Mercurial > repos > greg > insect_phenology_model

comparison insect_phenology_model.R @ 21:6349699fc9fa draft

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author greg
date Thu, 08 Mar 2018 08:11:43 -0500
parents 214217142600
children 36d7bb034285
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20:214217142600 21:6349699fc9fa
253 } 253 }
254 254
255 render_chart = function(date_labels, chart_type, plot_std_error, insect, location, latitude, start_date, end_date, days, maxval, 255 render_chart = function(date_labels, chart_type, plot_std_error, insect, location, latitude, start_date, end_date, days, maxval,
256 replications, life_stage, group, group_std_error, group2=NULL, group2_std_error=NULL, group3=NULL, group3_std_error=NULL, 256 replications, life_stage, group, group_std_error, group2=NULL, group2_std_error=NULL, group3=NULL, group3_std_error=NULL,
257 life_stages_adult=NULL, life_stages_nymph=NULL) { 257 life_stages_adult=NULL, life_stages_nymph=NULL) {
258 cat("In render_chart, chart_type: ", chart_type, "\n");
259 if (chart_type=="pop_size_by_life_stage") { 258 if (chart_type=="pop_size_by_life_stage") {
260 if (life_stage=="Total") { 259 if (life_stage=="Total") {
261 title = paste(insect, ": Reps", replications, ":", life_stage, "Pop :", location, ": Lat", latitude, ":", start_date, "-", end_date, sep=" "); 260 title = paste(insect, ": Reps", replications, ":", life_stage, "Pop :", location, ": Lat", latitude, ":", start_date, "-", end_date, sep=" ");
262 legend_text = c("Egg", "Nymph", "Adult"); 261 legend_text = c("Egg", "Nymph", "Adult");
263 columns = c(4, 2, 1); 262 columns = c(4, 2, 1);
313 title_str = paste(":", life_stages_nymph, "Nymph Pop by Gen", ":", sep=" "); 312 title_str = paste(":", life_stages_nymph, "Nymph Pop by Gen", ":", sep=" ");
314 } else if (life_stage=="Adult") { 313 } else if (life_stage=="Adult") {
315 title_str = paste(":", life_stages_adult, "Adult Pop by Gen", ":", sep=" "); 314 title_str = paste(":", life_stages_adult, "Adult Pop by Gen", ":", sep=" ");
316 } 315 }
317 title = paste(insect, ": Reps", replications, title_str, location, ": Lat", latitude, ":", start_date, "-", end_date, sep=" "); 316 title = paste(insect, ": Reps", replications, title_str, location, ": Lat", latitude, ":", start_date, "-", end_date, sep=" ");
318 cat("In render_chart, title: ", title, "\n");
319 cat("In render_chart, group: ", group, "\n");
320 cat("In render_chart, group2: ", group2, "\n");
321 cat("In render_chart, group3: ", group3, "\n");
322 legend_text = c("P", "F1", "F2"); 317 legend_text = c("P", "F1", "F2");
323 columns = c(1, 2, 4); 318 columns = c(1, 2, 4);
324 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); 319 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);
325 legend("topleft", legend_text, lty=c(1, 1, 1), col=columns, cex=3); 320 legend("topleft", legend_text, lty=c(1, 1, 1), col=columns, cex=3);
326 lines(days, group2, lwd=2, lty=1, col=2); 321 lines(days, group2, lwd=2, lty=1, col=2);
411 } else if (life_stage_adult=="Total") { 406 } else if (life_stage_adult=="Total") {
412 process_total_adults = TRUE; 407 process_total_adults = TRUE;
413 } 408 }
414 } 409 }
415 } 410 }
416 cat("process_eggs: ", process_eggs, "\n");
417 cat("process_nymphs: ", process_nymphs, "\n");
418 cat("process_young_nymphs: ", process_young_nymphs, "\n");
419 cat("process_old_nymphs: ", process_old_nymphs, "\n");
420 cat("process_total_nymphs: ", process_total_nymphs, "\n");
421 cat("process_adults: ", process_adults, "\n");
422 cat("process_previtellogenic_adults: ", process_previtellogenic_adults, "\n");
423 cat("process_vitellogenic_adults: ", process_vitellogenic_adults, "\n");
424 cat("process_diapausing_adults: ", process_diapausing_adults, "\n");
425 cat("process_total_adults: ", process_total_adults, "\n");
426 cat("life_stages: ", life_stages, "\n");
427 cat("life_stages_nymph: ", life_stages_nymph, "\n");
428 cat("life_stages_adult: ", life_stages_adult, "\n");
429 411
430 # Initialize matrices. 412 # Initialize matrices.
431 if (process_eggs) { 413 if (process_eggs) {
432 Eggs.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications); 414 Eggs.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
433 } 415 }
434 cat("process_young_nymphs==TRUE: ", process_young_nymphs==TRUE, "\n");
435 cat("process_total_nymphs==TRUE: ", process_total_nymphs==TRUE, "\n");
436 if (process_young_nymphs==TRUE | process_total_nymphs==TRUE) { 416 if (process_young_nymphs==TRUE | process_total_nymphs==TRUE) {
437 YoungNymphs.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications); 417 YoungNymphs.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
438 } 418 }
439 if (process_old_nymphs==TRUE | process_total_nymphs==TRUE) { 419 if (process_old_nymphs==TRUE | process_total_nymphs==TRUE) {
440 OldNymphs.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications); 420 OldNymphs.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
1074 # Information needed for plots plots. 1054 # Information needed for plots plots.
