Mercurial > repos > greg > extract_ipm_date_interval
changeset 0:1868b7913590 draft
Uploaded
| author | greg |
|---|---|
| date | Tue, 07 Aug 2018 13:05:10 -0400 |
| parents | |
| children | 459b422e5df6 |
| files | .shed.yml extract_ipm_date_interval.R extract_ipm_date_interval.xml utils.R |
| diffstat | 4 files changed, 1153 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/.shed.yml Tue Aug 07 13:05:10 2018 -0400 @@ -0,0 +1,13 @@ +name: extract_ipm_date_interval +owner: greg +description: | + Contains a tool that extracts a date interval from the dataset collection produced by the insect_phenology_model tool. +homepage_url: https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/entomology/extract_ipm_date_interval +long_description: | + Contains a tool that extracts a date interval from the (data) dataset collection produced by the insect_phenology_model + tool and zooms into the interval by producing plots with daily ticks on the x axis instead of weekly) tick marks. The + (data) dataset collection consisting of the restricted date interval is also produced. +remote_repository_url: https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/entomology/extract_ipm_date_interval +type: unrestricted +categories: +- Entomology
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/extract_ipm_date_interval.R Tue Aug 07 13:05:10 2018 -0400 @@ -0,0 +1,720 @@ +#!/usr/bin/env Rscript + +suppressPackageStartupMessages(library("data.table")) +suppressPackageStartupMessages(library("hash")) +suppressPackageStartupMessages(library("optparse")) + +option_list <- list( + make_option(c("--input_data_dir"), action="store", dest="input_data_dir", help="Directory containing .csv outputs from insect_phenology_model"), + make_option(c("--end_date"), action="store", dest="end_date", help="End date for date interval"), + make_option(c("--start_date"), action="store", dest="start_date", help="Start date for date interval"), + make_option(c("--script_dir"), action="store", dest="script_dir", help="R script source directory"), + make_option(c("--tool_parameters"), action="store", dest="tool_parameters", help="Users defined parameters for executing the insect_phenology_model inputs") +) + +parser <- OptionParser(usage="%prog [options] file", option_list=option_list); +args <- parse_args(parser, positional_arguments=TRUE); +opt <- args$options; + +get_new_temperature_data_frame = function(input_data_file) { + # Read a csv file to produce a data frame + # consisting of the data which was produced + # by the insect_phenology_model tool. + temperature_data_frame = read.csv(file=input_data_file, header=T, strip.white=TRUE, stringsAsFactors=FALSE, sep=","); + return(temperature_data_frame); +} + +parse_tool_parameters = function(tool_parameters) { + # Parse the tool parameters that were used to produce + # the input datasets found in input_data_dir. These + # datasets were produced by the insect_phenology_model + # tool. + raw_params = sub("^__SeP__", "", tool_parameters); + raw_param_items = strsplit(raw_params, "__SeP__")[[1]]; + keys = raw_param_items[c(T, F)]; + values = raw_param_items[c(F, T)]; + num_keys_and_vals = length(keys); + for (i in 1:num_keys_and_vals) { + values[i] = restore_text(values[[i]]); + } + for (i in 1:num_keys_and_vals) { + key = keys[i]; + if (endsWith(key, "cond")) { + value = values[i]; + # Galaxy passes some input job parameters as json-like strings + # for complex objects like conditionals, so we should see if + # we can re-implement this using r-jsonlite if possible. An + # exception is currently thrown when we do this: + # params_hash = fromJSON(opt$tool_parameters); + # Error: lexical error: invalid char in json text. + # __SeP__adult_mortality__SeP____ + # (right here) ------^ + # Here is an example complex object parameter value, in + # this case the parameter name is plot_nymph_life_stage_cond. + # {"life_stages_nymph": ["Total"], "__current_case__": 0, "plot_nymph_life_stage": "yes"} + # This code is somewhat brittle, so a better approach is + # warranted if possible. + if (key == "merge_ytd_temperature_data_cond") { + val = grep("yes", value); + if (length(val)>0) { + # Get the location. + items = strsplit(value, "\"location\": ")[[1]]; + location_str = items[2]; + val = grep("\",", location_str); + if (length(val)>0) { + items = strsplit(location_str, "\",")[[1]]; + location = items[1]; + } else { + location = items[1]; + } + if (location == "\"") { + location = ""; + } + keys[i] = "location"; + values[i] = location; + } + } else if (key =="plot_nymph_life_stage_cond") { + val = grep("yes", value); + if (length(val)==0) { + keys[i] = "plot_nymph_life_stage"; + values[i] = "no"; + } else { + # Get the value for "life_stages_nymph". + items = strsplit(value, "\"life_stages_nymph\": ")[[1]]; + life_stages_nymph_str = items[2]; + if (grep("],", life_stages_nymph_str)[[1]] > 0) { + items = strsplit(life_stages_nymph_str, "],")[[1]]; + life_stages_nymph_str = items[1]; + #life_stages_nymph_str = sub("^\\[", "", life_stages_nymph_str); + num_curent_keys = length(keys); + keys[num_curent_keys+1] = "life_stages_nymph"; + values[num_curent_keys+1] = life_stages_nymph_str; + } + keys[i] = "plot_nymph_life_stage"; + values[i] = "yes"; + } + } else if (key =="plot_adult_life_stage_cond") { + val = grep("yes", value); + # The value of val is an integer if the pattern is not found. + if (length(val)==0) { + keys[i] = "plot_adult_life_stage"; + values[i] = "no"; + } else { + # Get the value for "life_stages_adult". + items = strsplit(value, "\"life_stages_adult\": ")[[1]]; + life_stages_adult_str = items[2]; + if (grep("],", life_stages_adult_str)[[1]] > 0) { + items = strsplit(life_stages_adult_str, "],")[[1]]; + life_stages_adult_str = items[1]; + #life_stages_adult_str = sub("^\\[", "", life_stages_adult_str); + num_curent_keys = length(keys); + keys[num_curent_keys+1] = "life_stages_adult"; + values[num_curent_keys+1] = life_stages_adult_str; + } + keys[i] = "plot_adult_life_stage"; + values[i] = "yes"; + } + } + } + } + # Strip all double qu0tes from values. + for (i in 1:length(values)) { + value = values[i]; + value = gsub("\"", "", value); + values[i] = value; + } + return(hash(keys, values)); +} + +prepare_plot = function(life_stage, file_path, maxval, ticks, date_labels, chart_type, plot_std_error, insect, location, + latitude, start_date, end_date, total_days_vector, replications, group, group_std_error, group2, group2_std_error, + group3, group3_std_error, sub_life_stage=NULL) { + # Start PDF device driver. + dev.new(width=20, height=30); + pdf(file=file_path, width=20, height=30, bg="white"); + par(mar=c(5, 6, 4, 4), mfrow=c(3, 1)); + render_chart(ticks, date_labels, chart_type, plot_std_error, insect, location, latitude, start_date, end_date, + total_days_vector, maxval, 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, sub_life_stage=sub_life_stage); + # Turn off device driver to flush output. + dev.off(); +} + +restore_text = function(text) { + # Un-escape characters that are escaped by the + # Galaxy tool parameter handlers. + if (is.null(text) || length(text) == 0) { + return(text); + } + chars = list(">", "<", "'", '"', "[", "]", "{", "}", "@", "\n", "\r", "\t", "#"); + mapped_chars = list("__gt__", "__lt__", "__sq__", "__dq__", "__ob__", "__cb__", + "__oc__", "__cc__", "__at__", "__cn__", "__cr__", "__tc__", "__pd__"); + for (i in 1:length(mapped_chars)) { + char = chars[[i]]; + mapped_char = mapped_chars[[i]]; + text = gsub(mapped_char, char, text); + } + return(text); +} + +# Import the shared utility functions. +utils_path <- paste(opt$script_dir, "utils.R", sep="/"); +source(utils_path); + +params_hash = parse_tool_parameters(opt$tool_parameters); + +# Determine the data we need to generate for plotting. +if (params_hash$plot_generations_separately == "yes") { + plot_generations_separately = TRUE; +} else { + plot_generations_separately = FALSE; +} +if (params_hash$plot_std_error == "yes") { + plot_std_error = TRUE; +} else { + plot_std_error = FALSE; +} +process_eggs = FALSE; +process_nymphs = FALSE; +process_young_nymphs = FALSE; +process_old_nymphs = FALSE; +process_total_nymphs = FALSE; +process_adults = FALSE; +process_previttelogenic_adults = FALSE; +process_vittelogenic_adults = FALSE; +process_diapausing_adults = FALSE; +process_total_adults = FALSE; +if (params_hash$plot_egg_life_stage == "yes") { + process_eggs = TRUE; +} +if (params_hash$plot_nymph_life_stage == "yes") { + process_nymphs = TRUE; + # Get the selected life stages. + value = params_hash$life_stages_nymph; + val = grep("Young", value); + if (length(val)>0) { + process_young_nymphs = TRUE; + } + val = grep("Old", value); + if (length(val)>0) { + process_old_nymphs = TRUE; + } + val = grep("Total", value); + if (length(val)>0) { + process_total_nymphs = TRUE; + } +} +if (params_hash$plot_adult_life_stage == "yes") { + process_adults = TRUE; + # Get the selected life stages. + value = params_hash$life_stages_adult; + val = grep("Pre-vittelogenic", value); + if (length(val)>0) { + process_previttelogenic_adults = TRUE; + } + val = grep("Vittelogenic", value); + if (length(val)>0) { + process_vittelogenic_adults = TRUE; + } + val = grep("Diapausing", value); + if (length(val)>0) { + process_diapausing_adults = TRUE; + } + val = grep("Total", value); + if (length(val)>0) { + process_total_adults = TRUE; + } +} + +if (params_hash$plot_egg_life_stage == "yes" & params_hash$plot_nymph_life_stage == "yes" & params_hash$plot_adult_life_stage == "yes") { + process_total = TRUE; +} else { + process_total = FALSE; +} + + +# 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. +start_date = format(opt$start_date); +end_date = format(opt$end_date); + +# Calaculate the number of days in the date interval. +start_date = validate_date(start_date); +# Validate end_date. +end_date = validate_date(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."); +} +# 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"); + +# Create the csv data files consisting of the date interval. +input_data_files = list.files(path=opt$input_data_dir, full.names=TRUE); +for (input_data_file in input_data_files) { + file_name = basename(input_data_file); + temperature_data_frame = get_new_temperature_data_frame(input_data_file); + start_date_row = which(temperature_data_frame$DATE==start_date); + end_date_row = which(temperature_data_frame$DATE==end_date); + # Extract the date interval. + temperature_data_frame = temperature_data_frame[start_date_row:end_date_row,]; + # Save the date interval data into an output file + # named the same as the input. + file_path = paste("output_data_dir", file_name, sep="/"); + write.csv(temperature_data_frame, file=file_path, row.names=F); +} + +# Extract the vectors needed for plots from the input data files +# produced by the insect_phenology_model tool. +total_days_vector = NULL; +ticks_and_labels = NULL; +latitude = NULL; +input_data_files = list.files(path="output_data_dir", full.names=TRUE); +for (input_data_file in input_data_files) { + file_name = basename(input_data_file); + temperature_data_frame = get_new_temperature_data_frame(input_data_file); + # Initialize the total_days_vector for later plotting. + if (is.null(total_days_vector)) { + total_days_vector = c(1:dim(temperature_data_frame)[1]); + } + if (is.null(ticks_and_labels)) { + # Get the ticks date labels for later plotting + ticks_and_labels = get_x_axis_ticks_and_labels(temperature_data_frame, date_interval=TRUE); + ticks = c(unlist(ticks_and_labels[1])); + date_labels = c(unlist(ticks_and_labels[2])); + } + if (is.null(latitude)) { + # Get the latitude for later plotting. + latitude = temperature_data_frame$LATITUDE[1]; + } + + if (file_name == "04_combined_generations.csv") { + if (process_eggs) { + eggs = temperature_data_frame$EGG; + if (plot_std_error) { + eggs.std_error = temperature_data_frame$EGGSE; + } + } + if (process_young_nymphs) { + young_nymphs = temperature_data_frame$YOUNGNYMPH; + if (plot_std_error) { + young_nymphs.std_error = temperature_data_frame$YOUNGNYMPHSE; + } + } + if (process_old_nymphs) { + old_nymphs = temperature_data_frame$OLDNYMPH; + if (plot_std_error) { + old_nymphs.std_error = temperature_data_frame$OLDNYMPHSE; + } + } + if (process_total_nymphs) { + total_nymphs = temperature_data_frame$TOTALNYMPH; + if (plot_std_error) { + total_nymphs.std_error = temperature_data_frame$TOTALNYMPHSE; + } + } + if (process_previttelogenic_adults) { + previttelogenic_adults = temperature_data_frame$PRE.VITADULT; + if (plot_std_error) { + previttelogenic_adults.std_error = temperature_data_frame$PRE.VITADULTSE; + } + } + if (process_vittelogenic_adults) { + vittelogenic_adults = temperature_data_frame$VITADULT; + if (plot_std_error) { + vittelogenic_adults.std_error = temperature_data_frame$VITADULTSE; + } + } + if (process_diapausing_adults) { + diapausing_adults = temperature_data_frame$DIAPAUSINGADULT; + if (plot_std_error) { + diapausing_adults.std_error = temperature_data_frame$DIAPAUSINGADULTSE; + } + } + if (process_total_adults) { + total_adults = temperature_data_frame$TOTALADULT; + if (plot_std_error) { + total_adults.std_error = temperature_data_frame$TOTALADULTSE; + } + } + } else