Mean value for F1 eggs.
+ − 903 F1_eggs = apply(F1_eggs.replications, 1, mean);
+ − 904 # Standard error for F1 eggs.
+ − 905 F1_eggs.std_error = apply(F1_eggs.replications, 1, sd) / sqrt(opt$replications);
+ − 906 # Mean value for F2 eggs.
+ − 907 F2_eggs = apply(F2_eggs.replications, 1, mean);
+ − 908 # Standard error for F2 eggs.
+ − 909 F2_eggs.std_error = apply(F2_eggs.replications, 1, sd) / sqrt(opt$replications);
+ − 910 }
+ − 911 if (process_nymphs) {
+ − 912 # Mean value for P nymphs.
+ − 913 P_nymphs = apply(P_nymphs.replications, 1, mean);
+ − 914 # Standard error for P_nymphs.
+ − 915 P_nymphs.std_error = apply(P_nymphs.replications, 1, sd) / sqrt(opt$replications);
+ − 916 # Mean value for F1 nymphs.
+ − 917 F1_nymphs = apply(F1_nymphs.replications, 1, mean);
+ − 918 # Standard error for F1 nymphs.
+ − 919 F1_nymphs.std_error = apply(F1_nymphs.replications, 1, sd) / sqrt(opt$replications);
+ − 920 # Mean value for F2 nymphs.
+ − 921 F2_nymphs = apply(F2_nymphs.replications, 1, mean);
+ − 922 # Standard error for F2 eggs.
+ − 923 F2_nymphs.std_error = apply(F2_nymphs.replications, 1, sd) / sqrt(opt$replications);
+ − 924 }
+ − 925 if (process_adults) {
+ − 926 # Mean value for P adults.
+ − 927 P_adults = apply(P_adults.replications, 1, mean);
+ − 928 # Standard error for P_adults.
+ − 929 P_adults.std_error = apply(P_adults.replications, 1, sd) / sqrt(opt$replications);
+ − 930 # Mean value for F1 adults.
+ − 931 F1_adults = apply(F1_adults.replications, 1, mean);
+ − 932 # Standard error for F1 adults.
+ − 933 F1_adults.std_error = apply(F1_adults.replications, 1, sd) / sqrt(opt$replications);
+ − 934 # Mean value for F2 adults.
+ − 935 F2_adults = apply(F2_adults.replications, 1, mean);
+ − 936 # Standard error for F2 adults.
+ − 937 F2_adults.std_error = apply(F2_adults.replications, 1, sd) / sqrt(opt$replications);
+ − 938 }
+ − 939 }
6
+ − 940
+ − 941 # Display the total number of days in the Galaxy history item blurb.
8
+ − 942 cat("Number of days: ", opt$num_days, "\n");
5
+ − 943
10
+ − 944 # Information needed for plots plots.
8
+ − 945 days = c(1:opt$num_days);
+ − 946 start_date = temperature_data_frame$DATE[1];
+ − 947 end_date = temperature_data_frame$DATE[opt$num_days];
5
+ − 948
10
+ − 949 if (plot_generations_separately) {
15
+ − 950 for (life_stage in life_stages) {
10
+ − 951 if (life_stage == "Egg") {
+ − 952 # Start PDF device driver.
+ − 953 dev.new(width=20, height=30);
19
+ − 954 file_path = get_file_path(life_stage, "egg_pop_by_generation.pdf")
10
+ − 955 pdf(file=file_path, width=20, height=30, bg="white");
+ − 956 par(mar=c(5, 6, 4, 4), mfrow=c(3, 1));
+ − 957 # Egg population size by generation.
18
+ − 958 maxval = max(P_eggs+F1_eggs+F2_eggs) + 100;
10
+ − 959 render_chart(date_labels, "pop_size_by_generation", opt$plot_std_error, opt$insect, opt$location, latitude, start_date, end_date, days, maxval,
+ − 960 opt$replications, life_stage, group=P_eggs, group_std_error=P_eggs.std_error, group2=F1_eggs, group2_std_error=F1_eggs.std_error, group3=F2_eggs,
+ − 961 group3_std_error=F2_eggs.std_error);
+ − 962 # Turn off device driver to flush output.
+ − 963 dev.off();
+ − 964 } else if (life_stage == "Nymph") {
16
+ − 965 for (life_stage_nymph in life_stages_nymph) {
+ − 966 # Start PDF device driver.
