Mercurial > repos > greg > extract_ipm_date_interval

comparison utils.R @ 10:c2eb16ef23c0 draft

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author greg
date Tue, 07 Aug 2018 13:02:58 -0400
parents 0d9a74365270
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9:fd41f452c9fe 10:c2eb16ef23c0
1 #!/usr/bin/env Rscript 1 #!/usr/bin/env Rscript
2 2
3 get_file_path = function(life_stage, base_name, life_stage_nymph=NULL, life_stage_adult=NULL) { 3 get_file_path = function(life_stage, base_name, sub_life_stage=NULL) {
4 if (!is.null(life_stage_nymph)) { 4 if (is.null(sub_life_stage)) {
5 lsi = get_life_stage_index(life_stage, life_stage_nymph=life_stage_nymph);
6 file_name = paste(lsi, tolower(life_stage_nymph), base_name, sep="_");
7 } else if (!is.null(life_stage_adult)) {
8 lsi = get_life_stage_index(life_stage, life_stage_adult=life_stage_adult);
9 file_name = paste(lsi, tolower(life_stage_adult), base_name, sep="_");
10 } else {
11 lsi = get_life_stage_index(life_stage); 5 lsi = get_life_stage_index(life_stage);
12 file_name = paste(lsi, base_name, sep="_"); 6 file_name = paste(lsi, base_name, sep="_");
7 } else {
8 lsi = get_life_stage_index(life_stage, sub_life_stage=sub_life_stage);
9 file_name = paste(lsi, tolower(sub_life_stage), base_name, sep="_");
13 } 10 }
14 file_path = paste("output_plots_dir", file_name, sep="/"); 11 file_path = paste("output_plots_dir", file_name, sep="/");
15 return(file_path); 12 return(file_path);
16 } 13 }
17 14
18 get_year_from_date = function(date_str) { 15 get_year_from_date = function(date_str) {
19 date_str_items = strsplit(date_str, "-")[[1]]; 16 date_str_items = strsplit(date_str, "-")[[1]];
20 return (date_str_items[1]); 17 return (date_str_items[1]);
21 } 18 }
22 19
23 get_life_stage_index = function(life_stage, life_stage_nymph=NULL, life_stage_adult=NULL) { 20 get_life_stage_index = function(life_stage, sub_life_stage=NULL) {
24 # Name collection elements so that they 21 # Name collection elements so that they
25 # are displayed in logical order. 22 # are displayed in logical order.
26 if (life_stage=="Egg") { 23 if (life_stage=="Egg") {
27 lsi = "01"; 24 lsi = "01";
28 } else if (life_stage=="Nymph") { 25 } else if (life_stage=="Nymph") {
29 if (life_stage_nymph=="Young") { 26 if (sub_life_stage=="Young") {
30 lsi = "02"; 27 lsi = "02";
31 } else if (life_stage_nymph=="Old") { 28 } else if (sub_life_stage=="Old") {
32 lsi = "03"; 29 lsi = "03";
33 } else if (life_stage_nymph=="Total") { 30 } else if (sub_life_stage=="Total") {
34 lsi="04"; 31 lsi="04";
35 } 32 }
36 } else if (life_stage=="Adult") { 33 } else if (life_stage=="Adult") {
37 if (life_stage_adult=="Pre-vittelogenic") { 34 if (sub_life_stage=="Pre-vittelogenic") {
38 lsi = "05"; 35 lsi = "05";
39 } else if (life_stage_adult=="Vittelogenic") { 36 } else if (sub_life_stage=="Vittelogenic") {
40 lsi = "06"; 37 lsi = "06";
41 } else if (life_stage_adult=="Diapausing") { 38 } else if (sub_life_stage=="Diapausing") {
42 lsi = "07"; 39 lsi = "07";
43 } else if (life_stage_adult=="Total") { 40 } else if (sub_life_stage=="Total") {
44 lsi = "08"; 41 lsi = "08";
45 } 42 }
46 } else if (life_stage=="Total") { 43 } else if (life_stage=="Total") {
47 lsi = "09"; 44 lsi = "09";
48 } 45 }
221 return(list(ticks, tick_labels)); 218 return(list(ticks, tick_labels));
222 } 219 }
223 220
224 render_chart = function(ticks, date_labels, chart_type, plot_std_error, insect, location, latitude, start_date, end_date, days, maxval, 221 render_chart = function(ticks, date_labels, chart_type, plot_std_error, insect, location, latitude, start_date, end_date, days, maxval,
225 replications, life_stage, group, group_std_error, group2=NULL, group2_std_error=NULL, group3=NULL, group3_std_error=NULL, 222 replications, life_stage, group, group_std_error, group2=NULL, group2_std_error=NULL, group3=NULL, group3_std_error=NULL,
226 life_stages_adult=NULL, life_stages_nymph=NULL) { 223 sub_life_stage=NULL) {
227 if (chart_type=="pop_size_by_life_stage") { 224 if (chart_type=="pop_size_by_life_stage") {
228 if (life_stage=="Total") { 225 if (life_stage=="Total") {
