November 9, 2005

 

 

 

 

 

 

Data Analysis and Visualization Engine (DAVE) User’s Guide

ICF Subcontract number: 23BL00150

 

 

 

 

Prepared for:

 

ICF Consulting

3200 NC-54 East, Suite 101

P.O. Box 14348

Research Triangle Park, NC 27709

 

 

Prepared by:

 

Alison Eyth and Prashant Pai

            Carolina Environmental Program

            University of North Carolina at Chapel Hill

            Bank of America Plaza, CB# 6116

            Chapel Hill, NC 27599-6116

 

 

 

 


 


Contents

1... Introduction. 1

2... Starting DAVE and Selecting a Database. 2

3... Exporting Databases from DAVE. 4

4... Analyzing Databases with DAVE. 5

5... Creating Tables. 10

6... Creating Plots. 16

 

 


1.        Introduction

 

The U.S. EPA’s Total Risk Integrated Methodology (TRIM)[1] provides a modeling system for assessing the human health and ecological risks associated with exposures to air pollutants.  It provides capabilities to model the fate of multiple pollutants through different media types and exposure by multiple pathways.  The Carolina Environmental Program (CEP) at the University of North Carolina at Chapel Hill is working to integrate TRIM within EPA’s Multimedia Integrated Modeling System (MIMS) framework[2].  As part of this integration, CEP has designed a data analysis tool for visualizing output data from TRIM.

 

The Data Analysis and Visualization Engine (DAVE) is designed to create plots and tables using data contained in relational databases that are generated by TRIM modules.  Such databases are currently stored using MySQL, as opposed to the ASCII files that are also output from some modules.  DAVE can also be used to export the data into delimited text files for import into other analysis programs.  DAVE has customized windows with content that varies based on the type of database being analyzed.  The software currently reads the following database types:

 

·        Ecological Risk

·        Human Inhalation Exposure

·        Human Health Risk

·        Human Health Risk Metrics

 

Each database type has a unique configuration.  The Human Inhalation Exposure, Human Health Risk, and Human Health Risk Metrics databases can be based on data generated using either of two methods: TRIM.ExpoInhalation (also known as APEX) or the Hazardous Air Pollutant Exposure Model (HAPEM) [3].  Once data of interest in the databases is selected using DAVE, it is passed to the MIMS Analysis Engine for further analysis in the form of plots and tables.  The MIMS Analysis Engine provides functionality to support the needs of its user community and can be further customized in the future.  See the documentation of the MIMS Analysis Engine in the docs folder of the TRIM installation for further guidance on using the features of the Analysis Engine.


2.        Starting DAVE and Selecting a Database


DAVE can be accessed through one of two methods: (1) from within a MIMS scenario, or (2) as a stand-alone program.   A file called rundave.bat is provided as part of the TRIM installation package to assist you with running DAVE as a stand-alone program.  This batch file contains references to the Java files needed to run DAVE.  If TRIM has been installed through the installer, a shortcut to rundave.bat is added to the current user’s Start menu on Windows.  Simply click Start, and then choose All Programs, TRIM, and DAVE.  This should start DAVE if the TRIM installation was done properly.

 

If you have problems starting DAVE from All Programs and need to locate the file rundave.bat, use My Computer or the Windows explorer to browse to the “bat” folder contained in your TRIM installation folder.  To execute the batch file, double-click on the rundave.bat icon.  If you still have problems, check the settings in the trimvars.bat file in the same directory and make sure they are correct for your computer.  [Note: If you expect to run DAVE frequently, you can create a shortcut on your desktop by right-clicking on the icon and choosing Create Shortcut from the pop-up menu that appears.  After the shortcut appears, you can drag it onto your desktop and from there you can rename it, if desired.]

 

After starting DAVE, a DAVE Database Selector window appears (Figure 1).  The table in the window is populated with a list of databases that are located in the data directory of your MySQL installation (e.g., C:\mysql\data).[4]

Figure 1: DAVE Database Selector window.

Only the databases that exist on your computer and can be analyzed by DAVE are listed in the table.  Therefore, you may have more databases in your MySQL data directory than the ones shown in the DAVE Database Selector window.  Each database is of a particular database type: Ecological Risk, Human Inhalation Exposure, Human Health Risk, or Human Health Risk Metrics.  As noted earlier, the Human Inhalation Exposure, Human Health Risk, and Human Health Risk Metrics databases can be generated using either TRIM.ExpoInhalation or HAPEM; the database structure differs depending on which model was used to create it.  Within DAVE, the databases generated using the current version of HAPEM are followed by “(HAPEM5),” and databases generated by the default TRIM.ExpoInhalation processor are annotated by the relevant TRIM.ExpoInhalation version (e.g. APEX3.3).  DAVE also supports analysis of inhalation exposure databases created with the previous version of HAPEM, HAPEM4, although risk databases generated with HAPEM4 are not supported.

