# HG changeset patch # User greg # Date 1533661100 14400 # Node ID 24f389a2dd93854d99af22f24615cfe63685d609 # Parent 534658644efec0a99425a5414f79d9186b68ea2f Uploaded diff -r 534658644efe -r 24f389a2dd93 insect_phenology_model.R --- a/insect_phenology_model.R Fri Jun 01 08:00:53 2018 -0400 +++ b/insect_phenology_model.R Tue Aug 07 12:58:20 2018 -0400 @@ -6,7 +6,6 @@ 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("--end_date"), action="store", dest="end_date", default=NULL, help="End date for custom date interval"), 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", default=NULL, help="Year-to-date temperature data for selected location"), make_option(c("--insect"), action="store", dest="insect", help="Insect name"), @@ -25,7 +24,7 @@ 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"), make_option(c("--plot_std_error"), action="store", dest="plot_std_error", help="Plot Standard error"), make_option(c("--replications"), action="store", dest="replications", type="integer", help="Number of replications"), - make_option(c("--start_date"), action="store", dest="start_date", default=NULL, help="Start date for custom date interval"), + make_option(c("--script_dir"), action="store", dest="script_dir", help="R script source directory"), make_option(c("--young_nymph_accumulation"), action="store", dest="young_nymph_accumulation", type="integer", help="Adjustment of degree-days accumulation (egg->young nymph)") ) @@ -35,7 +34,7 @@ add_daylight_length = function(temperature_data_frame) { # Return temperature_data_frame with an added column - # of daylight length (photoperido profile). + # of daylight length (photoperiod profile). num_rows = dim(temperature_data_frame)[1]; # From Forsythe 1995. p = 0.8333; @@ -66,82 +65,61 @@ return(data_frame); } -extract_date_interval_rows = function(df, start_date, end_date) { - date_interval_rows = df[df$DATE >= start_date & df$DATE <= end_date]; - return(date_interval_rows); -} - -from_30_year_normals = function(temperature_data_frame, norm_data_frame, start_date_doy, end_date_doy) { +from_30_year_normals = function(norm_data_frame, start_date_doy, end_date_doy, year) { # The data we want is fully contained within the 30 year normals data. first_norm_row = which(norm_data_frame$DOY==start_date_doy); last_norm_row = which(norm_data_frame$DOY==end_date_doy); - norm_data_frame_rows = last_norm_row - first_norm_row; + # Add 1 to the number of rows to ensure that the end date is included. + tmp_data_frame_rows = last_norm_row - first_norm_row + 1; + tmp_data_frame = get_new_temperature_data_frame(nrow=tmp_data_frame_rows); 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, i); + tmp_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) { - if (!is.null(life_stage_nymph)) { - lsi = get_life_stage_index(life_stage, life_stage_nymph=life_stage_nymph); - file_name = paste(lsi, tolower(life_stage_nymph), base_name, sep="_"); - } else if (!is.null(life_stage_adult)) { - lsi = get_life_stage_index(life_stage, life_stage_adult=life_stage_adult); - file_name = paste(lsi, tolower(life_stage_adult), base_name, sep="_"); - } else { - lsi = get_life_stage_index(life_stage); - file_name = paste(lsi, base_name, sep="_"); - } - file_path = paste("output_plots_dir", file_name, sep="/"); - return(file_path); + return (tmp_data_frame); } -get_life_stage_index = function(life_stage, life_stage_nymph=NULL, life_stage_adult=NULL) { - # Name collection elements so that they - # are displayed in logical order. - if (life_stage=="Egg") { - lsi = "01"; - } else if (life_stage=="Nymph") { - if (life_stage_nymph=="Young") { - lsi = "02"; - } else if (life_stage_nymph=="Old") { - lsi = "03"; - } else if (life_stage_nymph=="Total") { - lsi="04"; +get_new_norm_data_frame = function(is_leap_year, input_norm=NULL, nrow=0) { + # The input_norm data has the following 10 columns: + # STATIONID, LATITUDE, LONGITUDE, ELEV_M, NAME, ST, MMDD, DOY, TMIN, TMAX + column_names = c("STATIONID", "LATITUDE","LONGITUDE", "ELEV_M", "NAME", "ST", "MMDD", "DOY", "TMIN", "TMAX"); + if (is.null(input_norm)) { + norm_data_frame = data.frame(matrix(ncol=10, nrow)); + # Set the norm_data_frame column names for access. + colnames(norm_data_frame) = column_names; + } else { + 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. + colnames(norm_data_frame) = column_names; + if (!is_leap_year) { + # 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. + norm_data_frame = norm_data_frame[-c(60),]; + # Since we've removed row 60, we need to subtract 1 from + # each value in the DOY column of the data frame starting + # with the 60th row. + num_rows = dim(norm_data_frame)[1]; + for (i in 60:num_rows) { + leap_year_doy = norm_data_frame$DOY[i]; + non_leap_year_doy = leap_year_doy - 1; + norm_data_frame$DOY[i] = non_leap_year_doy; + } } - } else if (life_stage=="Adult") { - if (life_stage_adult=="Pre-vittelogenic") { - lsi = "05"; - } else if (life_stage_adult=="Vittelogenic") { - lsi = "06"; - } else if (life_stage_adult=="Diapausing") { - lsi = "07"; - } else if (life_stage_adult=="Total") { - lsi = "08"; - } - } else if (life_stage=="Total") { - lsi = "09"; } - return(lsi); + return (norm_data_frame); } -get_mean_and_std_error = function(p_replications, f1_replications, f2_replications) { - # P mean. - p_m = apply(p_replications, 1, mean); - # P standard error. - p_se = apply(p_replications, 1, sd) / sqrt(opt$replications); - # F1 mean. - f1_m = apply(f1_replications, 1, mean); - # F1 standard error. - f1_se = apply(f1_replications, 1, sd) / sqrt(opt$replications); - # F2 mean. - f2_m = apply(f2_replications, 1, mean); - # 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_new_temperature_data_frame = function(input_ytd=NULL, nrow=0) { + # The input_ytd data has the following 6 columns: + # LATITUDE, LONGITUDE, DATE, DOY, TMIN, TMAX + if (is.null(input_ytd)) { + temperature_data_frame = data.frame(matrix(ncol=6, nrow)); + } else { + temperature_data_frame = read.csv(file=input_ytd, header=T, strip.white=TRUE, stringsAsFactors=FALSE, sep=","); + } + colnames(temperature_data_frame) = c("LATITUDE", "LONGITUDE", "DATE", "DOY", "TMIN", "TMAX"); + return(temperature_data_frame); } get_next_normals_row = function(norm_data_frame, year, index) { @@ -229,124 +207,6 @@ 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<3) { - 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_total_days = function(is_leap_year) { - # Get the total number of days in the current year. - if (is_leap_year) { - return(366); - } else { - return(365); - } -} - -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 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; - } - if (append_start_doy_norm > 0) { - append_start_norm_row = which(temperature_data_frame$DOY==append_start_doy_norm); - } else { - append_start_norm_row = 0; - } - num_rows = dim(temperature_data_frame)[1]; - month_labels = list(); - ticks = list(); - current_month_label = NULL; - last_tick = 0; - for (i in 1:num_rows) { - # We're plotting the entire year, so ticks will - # occur on Sundays and the first of each month. - if (i == prepend_end_norm_row) { - # Add a tick for the end of the 30 year