extract_ipm_date_interval: utils.R comparison

comparison utils.R @ 0:4dccc60b3525 draft

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author	greg
date	Tue, 31 Jul 2018 14:36:56 -0400
parents
children	9c5a4d07edb8

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--1:000000000000
+:4dccc60b3525
+#!/usr/bin/env Rscript
+get_file_path = function(life_stage, base_name, life_stage_nymph=NULL, life_stage_adult=NULL) {
+if (!is.null(life_stage_nymph)) {
+lsi = get_life_stage_index(life_stage, life_stage_nymph=life_stage_nymph);
+file_name = paste(lsi, tolower(life_stage_nymph), base_name, sep="_");
+} else if (!is.null(life_stage_adult)) {
+lsi = get_life_stage_index(life_stage, life_stage_adult=life_stage_adult);
+file_name = paste(lsi, tolower(life_stage_adult), base_name, sep="_");
+} else {
+lsi = get_life_stage_index(life_stage);
+file_name = paste(lsi, base_name, sep="_");
+}
+file_path = paste("output_plots_dir", file_name, sep="/");
+return(file_path);
+}
+get_life_stage_index = function(life_stage, life_stage_nymph=NULL, life_stage_adult=NULL) {
+# Name collection elements so that they
+# are displayed in logical order.
+if (life_stage=="Egg") {
+lsi = "01";
+} else if (life_stage=="Nymph") {
+if (life_stage_nymph=="Young") {
+lsi = "02";
+} else if (life_stage_nymph=="Old") {
+lsi = "03";
+} else if (life_stage_nymph=="Total") {
+lsi="04";
+}
+} else if (life_stage=="Adult") {
+if (life_stage_adult=="Pre-vittelogenic") {
+lsi = "05";
+} else if (life_stage_adult=="Vittelogenic") {
+lsi = "06";
+} else if (life_stage_adult=="Diapausing") {
+lsi = "07";
+} else if (life_stage_adult=="Total") {
+lsi = "08";
+}
+} else if (life_stage=="Total") {
+lsi = "09";
+}
+return(lsi);
+}
+get_mean_and_std_error = function(p_replications, f1_replications, f2_replications) {
+# P mean.
+p_m = apply(p_replications, 1, mean);
+# P standard error.
+p_se = apply(p_replications, 1, sd) / sqrt(opt$replications);
+# F1 mean.
+f1_m = apply(f1_replications, 1, mean);
+# F1 standard error.
+f1_se = apply(f1_replications, 1, sd) / sqrt(opt$replications);
+# F2 mean.
+f2_m = apply(f2_replications, 1, mean);
+# F2 standard error.
+f2_se = apply(f2_replications, 1, sd) / sqrt(opt$replications);
+return(list(p_m, p_se, f1_m, f1_se, f2_m, f2_se))
+}
+get_tick_index = function(index, last_tick, ticks, tick_labels, tick_sep) {
+# The R code tries hard not to draw overlapping tick labels, and so
+# will omit labels where they would abut or overlap previously drawn
+# labels. This can result in, for example, every other tick being
+# labelled.  We'll keep track of the last tick to make sure all of
+# the month labels are displayed, and missing ticks are restricted
+# to Sundays which have no labels anyway.
+if (last_tick==0) {
+return(length(ticks)+1);
+}
+last_saved_tick = ticks[[length(ticks)]];
+if (index-last_saved_tick<tick_sep) {
+last_saved_month = tick_labels[[length(tick_labels)]];
+if (last_saved_month=="") {
+# We're safe overwriting a tick
+# with no label (i.e., a Sunday tick).
+return(length(ticks));
+} else {
+# Don't eliminate a Month label.
+return(NULL);
+}
+}
+return(length(ticks)+1);
+}
+get_total_days = function(is_leap_year) {
+# Get the total number of days in the current year.
+if (is_leap_year) {
+return(366);
+} else {
+return(365);
+}
+}
+get_x_axis_ticks_and_labels = function(temperature_data_frame, prepend_end_doy_norm, append_start_doy_norm, date_interval=FALSE) {
+# Generate a list of ticks and labels for plotting the x axis.
+if (prepend_end_doy_norm > 0) {
+prepend_end_norm_row = which(temperature_data_frame$DOY==prepend_end_doy_norm);
+} else {
+prepend_end_norm_row = 0;
+}
+if (append_start_doy_norm > 0) {
+append_start_norm_row = which(temperature_data_frame$DOY==append_start_doy_norm);
+} else {
+append_start_norm_row = 0;
+}
+num_rows = dim(temperature_data_frame)[1];