if (file_name == "01_generation_P.csv") { + if (process_eggs) { + P_eggs = temperature_data_frame$EGG.P; + if (plot_std_error) { + P_eggs.std_error = temperature_data_frame$EGG.P.SE; + } + } + if (process_young_nymphs) { + P_young_nymphs = temperature_data_frame$YOUNGNYMPH.P; + if (plot_std_error) { + P_young_nymphs.std_error = temperature_data_frame$YOUNGNYMPH.P.SE; + } + } + if (process_old_nymphs) { + P_old_nymphs = temperature_data_frame$OLDNYMPH.P; + if (plot_std_error) { + P_old_nymphs.std_error = temperature_data_frame$OLDNYMPH.P.SE; + } + } + if (process_total_nymphs) { + P_total_nymphs = temperature_data_frame$TOTALNYMPH.P; + if (plot_std_error) { + P_total_nymphs.std_error = temperature_data_frame$TOTALNYMPH.P.SE; + } + } + if (process_previttelogenic_adults) { + P_previttelogenic_adults = temperature_data_frame$PRE.VITADULT.P; + if (plot_std_error) { + P_previttelogenic_adults.std_error = temperature_data_frame$PRE.VITADULT.P.SE; + } + } + if (process_vittelogenic_adults) { + P_vittelogenic_adults = temperature_data_frame$VITADULT.P; + if (plot_std_error) { + P_vittelogenic_adults.std_error = temperature_data_frame$VITADULT.P.SE; + } + } + if (process_diapausing_adults) { + P_diapausing_adults = temperature_data_frame$DIAPAUSINGADULT.P; + if (plot_std_error) { + P_diapausing_adults.std_error = temperature_data_frame$DIAPAUSINGADULT.P.SE; + } + } + if (process_total_adults) { + P_total_adults = temperature_data_frame$TOTALADULT.P; + if (plot_std_error) { + P_total_adults.std_error = temperature_data_frame$TOTALADULT.P.SE; + } + } + } else if (file_name == "02_generation_F1.csv") { + if (process_eggs) { + F1_eggs = temperature_data_frame$EGG.F1; + if (plot_std_error) { + F1_eggs.std_error = temperature_data_frame$EGG.F1.SE; + } + } + if (process_young_nymphs) { + F1_young_nymphs = temperature_data_frame$YOUNGNYMPH.F1; + if (plot_std_error) { + F1_young_nymphs.std_error = temperature_data_frame$YOUNGNYMPH.F1.SE; + } + } + if (process_old_nymphs) { + F1_old_nymphs = temperature_data_frame$OLDNYMPH.F1; + if (plot_std_error) { + F1_old_nymphs.std_error = temperature_data_frame$OLDNYMPH.F1.SE; + } + } + if (process_total_nymphs) { + F1_total_nymphs = temperature_data_frame$TOTALNYMPH.F1; + if (plot_std_error) { + F1_total_nymphs.std_error = temperature_data_frame$TOTALNYMPH.F1.SE; + } + } + if (process_previttelogenic_adults) { + F1_previttelogenic_adults = temperature_data_frame$PRE.VITADULT.F1; + if (plot_std_error) { + F1_previttelogenic_adults.std_error = temperature_data_frame$PRE.VITADULT.F1.SE; + } + } + if (process_vittelogenic_adults) { + F1_vittelogenic_adults = temperature_data_frame$VITADULT.F1; + if (plot_std_error) { + F1_vittelogenic_adults.std_error = temperature_data_frame$VITADULT.F1.SE; + } + } + if (process_diapausing_adults) { + F1_diapausing_adults = temperature_data_frame$DIAPAUSINGADULT.F1; + if (plot_std_error) { + F1_diapausing_adults.std_error = temperature_data_frame$DIAPAUSINGADULT.F1.SE; + } + } + if (process_total_adults) { + F1_total_adults = temperature_data_frame$TOTALADULT.F1; + if (plot_std_error) { + F1_total_adults.std_error = temperature_data_frame$TOTALADULT.F1.SE; + } + } + } else if (file_name == "03_generation_F2.csv") { + if (process_eggs) { + F2_eggs = temperature_data_frame$EGG.F2; + if (plot_std_error) { + F2_eggs.std_error = temperature_data_frame$EGG.F2.SE; + } + } + if (process_young_nymphs) { + F2_young_nymphs = temperature_data_frame$YOUNGNYMPH.F2; + if (plot_std_error) { + F2_young_nymphs.std_error = temperature_data_frame$YOUNGNYMPH.F2.SE; + } + } + if (process_old_nymphs) { + F2_old_nymphs = temperature_data_frame$OLDNYMPH.F2; + if (plot_std_error) { + F2_old_nymphs.std_error = temperature_data_frame$OLDNYMPH.F2.SE; + } + } + if (process_total_nymphs) { + F2_total_nymphs = temperature_data_frame$TOTALNYMPH.F2; + if (plot_std_error) { + F2_total_nymphs.std_error = temperature_data_frame$TOTALNYMPH.F2.SE; + } + } + if (process_previttelogenic_adults) { + F2_previttelogenic_adults = temperature_data_frame$PRE.VITADULT.F2; + if (plot_std_error) { + F2_previttelogenic_adults.std_error = temperature_data_frame$PRE.VITADULT.F2.SE; + } + } + if (process_vittelogenic_adults) { + F2_vittelogenic_adults = temperature_data_frame$VITADULT.F2; + if (plot_std_error) { + F2_vittelogenic_adults.std_error = temperature_data_frame$VITADULT.F2.SE; + } + } + if (process_diapausing_adults) { + F2_diapausing_adults = temperature_data_frame$DIAPAUSINGADULT.F2; + if (plot_std_error) { + F2_diapausing_adults.std_error = temperature_data_frame$DIAPAUSINGADULT.F2.SE; + } + } + if (process_total_adults) { + F2_total_adults = temperature_data_frame$TOTALADULT.F2; + if (plot_std_error) { + F2_total_adults.std_error = temperature_data_frame$TOTALADULT.F2.SE; + } + } + } +} + +# Create the pdf plot files based on the date interval. +if (plot_generations_separately) { + chart_type = "pop_size_by_generation"; + if (process_eggs) { + # Total population size by generation. + life_stage = "Egg"; + file_path = get_file_path(life_stage, "egg_pop_by_generation.pdf") + maxval = max(P_eggs+F1_eggs+F2_eggs) + 100; + prepare_plot(life_stage, file_path, maxval, ticks, date_labels, chart_type, params_hash$plot_std_error, + params_hash$insect, params_hash$location, latitude, start_date, end_date, total_days_vector, + params_hash$replications, group=P_eggs, group_std_error=P_eggs.std_error, group2=F1_eggs, + group2_std_error=F1_eggs.std_error, group3=F2_eggs, group3_std_error=F2_eggs.std_error); + } + if (process_nymphs) { + life_stage = "Nymph"; + if (process_young_nymphs) { + # Young nymph population size by generation. + sub_life_stage = "Young"; + file_path = get_file_path(life_stage, "nymph_pop_by_generation.pdf", sub_life_stage=sub_life_stage) + maxval = max(P_young_nymphs+F1_young_nymphs+F2_young_nymphs) + 100; + prepare_plot(life_stage, file_path, maxval, ticks, date_labels, chart_type, params_hash$plot_std_error, + params_hash$insect, params_hash$location, latitude, start_date, end_date, total_days_vector, + params_hash$replications, group=P_young_nymphs, group_std_error=P_young_nymphs.std_error, + group2=F1_young_nymphs, group2_std_error=F1_young_nymphs.std_error, group3=F2_young_nymphs, + group3_std_error=F2_young_nymphs.std_error, sub_life_stage=sub_life_stage); + } + if (process_old_nymphs) { + # Old nymph population size by generation. + sub_life_stage = "Old"; + file_path = get_file_path(life_stage, "nymph_pop_by_generation.pdf", sub_life_stage=sub_life_stage) + maxval = max(P_old_nymphs+F1_old_nymphs+F2_old_nymphs) + 100; + prepare_plot(life_stage, file_path, maxval, ticks, date_labels, chart_type, params_hash$plot_std_error, + params_hash$insect, params_hash$location, latitude, start_date, end_date, total_days_vector, + params_hash$replications, group=P_old_nymphs, group_std_error=P_old_nymphs.std_error, + group2=F1_old_nymphs, group2_std_error=F1_old_nymphs.std_error, group3=F2_old_nymphs, + group3_std_error=F2_old_nymphs.std_error, sub_life_stage=sub_life_stage); + } + if (process_total_nymphs) { + # Total nymph population size by generation. + sub_life_stage = "Total"; + file_path = get_file_path(life_stage, "nymph_pop_by_generation.pdf", sub_life_stage=sub_life_stage) + maxval = max(P_total_nymphs+F1_total_nymphs+F2_total_nymphs) + 100; + prepare_plot(life_stage, file_path, maxval, ticks, date_labels, chart_type, params_hash$plot_std_error, + params_hash$insect, params_hash$location, latitude, start_date, end_date, total_days_vector, + params_hash$replications, group=P_total_nymphs, group_std_error=P_total_nymphs.std_error, + group2=F1_total_nymphs, group2_std_error=F1_total_nymphs.std_error, group3=F2_total_nymphs, + group3_std_error=F2_total_nymphs.std_error, sub_life_stage=sub_life_stage); + } + } + if (process_adults) { + life_stage = "Adult"; + if (process_previttelogenic_adults) { + # Pre-vittelogenic adult population size by generation. + sub_life_stage = "Pre-vittelogenic"; + file_path = get_file_path(life_stage, "adult_pop_by_generation.pdf", sub_life_stage=sub_life_stage) + maxval = max(P_previttelogenic_adults+F1_previttelogenic_adults+F2_previttelogenic_adults) + 100; + prepare_plot(life_stage, file_path, maxval, ticks, date_labels, chart_type, params_hash$plot_std_error, + params_hash$insect, params_hash$location, latitude, start_date, end_date, total_days_vector, + params_hash$replications, group=P_previttelogenic_adults, + group_std_error=P_previttelogenic_adults.std_error, group2=F1_previttelogenic_adults, + group2_std_error=F1_previttelogenic_adults.std_error, group3=F2_previttelogenic_adults, + group3_std_error=F2_previttelogenic_adults.std_error, sub_life_stage=sub_life_stage); + } + if (process_vittelogenic_adults) { + # Vittelogenic adult population size by generation. + sub_life_stage = "Vittelogenic"; + file_path = get_file_path(life_stage, "adult_pop_by_generation.pdf", sub_life_stage=sub_life_stage) + maxval = max(P_vittelogenic_adults+F1_vittelogenic_adults+F2_vittelogenic_adults) + 100; + prepare_plot(life_stage, file_path, maxval, ticks, date_labels, chart_type, params_hash$plot_std_error, + params_hash$insect, params_hash$location, latitude, start_date, end_date, total_days_vector, + params_hash$replications, group=P_vittelogenic_adults, + group_std_error=P_vittelogenic_adults.std_error, group2=F1_vittelogenic_adults, + group2_std_error=F1_vittelogenic_adults.std_error, group3=F2_vittelogenic_adults, + group3_std_error=F2_vittelogenic_adults.std_error, sub_life_stage=sub_life_stage); + } + if (process_diapausing_adults) { + # Diapausing adult population size by generation. + sub_life_stage = "Diapausing"; + file_path = get_file_path(life_stage, "adult_pop_by_generation.pdf", sub_life_stage=sub_life_stage) + maxval = max(P_diapausing_adults+F1_diapausing_adults+F2_diapausing_adults) + 100; + prepare_plot(life_stage, file_path, maxval, ticks, date_labels, chart_type, params_hash$plot_std_error, + params_hash$insect, params_hash$location, latitude, start_date, end_date, total_days_vector, + params_hash$replications, group=P_diapausing_adults, group_std_error=P_diapausing_adults.std_error, + group2=F1_diapausing_adults, group2_std_error=F1_diapausing_adults.std_error, group3=F2_diapausing_adults, + group3_std_error=F2_diapausing_adults.std_error, sub_life_stage=sub_life_stage); + } + if (process_total_adults) { + # Total adult population size by generation. + sub_life_stage = "Total"; + file_path = get_file_path(life_stage, "adult_pop_by_generation.pdf", sub_life_stage=sub_life_stage) + maxval = max(P_total_adults+F1_total_adults+F2_total_adults) + 100; + prepare_plot(life_stage, file_path, maxval, ticks, date_labels, chart_type, params_hash$plot_std_error, + params_hash$insect, params_hash$location, latitude, start_date, end_date, total_days_vector, + params_hash$replications, group=P_total_adults, group_std_error=P_total_adults.std_error, + group2=F1_total_adults, group2_std_error=F1_total_adults.std_error, group3=F2_total_adults, + group3_std_error=F2_total_adults.std_error, sub_life_stage=sub_life_stage); + } + } + if (process_total) { + life_stage = "Total"; + # Total population size for egg, nymph and adult by generation. + file_path = get_file_path(life_stage, "total_pop_by_generation.pdf") + maxval = max(total_adults+eggs+total_nymphs) + 100; + # P == total_adults + # P.std_error == total_adults.std_error + # F1 == eggs + # F1.std_error == eggs.std_error + # F2 == ??? + # F2.std_error == ??? + # FIXME: testing demonstrates that P and F1 are properly assigned + # above, but F2 cannot be determined. F2 should undoubtedly be + # total_nymphs, but the data is not the same bewteen the output + # from the insect_phenology_model tool and the date interval from + # this tool. We won't plot the total until we get time to figure + # this out. + #prepare_plot(life_stage, file_path, maxval, ticks, date_labels, chart_type, params_hash$plot_std_error, + # params_hash$insect, params_hash$location, latitude, start_date, end_date, total_days_vector, + # params_hash$replications, group=total_adults, group_std_error=total_adults.std_error, group2=eggs, + # group2_std_error=eggs.std_error, group3=total_nymphs, group3_std_error=total_nymphs.std_error); + } +} else { + chart_type = "pop_size_by_life_stage"; + if (process_eggs) { + # Egg population size. + life_stage = "Egg"; + file_path = get_file_path(life_stage, "egg_pop.pdf") + maxval = max(eggs+eggs.std_error) + 100; + prepare_plot(life_stage, file_path, maxval, ticks, date_labels, chart_type, params_hash$plot_std_error, + params_hash$insect, params_hash$location, latitude, start_date, end_date, total_days_vector, + params_hash$replications, group=eggs, group_std_error=eggs.std_error); + } + if (process_nymphs) { + life_stage = "Nymph"; + if (process_young_nymphs) { + # Young nymph population size. + sub_life_stage = "Young"; + file_path = get_file_path(life_stage, "nymph_pop.pdf", sub_life_stage=sub_life_stage) + maxval = max(young_nymphs+young_nymphs.std_error) + 100; + prepare_plot(life_stage, file_path, maxval, ticks, date_labels, chart_type, params_hash$plot_std_error, + params_hash$insect, params_hash$location, latitude, start_date, end_date, total_days_vector, + params_hash$replications, group=young_nymphs, group_std_error=young_nymphs.std_error, + sub_life_stage=sub_life_stage); + } + if (process_old_nymphs) { + # Old nymph population size. + sub_life_stage = "Old"; + file_path = get_file_path(life_stage, "nymph_pop.pdf", sub_life_stage=sub_life_stage) + maxval = max(old_nymphs+old_nymphs.std_error) + 100; + prepare_plot(life_stage, file_path, maxval, ticks, date_labels, chart_type, params_hash$plot_std_error, + params_hash$insect, params_hash$location, latitude, start_date, end_date, total_days_vector, + params_hash$replications, group=old_nymphs, group_std_error=old_nymphs.std_error, + sub_life_stage=sub_life_stage); + } + if (process_total_nymphs) { + # Total nymph population size. + sub_life_stage = "Total"; + file_path = get_file_path(life_stage, "nymph_pop.pdf", sub_life_stage=sub_life_stage) + maxval = max(total_nymphs+total_nymphs.std_error) + 100; + prepare_plot(life_stage, file_path, maxval, ticks, date_labels, chart_type, params_hash$plot_std_error, + params_hash$insect, params_hash$location, latitude, start_date, end_date, total_days_vector, + params_hash$replications, group=total_nymphs, group_std_error=total_nymphs.std_error, + sub_life_stage=sub_life_stage); + } + } + if (process_adults) { + life_stage = "Adult"; + if (process_previttelogenic_adults) { + # Pre-vittelogenic adult population size. + sub_life_stage = "Pre-vittelogenic"; + file_path = get_file_path(life_stage, "adult_pop.pdf", sub_life_stage=sub_life_stage) + maxval = max(previttelogenic_adults+previttelogenic_adults.std_error) + 100; + prepare_plot(life_stage, file_path, maxval, ticks, date_labels, chart_type, params_hash$plot_std_error, + params_hash$insect, params_hash$location, latitude, start_date, end_date, total_days_vector, + params_hash$replications, group=previttelogenic_adults, + group_std_error=previttelogenic_adults.std_error, sub_life_stage=sub_life_stage); + } + if (process_vittelogenic_adults) { + # Vittelogenic adult population size. + sub_life_stage = "Vittelogenic"; + file_path = get_file_path(life_stage, "adult_pop.pdf", sub_life_stage=sub_life_stage) + maxval = max(vittelogenic_adults+vittelogenic_adults.std_error) + 100; + prepare_plot(life_stage, file_path, maxval, ticks, date_labels, chart_type, params_hash$plot_std_error, + params_hash$insect, params_hash$location, latitude, start_date, end_date, total_days_vector, + params_hash$replications, group=vittelogenic_adults, + group_std_error=vittelogenic_adults.std_error, sub_life_stage=sub_life_stage); + } + if (process_diapausing_adults) { + # Diapausing adult population size. + sub_life_stage = "Diapausing"; + file_path = get_file_path(life_stage, "adult_pop.pdf", sub_life_stage=sub_life_stage) + maxval = max(diapausing_adults+diapausing_adults.std_error) + 100; + prepare_plot(life_stage, file_path, maxval, ticks, date_labels, chart_type, params_hash$plot_std_error, + params_hash$insect, params_hash$location, latitude, start_date, end_date, total_days_vector, + params_hash$replications, group=diapausing_adults, group_std_error=diapausing_adults.std_error, + sub_life_stage=sub_life_stage); + } + if (process_total_adults) { + # Total adult population size. + sub_life_stage = "Total"; + file_path = get_file_path(life_stage, "adult_pop.pdf", sub_life_stage=sub_life_stage) + maxval = max(total_adults+total_adults.std_error) + 100; + prepare_plot(life_stage, file_path, maxval, ticks, date_labels, chart_type, params_hash$plot_std_error, + params_hash$insect, params_hash$location, latitude, start_date, end_date, total_days_vector, + params_hash$replications, group=total_adults, group_std_error=total_adults.std_error, + sub_life_stage=sub_life_stage); + } + } + if (process_total) { + # Total population size. + life_stage = "Total"; + file_path = get_file_path(life_stage, "total_pop.pdf") + maxval = max(eggs+eggs.std_error, total_nymphs+total_nymphs.std_error, total_adults+total_adults.std_error) + 100; + prepare_plot(life_stage, file_path, maxval, ticks, date_labels, chart_type, params_hash$plot_std_error, + params_hash$insect, params_hash$location, latitude, start_date, end_date, total_days_vector, + params_hash$replications, group=total_adults, group_std_error=total_adults.std_error, + group2=total_nymphs, group2_std_error=total_nymphs.std_error, group3=eggs, group3_std_error=eggs.std_error); + } +} +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/extract_ipm_date_interval.xml