normnals data - # that was prepended to the year-to-date data. - tick_index = get_tick_index(i, last_tick, ticks, month_labels) - ticks[tick_index] = i; - month_labels[tick_index] = "End prepended 30 year normals"; - last_tick = i; - } else if (i == append_start_doy_norm) { - # Add a tick for the start of the 30 year normnals data - # that was appended to the year-to-date data. - tick_index = get_tick_index(i, last_tick, ticks, month_labels) - ticks[tick_index] = i; - month_labels[tick_index] = "Start appended 30 year normals"; - last_tick = i; - } else if (i==num_rows) { - # Add a tick for the last day of the year. - tick_index = get_tick_index(i, last_tick, ticks, month_labels) - ticks[tick_index] = i; - month_labels[tick_index] = ""; - last_tick = i; - } else { - # Get the year and month from the date which - # has the format YYYY-MM-DD. - date = format(temperature_data_frame$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 a tick for the month. - tick_index = get_tick_index(i, last_tick, ticks, month_labels) - ticks[tick_index] = i; - month_labels[tick_index] = month_label; - 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 (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; - } else { - # Get the day. - day = weekdays(as.Date(date)); - if (day=="Sunday") { - # Add a 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)); -} - is_leap_year = function(date_str) { # Extract the year from the date_str. date = format(date_str); @@ -397,64 +257,72 @@ prepend_end_doy_norm = 0; # The start DOY for norm data appended to ytd data. append_start_doy_norm = 0; + if (is.null(start_date) && is.null(end_date)) { + # We're not dealing with a date interval. + date_interval = FALSE; + if (is.null(input_ytd)) { + # Base all dates on the current date since 30 year + # normals data does not include any dates. + year = format(Sys.Date(), "%Y"); + } + } else { + date_interval = TRUE; + year = get_year_from_date(start_date); + # Get the DOY for start_date and end_date. + start_date_doy = as.integer(strftime(start_date, format="%j")); + end_date_doy = as.integer(strftime(end_date, format="%j")); + } if (is.null(input_ytd)) { # We're processing only the 30 year normals data. processing_year_to_date_data = FALSE; + if (is.null(start_date) && is.null(end_date)) { + # We're processing the entire year, so we can + # set the start_date to Jan 1. + start_date = paste(year, "01", "01", sep="-"); + } } else { processing_year_to_date_data = TRUE; + # Read the input_ytd temperature data file into a data frame. + temperature_data_frame = get_new_temperature_data_frame(input_ytd=input_ytd); + num_ytd_rows = dim(temperature_data_frame)[1]; + if (!date_interval) { + start_date = temperature_data_frame$DATE[1]; + year = get_year_from_date(start_date); + } } - if (is.null(start_date) && is.null(end_date)) { - # We're processing the entire year, possibly merging - # data from input_norm with data from input_ytd. - date_interval = FALSE; - } else { - date_interval = TRUE; - # Get the DOY for start_date and end_date. - start_date_doy = strftime(start_date, format="%j"); - end_date_doy = strftime(end_date, format="%j"); - } + # See if we're in a leap year. + is_leap_year = is_leap_year(start_date); # Read the input_norm temperature datafile into a data frame. - # The input_norm data has the following 10 columns: - # STATIONID, LATITUDE, LONGITUDE, ELEV_M, NAME, ST, MMDD, DOY, TMIN, TMAX - norm_data_frame = read.csv(file=input_norm, header=T, strip.white=TRUE, stringsAsFactors=FALSE, sep=","); - # Set the norm_data_frame column names for access. - colnames(norm_data_frame) = c("STATIONID", "LATITUDE","LONGITUDE", "ELEV_M", "NAME", "ST", "MMDD", "DOY", "TMIN", "TMAX"); + norm_data_frame = get_new_norm_data_frame(is_leap_year, input_norm=input_norm); if (processing_year_to_date_data) { - # Read the input_ytd temperature data file into a data frame. - # The input_ytd data has the following 6 columns: - # LATITUDE, LONGITUDE, DATE, DOY, TMIN, TMAX - temperature_data_frame = read.csv(file=input_ytd, header=T, strip.white=TRUE, stringsAsFactors=FALSE, sep=","); - # Set the temperature_data_frame column names for access. - colnames(temperature_data_frame) = c("LATITUDE", "LONGITUDE", "DATE", "DOY", "TMIN", "TMAX"); if (date_interval) { # We're plotting a date interval. start_date_ytd_row = which(temperature_data_frame$DATE==start_date); - if (start_date_ytd_row > 0) { + if (length(start_date_ytd_row) > 0) { # The start date is contained within the input_ytd data. + start_date_ytd_row = start_date_ytd_row[1]; start_doy_ytd = as.integer(temperature_data_frame$DOY[start_date_ytd_row]); } else { # The start date is contained within the input_norm data. - start_date_norm_row = which(norm_data_frame$DATE==start_date); + start_date_ytd_row = 0; + start_date_norm_row = which(norm_data_frame$DOY==start_date_doy); } end_date_ytd_row = which(temperature_data_frame$DATE==end_date); - if (end_date_ytd_row > 0) { + if (length(end_date_ytd_row) > 0) { + end_date_ytd_row = end_date_ytd_row[1]; # The end date is contained within the input_ytd data. end_doy_ytd = as.integer(temperature_data_frame$DOY[end_date_ytd_row]); + } else { + end_date_ytd_row = 0; } - date_str = start_date; - # Extract the year from the start date. - date_str_items = strsplit(date_str, "-")[[1]]; - year = date_str_items[1]; } else { # We're plotting an entire year. - # Get the number of days contained in temperature_data_frame. - num_rows = dim(temperature_data_frame)[1]; # Get the start date and end date from temperature_data_frame. start_date_ytd_row = 1; # Temporarily set start_date to get the year. start_date = temperature_data_frame$DATE[1]; - end_date_ytd_row = num_rows; - end_date = temperature_data_frame$DATE[num_rows]; + end_date_ytd_row = num_ytd_rows; + end_date = temperature_data_frame$DATE[num_ytd_rows]; date_str = format(start_date); # Extract the year from the start date. date_str_items = strsplit(date_str, "-")[[1]]; @@ -466,14 +334,13 @@ 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]); + end_doy_ytd = as.integer(temperature_data_frame$DOY[num_ytd_rows]); } } else { # We're processing only the 30 year normals data, so create an empty # data frame for containing temperature data after it is converted # from the 30 year normals format to the year-to-date format. - temperature_data_frame = data.frame(matrix(ncol=6, nrow=0)); - colnames(temperature_data_frame) = c("LATITUDE", "LONGITUDE", "DATE", "DOY", "TMIN", "TMAX"); + temperature_data_frame = get_new_temperature_data_frame(); if (date_interval) { # We're plotting a date interval. # Extract the year, month and day from the start date. @@ -491,20 +358,10 @@ end_date = paste(year, end_date_month, end_date_day, sep="-"); } else { # We're plotting an entire year. - # Base all dates on the current date since 30 year - # normals data does not include any dates. - year = format(Sys.Date(), "%Y"); start_date = paste(year, "01", "01", sep="-"); end_date = paste(year, "12", "31", sep="-"); } } - # See if we're in a leap year. - is_leap_year = is_leap_year(start_date); - # All normals data includes Feb 29 which is row 60 in - # the data, so