 

If you started DAVE from a MIMS scenario, one of the databases may already be selected for you.  In this case, the selected database will be highlighted in light blue.  If no database is selected, or if you want to choose a different database, click on the database you wish to analyze or export.  You may first want to narrow down the list of databases by selecting a type from the “Database Type” pull-down menu.  The list will then show only databases of the chosen type (e.g., “Ecological Risk” database names). 

 

There is an “Available Metrics” pull-down menu below the table of databases.  This will be enabled only if the database you have selected is a Human Health Risk Metrics database.  The menu lists the metrics that are available in the selected database (e.g. Annualized Cancer Risk, Annualized Non-cancer Hazard Quotient, Population-weighted Hazard Frequency Distribution).  If you are analyzing a database of this type, choose the metric to analyze or export.

 

DAVE has two primary and separate functions that can be performed on databases: analyze and export.  The analyze function allows you to see what is in a database and to select data to present in plots or tables.  The export function is used to export data from a database into a workable format that can be used by programs other than MySQL and DAVE.  Each of the database types recognized by DAVE has a different structure.  The analysis and export functions automatically adjust to accommodate the differences in structure.  If you click on the “Analyze” button, the database selected in the table will be loaded into the DAVE Analysis window.  If you click on the “Export” button, DAVE will bring up a dialog that allows you to choose a delimiter for the data and the location in which to place the exported file; for some types of databases, you can also choose the parts of the database to export.  Note that the export function is not supported for Human Inhalation Exposure (APEX and HAPEM) database types at the time of the initial release.

 

Aside from Analyze and Export, three other buttons are available on the Database Selector window:

 

·      Clicking on the “Help” button brings up a window that shows the DAVE User Guide.

·      The “About DAVE…” button brings up a dialog that shows the version of DAVE you are running.

·      The “Exit” button causes DAVE to close.

3.        Exporting Databases from DAVE

 

The export feature in DAVE allows you to export data into a delimited file for use within other programs (e.g., Microsoft Excel or Notepad).  After you click on the “Export” button, DAVE will check the type of the selected database against the list of types that can be exported.  If the database is a Human Inhalation Exposure database (APEX or HAPEM), which cannot currently be exported, an error message will appear.  For all other database types,  an Export Database window will appear.  An example is shown in Figure 2.  This window allows you to specify the delimiter to be used to separate the values in the output file, and the name of the output file that will contain the exported data.  You can either type the path and file name directly into the “Output File” text field or create it by clicking on the “Browse” button, navigating to the desired directory, and typing in a name for the new file.   [Note: If you want to limit the files shown in the browser to those with a certain extension, you can type an entry containing a wildcard (for example, “*.txt”) into the “File Name” text field, then press “Enter” on the keyboard.]  After you have finished typing your file name into the “File Name” text field, click on “Accept” to return to the Export Database window.

Figure 2: DAVE Export Database dialog.

By default, DAVE will create a “comma separated value,” or .csv file.  If you choose a delimiter other than a comma, we recommend that you give the file an extension of .txt.  DAVE will not automatically give the file an extension, so you need to include an extension as part of the name you create.  After you are satisfied with the name showing in the “Output File” text field in the Export Database window, click on “OK.”  If the data are exported successfully, a dialog will appear that informs you of this and reminds you where the data are stored.  If the database cannot be exported as requested, an appropriate error dialog will appear.  Note that some types of databases contain data for multiple variables.  For example, Human Health Risk databases contain data for both cancer risk and non-cancer hazard quotients.  However, only one type of data can be exported at a time.  In these situations, there is an additional “Export options” pull-down menu from which you can choose the type of data to export.

4.        Analyzing Databases with DAVE

 

Clicking on the “Analyze” button from the Database Selector window allows you to analyze the chosen database by creating tables and plots that show subsets of the data.  [Note that the “Analyze” button is “clicked on” automatically if you double-click on a database in the Database Selector window.  Also note that default buttons in all of the windows are indicated by the thicker border around them].  The “Analyze” button is disabled for certain “Available Metrics” in the Risk Metrics databases that cannot be analyzed with this feature currently[5].    

 

The remaining sections of this manual explain the various aspects of the analysis function.  Once you have chosen to analyze a particular database, DAVE brings up an Analysis window similar to the one shown in Figure 3.  Each database type has a different set of variables displayed in this window; Figure 3 is an example based on the Human Health Risk (HAPEM5) database type.

 

The Analysis window consists of several parts:

·        At the top are the database type and description.  Descriptions are available for some types of databases, such as human health risk metrics; in this case the description would provide some information about the metric being analyzed.

·        The next section of the window addresses the dependent variables in the database.  The dependent variables are those for which there are values stored in the database.  These are the values that will be shown on any plots and tables that are created.  There can be more than one dependent variable in a database.  For example, the Human Health Risk databases contain two dependent variables: cancer risk and non-cancer hazard quotient.

