Mercurial > repos > greg > insect_phenology_model

comparison insect_phenology_model.R @ 34:7aa848b0e55c draft

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author greg
date Mon, 19 Mar 2018 14:49:05 -0400
parents ef6aa8c21729
children 29ec818b1c29
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33:ef5add7dea47 34:7aa848b0e55c
16 make_option(c("--min_clutch_size"), action="store", dest="min_clutch_size", type="integer", help="Adjustment of minimum clutch size"), 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"), 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("--num_days"), action="store", dest="num_days", type="integer", help="Total number of days in the temperature dataset"), 18 make_option(c("--num_days"), action="store", dest="num_days", type="integer", help="Total number of days in the temperature dataset"),
19 make_option(c("--nymph_mortality"), action="store", dest="nymph_mortality", type="integer", help="Adjustment rate for nymph mortality"), 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)"), 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("--output_combined"), action="store", dest="output_combined", help="Dataset containing analyzed data for combined generations"),
22 make_option(c("--output_f1"), action="store", dest="output_f1", default=NULL, help="Dataset containing analyzed data for generation F1"),
23 make_option(c("--output_f2"), action="store", dest="output_f2", default=NULL, help="Dataset containing analyzed data for generation F2"),
24 make_option(c("--output_p"), action="store", dest="output_p", default=NULL, help="Dataset containing analyzed data for generation P"),
25 make_option(c("--oviposition"), action="store", dest="oviposition", type="integer", help="Adjustment for oviposition rate"), 21 make_option(c("--oviposition"), action="store", dest="oviposition", type="integer", help="Adjustment for oviposition rate"),
26 make_option(c("--photoperiod"), action="store", dest="photoperiod", type="double", help="Critical photoperiod for diapause induction/termination"), 22 make_option(c("--photoperiod"), action="store", dest="photoperiod", type="double", help="Critical photoperiod for diapause induction/termination"),
27 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"), 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"),
28 make_option(c("--plot_std_error"), action="store", dest="plot_std_error", help="Plot Standard error"), 24 make_option(c("--plot_std_error"), action="store", dest="plot_std_error", help="Plot Standard error"),
29 make_option(c("--replications"), action="store", dest="replications", type="integer", help="Number of replications"), 25 make_option(c("--replications"), action="store", dest="replications", type="integer", help="Number of replications"),
64 # Reset the column names with the additional column for later access. 60 # Reset the column names with the additional column for later access.
65 colnames(data_frame) = append(current_column_names, new_column_name); 61 colnames(data_frame) = append(current_column_names, new_column_name);
66 return(data_frame); 62 return(data_frame);
67 } 63 }
68 64
69 get_date_labels = function(temperature_data_frame, num_rows) { 65 get_x_axis_ticks_and_labels = function(temperature_data_frame, num_rows) {
70 # Keep track of the years to see if spanning years. 66 # Keep track of the years to see if spanning years.
71 month_labels = list(); 67 month_labels = list();
68 ticks = list();
72 current_month_label = NULL; 69 current_month_label = NULL;
73 for (i in 1:num_rows) { 70 for (i in 1:num_rows) {
74 # Get the year and month from the date which 71 # Get the year and month from the date which
75 # has the format YYYY-MM-DD. 72 # has the format YYYY-MM-DD.
76 date = format(temperature_data_frame$DATE[i]); 73 date = format(temperature_data_frame$DATE[i]);
74 # Get the month label.
77 items = strsplit(date, "-")[[1]]; 75 items = strsplit(date, "-")[[1]];
78 month = items[2]; 76 month = items[2];
79 month_label = month.abb[as.integer(month)]; 77 month_label = month.abb[as.integer(month)];
80 if (!identical(current_month_label, month_label)) { 78 if (!identical(current_month_label, month_label)) {
79 # Add an x-axis tick for the month.
80 ticks[length(ticks)+1] = i;
81 month_labels[length(month_labels)+1] = month_label; 81 month_labels[length(month_labels)+1] = month_label;
82 current_month_label = month_label; 82 current_month_label = month_label;
83 } 83 }
84 } 84 # Get the day.