delete that row if we're not in a leap year. - if (!is_leap_year) { - norm_data_frame = norm_data_frame[-c(60),]; - } # Set the location to be the station name if the user elected not to enter it. if (is.null(location) | length(location) == 0) { location = norm_data_frame$NAME[1]; @@ -528,36 +385,36 @@ prepend_end_doy_norm = first_ytd_doy - 1; # Get the number of rows for the restricted date interval # that are contained in temperature_data_frame. - temperature_data_frame_rows = end_date_ytd_row; + num_temperature_data_frame_rows = end_date_ytd_row; # Get the last row needed from the 30 year normals data. last_norm_row = which(norm_data_frame$DOY==prepend_end_doy_norm); # Get the number of rows for the restricted date interval # that are contained in norm_data_frame. - norm_data_frame_rows = last_norm_row - first_norm_row; + num_norm_data_frame_rows = last_norm_row - first_norm_row; # Create a temporary data frame to contain the 30 year normals # data from the start date to the date immediately prior to the # 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)); + tmp_norm_data_frame = get_new_temperature_data_frame(nrow=num_temperature_data_frame_rows+num_norm_data_frame_rows); + j = 1; 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, i); + tmp_norm_data_frame[j,] = get_next_normals_row(norm_data_frame, year, i); + j = j + 1; } # 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,]; + tmp_temperature_data_frame = temperature_data_frame[1:num_temperature_data_frame_rows,]; # Merge the 2 temporary data frames. temperature_data_frame = rbind(tmp_norm_data_frame, tmp_temperature_data_frame); } else if (start_date_ytd_row > 0 & end_date_ytd_row == 0) { # The date interval starts in input_ytd and ends in input_norm, # so append appropriate rows from input_norm to appropriate rows - # from input_ytd. - num_rows = dim(temperature_data_frame)[1]; - # Get the number of rows for the restricted date interval - # that are contained in temperature_data_frame. - temperature_data_frame_rows = num_rows - start_date_ytd_row + # from input_ytd. First, get the number of rows for the restricted + # date interval that are contained in temperature_data_frame. + num_temperature_data_frame_rows = num_ytd_rows - start_date_ytd_row + 1; # Get the DOY of the last row in the input_ytd data. - last_ytd_doy = temperature_data_frame$DOY[num_rows]; + last_ytd_doy = temperature_data_frame$DOY[num_ytd_rows]; # Get the DOYs for the first and last rows from norm_data_frame # that will be appended to temperature_data_frame. append_start_doy_norm = last_ytd_doy + 1; @@ -567,21 +424,29 @@ last_norm_row = which(norm_data_frame$DOY == end_date_doy); # Get the number of rows for the restricted date interval # that are contained in norm_data_frame. - norm_data_frame_rows = last_norm_row - first_norm_row; + num_norm_data_frame_rows = last_norm_row - first_norm_row; # Create a temporary data frame to contain the data - # taken from both temperateu_data_frame and norm_data_frame + # taken from both temperature_data_frame and norm_data_frame # for the date interval. - tmp_data_frame = data.frame(matrix(ncol=6, nrow=temperature_data_frame_rows+norm_data_frame_rows)); + tmp_data_frame = get_new_temperature_data_frame(nrow=num_temperature_data_frame_rows+num_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,]; + j = start_date_ytd_row; + for (i in 1:num_temperature_data_frame_rows) { + tmp_data_frame[i,] = temperature_data_frame[j,]; + j = j + 1; + } # 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, i); + current_iteration = num_temperature_data_frame_rows + 1; + num_iterations = current_iteration + num_norm_data_frame_rows; + j = first_norm_row; + for (i in current_iteration:num_iterations) { + tmp_data_frame[i,] = get_next_normals_row(norm_data_frame, year, j); + j = j + 1; } 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); + temperature_data_frame = from_30_year_normals(norm_data_frame, start_date_doy, end_date_doy, year); } } else { # We're plotting an entire year. @@ -616,7 +481,7 @@ # We're processing only the 30 year normals data. 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); + temperature_data_frame = from_30_year_normals(norm_data_frame, start_date_doy, end_date_doy, year); } else { total_days = get_total_days(is_leap_year); for (i in 1:total_days) { @@ -629,103 +494,9 @@ return(list(temperature_data_frame, start_date, end_date, prepend_end_doy_norm, append_start_doy_norm, is_leap_year, location)); } -render_chart = function(ticks, date_labels, chart_type, plot_std_error, insect, location, latitude, start_date, end_date, days, maxval, - replications, life_stage, group, group_std_error, group2=NULL, group2_std_error=NULL, group3=NULL, group3_std_error=NULL, - life_stages_adult=NULL, life_stages_nymph=NULL) { - 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=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, las=2, font.axis=3, xpd=TRUE, cex=3, cex.lab=3, cex.axis=3, cex.main=3); - 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. - lines(days, group2+group2_std_error, col=2, lty=2); - lines(days, group2-group2_std_error, col=2, lty=2); - # Standard error for group3. - lines(days, group3+group3_std_error, col=4, lty=2); - lines(days, group3-group3_std_error, col=4, lty=2); - } - } else { - if (life_stage=="Egg") { - title = paste(insect, ": Reps", replications, ":", life_stage, "Pop :", location, ": Lat", latitude, ":", start_date, "-", end_date, sep=" "); - legend_text = c(life_stage); - columns = c(4); - } else if (life_stage=="Nymph") { - stage = paste(life_stages_nymph, "Nymph Pop :", sep=" "); - title = paste(insect, ": Reps", replications, ":", stage, location, ": Lat", latitude, ":", start_date, "-", end_date, sep=" "); - legend_text = c(paste(life_stages_nymph, life_stage, sep=" ")); - columns = c(2); - } else if (life_stage=="Adult") { - 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=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, las=2, font.axis=3, xpd=TRUE, cex=3, cex.lab=3, cex.axis=3, cex.main=3); - 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); - } - } - } else if (chart_type=="pop_size_by_generation") { - if (life_stage=="Total") { - title_str = ": Total Pop by Gen :"; - } else if (life_stage=="Egg") { - title_str = ": Egg Pop by Gen :"; - } else if (life_stage=="Nymph") { - title_str = paste(":", life_stages_nymph, "Nymph Pop by Gen", ":", sep=" "); - } else if (life_stage=="Adult") { - 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=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, las=2, font.axis=3, xpd=TRUE, cex=3, cex.lab=3, cex.axis=3, cex.main=3); - 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. - lines(days, group2+group2_std_error, col=2, lty=2); - lines(days, group2-group2_std_error, col=2, lty=2); - # Standard error for group3. - lines(days, group3+group3_std_error, col=4, lty=2); - lines(days, group3-group3_std_error, col=4, lty=2); - } - } -} - -stop_err = function(msg) { - cat(msg, file=stderr()); - quit(save="no", status=1); -} - -validate_date = function(date_str) { - valid_date = as.Date(date_str, format="%Y-%m-%d"); - if( class(valid_date)=="try-error" || is.na(valid_date)) { - msg = paste("Invalid date: ", date_str, ", valid date format is yyyy-mm-dd.", sep=""); - stop_err(msg); - } - return(valid_date); -} +# Import the shared utility functions. +utils_path <- paste(opt$script_dir, "utils.R", sep="/"); +source(utils_path); if (is.null(opt$input_ytd)) { processing_year_to_date_data = FALSE; @@ -750,44 +521,19 @@ 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) { - cat("Number of days year-to-date: ", opt$num_days_ytd, "\n"); - } else { - if (is_leap_year) { - num_days = 366; - } else { - num_days = 365; - } - cat("Number of days in year: ", num_days, "\n"); - } +# We're plotting an entire year. +# Display the total number of days in the Galaxy history item blurb. +if (processing_year_to_date_data) { + cat("Number of days year-to-date: ", opt$num_days_ytd, "\n"); } else { - # 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."); + if (is_leap_year) { + num_days = 366; + } else { + num_days = 365; } - # 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"); + cat("Number of days in year: ", 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); @@ -796,7 +542,7 @@ } # 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, date_interval); +ticks_and_labels = get_x_axis_ticks_and_labels(temperature_data_frame, prepend_end_doy_norm, append_start_doy_norm); 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. @@ -1533,10 +1279,10 @@ if (life_stage_adult == "Pre-vittelogenic") { # Mean value for previttelogenic adults. previttelogenic_adults = apply(Previttelogenic.replications, 1, mean); - temperature_data_frame = append_vector(temperature_data_frame, previttelogenic_adults, "PRE-VITADULT"); + temperature_data_frame = append_vector(temperature_data_frame, previttelogenic_adults, "PRE.VITADULT"); # Standard error for previttelogenic adults. previttelogenic_adults.std_error = apply(Previttelogenic.replications, 1, sd) / sqrt(opt$replications); - temperature_data_frame = append_vector(temperature_data_frame, previttelogenic_adults.std_error, "PRE-VITADULTSE"); + temperature_data_frame = append_vector(temperature_data_frame, previttelogenic_adults.std_error, "PRE.VITADULTSE"); } else if (life_stage_adult == "Vittelogenic") { # Mean value for vittelogenic adults. vittelogenic_adults = apply(Vittelogenic.replications, 1, mean); @@ -1574,121 +1320,121 @@ m_se = get_mean_and_std_error(P_eggs.replications, F1_eggs.replications, F2_eggs.replications); P_eggs = m_se[[1]]; P_eggs.std_error = m_se[[2]]; - temperature_data_frame_P = append_vector(temperature_data_frame_P, P_eggs, "EGG-P"); - temperature_data_frame_P = append_vector(temperature_data_frame_P, P_eggs.std_error, "EGG-P-SE"); + temperature_data_frame_P = append_vector(temperature_data_frame_P, P_eggs, "EGG.P"); + temperature_data_frame_P = append_vector(temperature_data_frame_P, P_eggs.std_error, "EGG.P.SE"); F1_eggs = m_se[[3]]; F1_eggs.std_error = m_se[[4]]; - temperature_data_frame_F1 = append_vector(temperature_data_frame_F1, F1_eggs, "EGG-F1"); - temperature_data_frame_F1 = append_vector(temperature_data_frame_F1, F1_eggs.std_error, "EGG-F1-SE"); + temperature_data_frame_F1 = append_vector(temperature_data_frame_F1, F1_eggs, "EGG.F1"); + temperature_data_frame_F1 = append_vector(temperature_data_frame_F1, F1_eggs.std_error, "EGG.F1.SE"); F2_eggs = m_se[[5]]; F2_eggs.std_error = m_se[[6]]; - temperature_data_frame_F2 = append_vector(temperature_data_frame_F2, F2_eggs, "EGG-F2"); - temperature_data_frame_F2 = append_vector(temperature_data_frame_F2, F2_eggs.std_error, "EGG-F2-SE"); + temperature_data_frame_F2 = append_vector(temperature_data_frame_F2, F2_eggs, "EGG.F2"); + temperature_data_frame_F2 = append_vector(temperature_data_frame_F2, F2_eggs.std_error, "EGG.F2.SE"); } if (process_young_nymphs) { m_se = get_mean_and_std_error(P_young_nymphs.replications, F1_young_nymphs.replications, F2_young_nymphs.replications); P_young_nymphs = m_se[[1]]; P_young_nymphs.std_error = m_se[[2]]; - temperature_data_frame_P = append_vector(temperature_data_frame_P, P_young_nymphs, "YOUNGNYMPH-P"); - temperature_data_frame_P = append_vector(temperature_data_frame_P, P_young_nymphs.std_error, "YOUNGNYMPH-P-SE"); + temperature_data_frame_P = append_vector(temperature_data_frame_P, P_young_nymphs, "YOUNGNYMPH.P"); + temperature_data_frame_P = append_vector(temperature_data_frame_P, P_young_nymphs.std_error, "YOUNGNYMPH.P.SE"); F1_young_nymphs = m_se[[3]]; F1_young_nymphs.std_error = m_se[[4]]; - temperature_data_frame_F1 = append_vector(temperature_data_frame_F1, F1_young_nymphs, "YOUNGNYMPH-F1"); - temperature_data_frame_F1 = append_vector(temperature_data_frame_F1, F1_young_nymphs.std_error, "YOUNGNYMPH-F1-SE"); + temperature_data_frame_F1 = append_vector(temperature_data_frame_F1, F1_young_nymphs, "YOUNGNYMPH.F1"); + temperature_data_frame_F1 = append_vector(temperature_data_frame_F1, F1_young_nymphs.std_error, "YOUNGNYMPH.F1.SE"); F2_young_nymphs = m_se[[5]]; F2_young_nymphs.std_error = m_se[[6]]; - temperature_data_frame_F2 = append_vector(temperature_data_frame_F2, F2_young_nymphs, "YOUNGNYMPH-F2"); - temperature_data_frame_F2 = append_vector(temperature_data_frame_F2, F2_young_nymphs.std_error, "YOUNGNYMPH-F2-SE"); + temperature_data_frame_F2 = append_vector(temperature_data_frame_F2, F2_young_nymphs, "YOUNGNYMPH.F2"); + temperature_data_frame_F2 = append_vector(temperature_data_frame_F2, F2_young_nymphs.std_error, "YOUNGNYMPH.F2.SE"); } if (process_old_nymphs) { m_se = get_mean_and_std_error(P_old_nymphs.replications, F1_old_nymphs.replications, F2_old_nymphs.replications); P_old_nymphs = m_se[[1]]; P_old_nymphs.std_error = m_se[[2]]; - temperature_data_frame_P = append_vector(temperature_data_frame_P, P_old_nymphs, "OLDNYMPH-P"); - temperature_data_frame_P = append_vector(temperature_data_frame_P, P_old_nymphs.std_error, "OLDNYMPH-P-SE"); + temperature_data_frame_P = append_vector(temperature_data_frame_P, P_old_nymphs, "OLDNYMPH.P"); + temperature_data_frame_P = append_vector(temperature_data_frame_P, P_old_nymphs.std_error, "OLDNYMPH.P.SE"); F1_old_nymphs = m_se[[3]]; F1_old_nymphs.std_error = m_se[[4]]; - temperature_data_frame_F1 = append_vector(temperature_data_frame_F1, F1_old_nymphs, "OLDNYMPH-F1"); - temperature_data_frame_F1 = append_vector(temperature_data_frame_F1, F1_old_nymphs.std_error, "OLDNYMPH-F1-SE"); + temperature_data_frame_F1 = append_vector(temperature_data_frame_F1, F1_old_nymphs, "OLDNYMPH.F1"); + temperature_data_frame_F1 = append_vector(temperature_data_frame_F1, F1_old_nymphs.std_error, "OLDNYMPH.F1.SE"); F2_old_nymphs = m_se[[5]]; F2_old_nymphs.std_error = m_se[[6]]; - temperature_data_frame_F2 = append_vector(temperature_data_frame_F2, F2_old_nymphs, "OLDNYMPH-F2"); - temperature_data_frame_F2 = append_vector(temperature_data_frame_F2, F2_old_nymphs.std_error, "OLDNYMPH-F2-SE"); + temperature_data_frame_F2 = append_vector(temperature_data_frame_F2, F2_old_nymphs, "OLDNYMPH.F2"); + temperature_data_frame_F2 = append_vector(temperature_data_frame_F2, F2_old_nymphs.std_error, "OLDNYMPH.F2.SE"); } if (process_total_nymphs) { m_se = get_mean_and_std_error(P_total_nymphs.replications, F1_total_nymphs.replications, F2_total_nymphs.replications); P_total_nymphs = m_se[[1]]; P_total_nymphs.std_error = m_se[[2]]; - temperature_data_frame_P = append_vector(temperature_data_frame_P, P_total_nymphs, "TOTALNYMPH-P"); - temperature_data_frame_P = append_vector(temperature_data_frame_P, P_total_nymphs.std_error, "TOTALNYMPH-P-SE"); + temperature_data_frame_P = append_vector(temperature_data_frame_P, P_total_nymphs, "TOTALNYMPH.P"); + temperature_data_frame_P = append_vector(temperature_data_frame_P, P_total_nymphs.std_error, "TOTALNYMPH.P.SE"); F1_total_nymphs = m_se[[3]]; F1_total_nymphs.std_error = m_se[[4]]; - temperature_data_frame_F1 = append_vector(temperature_data_frame_F1, F1_total_nymphs, "TOTALNYMPH-F1"); - temperature_data_frame_F1 = append_vector(temperature_data_frame_F1, F1_total_nymphs.std_error, "TOTALNYMPH-F1-SE"); + temperature_data_frame_F1 = append_vector(temperature_data_frame_F1, F1_total_nymphs, "TOTALNYMPH.F1"); + temperature_data_frame_F1 = append_vector(temperature_data_frame_F1, F1_total_nymphs.std_error, "TOTALNYMPH.F1.SE"); F2_total_nymphs = m_se[[5]]; F2_total_nymphs.std_error = m_se[[6]]; - temperature_data_frame_F2 = append_vector(temperature_data_frame_F2, F2_total_nymphs, "TOTALNYMPH-F2"); - temperature_data_frame_F2 = append_vector(temperature_data_frame_F2, F2_total_nymphs.std_error, "TOTALNYMPH-F2-SE"); + temperature_data_frame_F2 = append_vector(temperature_data_frame_F2, F2_total_nymphs, "TOTALNYMPH.F2"); + temperature_data_frame_F2 = append_vector(temperature_data_frame_F2, F2_total_nymphs.std_error, "TOTALNYMPH.F2.SE"); } if (process_previttelogenic_adults) { m_se = get_mean_and_std_error(P_previttelogenic_adults.replications, F1_previttelogenic_adults.replications, F2_previttelogenic_adults.replications); P_previttelogenic_adults = m_se[[1]]; P_previttelogenic_adults.std_error = m_se[[2]]; - temperature_data_frame_P = append_vector(temperature_data_frame_P, P_previttelogenic_adults, "PRE-VITADULT-P"); - temperature_data_frame_P = append_vector(temperature_data_frame_P, P_previttelogenic_adults.std_error, "PRE-VITADULT-P-SE"); + temperature_data_frame_P = append_vector(temperature_data_frame_P, P_previttelogenic_adults, "PRE.VITADULT.P"); + temperature_data_frame_P = append_vector(temperature_data_frame_P, P_previttelogenic_adults.std_error, "PRE.VITADULT.P.SE"); F1_previttelogenic_adults = m_se[[3]]; F1_previttelogenic_adults.std_error = m_se[[4]]; - temperature_data_frame_F1 = append_vector(temperature_data_frame_F1, F1_previttelogenic_adults, "PRE-VITADULT-F1"); - temperature_data_frame_F1 = append_vector(temperature_data_frame_F1, F1_previttelogenic_adults.std_error, "PRE-VITADULT-F1-SE"); + temperature_data_frame_F1 = append_vector(temperature_data_frame_F1, F1_previttelogenic_adults, "PRE.VITADULT.F1"); + temperature_data_frame_F1 = append_vector(temperature_data_frame_F1, F1_previttelogenic_adults.std_error, "PRE.VITADULT.F1.SE"); F2_previttelogenic_adults = m_se[[5]]; F2_previttelogenic_adults.std_error = m_se[[6]]; - temperature_data_frame_F2 = append_vector(temperature_data_frame_F2, F2_previttelogenic_adults, "PRE-VITADULT-F2"); - temperature_data_frame_F2 = append_vector(temperature_data_frame_F2, F2_previttelogenic_adults.std_error, "PRE-VITADULT-F2-SE"); + temperature_data_frame_F2 = append_vector(temperature_data_frame_F2, F2_previttelogenic_adults, "PRE.VITADULT.F2"); + temperature_data_frame_F2 = append_vector(temperature_data_frame_F2, F2_previttelogenic_adults.std_error, "PRE.VITADULT.F2.SE"); } if (process_vittelogenic_adults) { m_se = get_mean_and_std_error(P_vittelogenic_adults.replications, F1_vittelogenic_adults.replications, F2_vittelogenic_adults.replications); P_vittelogenic_adults = m_se[[1]]; P_vittelogenic_adults.std_error = m_se[[2]]; - temperature_data_frame_P = append_vector(temperature_data_frame_P, P_vittelogenic_adults, "VITADULT-P"); - temperature_data_frame_P = append_vector(temperature_data_frame_P, P_vittelogenic_adults.std_error, "VITADULT-P-SE"); + temperature_data_frame_P = append_vector(temperature_data_frame_P, P_vittelogenic_adults, "VITADULT.P"); + temperature_data_frame_P = append_vector(temperature_data_frame_P, P_vittelogenic_adults.std_error, "VITADULT.P.SE"); F1_vittelogenic_adults = m_se[[3]]; F1_vittelogenic_adults.std_error = m_se[[4]]; - temperature_data_frame_F1 = append_vector(temperature_data_frame_F1, F1_vittelogenic_adults, "VITADULT-F1"); - temperature_data_frame_F1 = append_vector(temperature_data_frame_F1, F1_vittelogenic_adults.std_error, "VITADULT-F1-SE"); + temperature_data_frame_F1 = append_vector(temperature_data_frame_F1, F1_vittelogenic_adults, "VITADULT.F1"); + temperature_data_frame_F1 = append_vector(temperature_data_frame_F1, F1_vittelogenic_adults.std_error, "VITADULT.F1.SE"); F2_vittelogenic_adults = m_se[[5]]; F2_vittelogenic_adults.std_error = m_se[[6]]; - temperature_data_frame_F2 = append_vector(temperature_data_frame_F2, F2_vittelogenic_adults, "VITADULT-F2"); - temperature_data_frame_F2 = append_vector(temperature_data_frame_F2, F2_vittelogenic_adults.std_error, "VITADULT-F2-SE"); + temperature_data_frame_F2 = append_vector(temperature_data_frame_F2, F2_vittelogenic_adults, "VITADULT.F2"); + temperature_data_frame_F2 = append_vector(temperature_data_frame_F2, F2_vittelogenic_adults.std_error, "VITADULT.F2.SE"); } if (process_diapausing_adults) { m_se = get_mean_and_std_error(P_diapausing_adults.replications, F1_diapausing_adults.replications, F2_diapausing_adults.replications); P_diapausing_adults = m_se[[1]]; P_diapausing_adults.std_error = m_se[[2]]; - temperature_data_frame_P = append_vector(temperature_data_frame_P, P_diapausing_adults, "DIAPAUSINGADULT-P"); - temperature_data_frame_P = append_vector(temperature_data_frame_P, P_diapausing_adults.std_error, "DIAPAUSINGADULT-P-SE"); + temperature_data_frame_P = append_vector(temperature_data_frame_P, P_diapausing_adults, "DIAPAUSINGADULT.P"); + temperature_data_frame_P = append_vector(temperature_data_frame_P, P_diapausing_adults.std_error, "DIAPAUSINGADULT.P.SE"); F1_diapausing_adults = m_se[[3]]; F1_diapausing_adults.std_error = m_se[[4]]; - temperature_data_frame_F1 = append_vector(temperature_data_frame_F1, F1_diapausing_adults, "DIAPAUSINGADULT-F1"); - temperature_data_frame_F1 = append_vector(temperature_data_frame_F1, F1_diapausing_adults.std_error, "DIAPAUSINGADULT-F1-SE"); + temperature_data_frame_F1 = append_vector(temperature_data_frame_F1, F1_diapausing_adults, "DIAPAUSINGADULT.F1"); + temperature_data_frame_F1 = append_vector(temperature_data_frame_F1, F1_diapausing_adults.std_error, "DIAPAUSINGADULT.F1.SE"); F2_diapausing_adults = m_se[[5]]; F2_diapausing_adults.std_error = m_se[[6]]; - temperature_data_frame_F2 = append_vector(temperature_data_frame_F2, F2_diapausing_adults, "DIAPAUSINGADULT-F2"); - temperature_data_frame_F2 = append_vector(temperature_data_frame_F2, F2_diapausing_adults.std_error, "DIAPAUSINGADULT-F2-SE"); + temperature_data_frame_F2 = append_vector(temperature_data_frame_F2, F2_diapausing_adults, "DIAPAUSINGADULT.F2"); + temperature_data_frame_F2 = append_vector(temperature_data_frame_F2, F2_diapausing_adults.std_error, "DIAPAUSINGADULT.F2.SE"); } if (process_total_adults) { m_se = get_mean_and_std_error(P_total_adults.replications, F1_total_adults.replications, F2_total_adults.replications); P_total_adults = m_se[[1]]; P_total_adults.std_error = m_se[[2]]; - temperature_data_frame_P = append_vector(temperature_data_frame_P, P_total_adults, "TOTALADULT-P"); - temperature_data_frame_P = append_vector(temperature_data_frame_P, P_total_adults.std_error, "TOTALADULT-P-SE"); + temperature_data_frame_P = append_vector(temperature_data_frame_P, P_total_adults, "TOTALADULT.P"); + temperature_data_frame_P = append_vector(temperature_data_frame_P, P_total_adults.std_error, "TOTALADULT.P.SE"); F1_total_adults = m_se[[3]]; F1_total_adults.std_error = m_se[[4]]; - temperature_data_frame_F1 = append_vector(temperature_data_frame_F1, F1_total_adults, "TOTALADULT-F1"); - temperature_data_frame_F1 = append_vector(temperature_data_frame_F1, F1_total_adults.std_error, "TOTALADULT-F1-SE"); + temperature_data_frame_F1 = append_vector(temperature_data_frame_F1, F1_total_adults, "TOTALADULT.F1"); + temperature_data_frame_F1 = append_vector(temperature_data_frame_F1, F1_total_adults.std_error, "TOTALADULT.F1.SE"); F2_total_adults = m_se[[5]]; F2_total_adults.std_error = m_se[[6]]; - temperature_data_frame_F2 = append_vector(temperature_data_frame_F2, F2_total_adults, "TOTALADULT-F2"); - temperature_data_frame_F2 = append_vector(temperature_data_frame_F2, F2_total_adults.std_error, "TOTALADULT-F2-SE"); + temperature_data_frame_F2 = append_vector(temperature_data_frame_F2, F2_total_adults, "TOTALADULT.F2"); + temperature_data_frame_F2 = append_vector(temperature_data_frame_F2, F2_total_adults.std_error, "TOTALADULT.F2.SE"); } } @@ -1727,7 +1473,7 @@ for (life_stage_nymph in life_stages_nymph) { # Start PDF device driver. dev.new(width=20, height=30); - file_path = get_file_path(life_stage, "nymph_pop_by_generation.pdf", life_stage_nymph=life_stage_nymph) + file_path = get_file_path(life_stage, "nymph_pop_by_generation.pdf", sub_life_stage=life_stage_nymph) pdf(file=file_path, width=20, height=30, bg="white"); par(mar=c(5, 6, 4, 4), mfrow=c(3, 1)); if (life_stage_nymph=="Young") { @@ -1760,7 +1506,7 @@ } render_chart(ticks, date_labels, "pop_size_by_generation", opt$plot_std_error, opt$insect, location, latitude, start_date, end_date, total_days_vector, maxval, opt$replications, life_stage, group=group, group_std_error=group_std_error, - group2=group2, group2_std_error=group2_std_error, group3=group3, group3_std_error=group3_std_error, life_stages_nymph=life_stage_nymph); + group2=group2, group2_std_error=group2_std_error, group3=group3, group3_std_error=group3_std_error, sub_life_stage=life_stage_nymph); # Turn off device driver to flush output. dev.off(); } @@ -1768,7 +1514,7 @@ for (life_stage_adult in life_stages_adult) { # Start PDF device driver. dev.new(width=20, height=30); - file_path = get_file_path(life_stage, "adult_pop_by_generation.pdf", life_stage_adult=life_stage_adult) + file_path = get_file_path(life_stage, "adult_pop_by_generation.pdf", sub_life_stage=life_stage_adult) pdf(file=file_path, width=20, height=30, bg="white"); par(mar=c(5, 6, 4, 4), mfrow=c(3, 1)); if (life_stage_adult=="Pre-vittelogenic") { @@ -1810,7 +1556,7 @@ } render_chart(ticks, date_labels, "pop_size_by_generation", opt$plot_std_error, opt$insect, location, latitude, start_date, end_date, total_days_vector, maxval, opt$replications, life_stage, group=group, group_std_error=group_std_error, - group2=group2, group2_std_error=group2_std_error, group3=group3, group3_std_error=group3_std_error, life_stages_adult=life_stage_adult); + group2=group2, group2_std_error=group2_std_error, group3=group3, group3_std_error=group3_std_error, sub_life_stage=life_stage_adult); # Turn off device driver to flush output. dev.off(); } @@ -1849,7 +1595,7 @@ for (life_stage_nymph in life_stages_nymph) { # Start PDF device driver. dev.new(width=20, height=30); - file_path = get_file_path(life_stage, "nymph_pop.pdf", life_stage_nymph=life_stage_nymph) + file_path = get_file_path(life_stage, "nymph_pop.pdf", sub_life_stage=life_stage_nymph) pdf(file=file_path, width=20, height=30, bg="white"); par(mar=c(5, 6, 4, 4), mfrow=c(3, 1)); if (life_stage_nymph=="Total") { @@ -1868,7 +1614,7 @@ maxval = max(group+group_std_error) + 100; render_chart(ticks, date_labels, "pop_size_by_life_stage", opt$plot_std_error, opt$insect, location, latitude, start_date, end_date, total_days_vector, maxval, opt$replications, life_stage, group=group, group_std_error=group_std_error, - life_stages_nymph=life_stage_nymph); + sub_life_stage=life_stage_nymph); # Turn off device driver to flush output. dev.off(); } @@ -1876,7 +1622,7 @@ for (life_stage_adult in life_stages_adult) { # Start PDF device driver. dev.new(width=20, height=30); - file_path = get_file_path(life_stage, "adult_pop.pdf", life_stage_adult=life_stage_adult) + file_path = get_file_path(life_stage, "adult_pop.pdf", sub_life_stage=life_stage_adult) pdf(file=file_path, width=20, height=30, bg="white"); par(mar=c(5, 6, 4, 4), mfrow=c(3, 1)); if (life_stage_adult=="Total") { @@ -1899,7 +1645,7 @@ maxval = max(group+group_std_error) + 100; render_chart(ticks, date_labels, "pop_size_by_life_stage", opt$plot_std_error, opt$insect, location, latitude, start_date, end_date, total_days_vector, maxval, opt$replications, life_stage, group=group, group_std_error=group_std_error, - life_stages_adult=life_stage_adult); + sub_life_stage=life_stage_adult); # Turn off device driver to flush output. dev.off(); } diff -r 534658644efe -r 24f389a2dd93 insect_phenology_model.xml --- a/insect_phenology_model.xml Fri Jun 01 08:00:53 2018 -0400 +++ b/insect_phenology_model.xml Tue Aug 07 12:58:20 2018 -0400 @@ -8,7 +8,6 @@ #set output_data_dir = "output_data_dir" #set output_plots_dir = "output_plots_dir" #set error_file = $os.path.join($output_data_dir, "04_combined_generations.csv") -#set custom_date_interval = $custom_date_interval_cond.custom_date_interval #set life_stages = list() #set plot_adult_life_stage = $plot_adult_life_stage_cond.plot_adult_life_stage #set plot_nymph_life_stage = $plot_nymph_life_stage_cond.plot_nymph_life_stage @@ -55,10 +54,7 @@ --plot_generations_separately $plot_generations_separately --plot_std_error $plot_std_error --replications $replications -#if str($custom_date_interval) == "yes": - --start_date '$custom_date_interval_cond.start_date' - --end_date '$custom_date_interval_cond.end_date' -#end if +--script_dir '$__tool_directory__' --young_nymph_accumulation $young_nymph_accumulation &>ipm_log.txt; if [[ $? -ne 0 ]]; then @@ -97,21 +93,6 @@ - - - - - - - - - len(value.split('-')[0])==4 and int(value.split('-')[0]) and len(value.split('-')[1])==2 and int(value.split('-')[1]) and len(value.split('-')[2])==2 and int(value.split('-')[2]) - - - len(value.split('-')[0])==4 and int(value.split('-')[0]) and len(value.split('-')[1])==2 and int(value.split('-')[1]) and len(value.split('-')[2])==2 and int(value.split('-')[2]) - - - diff -r 534658644efe -r 24f389a2dd93 test-data/output_combined1.csv --- a/test-data/output_combined1.csv Fri Jun 01 08:00:53 2018 -0400 +++ b/test-data/output_combined1.csv Tue Aug 07 12:58:20 2018 -0400 @@ -1,1 +1,1 @@ -"LATITUDE","LONGITUDE","DATE","DOY","TMIN","TMAX","DAYLEN","YOUNGNYMPH","YOUNGNYMPHSE","PRE-VITADULT","PRE-VITADULTSE" +"LATITUDE","LONGITUDE","DATE","DOY","TMIN","TMAX","DAYLEN","YOUNGNYMPH","YOUNGNYMPHSE","PRE.VITADULT","PRE.VITADULTSE" diff -r 534658644efe -r 24f389a2dd93 test-data/output_combined6.