·        The middle portion of the Analysis window shows the independent variables available in the database.  Independent variables are variables for which different values of the dependent variables exist.  The number of options available for the independent and dependent variables are shown in parentheses next to the variable names.  For example, Figure 3 shows that in this example database there are six different source types and 18030 people with cancer risk values.  Additional cancer risk values could be stored for multiple chemicals, start years, and counties (the remaining three independent variables), but in this database all the data are for the same chemical, start year, and county.

·        Lists of the available types of plots and tables are shown in the lower portion of the window.  More information on these analysis products is given later in the document.  A directory in which to place the analysis products can be specified at the bottom of the window, either by typing in the “Directory for output files” text field or by using the “Browse” button to find a directory.

Figure 3: Example DAVE Analysis window.

To create tables and/or plots, you must first specify the independent and dependent variables DAVE should use to subset the data so that only the data of interest are displayed in the plot or table.  Table 1 lists all of the variables for each of the database types.  The dependent variables are those for which values will be plotted or shown in tables (e.g., cancer risk, hazard quotient[6]); the independent variables (e.g., chemical, start year) are the qualifying parameters whose values are used to select the appropriate value of the dependent variable from the database.  For example, each hazard quotient value in an ecological risk database is for a specific ecological benchmark, chemical, receptor, volume element, and time.

Table 1: Dependent and independent variables for each database type.

Database Type

Dependent Variables

Independent Variables

Ecological risk

Ecological risk (e.g., hazard quotient)

Ecological benchmarks, chemicals, ecological receptors, volume elements, times

Human health risk (APEX 3.3)

Human health endpoints (e.g., cancer risk, non-cancer hazard quotient)

Chemicals, persons, start years, source types, facilities

Human health risk (HAPEM5)

Human health endpoints (e.g., cancer risk, non-cancer hazard quotient)

Chemicals, persons, start years, source types, counties

Human health risk metrics (APEX3.3)

Specific to the metric that is being analyzed

Metric specific (more detail will be provided in a later version of this manual)

Human health risk metrics (HAPEM5)

Specific to the metric that is being analyzed

Metric specific (more detail will be provided in a later version of this manual)

Human inhalation exposure (APEX3.3)

Exposure or dose (e.g., average dose, average exposure, maximum dose, maximum exposure)

Chemicals, persons, date ranges, source types, facilities, study areas

Human inhalation exposure (HAPEM5)

Exposure or dose (e.g., average exposure)

Chemicals, persons, counties, source types

Human inhalation exposure (HAPEM4)

Exposure or dose (e.g., average exposure)

Chemicals, demographic groups, home sectors, replicates

 

As noted above, after each variable name in the Analysis window is a number in parentheses.  This indicates the number of possible values that you can choose from for a given variable.  Some of the variables have only one possible value; for example, in the ecological risk database example, the dependent variable can be only hazard quotient.  Other variables have multiple possible values, ranging from two values to thousands of values.  If there is just one possible value, the “Selected Values” text field beside the variable name will already contain that value, and the “Choose” button will be grayed out.  If there is more than one possible value, you use the “Choose” button to select what value you want to use in generating plots or tables.

 

When you click on “Choose” for a given variable, a Select Values window opens.  It contains a list of all the possible values for that variable.  At this point the procedure for dependent and independent variables is slightly different.

 

  • For dependent variables, you can work with only one value at a time in the plots and tables.  Highlight the value you want and then click on “OK” (or simply hit return).  The value you highlighted will then show up in the “Selected Values” text field beside the name of the variable in the Analysis window.
  • For independent variables, the Select Values window includes a “Choose” pull-down menu above the list of possible values.  This menu contains the following choices (Sorted Values also available).

 

·        One – Allows you to select one value for the variable (e.g., for an ecological risk database, benzo(a)pyrene as the chemical, or 1987-01-03 00:00:00 as the time).

·        All – This will cause DAVE to provide values of the dependent variable for every value of the independent variable.  For example, for an ecological risk database, if you select “All” for Chemicals, there will be one hazard quotient value for each chemical in the database (e.g., benzo(a)pyrene, divalent mercury, and methylmercury).

·        One for each – DAVE will create a table or plot for each value of the selected independent variable (e.g., a table/plot for each chemical or for each year).

·        Maximum – DAVE will determine the maximum value for the dependent variable across all of the values for the given independent variable (e.g., when using a human health risk database and using Cancer Risk as the dependent variable, selecting Maximum for the Persons independent variable will cause DAVE to search through all the cancer risk values for the variable Persons and find the highest risk to any person, then use that value in the analysis).  Maximum is disabled if Sum Over and Mean is disabled.

·        Minimum – DAVE will determine the minimum value across all of the values for the given independent variable (e.g., when using a human health risk database and using “Cancer Risk” as the dependent variable, selecting Minimum for the Chemicals independent variable will cause DAVE to search through all the cancer risk values for the variable Chemicals and find the lowest value, then use that value in the analysis).  Minimum is disabled if Sum Over and Mean is disabled.

