insect_phenology_model: insect_phenology

comparison insect_phenology_model.R @ 123:e69e30d853fb draft

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author	greg
date	Thu, 31 May 2018 14:08:46 -0400
parents	8946ddb9d72c
children	534658644efe

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-:8946ddb9d72c
+:e69e30d853fb
 } else {
 return(365);
 }
 }
-get_x_axis_ticks_and_labels = function(temperature_data_frame, prepend_end_doy_norm, append_start_doy_norm, restricted_date_interval) {
+get_x_axis_ticks_and_labels = function(temperature_data_frame, prepend_end_doy_norm, append_start_doy_norm, date_interval) {
 # Generate a list of ticks and labels for plotting the
 # x axis.  There are several scenarios that affect this.
-# 1. If restricted_date_interval is TRUE:
+# 1. If date_interval is TRUE:
 #    a.
 if (prepend_end_doy_norm > 0) {
 prepend_end_norm_row = which(temperature_data_frame$DOY==prepend_end_doy_norm);
 } else {
 prepend_end_norm_row = 0;
 current_month_label = month_label;
 last_tick = i;
 }
 tick_index = get_tick_index(i, last_tick, ticks, month_labels)
 if (!is.null(tick_index)) {
-if (restricted_date_interval) {
+if (date_interval) {
 # Add a tick for every day.
 ticks[tick_index] = i;
 # Add a blank month label so it is not displayed.
 month_labels[tick_index] = "";
 last_tick = i;
 processing_year_to_date_data = TRUE;
 }
 if (is.null(start_date) && is.null(end_date)) {
 # We're processing the entire year, possibly merging
 # data from input_norm with data from input_ytd.
-restricted_date_interval = FALSE;
+date_interval = FALSE;
 } else {
-restricted_date_interval = TRUE;
+date_interval = TRUE;
 # Get the DOY for start_date and end_date.
 start_date_doy = strftime(start_date, format="%j");
 end_date_doy = strftime(end_date, format="%j");
 }
 # Read the input_norm temperature datafile into a data frame.
 # The input_ytd data has the following 6 columns:
 # LATITUDE, LONGITUDE, DATE, DOY, TMIN, TMAX
 temperature_data_frame = read.csv(file=input_ytd, header=T, strip.white=TRUE, stringsAsFactors=FALSE, sep=",");
 # Set the temperature_data_frame column names for access.
 colnames(temperature_data_frame) = c("LATITUDE", "LONGITUDE", "DATE", "DOY", "TMIN", "TMAX");
-if (restricted_date_interval) {
+if (date_interval) {
 # We're plotting a date interval.
 start_date_ytd_row = which(temperature_data_frame$DATE==start_date);
 if (start_date_ytd_row > 0) {
 # The start date is contained within the input_ytd data.
 start_doy_ytd = as.integer(temperature_data_frame$DOY[start_date_ytd_row]);
 if (end_date_ytd_row > 0) {
 # The end date is contained within the input_ytd data.
 end_doy_ytd = as.integer(temperature_data_frame$DOY[end_date_ytd_row]);
 }
 date_str = start_date;
+# Extract the year from the start date.
+date_str_items = strsplit(date_str, "-")[[1]];
+year = date_str_items[1];
 } else {
 # We're plotting an entire year.
 # Get the number of days contained in temperature_data_frame.
 num_rows = dim(temperature_data_frame)[1];
 # Get the start date and end date from temperature_data_frame.
 start_date_ytd_row = 1;
+# Temporarily set start_date to get the year.
 start_date = temperature_data_frame$DATE[1];
 end_date_ytd_row = num_rows;
 end_date = temperature_data_frame$DATE[num_rows];
 date_str = format(start_date);
+# Extract the year from the start date.
+date_str_items = strsplit(date_str, "-")[[1]];
+# Get the year.
+year = date_str_items[1];
+# Properly set the start_date to be Jan 1 of the year.
+start_date = paste(year, "01", "01", sep="-");
+# Properly set the end_date to be Dec 31 of the year.
+end_date = paste(year, "12", "31", sep="-");
 # Save the first DOY to later check if start_date is Jan 1.
 start_doy_ytd = as.integer(temperature_data_frame$DOY[1]);
 end_doy_ytd = as.integer(temperature_data_frame$DOY[num_rows]);
 }
-# Extract the year from the start date.
