| Previous changeset 42:64132300c62e (2018-04-23) Next changeset 44:c61d3d9d44db (2018-04-23) |
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modified:
insect_phenology_model.R |
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| diff -r 64132300c62e -r fd3c00392fce insect_phenology_model.R --- a/insect_phenology_model.R Mon Apr 23 09:48:58 2018 -0400 +++ b/insect_phenology_model.R Mon Apr 23 09:49:08 2018 -0400 |
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| b'@@ -7,7 +7,7 @@\n make_option(c("--adult_accumulation"), action="store", dest="adult_accumulation", type="integer", help="Adjustment of degree-days accumulation (old nymph->adult)"),\n make_option(c("--egg_mortality"), action="store", dest="egg_mortality", type="integer", help="Adjustment rate for egg mortality"),\n make_option(c("--input_norm"), action="store", dest="input_norm", help="30 year normals temperature data for selected station"),\n- make_option(c("--input_ytd"), action="store", dest="input_ytd", help="Year-to-date temperature data for selected location"),\n+ make_option(c("--input_ytd"), action="store", dest="input_ytd", default=NULL, help="Year-to-date temperature data for selected location"),\n make_option(c("--insect"), action="store", dest="insect", help="Insect name"),\n make_option(c("--insects_per_replication"), action="store", dest="insects_per_replication", type="integer", help="Number of insects with which to start each replication"),\n make_option(c("--life_stages"), action="store", dest="life_stages", help="Selected life stages for plotting"),\n@@ -16,7 +16,7 @@\n make_option(c("--location"), action="store", dest="location", help="Selected location"),\n make_option(c("--min_clutch_size"), action="store", dest="min_clutch_size", type="integer", help="Adjustment of minimum clutch size"),\n make_option(c("--max_clutch_size"), action="store", dest="max_clutch_size", type="integer", help="Adjustment of maximum clutch size"),\n- make_option(c("--num_days_ytd"), action="store", dest="num_days_ytd", type="integer", help="Total number of days in the temperature dataset"),\n+ 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"),\n make_option(c("--nymph_mortality"), action="store", dest="nymph_mortality", type="integer", help="Adjustment rate for nymph mortality"),\n make_option(c("--old_nymph_accumulation"), action="store", dest="old_nymph_accumulation", type="integer", help="Adjustment of degree-days accumulation (young nymph->old nymph)"),\n make_option(c("--oviposition"), action="store", dest="oviposition", type="integer", help="Adjustment for oviposition rate"),\n@@ -262,7 +262,7 @@\n ticks[tick_index] = i;\n month_labels[tick_index] = "End prepended 30 year normals";\n last_tick = i;\n- } else if (i==end_doy_ytd+1) {\n+ } else if (end_doy_ytd > 0 & i==end_doy_ytd+1) {\n # Add a tick for the start of the 30 year normnals data\n # that was appended to the year-to-date data.\n tick_index = get_tick_index(i, last_tick, ticks, month_labels)\n@@ -354,26 +354,42 @@\n }\n \n parse_input_data = function(input_ytd, input_norm, num_days_ytd) {\n- # Read the input_ytd temperature datafile into a data frame.\n- # The input_ytd data has the following 6 columns:\n- # LATITUDE, LONGITUDE, DATE, DOY, TMIN, TMAX\n- temperature_data_frame = read.csv(file=input_ytd, header=T, strip.white=TRUE, stringsAsFactors=FALSE, sep=",");\n- # Set the temperature_data_frame column names for access.\n- colnames(temperature_data_frame) = c("LATITUDE", "LONGITUDE", "DATE", "DOY", "TMIN", "TMAX");\n- # Get the start date.\n- start_date = temperature_data_frame$DATE[1];\n- end_date = temperature_data_frame$DATE[num_days_ytd];\n+ if (is.null(input_ytd)) {\n+ # We\'re analysing only the 30 year normals data, so create an empty\n+ # data frame for containing temperature data after it is converted\n+ # from the 30 year normals format to the year-to-date format.