·        Sum Over – DAVE will sum the values of the dependent variable across all of the values for the given independent variable for which you have chosen “Sum over.”  For example, selecting Sum Over for Chemicals when using a human health risk (HAPEM) database and using Cancer Risk as the dependent variable will cause DAVE to sum the cancer risk for all chemicals and provide the results for each person for the selected year, source type, and county. 

·        Mean – Mean value across all of the values of the given independent variable.

·        Ignore – DAVE will ignore this variable in the analysis.  For example, with an ecological risk database, you can create a rank-order plot for a particular time and showing each chemical separately by selecting Ignore for benchmarks, receptors, and volume elements.  All of the hazard quotient values will appear on the plot, but the particular benchmark, receptor, and volume element that they correspond to will be ignored.

Below the variables section of the Analysis window (Figure 3) is a note about how many “multivalue independent variables” remain.  For independent variables that have more than one possible value (i.e., those that have a number greater than 1 in parentheses after the variable name, such as “Source types” in the human health risk database type), you have the option of choosing a value of “All” (as explained in the bullet above).  If you choose “All,” you will see an asterisk appear with that variable name.  This indicates that you have chosen to use all (i.e., multiple) values of that variable in your plot or table.  A variable with an asterisk is referred to as a multivalue independent variable.  The number of multivalue independent variables is very important because it determines what types of plots or tables you can create.  Thus, DAVE emphasizes this number by stating it in the note below the variables section of the window. 

 

The plots and tables that can be created by DAVE are shown in the lists of Available Plots and Available Tables in the lower portion of the Analysis window.  Each type of plot/table that you can select is followed by a note (e.g. “[a,b multi vars]”) indicating how many multivalue independent variables are allowed when preparing that type of plot/table.  For example, if the note says you have two multivalue independent variables, you could create a table (two dimensional table which has two places for independent variables, rows and columns, with the dependent variables in each cell), or a categorized (e.g. stacked) bar plot (which also presents two independent variables with multiple values [e.g., chemicals and receptors]).  If you have only one multivalue independent variable, you could do a simple bar plot, for instance, or a one-dimensional table.  Using zero multivalue independent variables results in a single value that is shown in a text window (i.e., the output of the table creation process is a single value for the dependent value).  If the number of multivalue independent variables in the note is not listed for the type of plot/table you select, an error message will appear when you try to create the plot/table.  For more information on how many multivalue independent variables are required by each table or plot type, see Section 5 or 6, respectively. 

 

You may specify a default directory to contain your plots and tables using the “Directory for output files” text field near the bottom of the Analysis window.  The directory is specified by either typing in the directory name or selecting it using the “Browse” button.  If you do not specify a directory in this field, a default value of your TRIM directory\data\dave will be used.  You will also have a chance to provide a specific file name (including a directory) for the plot or table in the Customize Plot or Customize Table dialog that appears after you click on the “Create” button (unless you chose the Single Value table, in which case there is nothing to customize).

Once the number of multivalue independent variables matches one of the numbers allowed for the plot or table of interest, you can begin the process of table/plot generation by clicking on the “Create” button.  If you are unsure of the contents of the database of interest, you may want to begin by analyzing your data with two-dimensional tables rather than plots, so that you can see what data is in two dimensions of the database.  If there are missing data values for some of the variable values, the tables will still be generated.  Note that trying to generate certain plots using a data set with missing values may result in an error message.

 

The “Help” button at the bottom of the Analysis window will bring up the DAVE user guide in a separate window.  The “Close” button will close the Analysis window and return you to the Database Selector window or to another open Analysis window.


5.        Creating Tables


In the list of available tables in the Analysis window (Figure 3), the first item is the Basic Table.  This one is different from all of the other tables.  It can be used to extract one value from the database, and can be selected when there are zero remaining multivalue independent variables.  The single value is shown in a Single Value Result text window (Figure 4).  From there, the value can be copied and pasted into another application using the Control-C and Control-V keys.  To close the Single Value Result text window, click on the X in the upper right corner.  Single values are not saved to files.

Figure 4: Single Value Result text window.

If you select any of the tables that require one or two multivalue independent variables, a Customize Table dialog will appear after you click on the “Create” button in the Analysis window.  An example of the Customize Table dialog for a two-dimensional table is shown in Figure 5.

 

  • In the first section of this dialog, you can specify which of the remaining two multivalue independent variables will appear as the rows in the table; the other variable will be the column headers.  If you have one variable with a lot more values than the other, the system will be faster if you specify that variable to be the rows.  Important note: If you have one variable with thousands of values, be sure to use that variable for the rows and not the columns, otherwise DAVE will be very slow to create the table.
  • The Text Labels section allows you to customize the text labels that will be placed in the table.
  • In the Table Configuration section, you can specify the format of the table.  The available formats are CSV (comma-separated value), custom delimited, or fixed width.  If you choose a custom-delimited table, you can specify a delimiter to use other than a comma.  If you choose to output a fixed-width table, you should specify the fixed-width spacing to use for each column.  The number of significant digits entry applies to all three table formats.  If the “Show the table after creation” checkbox is checked, the resulting table will be shown in the Sort Filter Table application that is part of the MIMS Analysis Engine[7]; this application is used when you show any type of table after its creation.  Note that the Sort Filter Table application can read CSV or custom-delimited files but not fixed-width tables.  An example of a two-dimensional table created using DAVE is provided in Table 2.
  • The file name for the table specified in the “File Name” text field will be used.  A default unique file name will be generated, but you may change it either by editing the value directly in the field or by browsing to the file name using the “Browse” button. 
  • The table is actually created after you click the OK at the bottom of the dialog.