-date_str_items = strsplit(date_str, "-")[[1]];
-year = date_str_items[1];
 } else {
 # We're processing only the 30 year normals data, so create an empty
 # data frame for containing temperature data after it is converted
 # from the 30 year normals format to the year-to-date format.
 temperature_data_frame = data.frame(matrix(ncol=6, nrow=0));
 colnames(temperature_data_frame) = c("LATITUDE", "LONGITUDE", "DATE", "DOY", "TMIN", "TMAX");
-if (restricted_date_interval) {
+if (date_interval) {
 # We're plotting a date interval.
 # Extract the year, month and day from the start date.
 start_date_str = format(start_date);
 start_date_str_items = strsplit(start_date_str, "-")[[1]];
 year = start_date_str_items[1];
 # Extract the month and day from the end date.
 end_date_str = format(start_date);
 end_date_str_items = strsplit(end_date_str, "-")[[1]];
 end_date_month = end_date_str_items[2];
 end_date_day = end_date_str_items[3];
-end_date = paste(year, start_date_month, start_date_day, sep="-");
+end_date = paste(year, end_date_month, end_date_day, sep="-");
 } else {
 # We're plotting an entire year.
 # Base all dates on the current date since 30 year
 # normals data does not include any dates.
 year = format(Sys.Date(), "%Y");
 if (is.null(location) | length(location) == 0) {
 location = norm_data_frame$NAME[1];
 }
 if (processing_year_to_date_data) {
 # Merge the year-to-date data with the 30 year normals data.
-if (restricted_date_interval) {
+if (date_interval) {
 # The values of start_date_ytd_row and end_date_ytd_row were set above.
 if (start_date_ytd_row > 0 & end_date_ytd_row > 0) {
 # The date interval is contained within the input_ytd
 # data, so we don't need to merge the 30 year normals data.
 temperature_data_frame = temperature_data_frame[start_date_ytd_row:end_date_ytd_row,];
 total_days = get_total_days(is_leap_year);
 if (end_doy_ytd < total_days) {
 # Define the next row for the year-to-date data from the 30 year normals data.
 append_start_doy_norm = end_doy_ytd + 1;
 first_norm_row = which(norm_data_frame$DOY == append_start_doy_norm);
-last_norm_row = which(norm_data_frame$DOY == total_days);
 # Append the 30 year normals data to the year-to-date data.
-for (i in first_norm_row:last_norm_row) {
+for (i in first_norm_row:total_days) {
 temperature_data_frame[i,] = get_next_normals_row(norm_data_frame, year, is_leap_year, i);
 }
 }
 }
 } else {
 # We're processing only the 30 year normals data.
-if (restricted_date_interval) {
+if (date_interval) {
 # Populate temperature_data_frame from norm_data_frame.
 temperature_data_frame = from_30_year_normals(temperature_data_frame, norm_data_frame, start_date_doy, end_date_doy);
 } else {
 total_days = get_total_days(is_leap_year);
 for (i in 1:total_days) {
 stop_err(msg);
 }
 return(valid_date);
 }
+if (is.null(opt$input_ytd)) {
+processing_year_to_date_data = FALSE;
+} else {
+processing_year_to_date_data = TRUE;
+}
+# Determine if we're plotting generations separately.
+if (opt$plot_generations_separately=="yes") {
+plot_generations_separately = TRUE;
+} else {
+plot_generations_separately = FALSE;
+}
+if (is.null(opt$start_date) && is.null(opt$end_date)) {
+# We're plotting an entire year.
+date_interval = FALSE;
+# Display the total number of days in the Galaxy history item blurb.
+if (processing_year_to_date_data) {
+cat("Number of days year-to-date: ", opt$num_days_ytd, "\n");
+} else {
+if (is_leap_year) {
+num_days = 366;
+} else {
+num_days = 365;
+}
+cat("Number of days in year: ", num_days, "\n");
+}
+} else {
+# FIXME: currently custom date fields are free text, but
+# Galaxy should soon include support for a date selector
+# at which point this tool should be enhanced to use it.
+# Validate start_date.
+date_interval = TRUE;
+# Calaculate the number of days in the date interval rather
+# than using the number of rows in the input temperature data.