+ − 967 dev.new(width=20, height=30);
19
+ − 968 file_path = get_file_path(life_stage, "nymph_pop_by_generation.pdf", life_stage_nymph=life_stage_nymph)
16
+ − 969 pdf(file=file_path, width=20, height=30, bg="white");
+ − 970 par(mar=c(5, 6, 4, 4), mfrow=c(3, 1));
+ − 971 # Nymph population size by generation.
18
+ − 972 maxval = max(P_nymphs+F1_nymphs+F2_nymphs) + 100;
16
+ − 973 render_chart(date_labels, "pop_size_by_generation", opt$plot_std_error, opt$insect, opt$location, latitude, start_date, end_date, days, maxval,
19
+ − 974 opt$replications, life_stage, group=P_nymphs, group_std_error=P_nymphs.std_error, group2=F1_nymphs, group2_std_error=F1_nymphs.std_error,
+ − 975 group3=F2_nymphs, group3_std_error=F2_nymphs.std_error, life_stages_nymph=life_stage_nymph);
16
+ − 976 # Turn off device driver to flush output.
+ − 977 dev.off();
+ − 978 }
10
+ − 979 } else if (life_stage == "Adult") {
16
+ − 980 for (life_stage_adult in life_stages_adult) {
+ − 981 # Start PDF device driver.
+ − 982 dev.new(width=20, height=30);
19
+ − 983 file_path = get_file_path(life_stage, "adult_pop_by_generation.pdf", life_stage_adult=life_stage_adult)
16
+ − 984 pdf(file=file_path, width=20, height=30, bg="white");
+ − 985 par(mar=c(5, 6, 4, 4), mfrow=c(3, 1));
+ − 986 # Adult population size by generation.
18
+ − 987 maxval = max(P_adults+F1_adults+F2_adults) + 100;
16
+ − 988 render_chart(date_labels, "pop_size_by_generation", opt$plot_std_error, opt$insect, opt$location, latitude, start_date, end_date, days, maxval,
+ − 989 opt$replications, life_stage, group=P_adults, group_std_error=P_adults.std_error, group2=F1_adults, group2_std_error=F1_adults.std_error,
+ − 990 group3=F2_adults, group3_std_error=F2_adults.std_error, life_stages_adult=life_stage_adult);
+ − 991 # Turn off device driver to flush output.
+ − 992 dev.off();
+ − 993 }
10
+ − 994 } else if (life_stage == "Total") {
+ − 995 # Start PDF device driver.
18
+ − 996 # Name collection elements so that they
+ − 997 # are displayed in logical order.
10
+ − 998 dev.new(width=20, height=30);
19
+ − 999 file_path = get_file_path(life_stage, "total_pop_by_generation.pdf")
10
+ − 1000 pdf(file=file_path, width=20, height=30, bg="white");
+ − 1001 par(mar=c(5, 6, 4, 4), mfrow=c(3, 1));
+ − 1002 # Total population size by generation.
18
+ − 1003 maxval = max(P+F1+F2) + 100;
10
+ − 1004 render_chart(date_labels, "pop_size_by_generation", opt$plot_std_error, opt$insect, opt$location, latitude, start_date, end_date, days, maxval,
+ − 1005 opt$replications, life_stage, group=P, group_std_error=P.std_error, group2=F1, group2_std_error=F1.std_error, group3=F2, group3_std_error=F2.std_error);
+ − 1006 # Turn off device driver to flush output.
+ − 1007 dev.off();
+ − 1008 }
15
+ − 1009 }
10
+ − 1010 } else {
+ − 1011 for (life_stage in life_stages) {
+ − 1012 if (life_stage == "Egg") {
+ − 1013 # Start PDF device driver.
+ − 1014 dev.new(width=20, height=30);
19
+ − 1015 file_path = get_file_path(life_stage, "egg_pop.pdf")
10
+ − 1016 pdf(file=file_path, width=20, height=30, bg="white");
+ − 1017 par(mar=c(5, 6, 4, 4), mfrow=c(3, 1));
+ − 1018 # Egg population size.
18
+ − 1019 maxval = max(eggs+eggs.std_error) + 100;
10
+ − 1020 render_chart(date_labels, "pop_size_by_life_stage", opt$plot_std_error, opt$insect, opt$location, latitude, start_date, end_date, days, maxval,
+ − 1021 opt$replications, life_stage, group=eggs, group_std_error=eggs.std_error);
+ − 1022 # Turn off device driver to flush output.
+ − 1023 dev.off();
+ − 1024 } else if (life_stage == "Nymph") {
16
+ − 1025 for (life_stage_nymph in life_stages_nymph) {
+ − 1026 # Start PDF device driver.