Figure 5: DAVE Customize Table dialog.

In addition to the Single Value table discussed earlier, the types of tables DAVE can generate are the following:

 

  • 2 Dimensional Table (requires 2 multivalue independent variables) – This option generates a two-dimensional table showing the values of the dependent variable as a function of two independent variables (see Table 2 for an example).  The values of one independent variable are shown as the columns and the other as the rows.  For the remaining independent variables in the database, either a constant value is used, or a function is computed based on the option you chose for each variable in the Analysis window (e.g., maximum, minimum, sum over).

Table 2: Example of a fixed-width two-dimensional table with “|” as a delimiter.

Values for Ecological Risk = Hazard Quotient ; Eco. Benchmarks = Dose : NOAEL : Reproductive success ; Eco. Receptors = White Tailed Deer ; Times = 1987-01-03 00:00:00

 

|                 |MethylMercury    |Benzo(A)Pyrene  

|SurfSoil_E1      |1.436E-10        |5.621E-10       

|SurfSoil_ESE2    |8.642E-11        |3.628E-10       

|SurfSoil_ESE3    |1.193E-10        |3.948E-05       

|SurfSoil_N2      |1.429E-10        |5.849E-10       

|SurfSoil_NE2     |9.771E-11        |4.268E-10       

|SurfSoil_SE1     |8.134E-11        |1.640E-05       

|SurfSoil_SSE2    |7.153E-11        |7.431E-06       

|SurfSoil_SSE3    |8.693E-11        |3.393E-10       

|SurfSoil_SSE4    |1.203E-10        |7.446E-07       

|SurfSoil_SW2     |9.102E-11        |3.500E-10       

|SurfSoil_W2      |7.507E-11        |3.122E-04       

 

  • 1 Dimensional Table (requires 1 multivalue independent variable) – This option provides a one-dimensional table showing the values of the dependent variable as a function of the independent variable with multiple values, given that each of the remaining independent variables is held constant as specified in the Analysis window (see Table 3 for an example).  This table is the same as the two-dimensional table, except it has just a single column of data after the first column of labels.  When you select this option, the Customize Table dialog will appear, but you will not be able to choose whether you want the remaining multivalue variable to be columns or rows; it will always be used for the rows.

Table 3: Example of a one-dimensional table.

" Maximum Values Across Persons/(CR per year exposure) for Chemicals = Benzene;  Start Years = 2001;  Counties = Harris County;"

 

"Source Types","Cancer Risk"

"BackgConc","3.7652E-08"

"SOURCE1","1.0561E-06"

"SOURCE2","5.9269E-08"

"SOURCE3","3.2136E-06"

"SOURCE4","1.5578E-08"

"Total Outdoor","3.3914E-06"

 

·        Histogram Tables: This type of table is available for either one or two multivalue independent variables.  It is used to present counts of how many times the value of a dependent variable falls within a particular range or bin.  After you enter information as needed into the Customize Table dialog and then click on “OK,” a Customize Histogram dialog appears; an example is shown in Figure 6.  In this dialog, you can specify whether the histogram table shows the frequency (i.e., a count), the percentage, or the probability (values between zero and one).  You can also specify the bins to use.

Figure 6: The Customize Histogram dialog.

Some configuration options are provided to make it easy to choose the bins:

o       For equally spaced bins, select the Equally Spaced option, specify the lower bound, upper bound, and number of bins, then click on the “Recompute” button.  The bins are computed using the minimum and maximum values of the data range.  The resulting bin break points are shown in the break points table on the right side of the window.

o       For bins that differ by a factor of 10, select the Factor of 10 option, specify the lower bound and the number of bins, then click on the “Recompute” button.  The resulting bin break points are shown in the break points table.

o       For totally customized bins, select the Custom option and edit the values of the bins in the break points table.  The buttons in the toolbar above this table can be used to insert or delete values, and you may edit the values in the break points table directly by double-clicking on a specific value.

You may customize the format of the bin labels by adjusting the items in the Format Labels section and then clicking on Apply Format.  If you would like to see the bins as the rows instead of the columns (the default), activate the “Bins as Rows?” checkbox (caution: do not use this checkbox if your independent variable has thousands of values).  An example of a histogram table for two multivalue independent variables (person and source type) is shown in Figure 7.  The software displaying the table is the MIMS Analysis Engine Sort Filter Table application.

