Mercurial > repos > greg > insect_phenology_model
changeset 50:927321ed0322 draft
Uploaded
| author | greg |
|---|---|
| date | Tue, 07 Aug 2018 12:59:06 -0400 |
| parents | 1b6864c5b50a |
| children | 3f827fe31756 |
| files | insect_phenology_model.R insect_phenology_model.xml test-data/output_combined1.csv test-data/output_combined6.csv test-data/output_combined7.csv test-data/output_f1_3.csv test-data/output_f1_4.csv test-data/output_f2_3.csv test-data/output_f2_4.csv test-data/output_p_3.csv test-data/output_p_4.csv utils.R |
| diffstat | 12 files changed, 431 insertions(+), 451 deletions(-) [+] |
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--- a/insect_phenology_model.R Tue Jun 05 07:52:59 2018 -0400 +++ b/insect_phenology_model.R Tue Aug 07 12:59:06 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; @@ -66,11 +65,6 @@ 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(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$DOY==start_date_doy); @@ -86,66 +80,6 @@ return (tmp_data_frame); } -get_file_path = function(life_stage, base_name, life_stage_nymph=NULL, life_stage_adult=NULL) { - if (!is.null(life_stage_nymph)) { - lsi = get_life_stage_index(life_stage, life_stage_nymph=life_stage_nymph); - file_name = paste(lsi, tolower(life_stage_nymph), base_name, sep="_"); - } else if (!is.null(life_stage_adult)) { - lsi = get_life_stage_index(life_stage, life_stage_adult=life_stage_adult); - file_name = paste(lsi, tolower(life_stage_adult), base_name, sep="_"); - } else { - lsi = get_life_stage_index(life_stage); - file_name = paste(lsi, base_name, sep="_"); - } - file_path = paste("output_plots_dir", file_name, sep="/"); - return(file_path); -} - -get_life_stage_index = function(life_stage, life_stage_nymph=NULL, life_stage_adult=NULL) { - # Name collection elements so that they - # are displayed in logical order. - if (life_stage=="Egg") { - lsi = "01"; - } else if (life_stage=="Nymph") { - if (life_stage_nymph=="Young") { - lsi = "02"; - } else if (life_stage_nymph=="Old") { - lsi = "03"; - } else if (life_stage_nymph=="Total") { - lsi="04"; - } - } else if (life_stage=="Adult") { - if (life_stage_adult=="Pre-vittelogenic") { - lsi = "05"; - } else if (life_stage_adult=="Vittelogenic") { - lsi = "06"; - } else if (life_stage_adult=="Diapausing") { - lsi = "07"; - } else if (life_stage_adult=="Total") { - lsi = "08"; - } - } else if (life_stage=="Total") { - lsi = "09"; - } - return(lsi); -} - -get_mean_and_std_error = function(p_replications, f1_replications, f2_replications) { - # P mean. - p_m = apply(p_replications, 1, mean); - # P standard error. - p_se = apply(p_replications, 1, sd) / sqrt(opt$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_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 @@ -273,167 +207,6 @@ return(c(curr_mean_temp, averages)) } -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<tick_sep) { - last_saved_month = tick_labels[[length(tick_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. - 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]; - 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)); -} - -get_year_from_date = function(date_str) { - date_str_items = strsplit(date_str, "-")[[1]]; - return (date_str_items[1]); -} - is_leap_year = function(date_str) { # Extract the year from the date_str. date = format(date_str); @@ -721,103 +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; @@ -842,48 +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(end_date, start_date, units=c("days")); - # Add 1 to the number of days to make the dates inclusive. For - # example, if the user enters a date range of 2018-01-01 to - # 2018-01-31, they likely expect the end date to be included. - num_days = num_days + 1; - 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); @@ -892,7 +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. @@ -1629,10 +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); @@ -1670,121 +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"); } } @@ -1823,7 +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") { @@ -1856,7 +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(); } @@ -1864,7 +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") { @@ -1906,7 +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$replications, life_stage, group=group, group_std_error=group_std_error, - group2=group2, group2_std_error=group2_std_error, group3=group3, group3_std_error=group3_std_error, life_stages_adult=life_stage_adult); + group2=group2, group2_std_error=group2_std_error, group3=group3, group3_std_error=group3_std_error, sub_life_stage=life_stage_adult); # Turn