--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/utils.R	Tue Aug 07 13:05:10 2018 -0400
@@ -0,0 +1,317 @@
+#!/usr/bin/env Rscript
+
+get_file_path = function(life_stage, base_name, sub_life_stage=NULL) {
+    if (is.null(sub_life_stage)) {
+        lsi = get_life_stage_index(life_stage);
+        file_name = paste(lsi, base_name, sep="_");
+    } else {
+        lsi = get_life_stage_index(life_stage, sub_life_stage=sub_life_stage);
+        file_name = paste(lsi, tolower(sub_life_stage), base_name, sep="_");
+    }
+    file_path = paste("output_plots_dir", file_name, sep="/");
+    return(file_path);
+}
+
+get_year_from_date = function(date_str) {
+    date_str_items = strsplit(date_str, "-")[[1]];
+    return (date_str_items[1]);
+}
+
+get_life_stage_index = function(life_stage, sub_life_stage=NULL) {
+    # Name collection elements so that they
+    # are displayed in logical order.
+    if (life_stage=="Egg") {
+        lsi = "01";
+    } else if (life_stage=="Nymph") {
+        if (sub_life_stage=="Young") {
+            lsi = "02";
+        } else if (sub_life_stage=="Old") {
+            lsi = "03";
+        } else if (sub_life_stage=="Total") {
+            lsi="04";
+        }
+    } else if (life_stage=="Adult") {
+        if (sub_life_stage=="Pre-vittelogenic") {
+            lsi = "05";
+        } else if (sub_life_stage=="Vittelogenic") {
+            lsi = "06";
+        } else if (sub_life_stage=="Diapausing") {
+            lsi = "07";
+        } else if (sub_life_stage=="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$replications);
+    return(list(p_m, p_se, f1_m, f1_se, f2_m, f2_se))
+}
+
+get_tick_index = function(index, last_tick, ticks, tick_labels, tick_sep) {
+    # The R code tries hard not to draw overlapping tick labels, and so
+    # will omit labels where they would abut or overlap previously drawn
+    # labels. This can result in, for example, every other tick being
+    # labelled.  We'll keep track of the last tick to make sure all of
+    # the month labels are displayed, and missing ticks are restricted
+    # to Sundays which have no labels anyway.
+    if (last_tick==0) {
+        return(length(ticks)+1);
+    }
+    last_saved_tick = ticks[[length(ticks)]];
+    if (index-last_saved_tick<tick_sep) {
+        last_saved_month = tick_labels[[length(tick_labels)]];
+        if (last_saved_month=="") {
+            # We're safe overwriting a tick
+            # with no label (i.e., a Sunday tick).
+            return(length(ticks));
+        } else {
+            # Don't eliminate a Month label.
+            return(NULL);
+        }
+    }
+    return(length(ticks)+1);
+}
+
+get_total_days = function(is_leap_year) {
+    # Get the total number of days in the current year.
+    if (is_leap_year) {
+        return(366);
+    } else {
+        return(365);
+    }
+}
+
+get_x_axis_ticks_and_labels = function(temperature_data_frame, prepend_end_doy_norm=0, append_start_doy_norm=0, date_interval=FALSE) {
+    # Generate a list of ticks and labels for plotting the x axis.
+    if (prepend_end_doy_norm > 0) {
+        prepend_end_norm_row = which(temperature_data_frame$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,
+            sub_life_stage=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(sub_life_stage, "Nymph Pop :", sep=" ");
+                title = paste(insect, ": Reps", replications, ":", stage, location, ": Lat", latitude, ":", start_date, "-", end_date, sep=" ");
+                legend_text = c(paste(sub_life_stage, life_stage, sep=" "));
+                columns = c(2);
+            } else if (life_stage=="Adult") {
+                stage = paste(sub_life_stage, "Adult Pop", sep=" ");
+                title = paste(insect, ": Reps", replications, ":", stage, location, ": Lat", latitude, ":", start_date, "-", end_date, sep=" ");
+                legend_text = c(paste(sub_life_stage, 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(":", sub_life_stage, "Nymph Pop by Gen", ":", sep=" ");
+        } else if (life_stage=="Adult") {
+            title_str = paste(":", sub_life_stage, "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);
+}