85 return(c(unlist(month_labels))); 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 }
92 }
93 return(list(ticks, month_labels));
86 } 94 }
87 95
88 get_file_path = function(life_stage, base_name, life_stage_nymph=NULL, life_stage_adult=NULL) { 96 get_file_path = function(life_stage, base_name, life_stage_nymph=NULL, life_stage_adult=NULL) {
89 if (!is.null(life_stage_nymph)) { 97 if (!is.null(life_stage_nymph)) {
90 lsi = get_life_stage_index(life_stage, life_stage_nymph=life_stage_nymph); 98 lsi = get_life_stage_index(life_stage, life_stage_nymph=life_stage_nymph);
94 file_name = paste(lsi, tolower(life_stage_adult), base_name, sep="_"); 102 file_name = paste(lsi, tolower(life_stage_adult), base_name, sep="_");
95 } else { 103 } else {
96 lsi = get_life_stage_index(life_stage); 104 lsi = get_life_stage_index(life_stage);
97 file_name = paste(lsi, base_name, sep="_"); 105 file_name = paste(lsi, base_name, sep="_");
98 } 106 }
99 file_path = paste("output_dir", file_name, sep="/"); 107 file_path = paste("output_plots_dir", file_name, sep="/");
100 return(file_path); 108 return(file_path);
101 } 109 }
102 110
103 get_life_stage_index = function(life_stage, life_stage_nymph=NULL, life_stage_adult=NULL) { 111 get_life_stage_index = function(life_stage, life_stage_nymph=NULL, life_stage_adult=NULL) {
104 # Name collection elements so that they 112 # Name collection elements so that they
263 temperature_data_frame = add_daylight_length(temperature_data_frame, num_rows); 271 temperature_data_frame = add_daylight_length(temperature_data_frame, num_rows);
264 } 272 }
265 return(temperature_data_frame); 273 return(temperature_data_frame);
266 } 274 }
267 275
268 render_chart = function(date_labels, chart_type, plot_std_error, insect, location, latitude, start_date, end_date, days, maxval, 276 render_chart = function(ticks, date_labels, chart_type, plot_std_error, insect, location, latitude, start_date, end_date, days, maxval,
269 replications, life_stage, group, group_std_error, group2=NULL, group2_std_error=NULL, group3=NULL, group3_std_error=NULL, 277 replications, life_stage, group, group_std_error, group2=NULL, group2_std_error=NULL, group3=NULL, group3_std_error=NULL,
270 life_stages_adult=NULL, life_stages_nymph=NULL) { 278 life_stages_adult=NULL, life_stages_nymph=NULL) {
271 if (chart_type=="pop_size_by_life_stage") { 279 if (chart_type=="pop_size_by_life_stage") {
272 if (life_stage=="Total") { 280 if (life_stage=="Total") {
273 title = paste(insect, ": Reps", replications, ":", life_stage, "Pop :", location, ": Lat", latitude, ":", start_date, "-", end_date, sep=" "); 281 title = paste(insect, ": Reps", replications, ":", life_stage, "Pop :", location, ": Lat", latitude, ":", start_date, "-", end_date, sep=" ");
275 columns = c(4, 2, 1); 283 columns = c(4, 2, 1);
276 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); 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);
277 legend("topleft", legend_text, lty=c(1, 1, 1), col=columns, cex=3); 285 legend("topleft", legend_text, lty=c(1, 1, 1), col=columns, cex=3);
278 lines(days, group2, lwd=2, lty=1, col=2); 286 lines(days, group2, lwd=2, lty=1, col=2);
279 lines(days, group3, lwd=2, lty=1, col=4); 287 lines(days, group3, lwd=2, lty=1, col=4);
280 axis(1, at=c(1:length(date_labels)) * 30 - 15, cex.axis=3, labels=date_labels); 288 axis(side=1, at=ticks, labels=date_labels);
281 axis(2, cex.axis=3); 289 axis(side=2);
282 if (plot_std_error=="yes") { 290 if (plot_std_error=="yes") {
283 # Standard error for group. 291 # Standard error for group.
284 lines(days, group+group_std_error, lty=2); 292 lines(days, group+group_std_error, lty=2);
285 lines(days, group-group_std_error, lty=2); 293 lines(days, group-group_std_error, lty=2);
286 # Standard error for group2. 294 # Standard error for group2.