+tick_labels = list();
+ticks = list();
+current_month_label = NULL;
+last_tick = 0;
+if (date_interval) {
+tick_sep = 0;
+} else {
+tick_sep = 3;
+}
+for (i in 1:num_rows) {
+# Get the year and month from the date which
+# has the format YYYY-MM-DD.
+date = format(temperature_data_frame$DATE[i]);
+# Get the month label.
+items = strsplit(date, "-")[[1]];
+month = items[2];
+month_label = month.abb[as.integer(month)];
+day = as.integer(items[3]);
+doy = as.integer(temperature_data_frame$DOY[i]);
+# We're plotting the entire year, so ticks will
+# occur on Sundays and the first of each month.
+if (i == prepend_end_norm_row) {
+# Add a tick for the end of the 30 year normnals data
+# that was prepended to the year-to-date data.
+label_str = "End prepended 30 year normals";
+tick_index = get_tick_index(i, last_tick, ticks, tick_labels, tick_sep)
+ticks[tick_index] = i;
+if (date_interval) {
+# Append the day to label_str
+tick_labels[tick_index] = paste(label_str, day, sep=" ");
+} else {
+tick_labels[tick_index] = label_str;
+}
+last_tick = i;
+} else if (doy == append_start_doy_norm) {
+# Add a tick for the start of the 30 year normnals data
+# that was appended to the year-to-date data.
+label_str = "Start appended 30 year normals";
+tick_index = get_tick_index(i, last_tick, ticks, tick_labels, tick_sep)
+ticks[tick_index] = i;
+if (!identical(current_month_label, month_label)) {
+# Append the month to label_str.
+label_str = paste(label_str, month_label, spe=" ");
+current_month_label = month_label;
+}
+if (date_interval) {
+# Append the day to label_str
+label_str = paste(label_str, day, sep=" ");
+}
+tick_labels[tick_index] = label_str;
+last_tick = i;
+} else if (i==num_rows) {
+# Add a tick for the last day of the year.
+label_str = "";
+tick_index = get_tick_index(i, last_tick, ticks, tick_labels, tick_sep)
+ticks[tick_index] = i;
+if (!identical(current_month_label, month_label)) {
+# Append the month to label_str.
+label_str = month_label;
+current_month_label = month_label;
+}
+if (date_interval) {
+# Append the day to label_str
+label_str = paste(label_str, day, sep=" ");
+}
+tick_labels[tick_index] = label_str;
+} else {
+if (!identical(current_month_label, month_label)) {
+# Add a tick for the month.
+tick_index = get_tick_index(i, last_tick, ticks, tick_labels, tick_sep)
+ticks[tick_index] = i;
+if (date_interval) {
+# Append the day to the month.
+tick_labels[tick_index] = paste(month_label, day, sep=" ");
+} else {
+tick_labels[tick_index] = month_label;
+}
+current_month_label = month_label;
+last_tick = i;
+}
+tick_index = get_tick_index(i, last_tick, ticks, tick_labels, tick_sep)
+if (!is.null(tick_index)) {
+if (date_interval) {
+# Add a tick for every day. The first tick is the
+# month label, so add a tick only if i is not 1
+if (i>1 & day>1) {
+tick_index = get_tick_index(i, last_tick, ticks, tick_labels, tick_sep)
+ticks[tick_index] = i;
+# Add the day as the label.
+tick_labels[tick_index] = day;
+last_tick = i;
+}
+} else {
+# Get the day.
+day = weekdays(as.Date(date));
+if (day=="Sunday") {
+# Add a tick if we're on a Sunday.
+ticks[tick_index] = i;
+# Add a blank month label so it is not displayed.
+tick_labels[tick_index] = "";
+last_tick = i;
+}
+}
+}
+}
+}
+return(list(ticks, tick_labels));
+}
+render_chart = function(ticks, date_labels, chart_type, plot_std_error, insect, location, latitude, start_date, end_date, days, maxval,
+replications, life_stage, group, group_std_error, group2=NULL, group2_std_error=NULL, group3=NULL, group3_std_error=NULL,
+life_stages_adult=NULL, life_stages_nymph=NULL) {
+if (chart_type=="pop_size_by_life_stage") {
+if (life_stage=="Total") {
+title = paste(insect, ": Reps", replications, ":", life_stage, "Pop :", location, ": Lat", latitude, ":", start_date, "-", end_date, sep=" ");
+legend_text = c("Egg", "Nymph", "Adult");
+columns = c(4, 2, 1);