+ − 1027 dev.new(width=20, height=30);
19
+ − 1028 file_path = get_file_path(life_stage, "nymph_pop.pdf", life_stage_nymph=life_stage_nymph)
16
+ − 1029 pdf(file=file_path, width=20, height=30, bg="white");
+ − 1030 par(mar=c(5, 6, 4, 4), mfrow=c(3, 1));
+ − 1031 if (life_stage_nymph=="Total") {
+ − 1032 # Total nymph population size.
+ − 1033 group = total_nymphs;
+ − 1034 group_std_error = total_nymphs.std_error;
+ − 1035 } else if (life_stage_nymph=="Young") {
+ − 1036 # Young nymph population size.
+ − 1037 group = young_nymphs;
+ − 1038 group_std_error = young_nymphs.std_error;
+ − 1039 } else if (life_stage_nymph=="Old") {
+ − 1040 # Old nymph population size.
+ − 1041 group = old_nymphs;
+ − 1042 group_std_error = old_nymphs.std_error;
+ − 1043 }
18
+ − 1044 maxval = max(group+group_std_error) + 100;
16
+ − 1045 render_chart(date_labels, "pop_size_by_life_stage", opt$plot_std_error, opt$insect, opt$location, latitude, start_date, end_date, days, maxval,
+ − 1046 opt$replications, life_stage, group=group, group_std_error=group_std_error, life_stages_nymph=life_stage_nymph);
+ − 1047 # Turn off device driver to flush output.
+ − 1048 dev.off();
+ − 1049 }
10
+ − 1050 } else if (life_stage == "Adult") {
16
+ − 1051 for (life_stage_adult in life_stages_adult) {
+ − 1052 # Start PDF device driver.
+ − 1053 dev.new(width=20, height=30);
19
+ − 1054 file_path = get_file_path(life_stage, "adult_pop.pdf", life_stage_adult=life_stage_adult)
16
+ − 1055 pdf(file=file_path, width=20, height=30, bg="white");
+ − 1056 par(mar=c(5, 6, 4, 4), mfrow=c(3, 1));
+ − 1057 if (life_stage_adult=="Total") {
+ − 1058 # Total adult population size.
+ − 1059 group = total_adults;
+ − 1060 group_std_error = total_adults.std_error
+ − 1061 } else if (life_stage_adult=="Pre-vittelogenic") {
+ − 1062 # Pre-vittelogenic adult population size.
+ − 1063 group = previttelogenic_adults;
+ − 1064 group_std_error = previttelogenic_adults.std_error
+ − 1065 } else if (life_stage_adult=="Vittelogenic") {
+ − 1066 # Vittelogenic adult population size.
+ − 1067 group = vittelogenic_adults;
+ − 1068 group_std_error = vittelogenic_adults.std_error
+ − 1069 } else if (life_stage_adult=="Diapausing") {
+ − 1070 # Diapausing adult population size.
+ − 1071 group = diapausing_adults;
+ − 1072 group_std_error = diapausing_adults.std_error
+ − 1073 }
18
+ − 1074 maxval = max(group+group_std_error) + 100;
16
+ − 1075 render_chart(date_labels, "pop_size_by_life_stage", opt$plot_std_error, opt$insect, opt$location, latitude, start_date, end_date, days, maxval,
+ − 1076 opt$replications, life_stage, group=group, group_std_error=group_std_error, life_stages_adult=life_stage_adult);
+ − 1077 # Turn off device driver to flush output.
+ − 1078 dev.off();
+ − 1079 }
10
+ − 1080 } else if (life_stage == "Total") {
+ − 1081 # Start PDF device driver.
+ − 1082 dev.new(width=20, height=30);
19
+ − 1083 file_path = get_file_path(life_stage, "total_pop.pdf")
10
+ − 1084 pdf(file=file_path, width=20, height=30, bg="white");
+ − 1085 par(mar=c(5, 6, 4, 4), mfrow=c(3, 1));
+ − 1086 # Total population size.
18
+ − 1087 maxval = max(eggs+eggs.std_error, total_nymphs+total_nymphs.std_error, total_adults+total_adults.std_error) + 100;
10
+ − 1088 render_chart(date_labels, "pop_size_by_life_stage", opt$plot_std_error, opt$insect, opt$location, latitude, start_date, end_date, days, maxval,
16
+ − 1089 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
+ − 1090 group3_std_error=eggs.std_error);
+ − 1091 # Turn off device driver to flush output.
+ − 1092 dev.off();
+ − 1093 }
+ − 1094 }
+ − 1095 }