306 legend_text = c(paste(life_stages_adult, life_stage, sep=" ")); 314 legend_text = c(paste(life_stages_adult, life_stage, sep=" "));
307 columns = c(1); 315 columns = c(1);
308 } 316 }
309 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); 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);
310 legend("topleft", legend_text, lty=c(1), col="black", cex=3); 318 legend("topleft", legend_text, lty=c(1), col="black", cex=3);
311 axis(1, at=c(1:length(date_labels)) * 30 - 15, cex.axis=3, labels=date_labels); 319 axis(side=1, at=ticks, labels=date_labels);
312 axis(2, cex.axis=3); 320 axis(side=2);
313 if (plot_std_error=="yes") { 321 if (plot_std_error=="yes") {
314 # Standard error for group. 322 # Standard error for group.
315 lines(days, group+group_std_error, lty=2); 323 lines(days, group+group_std_error, lty=2);
316 lines(days, group-group_std_error, lty=2); 324 lines(days, group-group_std_error, lty=2);
317 } 325 }
331 columns = c(1, 2, 4); 339 columns = c(1, 2, 4);
332 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); 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);
333 legend("topleft", legend_text, lty=c(1, 1, 1), col=columns, cex=3); 341 legend("topleft", legend_text, lty=c(1, 1, 1), col=columns, cex=3);
334 lines(days, group2, lwd=2, lty=1, col=2); 342 lines(days, group2, lwd=2, lty=1, col=2);
335 lines(days, group3, lwd=2, lty=1, col=4); 343 lines(days, group3, lwd=2, lty=1, col=4);
336 axis(1, at=c(1:length(date_labels)) * 30 - 15, cex.axis=3, labels=date_labels); 344 axis(side=1, at=ticks, labels=date_labels);
337 axis(2, cex.axis=3); 345 axis(side=2);
338 if (plot_std_error=="yes") { 346 if (plot_std_error=="yes") {
339 # Standard error for group. 347 # Standard error for group.
340 lines(days, group+group_std_error, lty=2); 348 lines(days, group+group_std_error, lty=2);
341 lines(days, group-group_std_error, lty=2); 349 lines(days, group-group_std_error, lty=2);
342 # Standard error for group2. 350 # Standard error for group2.
362 temperature_data_frame_P = data.frame(temperature_data_frame); 370 temperature_data_frame_P = data.frame(temperature_data_frame);
363 temperature_data_frame_F1 = data.frame(temperature_data_frame); 371 temperature_data_frame_F1 = data.frame(temperature_data_frame);
364 temperature_data_frame_F2 = data.frame(temperature_data_frame); 372 temperature_data_frame_F2 = data.frame(temperature_data_frame);
365 } 373 }
366 # Get the date labels for plots. 374 # Get the date labels for plots.
367 date_labels = get_date_labels(temperature_data_frame, opt$num_days); 375 ticks_and_labels = get_x_axis_ticks_and_labels(temperature_data_frame, opt$num_days);
376 ticks = c(unlist(ticks_and_labels[1]));
377 date_labels = c(unlist(ticks_and_labels[2]));
368 # All latitude values are the same, so get the value for plots from the first row. 378 # All latitude values are the same, so get the value for plots from the first row.
369 latitude = temperature_data_frame$LATITUDE[1]; 379 latitude = temperature_data_frame$LATITUDE[1];
370 # Determine the specified life stages for processing. 380 # Determine the specified life stages for processing.
371 # Split life_stages into a list of strings for plots. 381 # Split life_stages into a list of strings for plots.
372 life_stages_str = as.character(opt$life_stages); 382 life_stages_str = as.character(opt$life_stages);
1254 temperature_data_frame_F2 = append_vector(temperature_data_frame_F2, F2_total_adults.std_error, "TOTALADULT-F2-SE"); 1264 temperature_data_frame_F2 = append_vector(temperature_data_frame_F2, F2_total_adults.std_error, "TOTALADULT-F2-SE");
1255 } 1265 }
1256 } 1266 }
1257 1267
1258 # Save the analyzed data for combined generations. 1268 # Save the analyzed data for combined generations.
