insect_phenology_model: insect_phenology

comparison insect_phenology_model.R @ 43:fd3c00392fce draft

Uploaded

author	greg
date	Mon, 23 Apr 2018 09:49:08 -0400
parents	f4d683709b7f
children	315c5e1bc44a

comparison

equal deleted inserted replaced

-:64132300c62e
+:fd3c00392fce
 option_list <- list(
 make_option(c("--adult_mortality"), action="store", dest="adult_mortality", type="integer", help="Adjustment rate for adult mortality"),
 make_option(c("--adult_accumulation"), action="store", dest="adult_accumulation", type="integer", help="Adjustment of degree-days accumulation (old nymph->adult)"),
 make_option(c("--egg_mortality"), action="store", dest="egg_mortality", type="integer", help="Adjustment rate for egg mortality"),
 make_option(c("--input_norm"), action="store", dest="input_norm", help="30 year normals temperature data for selected station"),
-make_option(c("--input_ytd"), action="store", dest="input_ytd", help="Year-to-date temperature data for selected location"),
+make_option(c("--input_ytd"), action="store", dest="input_ytd", default=NULL, help="Year-to-date temperature data for selected location"),
 make_option(c("--insect"), action="store", dest="insect", help="Insect name"),
 make_option(c("--insects_per_replication"), action="store", dest="insects_per_replication", type="integer", help="Number of insects with which to start each replication"),
 make_option(c("--life_stages"), action="store", dest="life_stages", help="Selected life stages for plotting"),
 make_option(c("--life_stages_adult"), action="store", dest="life_stages_adult", default=NULL, help="Adult life stages for plotting"),
 make_option(c("--life_stages_nymph"), action="store", dest="life_stages_nymph", default=NULL, help="Nymph life stages for plotting"),
 make_option(c("--location"), action="store", dest="location", help="Selected location"),
 make_option(c("--min_clutch_size"), action="store", dest="min_clutch_size", type="integer", help="Adjustment of minimum clutch size"),
 make_option(c("--max_clutch_size"), action="store", dest="max_clutch_size", type="integer", help="Adjustment of maximum clutch size"),
-make_option(c("--num_days_ytd"), action="store", dest="num_days_ytd", type="integer", help="Total number of days in the temperature dataset"),
+make_option(c("--num_days_ytd"), action="store", dest="num_days_ytd", default=NULL, type="integer", help="Total number of days in the year-to-date temperature dataset"),
 make_option(c("--nymph_mortality"), action="store", dest="nymph_mortality", type="integer", help="Adjustment rate for nymph mortality"),
 make_option(c("--old_nymph_accumulation"), action="store", dest="old_nymph_accumulation", type="integer", help="Adjustment of degree-days accumulation (young nymph->old nymph)"),
 make_option(c("--oviposition"), action="store", dest="oviposition", type="integer", help="Adjustment for oviposition rate"),
 make_option(c("--photoperiod"), action="store", dest="photoperiod", type="double", help="Critical photoperiod for diapause induction/termination"),
 make_option(c("--plot_generations_separately"), action="store", dest="plot_generations_separately", help="Plot Plot P, F1 and F2 as separate lines or pool across them"),
 # that was prepended to the year-to-date data.
 tick_index = get_tick_index(i, last_tick, ticks, month_labels)
 ticks[tick_index] = i;
 month_labels[tick_index] = "End prepended 30 year normals";
 last_tick = i;
-} else  if (i==end_doy_ytd+1) {
+} else  if (end_doy_ytd > 0 & i==end_doy_ytd+1) {
 # Add a tick for the start of the 30 year normnals data
 # that was appended to the year-to-date data.
 tick_index = get_tick_index(i, last_tick, ticks, month_labels)
 ticks[tick_index] = i;
 month_labels[tick_index] = "Start appended 30 year normals";
 }
 return(mortality.probability);
 }
 parse_input_data = function(input_ytd, input_norm, num_days_ytd) {
-# Read the input_ytd temperature datafile into a data frame.
+if (is.null(input_ytd)) {
-# The input_ytd data has the following 6 columns:
+# We're analysing only the 30 year normals data, so create an empty
-# LATITUDE, LONGITUDE, DATE, DOY, TMIN, TMAX
+# data frame for containing temperature data after it is converted
-temperature_data_frame = read.csv(file=input_ytd, header=T, strip.white=TRUE, stringsAsFactors=FALSE, sep=",");
+# from the 30 year normals format to the year-to-date format.
