insect_phenology_model: insect_phenology

comparison insect_phenology_model.R @ 35:29ec818b1c29 draft

Uploaded

author	greg
date	Tue, 20 Mar 2018 09:45:26 -0400
parents	7aa848b0e55c
children	5097cfeedc4f

comparison

equal deleted inserted replaced

-:7aa848b0e55c
+:29ec818b1c29
 # Append vector vec as a new column to data_frame.
 data_frame[,num_columns+1] = vec;
 # Reset the column names with the additional column for later access.
 colnames(data_frame) = append(current_column_names, new_column_name);
 return(data_frame);
-}
-get_x_axis_ticks_and_labels = function(temperature_data_frame, num_rows) {
-# Keep track of the years to see if spanning years.
-month_labels = list();
-ticks = list();
-current_month_label = NULL;
-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)];
-if (!identical(current_month_label, month_label)) {
-# Add an x-axis tick for the month.
-ticks[length(ticks)+1] = i;
-month_labels[length(month_labels)+1] = month_label;
-current_month_label = month_label;
-}
-# Get the day.
-day = weekdays(as.Date(date));
-if (day=="Sunday") {
-# Add an x-axis tick if we're on a Sunday.
-ticks[length(ticks)+1] = i;
-# Add a blank month label so it is not displayed.
-month_labels[length(month_labels)+1] = "";
-}
-}
-return(list(ticks, month_labels));
 }
 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);
 averages = sum(dh) / 24;
 }
 return(c(curr_mean_temp, averages))
 }
+get_tick_index = function(index, last_tick, ticks, month_labels) {
+# 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<6) {
+last_saved_month = month_labels[[length(month_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_x_axis_ticks_and_labels = function(temperature_data_frame, num_rows) {
+# Keep track of the years to see if spanning years.
+month_labels = list();
+ticks = list();
+current_month_label = NULL;
+last_tick = 0;
+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)];
+tick_index = get_tick_index(i, last_tick, ticks, month_labels)
+if (!is.null(tick_index)) {
+if (!identical(current_month_label, month_label)) {
+# Add an x-axis tick for the month.
+ticks[tick_index] = i;
+month_labels[tick_index] = month_label;
+current_month_label = month_label;
+last_tick = i;
+}
+# Get the day.
+day = weekdays(as.Date(date));
+if (day=="Sunday") {
+# Add an x-axis tick if we're on a Sunday.
+ticks[tick_index] = i;
+# Add a blank month label so it is not displayed.
+month_labels[tick_index] = "";
+last_tick = i;
+}
+}
+}
+return(list(ticks, month_labels));
+}
 mortality.adult = function(temperature) {
 if (temperature < 12.7) {
 mortality.probability = 0.002;
 }
 else {
 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=F, lwd=2, xlab="", ylab="", cex=3, cex.lab=3, cex.axis=3, cex.main=3);
+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);
+axis(side=1, at=ticks, labels=date_labels, font.axis=3, xpd=TRUE, cex=3, cex.lab=3, cex.axis=3, cex.main=3);
-axis(side=2);
+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.
 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=F, lwd=2, xlab="", ylab="", cex=3, cex.lab=3, cex.axis=3, cex.main=3);
+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);
+axis(side=1, at=ticks, labels=date_labels, font.axis=3, xpd=TRUE, cex=3, cex.lab=3, cex.axis=3, cex.main=3);
-axis(side=2);
+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);
 }
 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=F, lwd=2, xlab="", ylab="", cex=3, cex.lab=3, cex.axis=3, cex.main=3);
+plot(days, group, main=title, type="l", ylim=c(0, maxval), axes=FALSE, lwd=2, xlab="", ylab="");
 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);
+axis(side=1, at=ticks, labels=date_labels, font.axis=3, xpd=TRUE, cex=3, cex.lab=3, cex.axis=3, cex.main=3);
-axis(side=2);
+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.

Mercurial > repos > greg > insect_phenology_model

comparison insect_phenology_model.R @ 35:29ec818b1c29 draft