1075 days = c(1:opt$num_days); 1055 days = c(1:opt$num_days);
1076 start_date = temperature_data_frame$DATE[1]; 1056 start_date = temperature_data_frame$DATE[1];
1077 end_date = temperature_data_frame$DATE[opt$num_days]; 1057 end_date = temperature_data_frame$DATE[opt$num_days];
1078 1058
1079 cat("life_stages: ", toString(life_stages), "\n");
1080 cat("plot_generations_separately: ", plot_generations_separately, "\n");
1081 if (plot_generations_separately) { 1059 if (plot_generations_separately) {
1082 for (life_stage in life_stages) { 1060 for (life_stage in life_stages) {
1083 cat("life_stage: ", life_stage, "\n");
1084 if (life_stage == "Egg") { 1061 if (life_stage == "Egg") {
1085 # Start PDF device driver. 1062 # Start PDF device driver.
1086 dev.new(width=20, height=30); 1063 dev.new(width=20, height=30);
1087 file_path = get_file_path(life_stage, "egg_pop_by_generation.pdf") 1064 file_path = get_file_path(life_stage, "egg_pop_by_generation.pdf")
1088 pdf(file=file_path, width=20, height=30, bg="white"); 1065 pdf(file=file_path, width=20, height=30, bg="white");
1089 par(mar=c(5, 6, 4, 4), mfrow=c(3, 1)); 1066 par(mar=c(5, 6, 4, 4), mfrow=c(3, 1));
1090 # Egg population size by generation. 1067 # Egg population size by generation.
1091 maxval = max(P_eggs+F1_eggs+F2_eggs) + 100; 1068 maxval = max(P_eggs+F1_eggs+F2_eggs) + 100;
1092 cat("maxval: ", maxval, "\n");
1093 cat("P_eggs: ", toString(P_eggs), "\n");
1094 cat("is.vector(P_eggs): ", is.vector(P_eggs), "\n");
1095 cat("length(P_eggs): ", length(P_eggs), "\n");
1096 cat("P_eggs.std_error: ", toString(P_eggs.std_error), "\n");
1097 cat("F1_eggs: ", toString(F1_eggs), "\n");
1098 cat("F1_eggs.std_error: ", toString(F1_eggs.std_error), "\n");
1099 cat("F2_eggs: ", toString(F2_eggs), "\n");
1100 cat("F2_eggs.std_error: ", toString(F2_eggs.std_error), "\n");
1101 render_chart(date_labels, "pop_size_by_generation", opt$plot_std_error, opt$insect, opt$location, latitude, start_date, end_date, days, maxval, 1069 render_chart(date_labels, "pop_size_by_generation", opt$plot_std_error, opt$insect, opt$location, latitude, start_date, end_date, days, maxval,
1102 opt$replications, life_stage, group=P_eggs, group_std_error=P_eggs.std_error, group2=F1_eggs, group2_std_error=F1_eggs.std_error, group3=F2_eggs, 1070 opt$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,
1103 group3_std_error=F2_eggs.std_error); 1071 group3_std_error=F2_eggs.std_error);
1104 # Turn off device driver to flush output. 1072 # Turn off device driver to flush output.
1105 dev.off(); 1073 dev.off();
1106 } else if (life_stage == "Nymph") { 1074 } else if (life_stage == "Nymph") {
1107 for (life_stage_nymph in life_stages_nymph) { 1075 for (life_stage_nymph in life_stages_nymph) {
1108 cat("life_stage_nymph: ", life_stage_nymph, "\n");
1109 # Start PDF device driver. 1076 # Start PDF device driver.
1110 dev.new(width=20, height=30); 1077 dev.new(width=20, height=30);
1111 file_path = get_file_path(life_stage, "nymph_pop_by_generation.pdf", life_stage_nymph=life_stage_nymph) 1078 file_path = get_file_path(life_stage, "nymph_pop_by_generation.pdf", life_stage_nymph=life_stage_nymph)
1112 pdf(file=file_path, width=20, height=30, bg="white"); 1079 pdf(file=file_path, width=20, height=30, bg="white");
1113 par(mar=c(5, 6, 4, 4), mfrow=c(3, 1)); 1080 par(mar=c(5, 6, 4, 4), mfrow=c(3, 1));
1137 group2 = F1_total_nymphs; 1104 group2 = F1_total_nymphs;
1138 group2_std_error = F1_total_nymphs.std_error; 1105 group2_std_error = F1_total_nymphs.std_error;
1139 group3 = F2_total_nymphs; 1106 group3 = F2_total_nymphs;
1140 group3_std_error = F2_total_nymphs.std_error; 1107 group3_std_error = F2_total_nymphs.std_error;
1141 } 1108 }
1142 cat("XXX group: ", group, "\n");
1143 render_chart(date_labels, "pop_size_by_generation", opt$plot_std_error, opt$insect, opt$location, latitude, start_date, end_date, days, maxval, 1109 render_chart(date_labels, "pop_size_by_generation", opt$plot_std_error, opt$insect, opt$location, latitude, start_date, end_date, days, maxval,
1144 opt$replications, life_stage, group=group, group_std_error=group_std_error, group2=group2, group2_std_error=group2_std_error, 1110 opt$replications, life_stage, group=group, group_std_error=group_std_error, group2=group2, group2_std_error=group2_std_error,
1145 group3=group3, group3_std_error=group3_std_error, life_stages_nymph=life_stage_nymph); 1111 group3=group3, group3_std_error=group3_std_error, life_stages_nymph=life_stage_nymph);
1146 # Turn off device driver to flush output. 1112 # Turn off device driver to flush output.
1147 dev.off(); 1113 dev.off();