-# Set the temperature_data_frame column names for access.
+temperature_data_frame = data.frame(matrix(ncol=6, nrow=0));
 colnames(temperature_data_frame) = c("LATITUDE", "LONGITUDE", "DATE", "DOY", "TMIN", "TMAX");
-# Get the start date.
+# Base all dates on the current date since 30 year
-start_date = temperature_data_frame$DATE[1];
+# normals data does not include any dates.
-end_date = temperature_data_frame$DATE[num_days_ytd];
+year = format(Sys.Date(), "%Y");
+start_date = paste(year, "01", "01", sep="-");
+end_date = paste(year, "12", "31", sep="-");
+# Set invalid start and end DOY.
+start_doy_ytd = 0;
+end_doy_ytd = 0;
+} else {
+# Read the input_ytd 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");
+# Get the start date.
+start_date = temperature_data_frame$DATE[1];
+end_date = temperature_data_frame$DATE[num_days_ytd];
+# Extract the year from the start date.
+date_str = format(start_date);
+date_str_items = strsplit(date_str, "-")[[1]];
+year = date_str_items[1];
+# 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_days_ytd]);
+}
 # See if we're in a leap year.
 is_leap_year = is_leap_year(start_date);
 # Get the number of days in the year.
 total_days = get_total_days(is_leap_year);
-# Extract the year from the start date.
-date_str = format(start_date);
-date_str_items = strsplit(date_str, "-")[[1]];
-year = date_str_items[1];
-# 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_days_ytd]);
 # Read the input_norm temperature datafile into a data frame.
 # The input_norm data has the following 10 columns:
 # STATIONID, LATITUDE, LONGITUDE, ELEV_M, NAME, ST, MMDD, DOY, TMIN, TMAX
 norm_data_frame = read.csv(file=input_norm, header=T, strip.white=TRUE, stringsAsFactors=FALSE, sep=",");
 # Set the norm_data_frame column names for access.
 # All normals data includes Feb 29 which is row 60 in
 # the data, so delete that row if we're not in a leap year.
 if (!is_leap_year) {
 norm_data_frame = norm_data_frame[-c(60),];
 }
-if (start_doy_ytd > 1) {
+if (is.null(input_ytd)) {
-# The year-to-date data starts after Jan 1, so create a
+# Convert the 30 year normals data to the year-to-date format.
-# temporary data frame to contain the 30 year normals data
+for (i in 1:total_days) {
-# from Jan 1 to the date immediately prior to start_date.
+temperature_data_frame[i,] = get_next_normals_row(norm_data_frame, year, is_leap_year, i);
-tmp_data_frame = temperature_data_frame[FALSE,];
+}
-for (i in 1:start_doy_ytd-1) {
+} else {
-tmp_data_frame[i,] = get_next_normals_row(norm_data_frame, year, is_leap_year, i);
+# Merge the year-to-date data with the 30 year normals data.
-}
+if (start_doy_ytd > 1) {
-# Next merge the temporary data frame with the year-to-date data frame.
+# The year-to-date data starts after Jan 1, so create a
-temperature_data_frame = rbind(tmp_data_frame, temperature_data_frame);
+# temporary data frame to contain the 30 year normals data
-}
+# from Jan 1 to the date immediately prior to start_date.
-# Define the next row for the year-to-date data from the 30 year normals data.
+tmp_data_frame = temperature_data_frame[FALSE,];
-first_normals_append_row = end_doy_ytd + 1;
+for (i in 1:start_doy_ytd-1) {
-# Append the 30 year normals data to the year-to-date data.
+tmp_data_frame[i,] = get_next_normals_row(norm_data_frame, year, is_leap_year, i);
-for (i in first_normals_append_row:total_days) {
+}
-temperature_data_frame[i,] = get_next_normals_row(norm_data_frame, year, is_leap_year, i);
+# Next merge the temporary data frame with the year-to-date data frame.
+temperature_data_frame = rbind(tmp_data_frame, temperature_data_frame);
+}
+# Define the next row for the year-to-date data from the 30 year normals data.
+first_normals_append_row = end_doy_ytd + 1;
+# Append the 30 year normals data to the year-to-date data.
+for (i in first_normals_append_row:total_days) {
+temperature_data_frame[i,] = get_next_normals_row(norm_data_frame, year, is_leap_year, i);
+}
 }
 # Add a column containing the daylight length for each day.
 temperature_data_frame = add_daylight_length(temperature_data_frame, total_days);
 return(list(temperature_data_frame, start_date, end_date, start_doy_ytd, end_doy_ytd, is_leap_year, total_days));
 }

Mercurial > repos > greg > insect_phenology_model

comparison insect_phenology_model.R @ 43:fd3c00392fce draft