Figure 7: An example histogram table for two multivalue independent variables.

·        Percentile Tables: These tables are available for either one or two multivalue independent variables.  The percentile tables are similar to the histograms, but you specify percentiles to compute instead of a list of bin cutoffs.  When a percentile table is requested, a Customize Percentiles dialog (see the example in Figure 8) will appear after you click on “OK” in the Customize Table dialog.  This Customize Percentiles dialog is used to specify the percentiles to compute.  Some preconfigured options are available via the Quartiles (every 0.25), Quintiles (every 0.2), and Deciles (every 0.1) options at the top of the dialog.  After choosing one of these, you can then add additional percentiles if desired by specifying a minimum percentile, maximum percentile, and step size and then clicking on the “Add Percentiles” button.  You may also add or remove specific percentiles by using the buttons on the toolbar in the Percentiles section.  If you wish for the percentiles to appear as rows instead of columns (the default), activate the “Percentiles as rows?” checkbox.  Caution: Do not activate Percentiles as rows if your independent variable has thousands of values – a table with thousands of columns will result and it will be very slow.  An example of a Percentiles table for two multivalue independent variables (person and source type) is shown in Table 4.  This table was created from a CSV file that was output by DAVE

Figure 8: Percentile Editor dialog.

Table 4: An example percentiles table for two multivalue independent variables.

Percentile of Cancer Risk/(CR per year exposure) for Chemicals = Benzene;  Start Years = 2001;  Counties = Harris County;

Percentile

BackgConc

SOURCE1

SOURCE2

SOURCE3

SOURCE4

Total Outdoor

0.0 %

1.0435E-08

4.0783E-08

1.1756E-08

1.7405E-08

5.5402E-09

1.1244E-07

25.0 %

1.8297E-08

8.3460E-08

2.3411E-08

2.7434E-08

7.7476E-09

1.7690E-07

50.0 %

1.9623E-08

1.0316E-07

2.9328E-08

3.2955E-08

8.4273E-09

2.0450E-07

75.0 %

2.1361E-08

1.3371E-07

3.5980E-08

4.3658E-08

9.5316E-09

2.3981E-07

95.0 %

2.3277E-08

2.3199E-07

4.3702E-08

9.0932E-08

1.1889E-08

3.6987E-07

96.0 %

2.3478E-08

2.5443E-07

4.4525E-08

1.0346E-07

1.2224E-08

3.9605E-07

97.0 %

2.3690E-08

2.9084E-07

4.5553E-08

1.2302E-07

1.2591E-08

4.2457E-07

98.0 %

2.3991E-08

3.3263E-07

4.6989E-08

1.4265E-07

1.2981E-08

4.8406E-07

99.0 %

2.4489E-08

4.0807E-07

4.8847E-08

2.4358E-07

1.3795E-08

6.1130E-07

 

6.        Creating Plots

 

NOTE: As indicated at the end of Section 4, if you are unsure of the contents of the chosen database you may want to begin by analyzing your data using two-dimensional tables (as described in Section 5) rather than plots.  If there are missing data values for some of the variable values, tables can still be generated.

 

DAVE can create a variety of plot types using the data in the databases by passing the selected data to the MIMS Analysis Engine and having it create the plots.  After specifying the values for the dependent and independent variables in the Analysis window (Figure 3), you can choose the type of plot you wish to create from the Available Plots list located at the lower left of the Analysis window.  If you wish to specify a default directory in which to place the plots generated during your analysis, use the “Directory for output files” text field, as explained in Section 4.  After you click on the “Create” button, a Customize Plot dialog appears (see example in Figure 9); this is similar to the Customize Table dialog shown in Figure 5.  The Customize Plot dialog allows you to customize some of the items that will appear on your plot.

Figure 9: DAVE Customize Plot dialog.

  • At the top of the dialog is the Primary Data Selector section.  This allows you to specify which of your remaining multivalue independent variables will be the organizing basis for the data sets passed to the MIMS Analysis Engine for plotting.  The other independent variable will be used to specify the values contained in the data sets.  For example, if your multivalue independent variables are chemicals and source types, and you choose chemicals as the primary data, then one data set for each chemical will be passed to the analysis engine, and each of these data sets will contain values for all source types.  The way you “slice” the data affects how you can present them in plots.  The best way to understand how this works is through trial and error.  If you find that a plot you create is not showing the right variable, come back to the Customize Plot window and select the other variable as your primary data.

 

  • The Text Labels section of this window is especially useful if you are generating multiple plots using the “One for each” feature for one of the variables.  If you are not using the “One for each” feature, you can wait and customize your labels within the Analysis Engine window that will appear after you click on “OK” in the Customize Plot window. 

 

  • In the Plot Configuration section, you choose whether to use a new configuration or an existing template.  Templates are created from the MIMS Analysis Engine plot window that you will move to after leaving the DAVE Customize Plot window; their creation is discussed below.  You can specify that a template should be used by choosing the Template option and then either browsing to a template file or entering the name in the “Optional analysis engine configuration” text field.  If you do not have a template saved, you can either create a new configuration using the New option (the default) in this section of the window, or you can select the Previous option to use the configuration that was created and saved automatically by DAVE when you created your most recent plot.