off device driver to flush output. dev.off(); } @@ -1945,7 +1595,7 @@ for (life_stage_nymph in life_stages_nymph) { # Start PDF device driver. dev.new(width=20, height=30); - file_path = get_file_path(life_stage, "nymph_pop.pdf", life_stage_nymph=life_stage_nymph) + file_path = get_file_path(life_stage, "nymph_pop.pdf", sub_life_stage=life_stage_nymph) pdf(file=file_path, width=20, height=30, bg="white"); par(mar=c(5, 6, 4, 4), mfrow=c(3, 1)); if (life_stage_nymph=="Total") { @@ -1964,7 +1614,7 @@ maxval = max(group+group_std_error) + 100; render_chart(ticks, date_labels, "pop_size_by_life_stage", opt$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(); } @@ -1972,7 +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") { @@ -1995,7 +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(); }
--- a/insect_phenology_model.xml Tue Jun 05 07:52:59 2018 -0400 +++ b/insect_phenology_model.xml Tue Aug 07 12:59:06 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 @@ <param name="young_nymph_accumulation" type="integer" value="0" min="0" label="Adjustment of degree-days accumulation (egg->young nymph)"/> <param name="old_nymph_accumulation" type="integer" value="0" min="0" label="Adjustment of degree-days accumulation (young nymph->old nymph)"/> <param name="adult_accumulation" type="integer" value="0" min="0" label="Adjustment of degree-days accumulation (old nymph->adult)"/> - <conditional name="custom_date_interval_cond"> - <param name="custom_date_interval" type="select" label="Set date interval for plots?" help="Scales the x axis in plots from weeks to days"> - <option value="no" selected="true">No</option> - <option value="yes">Yes</option> - </param> - <when value="no"/> - <when value="yes"> - <param name="start_date" type="text" value="" label="Start date" help="Format must be yyyy-mm-dd"> - <validator type="expression" message="Date must have the format yyyy-mm-dd">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])</validator> - </param> - <param name="end_date" type="text" value="" label="End date" help="Format must be yyyy-mm-dd"> - <validator type="expression" message="Date must have the format yyyy-mm-dd">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])</validator> - </param> - </when> - </conditional> <param name="plot_generations_separately" type="select" label="Plot generations separately?"> <option value="yes" selected="True">Yes</option> <option value="no">No</option>
--- a/test-data/output_combined1.csv Tue Jun 05 07:52:59 2018 -0400 +++ b/test-data/output_combined1.csv Tue Aug 07 12:59:06 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"
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_combined6.csv Tue Aug 07 12:59:06 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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_combined7.csv Tue Aug 07 12:59:06 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
--- a/test-data/output_f1_3.csv Tue Jun 05 07:52:59 2018 -0400 +++ b/test-data/output_f1_3.csv Tue Aug 07 12:59:06 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"
--- a/test-data/output_f1_4.csv Tue Jun 05 07:52:59 2018 -0400 +++ b/test-data/output_f1_4.csv Tue Aug 07 12:59:06 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"
--- a/test-data/output_f2_3.csv Tue Jun 05 07:52:59 2018 -0400 +++ b/test-data/output_f2_3.csv Tue Aug 07 12:59:06 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"
--- a/test-data/output_f2_4.csv Tue Jun 05 07:52:59 2018 -0400 +++ b/test-data/output_f2_4.csv Tue Aug 07 12:59:06 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"
--- a/test-data/output_p_3.csv Tue Jun 05 07:52:59 2018 -0400 +++ b/test-data/output_p_3.csv Tue Aug 07 12:59:06 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"
--- a/test-data/output_p_4.csv Tue Jun 05 07:52:59 2018 -0400 +++ b/test-data/output_p_4.csv Tue Aug 07 12:59:06 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"
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/utils.R Tue Aug 07 12:59:06 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<tick_sep) { + last_saved_month = tick_labels[[length(tick_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=0, append_start_doy_norm=0, date_interval=FALSE) { + # Generate a list of ticks and labels for plotting the x axis. + 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]; + 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); +}