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_combined6.csv Tue Aug 07 12:58:20 2018 -0400 @@ -0,0 +1,16 @@ +"LATITUDE","LONGITUDE","DATE","DOY","TMIN","TMAX","DAYLEN","YOUNGNYMPH","YOUNGNYMPHSE","PRE.VITADULT","PRE.VITADULTSE" +40.81849,-77.84637,"2017-04-01",91,3.3,7.66,12.6361192995361 +40.81849,-77.84637,"2017-04-02",92,1.69,15.19,12.681126343138 +40.81849,-77.84637,"2017-04-03",93,3.48,18.81,12.7260513149927 +40.81849,-77.84637,"2017-04-04",94,9.28,18.75,12.7708878775247 +40.81849,-77.84637,"2017-04-05",95,8.14,19.01,12.8156295592851 +40.81849,-77.84637,"2017-04-06",96,4.59,12.02,12.8602697436611 +40.81849,-77.84637,"2017-04-07",97,1.19,3.66,12.9048016577475 +40.81849,-77.84637,"2017-04-08",98,-0.56,13.85,12.9492183613912 +40.81849,-77.84637,"2017-04-09",99,-2.32,21.96,12.9935127364246 +40.81849,-77.84637,"2017-04-10",100,7.9,26.25,13.037677476103 +40.81849,-77.84637,"2017-04-11",101,9.25,26.48,13.081705074763 +40.81849,-77.84637,"2017-04-12",102,8.95,19.78,13.1255878177204 +40.81849,-77.84637,"2017-04-13",103,4,15.47,13.1693177714296 +40.81849,-77.84637,"2017-04-14",104,5.09,20.1,13.2128867739251 +40.81849,-77.84637,"2017-04-15",105,8.44,25.02,13.2562864255699 diff -r 534658644efe -r 24f389a2dd93 test-data/output_combined7.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_combined7.csv Tue Aug 07 12:58:20 2018 -0400 @@ -0,0 +1,16 @@ +"LATITUDE","LONGITUDE","DATE","DOY","TMIN","TMAX","DAYLEN","YOUNGNYMPH","YOUNGNYMPHSE","PRE.VITADULT","PRE.VITADULTSE" +40.3844,-76.0339,"2017-01-01",1,-6.8,2.8,9.33687304211315 +40.3844,-76.0339,"2017-01-02",2,-6.8,2.7,9.34822021765528 +40.3844,-76.0339,"2017-01-03",3,-6.9,2.6,9.36062371263695 +40.3844,-76.0339,"2017-01-04",4,-7,2.6,9.3740716338922 +40.3844,-76.0339,"2017-01-05",5,-7.1,2.5,9.38855118408927 +40.3844,-76.0339,"2017-01-06",6,-7.1,2.5,9.40404870530151 +40.3844,-76.0339,"2017-01-07",7,-7.2,2.4,9.42054972475204 +40.3844,-76.0339,"2017-01-08",8,-7.2,2.4,9.43803900243173 +40.3844,-76.0339,"2017-01-09",9,-7.3,2.4,9.45650058028574 +40.3844,-76.0339,"2017-01-10",10,-7.3,2.3,9.4759178326624 +40.3844,-76.0339,"2017-01-11",11,-7.4,2.3,9.4962735177201 +40.3844,-76.0339,"2017-01-12",12,-7.4,2.3,9.51754982949216 +40.3844,-76.0339,"2017-01-13",13,-7.4,2.3,9.53972845031694 +40.3844,-76.0339,"2017-01-14",14,-7.5,2.3,9.56279060334963 +40.3844,-76.0339,"2017-01-15",15,-7.5,2.3,9.58671710488405 diff -r 534658644efe -r 24f389a2dd93 test-data/output_f1_3.csv --- a/test-data/output_f1_3.csv Fri Jun 01 08:00:53 2018 -0400 +++ b/test-data/output_f1_3.csv Tue Aug 07 12:58:20 2018 -0400 @@ -1,1 +1,1 @@ -"LATITUDE","LONGITUDE","DATE","DOY","TMIN","TMAX","DAYLEN","OLDNYMPH-F1","OLDNYMPH-F1-SE" +"LATITUDE","LONGITUDE","DATE","DOY","TMIN","TMAX","DAYLEN","OLDNYMPH.F1","OLDNYMPH.F1.SE" diff -r 534658644efe -r 24f389a2dd93 test-data/output_f1_4.csv --- a/test-data/output_f1_4.csv Fri Jun 01 08:00:53 2018 -0400 +++ b/test-data/output_f1_4.csv Tue Aug 07 12:58:20 2018 -0400 @@ -1,1 +1,1 @@ -"LATITUDE","LONGITUDE","DATE","DOY","TMIN","TMAX","DAYLEN","EGG-F1","EGG-F1-SE","TOTALNYMPH-F1","TOTALNYMPH-F1-SE","TOTALADULT-F1","TOTALADULT-F1-SE" +"LATITUDE","LONGITUDE","DATE","DOY","TMIN","TMAX","DAYLEN","EGG.F1","EGG.F1.SE","TOTALNYMPH.F1","TOTALNYMPH.F1.SE","TOTALADULT.F1","TOTALADULT.F1.SE" diff -r 534658644efe -r 24f389a2dd93 test-data/output_f2_3.csv --- a/test-data/output_f2_3.csv Fri Jun 01 08:00:53 2018 -0400 +++ b/test-data/output_f2_3.csv Tue Aug 07 12:58:20 2018 -0400 @@ -1,1 +1,1 @@ -"LATITUDE","LONGITUDE","DATE","DOY","TMIN","TMAX","DAYLEN","OLDNYMPH-F2","OLDNYMPH-F2-SE" +"LATITUDE","LONGITUDE","DATE","DOY","TMIN","TMAX","DAYLEN","OLDNYMPH.F2","OLDNYMPH.F2.SE" diff -r 534658644efe -r 24f389a2dd93 test-data/output_f2_4.csv --- a/test-data/output_f2_4.csv Fri Jun 01 08:00:53 2018 -0400 +++ b/test-data/output_f2_4.csv Tue Aug 07 12:58:20 2018 -0400 @@ -1,1 +1,1 @@ -"LATITUDE","LONGITUDE","DATE","DOY","TMIN","TMAX","DAYLEN","EGG-F2","EGG-F2-SE","TOTALNYMPH-F2","TOTALNYMPH-F2-SE","TOTALADULT-F2","TOTALADULT-F2-SE" +"LATITUDE","LONGITUDE","DATE","DOY","TMIN","TMAX","DAYLEN","EGG.F2","EGG.F2.SE","TOTALNYMPH.F2","TOTALNYMPH.F2.SE","TOTALADULT.F2","TOTALADULT.F2.SE" diff -r 534658644efe -r 24f389a2dd93 test-data/output_p_3.csv --- a/test-data/output_p_3.csv Fri Jun 01 08:00:53 2018 -0400 +++ b/test-data/output_p_3.csv Tue Aug 07 12:58:20 2018 -0400 @@ -1,1 +1,1 @@ -"LATITUDE","LONGITUDE","DATE","DOY","TMIN","TMAX","DAYLEN","OLDNYMPH-P","OLDNYMPH-P-SE" +"LATITUDE","LONGITUDE","DATE","DOY","TMIN","TMAX","DAYLEN","OLDNYMPH.P","OLDNYMPH.P.SE" diff -r 534658644efe -r 24f389a2dd93 test-data/output_p_4.csv --- a/test-data/output_p_4.csv Fri Jun 01 08:00:53 2018 -0400 +++ b/test-data/output_p_4.csv Tue Aug 07 12:58:20 2018 -0400 @@ -1,1 +1,1 @@ -"LATITUDE","LONGITUDE","DATE","DOY","TMIN","TMAX","DAYLEN","EGG-P","EGG-P-SE","TOTALNYMPH-P","TOTALNYMPH-P-SE","TOTALADULT-P","TOTALADULT-P-SE" +"LATITUDE","LONGITUDE","DATE","DOY","TMIN","TMAX","DAYLEN","EGG.P","EGG.P.SE","TOTALNYMPH.P","TOTALNYMPH.P.SE","TOTALADULT.P","TOTALADULT.P.SE" diff -r 534658644efe -r 24f389a2dd93 utils.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/utils.R Tue Aug 07 12:58:20 2018 -0400 @@ -0,0 +1,317 @@ +#!/usr/bin/env Rscript + +get_file_path = function(life_stage, base_name, sub_life_stage=NULL) { + if (is.null(sub_life_stage)) { + lsi = get_life_stage_index(life_stage); + file_name = paste(lsi, base_name, sep="_"); + } else { + lsi = get_life_stage_index(life_stage, sub_life_stage=sub_life_stage); + file_name = paste(lsi, tolower(sub_life_stage), base_name, sep="_"); + } + file_path = paste("output_plots_dir", file_name, sep="/"); + return(file_path); +} + +get_year_from_date = function(date_str) { + date_str_items = strsplit(date_str, "-")[[1]]; + return (date_str_items[1]); +} + +get_life_stage_index = function(life_stage, sub_life_stage=NULL) { + # Name collection elements so that they + # are displayed in logical order. + if (life_stage=="Egg") { + lsi = "01"; + } else if (life_stage=="Nymph") { + if (sub_life_stage=="Young") { + lsi = "02"; + } else if (sub_life_stage=="Old") { + lsi = "03"; + } else if (sub_life_stage=="Total") { + lsi="04"; + } + } else if (life_stage=="Adult") { + if (sub_life_stage=="Pre-vittelogenic") { + lsi = "05"; + } else if (sub_life_stage=="Vittelogenic") { + lsi = "06"; + } else if (sub_life_stage=="Diapausing") { + lsi = "07"; + } else if (sub_life_stage=="Total") { + lsi = "08"; + } + } else if (life_stage=="Total") { + lsi = "09"; + } + return(lsi); +} + +get_mean_and_std_error = function(p_replications, f1_replications, f2_replications) { + # P mean. + p_m = apply(p_replications, 1, mean); + # P standard error. + p_se = apply(p_replications, 1, sd) / sqrt(opt$replications); + # F1 mean. + f1_m = apply(f1_replications, 