+start_date = validate_date(opt$start_date);
+# Validate end_date.
+end_date = validate_date(opt$end_date);
+if (start_date >= end_date) {
+stop_err("The start date must be between 1 and 50 days before the end date when setting date intervals for plots.");
+}
+# Calculate the number of days in the date interval.
+num_days = difftime(start_date, end_date, units=c("days"));
+if (num_days > 50) {
+# We need to restrict date intervals since
+# plots render tick marks for each day.
+stop_err("Date intervals for plotting cannot exceed 50 days.");
+}
+# Display the total number of days in the Galaxy history item blurb.
+cat("Number of days in date interval: ", num_days, "\n");
+}
 # Parse the inputs.
 data_list = parse_input_data(opt$input_ytd, opt$input_norm, opt$location, opt$start_date, opt$end_date);
 temperature_data_frame = data_list[[1]];
 # Information needed for plots, some of these values are
 # being reset here since in some case they were set above.
 prepend_end_doy_norm = data_list[[4]];
 append_start_doy_norm = data_list[[5]];
 is_leap_year = data_list[[6]];
 location = data_list[[7]];
-if (is.null(input_ytd)) {
-processing_year_to_date_data = FALSE;
-} else {
-processing_year_to_date_data = TRUE;
-}
-# Determine if we're plotting generations separately.
-if (opt$plot_generations_separately=="yes") {
-plot_generations_separately = TRUE;
-} else {
-plot_generations_separately = FALSE;
-}
-if (is.null(opt$start_date) && is.null(opt$end_date)) {
-# We're plotting an entire year.
-restricted_date_interval = FALSE;
-# Display the total number of days in the Galaxy history item blurb.
-if (processing_year_to_date_data) {
-cat("Number of days year-to-date: ", opt$num_days_ytd, "\n");
-} else {
-if (is_leap_year) {
-num_days = 366;
-} else {
-num_days = 365;
-}
-cat("Number of days in year: ", num_days, "\n");
-}
-} else {
-# FIXME: currently custom date fields are free text, but
-# Galaxy should soon include support for a date selector
-# at which point this tool should be enhanced to use it.
-# Validate start_date.
-restricted_date_interval = TRUE;
-# Calaculate the number of days in the date interval rather
-# than using the number of rows in the input temperature data.
-start_date = validate_date(opt$start_date);
-# Validate end_date.
-end_date = validate_date(opt$end_date);
-if (start_date >= end_date) {
-stop_err("The start date must be between 1 and 50 days before the end date when setting date intervals for plots.");
-}
-# Calculate the number of days in the date interval.
-num_days = difftime(start_date, end_date, units=c("days"));
-if (num_days > 50) {
-# We need to restrict date intervals since
-# plots render tick marks for each day.
-stop_err("Date intervals for plotting cannot exceed 50 days.");
-}
-# Display the total number of days in the Galaxy history item blurb.
-cat("Number of days in date interval: ", num_days, "\n");
-}
 # Create copies of the temperature data for generations P, F1 and F2 if we're plotting generations separately.
 if (plot_generations_separately) {
 temperature_data_frame_P = data.frame(temperature_data_frame);
 temperature_data_frame_F1 = data.frame(temperature_data_frame);
 temperature_data_frame_F2 = data.frame(temperature_data_frame);
 }
 # Get the ticks date labels for plots.
-ticks_and_labels = get_x_axis_ticks_and_labels(temperature_data_frame, prepend_end_doy_norm, append_start_doy_norm, restricted_date_interval);
+ticks_and_labels = get_x_axis_ticks_and_labels(temperature_data_frame, prepend_end_doy_norm, append_start_doy_norm, date_interval);
 ticks = c(unlist(ticks_and_labels[1]));
 date_labels = c(unlist(ticks_and_labels[2]));
 # All latitude values are the same, so get the value for plots from the first row.
 latitude = temperature_data_frame$LATITUDE[1];

Mercurial > repos > greg > insect_phenology_model

comparison insect_phenology_model.R @ 123:e69e30d853fb draft