229 title = paste(insect, ": Reps", replications, ":", life_stage, "Pop :", location, ": Lat", latitude, ":", start_date, "-", end_date, sep=" "); 226 title = paste(insect, ": Reps", replications, ":", life_stage, "Pop :", location, ": Lat", latitude, ":", start_date, "-", end_date, sep=" ");
230 legend_text = c("Egg", "Nymph", "Adult"); 227 legend_text = c("Egg", "Nymph", "Adult");
231 columns = c(4, 2, 1); 228 columns = c(4, 2, 1);
250 if (life_stage=="Egg") { 247 if (life_stage=="Egg") {
251 title = paste(insect, ": Reps", replications, ":", life_stage, "Pop :", location, ": Lat", latitude, ":", start_date, "-", end_date, sep=" "); 248 title = paste(insect, ": Reps", replications, ":", life_stage, "Pop :", location, ": Lat", latitude, ":", start_date, "-", end_date, sep=" ");
252 legend_text = c(life_stage); 249 legend_text = c(life_stage);
253 columns = c(4); 250 columns = c(4);
254 } else if (life_stage=="Nymph") { 251 } else if (life_stage=="Nymph") {
255 stage = paste(life_stages_nymph, "Nymph Pop :", sep=" "); 252 stage = paste(sub_life_stage, "Nymph Pop :", sep=" ");
256 title = paste(insect, ": Reps", replications, ":", stage, location, ": Lat", latitude, ":", start_date, "-", end_date, sep=" "); 253 title = paste(insect, ": Reps", replications, ":", stage, location, ": Lat", latitude, ":", start_date, "-", end_date, sep=" ");
257 legend_text = c(paste(life_stages_nymph, life_stage, sep=" ")); 254 legend_text = c(paste(sub_life_stage, life_stage, sep=" "));
258 columns = c(2); 255 columns = c(2);
259 } else if (life_stage=="Adult") { 256 } else if (life_stage=="Adult") {
260 stage = paste(life_stages_adult, "Adult Pop", sep=" "); 257 stage = paste(sub_life_stage, "Adult Pop", sep=" ");
261 title = paste(insect, ": Reps", replications, ":", stage, location, ": Lat", latitude, ":", start_date, "-", end_date, sep=" "); 258 title = paste(insect, ": Reps", replications, ":", stage, location, ": Lat", latitude, ":", start_date, "-", end_date, sep=" ");
262 legend_text = c(paste(life_stages_adult, life_stage, sep=" ")); 259 legend_text = c(paste(sub_life_stage, life_stage, sep=" "));
263 columns = c(1); 260 columns = c(1);
264 } 261 }
265 plot(days, group, main=title, type="l", ylim=c(0, maxval), axes=FALSE, lwd=2, xlab="", ylab="", cex=3, cex.lab=3, cex.axis=3, cex.main=3); 262 plot(days, group, main=title, type="l", ylim=c(0, maxval), axes=FALSE, lwd=2, xlab="", ylab="", cex=3, cex.lab=3, cex.axis=3, cex.main=3);
266 legend("topleft", legend_text, lty=c(1), col="black", cex=3); 263 legend("topleft", legend_text, lty=c(1), col="black", cex=3);
267 axis(side=1, at=ticks, labels=date_labels, las=2, font.axis=3, xpd=TRUE, cex=3, cex.lab=3, cex.axis=3, cex.main=3); 264 axis(side=1, at=ticks, labels=date_labels, las=2, font.axis=3, xpd=TRUE, cex=3, cex.lab=3, cex.axis=3, cex.main=3);
276 if (life_stage=="Total") { 273 if (life_stage=="Total") {
277 title_str = ": Total Pop by Gen :"; 274 title_str = ": Total Pop by Gen :";
278 } else if (life_stage=="Egg") { 275 } else if (life_stage=="Egg") {
279 title_str = ": Egg Pop by Gen :"; 276 title_str = ": Egg Pop by Gen :";
280 } else if (life_stage=="Nymph") { 277 } else if (life_stage=="Nymph") {
281 title_str = paste(":", life_stages_nymph, "Nymph Pop by Gen", ":", sep=" "); 278 title_str = paste(":", sub_life_stage, "Nymph Pop by Gen", ":", sep=" ");
282 } else if (life_stage=="Adult") { 279 } else if (life_stage=="Adult") {
283 title_str = paste(":", life_stages_adult, "Adult Pop by Gen", ":", sep=" "); 280 title_str = paste(":", sub_life_stage, "Adult Pop by Gen", ":", sep=" ");
284 } 281 }
285 title = paste(insect, ": Reps", replications, title_str, location, ": Lat", latitude, ":", start_date, "-", end_date, sep=" "); 282 title = paste(insect, ": Reps", replications, title_str, location, ": Lat", latitude, ":", start_date, "-", end_date, sep=" ");
286 legend_text = c("P", "F1", "F2"); 283 legend_text = c("P", "F1", "F2");
287 columns = c(1, 2, 4); 284 columns = c(1, 2, 4);
288 plot(days, group, main=title, type="l", ylim=c(0, maxval), axes=FALSE, lwd=2, xlab="", ylab="", cex=3, cex.lab=3, cex.axis=3, cex.main=3); 285 plot(days, group, main=title, type="l", ylim=c(0, maxval), axes=FALSE, lwd=2, xlab="", ylab="", cex=3, cex.lab=3, cex.axis=3, cex.main=3);