1, mean); + # F1 standard error. + f1_se = apply(f1_replications, 1, sd) / sqrt(opt$replications); + # F2 mean. + f2_m = apply(f2_replications, 1, mean); + # F2 standard error. + f2_se = apply(f2_replications, 1, sd) / sqrt(opt$replications); + return(list(p_m, p_se, f1_m, f1_se, f2_m, f2_se)) +} + +get_tick_index = function(index, last_tick, ticks, tick_labels, tick_sep) { + # 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 0) { + prepend_end_norm_row = which(temperature_data_frame$DOY==prepend_end_doy_norm); + } else { + prepend_end_norm_row = 0; + } + if (append_start_doy_norm > 0) { + append_start_norm_row = which(temperature_data_frame$DOY==append_start_doy_norm); + } else { + append_start_norm_row = 0; + } + num_rows = dim(temperature_data_frame)[1]; + tick_labels = list(); + ticks = list(); + current_month_label = NULL; + last_tick = 0; + if (date_interval) { + tick_sep = 0; + } else { + tick_sep = 3; + } + 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$DATE[i]); + # Get the month label. + items = strsplit(date, "-")[[1]]; + month = items[2]; + month_label = month.abb[as.integer(month)]; + day = as.integer(items[3]); + doy = as.integer(temperature_data_frame$DOY[i]); + # We're plotting the entire year, so ticks will + # occur on Sundays and the first of each month. + if (i == prepend_end_norm_row) { + # Add a tick for the end of the 30 year normnals data + # that was prepended to the year-to-date data. + label_str = "End prepended 30 year normals"; + tick_index = get_tick_index(i, last_tick, ticks, tick_labels, tick_sep) + ticks[tick_index] = i; + if (date_interval) { + # Append the day to label_str + tick_labels[tick_index] = paste(label_str, day, sep=" "); + } else { + tick_labels[tick_index] = label_str; + } + last_tick = i; + } else if (doy == append_start_doy_norm) { + # Add a tick for the start of the 30 year normnals data + # that was appended to the year-to-date data. + label_str = "Start appended 30 year normals"; + tick_index = get_tick_index(i, last_tick, ticks, tick_labels, tick_sep) + ticks[tick_index] = i; + if (!identical(current_month_label, month_label)) { + # Append the month to label_str. + label_str = paste(label_str, month_label, spe=" "); + current_month_label = month_label; + } + if (date_interval) { + # Append the day to label_str + label_str = paste(label_str, day, sep=" "); + } + tick_labels[tick_index] = label_str; + last_tick = i; + } else if (i==num_rows) { + # Add a tick for the last day of the year. + label_str = ""; + tick_index = get_tick_index(i, last_tick, ticks, tick_labels, tick_sep) + ticks[tick_index] = i; + if (!identical(current_month_label, month_label)) { + # Append the month to label_str. + label_str = month_label; + current_month_label = month_label; + } + if (date_interval) { + # Append the day to label_str + label_str = paste(label_str, day, sep=" "); + } + tick_labels[tick_index] = label_str; + } else { + if (!identical(current_month_label, month_label)) { + # Add a tick for the month. + tick_index = get_tick_index(i, last_tick, ticks, tick_labels, tick_sep) + ticks[tick_index] = i; + if (date_interval) { + # Append the day to the month. + tick_labels[tick_index] = paste(month_label, day, sep=" "); + } else { + tick_labels[tick_index] = month_label; + } + current_month_label = month_label; + last_tick = i; + } + tick_index = get_tick_index(i, last_tick, ticks, tick_labels, tick_sep) + if (!is.null(tick_index)) { + if (date_interval) { + # Add a tick for every day. The first tick is the + # month label, so add a tick only if i is not 1 + if (i>1 & day>1) { + tick_index = get_tick_index(i, last_tick, ticks, tick_labels, tick_sep) + ticks[tick_index] = i; + # Add the day as the label. + tick_labels[tick_index] = day; + last_tick = i; + } + } else { + # Get the day. + day = weekdays(as.Date(date)); + if (day=="Sunday") { + # Add a tick if we're on a Sunday. + ticks[tick_index] = i; + # Add a blank month label so it is not displayed. + tick_labels[tick_index] = ""; + last_tick = i; + } + } + } + } + } + return(list(ticks, tick_labels)); +} + +render_chart = function(ticks, date_labels, chart_type, plot_std_error, insect, location, latitude, start_date, end_date, days, maxval, + replications, life_stage, group, group_std_error, group2=NULL, group2_std_error=NULL, group3=NULL, group3_std_error=NULL, + sub_life_stage=NULL) { + 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=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, las=2, font.axis=3, xpd=TRUE, cex=3, cex.lab=3, cex.axis=3, cex.main=3); + 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. + lines(days, group2+group2_std_error, col=2, lty=2); + lines(days, group2-group2_std_error, col=2, lty=2); + # Standard error for group3. + lines(days, group3+group3_std_error, col=4, lty=2); + lines(days, group3-group3_std_error, col=4, lty=2); + } + } else { + if (life_stage=="Egg") { + title = paste(insect, ": Reps", replications, ":", life_stage, "Pop :", location, ": Lat", latitude, ":", start_date, "-", end_date, sep=" "); + legend_text = c(life_stage); + columns = c(4); + } else if (life_stage=="Nymph") { + stage = paste(sub_life_stage, "Nymph Pop :", sep=" "); + title = paste(insect, ": Reps", replications, ":", stage, location, ": Lat", latitude, ":", start_date, "-", end_date, sep=" "); + legend_text = c(paste(sub_life_stage, life_stage, sep=" ")); + columns = c(2); + } else if (life_stage=="Adult") { + stage = paste(sub_life_stage, "Adult Pop", sep=" "); + title = paste(insect, ": Reps", replications, ":", stage, location, ": Lat", latitude, ":", start_date, "-", end_date, sep=" "); + legend_text = c(paste(sub_life_stage, life_stage, sep=" ")); + columns = c(1); + } + 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, las=2, font.axis=3, xpd=TRUE, cex=3, cex.lab=3, cex.axis=3, cex.main=3); + 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); + } + } + } else if (chart_type=="pop_size_by_generation") { + if (life_stage=="Total") { + title_str = ": Total Pop by Gen :"; + } else if (life_stage=="Egg") { + title_str = ": Egg Pop by Gen :"; + } else if (life_stage=="Nymph") { + title_str = paste(":", sub_life_stage, "Nymph Pop by Gen", ":", sep=" "); + } else if (life_stage=="Adult") { + title_str = paste(":", sub_life_stage, "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=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, las=2, font.axis=3, xpd=TRUE, cex=3, cex.lab=3, cex.axis=3, cex.main=3); + 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. + lines(days, group2+group2_std_error, col=2, lty=2); + lines(days, group2-group2_std_error, col=2, lty=2); + # Standard error for group3. + lines(days, group3+group3_std_error, col=4, lty=2); + lines(days, group3-group3_std_error, col=4, lty=2); + } + } +} + +stop_err = function(msg) { + cat(msg, file=stderr()); + quit(save="no", status=1); +} + +validate_date = function(date_str) { + valid_date = as.Date(date_str, format="%Y-%m-%d"); + if( class(valid_date)=="try-error" || is.na(valid_date)) { + msg = paste("Invalid date: ", date_str, ", valid date format is yyyy-mm-dd.", sep=""); + stop_err(msg); + } + return(valid_date); +}