1259 write.csv(temperature_data_frame, file=opt$output_combined, row.names=F); 1269 file_path = paste("output_data_dir", "04_combined_generations.csv", sep="/");
1270 write.csv(temperature_data_frame, file=file_path, row.names=F);
1260 if (plot_generations_separately) { 1271 if (plot_generations_separately) {
1261 # Save the analyzed data for generation P. 1272 # Save the analyzed data for generation P.
1262 write.csv(temperature_data_frame_P, file=opt$output_p, row.names=F); 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);
1263 # Save the analyzed data for generation F1. 1275 # Save the analyzed data for generation F1.
1264 write.csv(temperature_data_frame_F1, file=opt$output_f1, row.names=F); 1276 file_path = paste("output_data_dir", "02_generation_F1.csv", sep="/");
1277 write.csv(temperature_data_frame_F1, file=file_path, row.names=F);
1265 # Save the analyzed data for generation F2. 1278 # Save the analyzed data for generation F2.
1266 write.csv(temperature_data_frame_F2, file=opt$output_f2, row.names=F); 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);
1267 } 1281 }
1268 # Display the total number of days in the Galaxy history item blurb. 1282 # Display the total number of days in the Galaxy history item blurb.
1269 cat("Number of days: ", opt$num_days, "\n"); 1283 cat("Number of days: ", opt$num_days, "\n");
1270 # Information needed for plots plots. 1284 # Information needed for plots plots.
1271 days = c(1:opt$num_days); 1285 days = c(1:opt$num_days);
1280 file_path = get_file_path(life_stage, "egg_pop_by_generation.pdf") 1294 file_path = get_file_path(life_stage, "egg_pop_by_generation.pdf")
1281 pdf(file=file_path, width=20, height=30, bg="white"); 1295 pdf(file=file_path, width=20, height=30, bg="white");
1282 par(mar=c(5, 6, 4, 4), mfrow=c(3, 1)); 1296 par(mar=c(5, 6, 4, 4), mfrow=c(3, 1));
1283 # Egg population size by generation. 1297 # Egg population size by generation.
1284 maxval = max(P_eggs+F1_eggs+F2_eggs) + 100; 1298 maxval = max(P_eggs+F1_eggs+F2_eggs) + 100;
1285 render_chart(date_labels, "pop_size_by_generation", opt$plot_std_error, opt$insect, opt$location, latitude, start_date, end_date, days, maxval, 1299 render_chart(ticks, date_labels, "pop_size_by_generation", opt$plot_std_error, opt$insect, opt$location, latitude, start_date, end_date, days, maxval,
1286 opt$replications, life_stage, group=P_eggs, group_std_error=P_eggs.std_error, group2=F1_eggs, group2_std_error=F1_eggs.std_error, group3=F2_eggs, 1300 opt$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,
1287 group3_std_error=F2_eggs.std_error); 1301 group3_std_error=F2_eggs.std_error);
1288 # Turn off device driver to flush output. 1302 # Turn off device driver to flush output.
1289 dev.off(); 1303 dev.off();
1290 } else if (life_stage == "Nymph") { 1304 } else if (life_stage == "Nymph") {
1320 group2 = F1_total_nymphs; 1334 group2 = F1_total_nymphs;
1321 group2_std_error = F1_total_nymphs.std_error; 1335 group2_std_error = F1_total_nymphs.std_error;
1322 group3 = F2_total_nymphs; 1336 group3 = F2_total_nymphs;
1323 group3_std_error = F2_total_nymphs.std_error; 1337 group3_std_error = F2_total_nymphs.std_error;
1324 } 1338 }
1325 render_chart(date_labels, "pop_size_by_generation", opt$plot_std_error, opt$insect, opt$location, latitude, start_date, end_date, days, maxval, 1339 render_chart(ticks, date_labels, "pop_size_by_generation", opt$plot_std_error, opt$insect, opt$location, latitude, start_date, end_date, days, maxval,
1326 opt$replications, life_stage, group=group, group_std_error=group_std_error, group2=group2, group2_std_error=group2_std_error, 1340 opt$replications, life_stage, group=group, group_std_error=group_std_error, group2=group2, group2_std_error=group2_std_error,
1327 group3=group3, group3_std_error=group3_std_error, life_stages_nymph=life_stage_nymph); 1341 group3=group3, group3_std_error=group3_std_error, life_stages_nymph=life_stage_nymph);
1328 # Turn off device driver to flush output. 1342 # Turn off device driver to flush output.
