insect_phenology_model: insect_phenology

comparison insect_phenology_model.R @ 124:534658644efe draft

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author	greg
date	Fri, 01 Jun 2018 08:00:53 -0400
parents	e69e30d853fb
children	24f389a2dd93

comparison

equal deleted inserted replaced

-:e69e30d853fb
+:534658644efe
 last_norm_row = which(norm_data_frame$DOY==end_date_doy);
 norm_data_frame_rows = last_norm_row - first_norm_row;
 j = 0;
 for (i in first_norm_row:last_norm_row) {
 j = j + 1;
-temperature_data_frame[j,] = get_next_normals_row(norm_data_frame, year, is_leap_year, i);
+temperature_data_frame[j,] = get_next_normals_row(norm_data_frame, year, i);
 }
 return (temperature_data_frame);
 }
 get_file_path = function(life_stage, base_name, life_stage_nymph=NULL, life_stage_adult=NULL) {
 # F2 standard error.
 f2_se = apply(f2_replications, 1, sd) / sqrt(opt$replications);
 return(list(p_m, p_se, f1_m, f1_se, f2_m, f2_se))
 }
-get_next_normals_row = function(norm_data_frame, year, is_leap_year, index) {
+get_next_normals_row = function(norm_data_frame, year, index) {
 # Return the next 30 year normals row formatted
 # appropriately for the year-to-date data.
 latitude = norm_data_frame[index,"LATITUDE"][1];
 longitude = norm_data_frame[index,"LONGITUDE"][1];
 # Format the date.
 mmdd = norm_data_frame[index,"MMDD"][1];
 date_str = paste(year, mmdd, sep="-");
 doy = norm_data_frame[index,"DOY"][1];
-if (!is_leap_year) {
-# Since all normals data includes Feb 29, we have to
-# subtract 1 from DOY if we're not in a leap year since
-# we removed the Feb 29 row from the data frame above.
-doy = as.integer(doy) - 1;
-}
 tmin = norm_data_frame[index,"TMIN"][1];
 tmax = norm_data_frame[index,"TMAX"][1];
 return(list(latitude, longitude, date_str, doy, tmin, tmax));
 }
 # first row of the input_ytd data.
 tmp_norm_data_frame = data.frame(matrix(ncol=6, nrow=temperature_data_frame_rows+norm_data_frame_rows));
 for (i in first_norm_row:last_norm_row) {
 # Populate the temp_data_frame row with
 # values from norm_data_frame.
-tmp_norm_data_frame[i,] = get_next_normals_row(norm_data_frame, year, is_leap_year, i);
+tmp_norm_data_frame[i,] = get_next_normals_row(norm_data_frame, year, i);
 }
 # Create a second temporary data frame containing the
 # appropriate rows from temperature_data_frame.
 tmp_temperature_data_frame = temperature_data_frame[1:first_norm_row-1,];
 # Merge the 2 temporary data frames.
 tmp_data_frame = data.frame(matrix(ncol=6, nrow=temperature_data_frame_rows+norm_data_frame_rows));
 # Populate tmp_data_frame with the appropriate rows from temperature_data_frame.
 tmp_data_frame[temperature_data_frame_rows,] = temperature_data_frame[start_date_ytd_row:temperature_data_frame_rows,];
 # Apppend the appropriate rows from norm_data_frame to tmp_data_frame.
 for (i in first_norm_row:last_norm_row) {
-tmp_data_frame[i,] = get_next_normals_row(norm_data_frame, year, is_leap_year, i);
+tmp_data_frame[i,] = get_next_normals_row(norm_data_frame, year, i);
 }
 temperature_data_frame = tmp_data_frame[,];
 } else if (start_date_ytd_row == 0 & end_date_ytd_row == 0) {
 # The date interval is contained witin input_norm.
 temperature_data_frame = from_30_year_normals(temperature_data_frame, norm_data_frame, start_date_doy, end_date_doy);
 # We're plotting an entire year.
 if (start_doy_ytd > 1) {
 # The input_ytd data starts after Jan 1, so prepend
 # appropriate rows from input_norm to temperature_data_frame.
 prepend_end_doy_norm = start_doy_ytd - 1;
-first_norm_row = 1;
 last_norm_row = which(norm_data_frame$DOY == prepend_end_doy_norm);
 # Create a temporary data frame to contain the input_norm data
 # from Jan 1 to the date immediately prior to start_date.
 tmp_data_frame = temperature_data_frame[FALSE,];
 # Populate tmp_data_frame with appropriate rows from norm_data_frame.
-for (i in first_norm_row:last_norm_row) {
+for (i in 1:last_norm_row) {
-tmp_data_frame[i,] = get_next_normals_row(norm_data_frame, year, is_leap_year, i);
+tmp_data_frame[i,] = get_next_normals_row(norm_data_frame, year, i);
 }
 # Merge the temporary data frame with temperature_data_frame.
 temperature_data_frame = rbind(tmp_data_frame, temperature_data_frame);
 }
 # Set the value of total_days.
 # Define the next row for the year-to-date data from the 30 year normals data.
 append_start_doy_norm = end_doy_ytd + 1;
 first_norm_row = which(norm_data_frame$DOY == append_start_doy_norm);
 # Append the 30 year normals data to the year-to-date data.
 for (i in first_norm_row:total_days) {
-temperature_data_frame[i,] = get_next_normals_row(norm_data_frame, year, is_leap_year, i);
+temperature_data_frame[i,] = get_next_normals_row(norm_data_frame, year, i);
 }
 }
 }
 } else {
 # We're processing only the 30 year normals data.
 # 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) {
-temperature_data_frame[i,] = get_next_normals_row(norm_data_frame, year, is_leap_year, i);
+temperature_data_frame[i,] = get_next_normals_row(norm_data_frame, year, i);
 }
 }
 }
 # Add a column containing the daylight length for each day.
 temperature_data_frame = add_daylight_length(temperature_data_frame);
 if (opt$plot_generations_separately=="yes") {
 plot_generations_separately = TRUE;
 } else {
 plot_generations_separately = FALSE;
 }
+# Parse the inputs.
+data_list = parse_input_data(opt$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.
+start_date = data_list[[2]];
+end_date = data_list[[3]];
+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(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) {
 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.
-start_date = data_list[[2]];
-end_date = data_list[[3]];
-prepend_end_doy_norm = data_list[[4]];
-append_start_doy_norm = data_list[[5]];
-is_leap_year = data_list[[6]];
-location = data_list[[7]];
 # 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);

Mercurial > repos > greg > insect_phenology_model

comparison insect_phenology_model.R @ 124:534658644efe draft