 

  • If the “show analysis engine GUI” checkbox is activated, the GUI will appear and allow you to customize the plot.  If it is not activated, the plot(s) will be generated behind the scenes using the specified template.

 

  • You can specify the name to be used for the plot file in the “File Name” text field, or you can specify it later in the Analysis Engine plot window.

 

The data are passed to the MIMS Analysis Engine after you click on “OK” in the Customize Plot window.  In the analysis engine GUI, you can further sub-select which data to show on a specific plot.  You can also customize the analysis options for the plot, such as the plot title, axes labels, format of bars (e.g., color), how to output the plot (either to the screen or saved as an image), and the name of the file to be saved.  The remainder of this section uses the example of creating a bar plot.  We use Figure 10, a MIMS Analysis Engine example window for specifying the plot options needed to create bar plots, to illustrate this process in greater detail.[8]

 

  

Figure 10: MIMS Analysis Engine bar plot window.

The first item you encounter in this window is a File pull-down menu.  After you have customized the features of a plot from this MIMS window (as described below), you can save those customizations as a “plot template” that you can use later to create plots that look similar.  A template can be saved by choosing “Save plot Template” from the File pull-down menu.  Templates are accessed via the Customize Plot window, as already discussed in the description of Figure 9.

 

Before creating a plot, you must specify which data to plot.  Each type of plot requires different types of data series.  For example, a scatter plot requires an X data series and a Y data series.  A bar plot requires a “Bar Data Series.”  The data series required for the particular type of plot are listed in the Data Sets section of the MIMS window.  Note that the notation “1 to N needed” in this section means that the plot requires at least one data series, but can take any number (“N”) of them.  For plots that allow only a single data series, the notation would be “1 needed.”  To select the data sets to use in the bar plot, click on the “Set” button for the Bar Data Series option in the MIMS window.  A Select Data Sets window (Figure 11) appears that lists the data sets available to be plotted.  The contents of the Select Data Sets window are influenced by the variable you chose as the “primary data” in the Customize Plot window.  As explained earlier, when DAVE passes the data to the MIMS Analysis Engine, it provides them in terms of data sets organized by the independent variable you chose as primary.  In the process that led to the example window in Figure 11, Source Type was chosen as primary and the other variable was Persons.

Figure 11: Select Data Sets window for choosing what data set(s) to plot.

To select a data set from the Available Data Sets list on the right, highlight the data set and click “Add to Selected.” The data set will now be listed in the Selected Data Sets list on the left.  To remove a data set from the Selected Data Sets list, highlight the data set and click “Remove.” You can also view the data in the data sets in a separate window at any time by highlighting one or more data sets (hold down the Control or Shift key to choose more than one at a time) and clicking “View Data Sets.”  Note that many types of plots will not be able to effectively show more than 10 or 20 datasets at one time.  In addition, tests have shown that selecting more than 30 datasets sometimes creates problems with the R program.  Selecting fewer dataset will create clearer, more effective plots.  Once you are satisfied with the list of data sets you have selected, click “OK.”  Those data sets will now be associated with the Bar Data Series option in the MIMS Analysis Engine bar plot window (Figure 10) and the number of data sets you chose will now be listed beside the Bar Data Series option.  To exit the Select Data Sets window without adding any data sets or changing the list of selected data sets, click “Cancel” and the window will close and return to the MIMS Analysis Engine bar plot window.

 

The section of the bar plot window below the Data sets section is the Bar Plot Options section.  You use this section to customize the plot’s analysis options, such as the title text and its font, size, and color, the orientation and color of the bars, and so on.  Click on the “Edit” buttons to access dialogs that allow you to perform the customization by setting specific properties of each option.  For more detail on the specifics of the user interface for each analysis option, please see the MIMS Analysis Engine user guide (available in the docs folder of the TRIM installation).  The analysis options that are presented in the MIMS Analysis Engine window vary slightly by plot type, but title, subtitle, and footer are available for all types of plots.

 

Once you have configured the plot, you can view a temporary copy of it by clicking on the “View Plot” button.  On Windows machines, Adobe Acrobat will be used to display the plot.  The first time a plot is created, it takes a short while to open and configure Acrobat.  If you are creating multiple plots, it is best to leave Acrobat running in the background to shorten the time required to load the additional plots.  You may want to configure Acrobat to show an entire plot on the screen by setting the Preference for Display to “Fit in Window.” The location of this option varies according to the Acrobat version, but in Version 5 you access it by choosing Preferences → General from the Edit pull-down menu, then clicking on Display and setting Default Zoom to “Fit in Window.”