1329 dev.off(); 1343 dev.off();
1330 } 1344 }
1370 group2 = F1_total_adults; 1384 group2 = F1_total_adults;
1371 group2_std_error = F1_total_adults.std_error; 1385 group2_std_error = F1_total_adults.std_error;
1372 group3 = F2_total_adults; 1386 group3 = F2_total_adults;
1373 group3_std_error = F2_total_adults.std_error; 1387 group3_std_error = F2_total_adults.std_error;
1374 } 1388 }
1375 render_chart(date_labels, "pop_size_by_generation", opt$plot_std_error, opt$insect, opt$location, latitude, start_date, end_date, days, maxval, 1389 render_chart(ticks, date_labels, "pop_size_by_generation", opt$plot_std_error, opt$insect, opt$location, latitude, start_date, end_date, days, maxval,
1376 opt$replications, life_stage, group=group, group_std_error=group_std_error, group2=group2, group2_std_error=group2_std_error, 1390 opt$replications, life_stage, group=group, group_std_error=group_std_error, group2=group2, group2_std_error=group2_std_error,
1377 group3=group3, group3_std_error=group3_std_error, life_stages_adult=life_stage_adult); 1391 group3=group3, group3_std_error=group3_std_error, life_stages_adult=life_stage_adult);
1378 # Turn off device driver to flush output. 1392 # Turn off device driver to flush output.
1379 dev.off(); 1393 dev.off();
1380 } 1394 }
1386 file_path = get_file_path(life_stage, "total_pop_by_generation.pdf") 1400 file_path = get_file_path(life_stage, "total_pop_by_generation.pdf")
1387 pdf(file=file_path, width=20, height=30, bg="white"); 1401 pdf(file=file_path, width=20, height=30, bg="white");
1388 par(mar=c(5, 6, 4, 4), mfrow=c(3, 1)); 1402 par(mar=c(5, 6, 4, 4), mfrow=c(3, 1));
1389 # Total population size by generation. 1403 # Total population size by generation.
1390 maxval = max(P+F1+F2) + 100; 1404 maxval = max(P+F1+F2) + 100;
1391 render_chart(date_labels, "pop_size_by_generation", opt$plot_std_error, opt$insect, opt$location, latitude, start_date, end_date, days, maxval, 1405 render_chart(ticks, date_labels, "pop_size_by_generation", opt$plot_std_error, opt$insect, opt$location, latitude, start_date, end_date, days, maxval,
1392 opt$replications, life_stage, group=P, group_std_error=P.std_error, group2=F1, group2_std_error=F1.std_error, group3=F2, group3_std_error=F2.std_error); 1406 opt$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);
1393 # Turn off device driver to flush output. 1407 # Turn off device driver to flush output.
1394 dev.off(); 1408 dev.off();
1395 } 1409 }
1396 } 1410 }
1402 file_path = get_file_path(life_stage, "egg_pop.pdf") 1416 file_path = get_file_path(life_stage, "egg_pop.pdf")
1403 pdf(file=file_path, width=20, height=30, bg="white"); 1417 pdf(file=file_path, width=20, height=30, bg="white");
1404 par(mar=c(5, 6, 4, 4), mfrow=c(3, 1)); 1418 par(mar=c(5, 6, 4, 4), mfrow=c(3, 1));
1405 # Egg population size. 1419 # Egg population size.
1406 maxval = max(eggs+eggs.std_error) + 100; 1420 maxval = max(eggs+eggs.std_error) + 100;
1407 render_chart(date_labels, "pop_size_by_life_stage", opt$plot_std_error, opt$insect, opt$location, latitude, start_date, end_date, days, maxval, 1421 render_chart(ticks, date_labels, "pop_size_by_life_stage", opt$plot_std_error, opt$insect, opt$location, latitude, start_date, end_date, days, maxval,
1408 opt$replications, life_stage, group=eggs, group_std_error=eggs.std_error); 1422 opt$replications, life_stage, group=eggs, group_std_error=eggs.std_error);
1409 # Turn off device driver to flush output. 1423 # Turn off device driver to flush output.