+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);
+legend("topleft", legend_text, lty=c(1, 1, 1), col=columns, cex=3);
+lines(days, group2, lwd=2, lty=1, col=2);
+lines(days, group3, lwd=2, lty=1, col=4);
+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);
+axis(side=2, font.axis=3, xpd=TRUE, cex=3, cex.lab=3, cex.axis=3, cex.main=3);
+if (plot_std_error=="yes") {
+# Standard error for group.
+lines(days, group+group_std_error, lty=2);
+lines(days, group-group_std_error, lty=2);
+# Standard error for group2.
+lines(days, group2+group2_std_error, col=2, lty=2);
+lines(days, group2-group2_std_error, col=2, lty=2);
+# Standard error for group3.
+lines(days, group3+group3_std_error, col=4, lty=2);
+lines(days, group3-group3_std_error, col=4, lty=2);
+}
+} else {
+if (life_stage=="Egg") {
+title = paste(insect,  ": Reps", replications, ":", life_stage, "Pop :", location, ": Lat", latitude, ":", start_date, "-", end_date, sep=" ");
+legend_text = c(life_stage);
+columns = c(4);
+} else if (life_stage=="Nymph") {
+stage = paste(life_stages_nymph, "Nymph Pop :", sep=" ");
+title = paste(insect, ": Reps", replications, ":", stage, location, ": Lat", latitude, ":", start_date, "-", end_date, sep=" ");
+legend_text = c(paste(life_stages_nymph, life_stage, sep=" "));
+columns = c(2);
+} else if (life_stage=="Adult") {
+stage = paste(life_stages_adult, "Adult Pop", sep=" ");
+title = paste(insect, ": Reps", replications, ":", stage, location, ": Lat", latitude, ":", start_date, "-", end_date, sep=" ");
+legend_text = c(paste(life_stages_adult, life_stage, sep=" "));
+columns = c(1);
+}
+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);
+legend("topleft", legend_text, lty=c(1), col="black", cex=3);
+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);
+axis(side=2, font.axis=3, xpd=TRUE, cex=3, cex.lab=3, cex.axis=3, cex.main=3);
+if (plot_std_error=="yes") {
+# Standard error for group.
+lines(days, group+group_std_error, lty=2);
+lines(days, group-group_std_error, lty=2);
+}
+}
+} else if (chart_type=="pop_size_by_generation") {
+if (life_stage=="Total") {
+title_str = ": Total Pop by Gen :";
+} else if (life_stage=="Egg") {
+title_str = ": Egg Pop by Gen :";
+} else if (life_stage=="Nymph") {
+title_str = paste(":", life_stages_nymph, "Nymph Pop by Gen", ":", sep=" ");
+} else if (life_stage=="Adult") {
+title_str = paste(":", life_stages_adult, "Adult Pop by Gen", ":", sep=" ");
+}
+title = paste(insect, ": Reps", replications, title_str, location, ": Lat", latitude, ":", start_date, "-", end_date, sep=" ");
+legend_text = c("P", "F1", "F2");
+columns = c(1, 2, 4);
+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);
+legend("topleft", legend_text, lty=c(1, 1, 1), col=columns, cex=3);
+lines(days, group2, lwd=2, lty=1, col=2);
+lines(days, group3, lwd=2, lty=1, col=4);
+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);
+axis(side=2, font.axis=3, xpd=TRUE, cex=3, cex.lab=3, cex.axis=3, cex.main=3);
+if (plot_std_error=="yes") {
+# Standard error for group.
+lines(days, group+group_std_error, lty=2);
+lines(days, group-group_std_error, lty=2);
+# Standard error for group2.
+lines(days, group2+group2_std_error, col=2, lty=2);
+lines(days, group2-group2_std_error, col=2, lty=2);
+# Standard error for group3.
+lines(days, group3+group3_std_error, col=4, lty=2);
+lines(days, group3-group3_std_error, col=4, lty=2);
+}
+}
+}
+stop_err = function(msg) {
+cat(msg, file=stderr());
+quit(save="no", status=1);
+}
+validate_date = function(date_str) {
+valid_date = as.Date(date_str, format="%Y-%m-%d");
+if( class(valid_date)=="try-error" || is.na(valid_date)) {
+msg = paste("Invalid date: ", date_str, ", valid date format is yyyy-mm-dd.", sep="");
+stop_err(msg);
+}
+return(valid_date);
+}

Mercurial > repos > greg > extract_ipm_date_interval

comparison utils.R @ 0:4dccc60b3525 draft