 

You can save a copy of the plot by specifying a file name in the “File Name” text field that has one of these standard image file extensions: .jpg, .ps, .ptx, .png, or .pdf; this name will be passed to the Analysis Engine from DAVE.  You can use the default file name chosen by DAVE, or edit the file name either by typing directly into the File Name field or using the “Browse” button to specify one. 

 

A brief explanation of each plot type available in DAVE is provided below; this list is followed by an example of each plot type.  For additional information on the plotting options, consult the MIMS Analysis Engine user guide.

 

  • Simple bar plot (Figure 12) (with 1 multivalue independent variable) – Plots the values of the dependent variable for all values of one independent variable (e.g., source type) given that all other independent variables are held constant.

  • Categorized bar plot (Figure 13) (with 2 multivalue independent variables) – This is a stacked bar plot showing data from various data sets (e.g., a series of data sets consisting of one data set per chemical grouped by category (on the x-axis). 
  • Simple scatter plot (Figure 14) (with with 2 multivalue independent variables) – Plots the values of one subset of a dependent variable against another.  For example, plots the relationship between the risk for one chemical against another to see if there is a correlation of values for the two chemicals.
  • Rank-order plot (Figure 15) (with 2 multivalue independent variables) – Plots the values of the dependent variable using subsets based on two independent variables on a ranked scale, where the values for each variable are ordered by value and measured on an equal-interval scale.  It provides an analysis of how the values of the dependent variable are ranked relative to multiple independent variables.
  • Discrete-category plot (Figure 16) (with 2 multivalue independent variables) – Has a discrete categorical x-axis like a bar plot, and plots the values of the dependent variable as multiple symbols above each tick mark.  For example, plots hazard quotients for each source type (on the x-axis) and each chemical (as different symbols).
  • Box plot (Figure 17) (with 2 multivalue independent variables) – Plots the values of quartiles for the dependent variable with a box at the 25th and 75th variables and whiskers to the 0th and 100th percentiles.
  • CDF plot (supports 2 multivalue independent variables) – Plots a cumulative distribution function (CDF) curve for each value of the dependent variable.
  • Tornado plot (supports 2 multivalue independent variables) – Plots a flipped bar plot with values for the dependent variable along the x axis.
  • Time Series plot (supports 2 multivalue independent variables, out of which one represents time) – Plots the time variable along the x axis and the dependent variable along the y axis similar to a line plot.
  • Histogram plot (supports 1 multivalue independent variable) – Plots frequency of dependent variables’ values in each of the histogram bins (bins are specified by the user).
  • Percentile plot (supports 2 multivalue independent variables) – Plots the percentitles specified by the user for each of the dependent variables’.

 

 

Figure 12: Simple bar plot from DAVE.

Figure 13: Categorized bar plot from DAVE.

Figure 14: Scatter plot example from DAVE.

Figure 15: Rank-order plot from DAVE.

Figure 16: Discrete-category plot from DAVE.

 

Figure 17: Box plot from DAVE.

 



[1] Total Risk Integrated Methodology (TRIM) - General Information [http://www.epa.gov/ttn/fera/trim_gen.html].

[2] Fine, S. S., S. C. Howard, A. M. Eyth, D. A. Herington, K. J. Castleton, 2002, The EPA Multimedia Integrated Modeling System Software Suite, Second Federal Interagency Hydrologic Modeling Conference, July 28-August 1, Las Vegas, Nevada.

[3] Hazardous Air Pollutant Exposure Model (HAPEM) [http://www.epa.gov/ttnatw01/nata/hapem.html]

 

4 For more information on MySQL, please consult the MySQL web page at http://www.mysql.com.

[5] The metrics which cannot be analyzed with the “Analyze” feature are the “distribution” metrics:

        Population-weighted Cumulative Cancer Frequency Distribution for Lifetime Residency Period (PRD);

        Population-weighted Cumulative Cancer Frequency Distribution for Less-than-Lifetime Residency Period (PRD_LT);

        Population-weighted Cumulative Hazard Frequency Distribution (PHD);

        Population-weighted Cumulative Hazard Frequency Distribution for Lifetime Residency Period (PHD_L);

        Population-weighted Cumulative Hazard Frequency Distribution for Greatest 7-Year Hazard Quotient for Lifetime Residency Period (PHD_7_L);

        Population-weighted Cumulative Hazard Frequency Distributions for Less-than-Lifetime Residency Period (PHD_LT);

        Population-weighted Cumulative Hazard Frequency Distributions for the Maximum 7-Year Hazard Quotient for Less-than-Lifetime Residency Period (PHD_7_LT)

 

[6] A hazard quotient (HQ) is the result of dividing an estimated or actual value by a benchmark value. Thus, the HQ will be greater than 1 if the value exceeds the benchmark, and less than 1 if the value is less than the benchmark. HQs are commonly used in risk analyses.

[7] For more information on the Analysis Engine Table application, see the MIMS Analysis Engine documentation included in the docs folder of the TRIM installation.

[8]  Note that when the MIMS Analysis Engine window is open, you cannot make any selections in DAVE.