# HG changeset patch
# User greg
# Date 1533661510 14400
# Node ID 1868b79135908d74910188baf7f53af22e85bf14

Uploaded

diff -r 000000000000 -r 1868b7913590 .shed.yml
--- /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
diff -r 000000000000 -r 1868b7913590 extract_ipm_date_interval.R
--- /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);
+    }
+}
+
diff -r 000000000000 -r 1868b7913590 extract_ipm_date_interval.xml
--- /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>
diff -r 000000000000 -r 1868b7913590 utils.R
--- /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);
+}