\n+ temperature_data_frame = data.frame(matrix(ncol=6, nrow=0));\n+ colnames(temperature_data_frame) = c("LATITUDE", "LONGITUDE", "DATE", "DOY", "TMIN", "TMAX");\n+ # Base all dates on the current date since 30 year\n+ # normals data does not include any dates.\n+ year = format(Sys.Date(), "%Y"'..b'column names for access.\n+ colnames(temperature_data_frame) = c("LATITUDE", "LONGITUDE", "DATE", "DOY", "TMIN", "TMAX");\n+ # Get the start date.\n+ start_date = temperature_data_frame$DATE[1];\n+ end_date = temperature_data_frame$DATE[num_days_ytd];\n+ # Extract the year from the start date.\n+ date_str = format(start_date);\n+ date_str_items = strsplit(date_str, "-")[[1]];\n+ year = date_str_items[1];\n+ # Save the first DOY to later check if start_date is Jan 1.\n+ start_doy_ytd = as.integer(temperature_data_frame$DOY[1]);\n+ end_doy_ytd = as.integer(temperature_data_frame$DOY[num_days_ytd]);\n+ }\n # See if we\'re in a leap year.\n is_leap_year = is_leap_year(start_date);\n # Get the number of days in the year.\n total_days = get_total_days(is_leap_year);\n- # Extract the year from the start date.\n- date_str = format(start_date);\n- date_str_items = strsplit(date_str, "-")[[1]];\n- year = date_str_items[1];\n- # Save the first DOY to later check if start_date is Jan 1.\n- start_doy_ytd = as.integer(temperature_data_frame$DOY[1]);\n- end_doy_ytd = as.integer(temperature_data_frame$DOY[num_days_ytd]);\n # Read the input_norm temperature datafile into a data frame.\n # The input_norm data has the following 10 columns:\n # STATIONID, LATITUDE, LONGITUDE, ELEV_M, NAME, ST, MMDD, DOY, TMIN, TMAX\n@@ -385,22 +401,30 @@\n if (!is_leap_year) {\n norm_data_frame = norm_data_frame[-c(60),];\n }\n- if (start_doy_ytd > 1) {\n- # The year-to-date data starts after Jan 1, so create a\n- # temporary data frame to contain the 30 year normals data\n- # from Jan 1 to the date immediately prior to start_date.\n- tmp_data_frame = temperature_data_frame[FALSE,];\n- for (i in 1:start_doy_ytd-1) {\n- tmp_data_frame[i,] = get_next_normals_row(norm_data_frame, year, is_leap_year, i);\n+ if (is.null(input_ytd)) {\n+ # Convert the 30 year normals data to the year-to-date format.\n+ for (i in 1:total_days) {\n+ temperature_data_frame[i,] = get_next_normals_row(norm_data_frame, year, is_leap_year, i);\n }\n- # Next merge the temporary data frame with the year-to-date data frame.\n- temperature_data_frame = rbind(tmp_data_frame, temperature_data_frame);\n- }\n- # Define the next row for the year-to-date data from the 30 year normals data.\n- first_normals_append_row = end_doy_ytd + 1;\n- # Append the 30 year normals data to the year-to-date data.\n- for (i in first_normals_append_row:total_days) {\n- temperature_data_frame[i,] = get_next_normals_row(norm_data_frame, year, is_leap_year, i);\n+ } else {\n+ # Merge the year-to-date data with the 30 year normals data.\n+ if (start_doy_ytd > 1) {\n+ # The year-to-date data starts after Jan 1, so create a\n+ # temporary data frame to contain the 30 year normals data\n+ # from Jan 1 to the date immediately prior to start_date.\n+ tmp_data_frame = temperature_data_frame[FALSE,];\n+ for (i in 1:start_doy_ytd-1) {\n+ tmp_data_frame[i,] = get_next_normals_row(norm_data_frame, year, is_leap_year, i);\n+ }\n+ # Next merge the temporary data frame with the year-to-date data frame.\n+ temperature_data_frame = rbind(tmp_data_frame, temperature_data_frame);\n+ }\n+ # Define the next row for the year-to-date data from the 30 year normals data.\n+ first_normals_append_row = end_doy_ytd + 1;\n+ # Append the 30 year normals data to the year-to-date data.\n+ for (i in first_normals_append_row:total_days) {\n+ temperature_data_frame[i,] = get_next_normals_row(norm_data_frame, year, is_leap_year, i);\n+ }\n }\n # Add a column containing the daylight length for each day.\n temperature_data_frame = add_daylight_length(temperature_data_frame, total_days);\n' |