1410 dev.off(); 1424 dev.off();
1411 } else if (life_stage == "Nymph") { 1425 } else if (life_stage == "Nymph") {
1412 for (life_stage_nymph in life_stages_nymph) { 1426 for (life_stage_nymph in life_stages_nymph) {
1427 # Old nymph population size. 1441 # Old nymph population size.
1428 group = old_nymphs; 1442 group = old_nymphs;
1429 group_std_error = old_nymphs.std_error; 1443 group_std_error = old_nymphs.std_error;
1430 } 1444 }
1431 maxval = max(group+group_std_error) + 100; 1445 maxval = max(group+group_std_error) + 100;
1432 render_chart(date_labels, "pop_size_by_life_stage", opt$plot_std_error, opt$insect, opt$location, latitude, start_date, end_date, days, maxval, 1446 render_chart(ticks, date_labels, "pop_size_by_life_stage", opt$plot_std_error, opt$insect, opt$location, latitude, start_date, end_date, days, maxval,
1433 opt$replications, life_stage, group=group, group_std_error=group_std_error, life_stages_nymph=life_stage_nymph); 1447 opt$replications, life_stage, group=group, group_std_error=group_std_error, life_stages_nymph=life_stage_nymph);
1434 # Turn off device driver to flush output. 1448 # Turn off device driver to flush output.
1435 dev.off(); 1449 dev.off();
1436 } 1450 }
1437 } else if (life_stage == "Adult") { 1451 } else if (life_stage == "Adult") {
1457 # Diapausing adult population size. 1471 # Diapausing adult population size.
1458 group = diapausing_adults; 1472 group = diapausing_adults;
1459 group_std_error = diapausing_adults.std_error 1473 group_std_error = diapausing_adults.std_error
1460 } 1474 }
1461 maxval = max(group+group_std_error) + 100; 1475 maxval = max(group+group_std_error) + 100;
1462 render_chart(date_labels, "pop_size_by_life_stage", opt$plot_std_error, opt$insect, opt$location, latitude, start_date, end_date, days, maxval, 1476 render_chart(ticks, date_labels, "pop_size_by_life_stage", opt$plot_std_error, opt$insect, opt$location, latitude, start_date, end_date, days, maxval,
1463 opt$replications, life_stage, group=group, group_std_error=group_std_error, life_stages_adult=life_stage_adult); 1477 opt$replications, life_stage, group=group, group_std_error=group_std_error, life_stages_adult=life_stage_adult);
1464 # Turn off device driver to flush output. 1478 # Turn off device driver to flush output.
1465 dev.off(); 1479 dev.off();
1466 } 1480 }
1467 } else if (life_stage == "Total") { 1481 } else if (life_stage == "Total") {
1470 file_path = get_file_path(life_stage, "total_pop.pdf") 1484 file_path = get_file_path(life_stage, "total_pop.pdf")
1471 pdf(file=file_path, width=20, height=30, bg="white"); 1485 pdf(file=file_path, width=20, height=30, bg="white");
1472 par(mar=c(5, 6, 4, 4), mfrow=c(3, 1)); 1486 par(mar=c(5, 6, 4, 4), mfrow=c(3, 1));
1473 # Total population size. 1487 # Total population size.
1474 maxval = max(eggs+eggs.std_error, total_nymphs+total_nymphs.std_error, total_adults+total_adults.std_error) + 100; 1488 maxval = max(eggs+eggs.std_error, total_nymphs+total_nymphs.std_error, total_adults+total_adults.std_error) + 100;
1475 render_chart(date_labels, "pop_size_by_life_stage", opt$plot_std_error, opt$insect, opt$location, latitude, start_date, end_date, days, maxval, 1489 render_chart(ticks, date_labels, "pop_size_by_life_stage", opt$plot_std_error, opt$insect, opt$location, latitude, start_date, end_date, days, maxval,
1476 opt$replications, life_stage, group=total_adults, group_std_error=total_adults.std_error, group2=total_nymphs, group2_std_error=total_nymphs.std_error, group3=eggs, 1490 opt$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,
1477 group3_std_error=eggs.std_error); 1491 group3_std_error=eggs.std_error);
1478 # Turn off device driver to flush output. 1492 # Turn off device driver to flush output.
1479 dev.off(); 1493 dev.off();
1480 } 1494 }