Tue Aug 07 13:05:10 2018 -0400 @@ -0,0 +1,103 @@ +<tool id="ipm_date_interval" name="Extract date interval" version="1.1.0"> + <description>from insect phenology model data</description> + <requirements> + <requirement type="package" version="1.10.4">r-data.table</requirement> + <requirement type="package" version="2.2.6">r-hash</requirement> + <requirement type="package" version="1.4.4">r-optparse</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ +#import os +#set input_data_dir = 'input_data_dir' +#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 job = $input_data[0].creating_job +#set tool_parameters = "" +#for $p in $job.parameters: + #set tool_parameters = $tool_parameters + "__SeP__" + $p.name + #set tool_parameters = $tool_parameters + "__SeP__" + $p.value +#end for +mkdir $input_data_dir && +mkdir output_data_dir && +mkdir output_plots_dir && +#for $i in $input_data: + #set filename = $i.file_name + #set name = $i.name + ln -s $filename $input_data_dir/$name && +#end for +Rscript '$__tool_directory__/extract_ipm_date_interval.R' +--end_date '$end_date' +--input_data_dir '$input_data_dir' +--script_dir '$__tool_directory__' +--start_date '$start_date' +--tool_parameters '$tool_parameters' +&>eipmdi_log.txt; +if [[ $? -ne 0 ]]; then + cp eipmdi_log.txt '$error_file'; + exit 1; +fi]]></command> + <inputs> + <param name="input_data" type="data_collection" format="csv" collection_type="list" label="Insect phenology model data files" /> + <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> + </inputs> + <outputs> + <collection name="output_data_collection" type="list" label="${tool.name} (data), on ${on_string}"> + <discover_datasets pattern="__name__" directory="output_data_dir" format="csv"/> + </collection> + <collection name="output_plot_collection" type="list" label="${tool.name} (plots), on ${on_string}"> + <discover_datasets pattern="__name__" directory="output_plots_dir" format="pdf"/> + </collection> + </outputs> + <tests> + <test> + <!-- + FIXME: Here is a sort of layout for a test, but since the input collection will be uploaded, the test + will fail bacused the job parameters for the inputs will not be those produced by the insect_phenology_model + tool. Testing this tool will require using the workflow testing approach. + <param name="input_data"> + <collection type="list"> + <element name="input_p_1.csv" value="input_p_1.csv" ftype="csv"/> + <element name="input_f1_1.csv" value="input_f1_1.csv" ftype="csv"/> + <element name="input_f2_1.csv" value="input_f2_1.csv" ftype="csv"/> + <element name="input_combined1.csv" value="input_combined1.csv" ftype="csv"/> + </collection> + </param> + <param name="start_date" value="2017-04-01"/> + <param name="end_date" value="2017-04-15"/> + <output_collection name="output_data_collection" type="list"> + <element name="01_generation_P.csv" file="output_p_1.csv" ftype="csv" compare="contains"/> + <element name="02_generation_F1.csv" file="output_f1_1.csv" ftype="csv" compare="contains"/> + <element name="03_generation_F2.csv" file="output_f2_1.csv" ftype="csv" compare="contains"/> + <element name="04_combined_generations.csv" file="output_combined1.csv" ftype="csv" compare="contains"/> + </output_collection> + <output_collection name="output_plot_collection" type="list"> + <element name="01_egg_pop_by_generation.pdf" file="plot.pdf" ftype="pdf" compare="contains"/> + <element name="04_total_nymph_pop_by_generation.pdf" file="plot.pdf" ftype="pdf" compare="contains"/> + <element name="08_total_adult_pop_by_generation.pdf" file="plot.pdf" ftype="pdf" compare="contains"/> + <element name="09_total_pop_by_generation.pdf" file="plot.pdf" ftype="pdf" compare="contains"/> + </output_collection> + --> + </test> + </tests> + <help> +**What it does** + +Provides an agent-based stochastic model expressing stage-specific phenology and population dynamics for an insect species across geographic regions. + +----- + +**Required options** + + * **Plot standard error** - add standard error lines to plot. + </help> + <citations> + <citation type="doi">10.3389/fphys.2016.00165</citation> + <citation type="doi">10.1175/JTECH-D-11-00103.1</citation> + <citation type="doi">10.7289/V5D21VHZ</citation> + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/utils.R Tue Aug 07 13:05:10 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); +}