Inhalation Exposure Simulation Modeling Project

Please visit the [[Inhalation Exposure Simulation Modeling|IESM Summary Page]] for a quick description of the aims, investigators, and materials associated with the Inhalation Exposure Simulation Modeling (IESM) hosted project.

The IESM project integrates the results of other projects into a deterministic and stochastic modeling framework, which can be used to predict and explore human exposures to airborne pollutants for a wide range of locations and scenarios. The framework incorporates human activity patterns, indoor air monitoring data and models, building factors, and a range of simulation techniques. The framework is currently manifested as a series of routines programmed in the [[Human Exposure Research Package (heR)]].

The earliest activity-pattern based exposure model was developed by Wayne Ott in the 1980's, called the Simulation of Human Activity and Pollutant Exposure (SHAPE) model. The more recent THEM model, developed at Stanford University in the early 1990's, was an offshoot of this original model ([[A Total Human Exposure Model (THEM) for Respirable Suspended Particles (RSP)|Klepeis et al. 1994]]).

Most recently, investigators in the IESM project have simulated exposure to secondhand tobacco smoke (SHS) in residences ([[Modeling Residential Exposure to Secondhand Tobacco Smoke|Klepeis and Nazaroff 2006]]), for the purpose of identifying building and occupant-activity factors that most heavily influence exposure.

In the sections of this chapter, we describe in more detail the various sub-projects and software implementations that are part of the IESM project.

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The THEM Software Project

Introduction

This page describes the Total Human Exposure Model (THEM) for exploring particle exposures in the San Francisco Bay Area. Please visit the [[A Total Human Exposure Model (THEM)|THEM Summary Page]] for a complete list of all the THEM project details.

The Total Human Exposure Model (THEM) program, version 1.0 was developed at Stanford University from July 1991 to April 1994 by Wayne R. Ott, Neil E. Klepeis, and Elena Tracy. THEM is written in MicroSoft Professional BASIC Development System version 7.1.

THEM is not currently being maintained, but questions can be directed to Dr. Neil E. Klepeis.

THEM is released under the GNU General Public License.

The current version calculates exposure to Respirable Suspended Particles (RSP) from Environmental Tobacco Smoke (ETS) and ambient sources. It uses the California Activity Pattern (CAP) Survey data from the California Air Resources Board (Sacramento, CA) and ambient RSP data from the Bay Area Air Quality Management District (David Fairley). The so-called Sequential Cigarette Exposure Model (SCEM), based on the mass balance equation, is used to determine concentrations of secondhand tobacco smoke for single cigarettes.

There is a scientific paper and a user's and programmer's manual.

Download

A zipped archive is available containing all of the Microsoft Professional Basic source-code files, a variety of documentation files, and a Windows/DOS executable (themrsp3.exe).

[Download the THEM zipped archive]

Documentation

The user interface to the program is fairly self-explanatory.

Execution of THEM for the calculation of exposures across populations requires the input of (1) activity pattern data, (2) mass balance parameters, (3) microenvironmental distributions, (4) activity, location, and calculation method reduced codes, and (5) ambient data (optional).

All parameters are specified using input data files, which have already been set at default values for the simulation of exposure to RSP from cigarettes and ambient sources for people living in the San Francisco Bay Area.

The documentation files in the software distribution contain more information on using THEM.

The main reference for THEM is the following AWMA conference paper:

Klepeis NE, Ott WR, Switzer P. A Total Human Exposure Model (THEM) for Respirable Suspended Particles (RSP), Presented at the 87th Annual Meeting and Exhibition of the Air and Waste Management Association, Cincinnati, OH, June 1994.

Please cite this paper if you use or describe THEM in any published research.

The THEM user's and programmer's manual contains a technical description of the program, including all the subprograms and variable declarations.

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The heR Software Project

This page provides details on the human exposure research (heR) software project. You may also want to visit the [[Human Exposure Research Package (heR)|heR Summary Page]] page, which lists the main heR highlights.

The heR Project is officially part of the Inhalation Exposure Simulation Modeling project, because it includes sophisticated tools for modeling individual and population exposures. However, it also contains many tools, sub-models, and data sets that are likely to be useful in many different areas of human exposure research. For example, it contains subroutines for manipulating and statistically analyzing activity pattern data, and it also contains routines for executing advanced indoor air quality models.

Introduction

heR Logo

heR is a free software package implemented in the R computing environment that contains routines and data sets for use in conducting human exposure research. The field of human exposure is concerned with the processes by which environmental contaminants in air, water, soil, and food come into contact with human biological boundaries.

heR originated as part of the Ph.D. research of Neil E. Klepeis at the University of California at Berkeley. His research was focused on the simulation of residential secondhand tobacco smoke exposure. As a result, heR currently contains substantial functionality for airborne exposures, indoor air quality modeling, and human activity pattern analysis.

The aim is for heR to be a community-supported project, containing the most advanced techniques in all types of exposure-related modeling and data analysis.

Both R and heR are free software released under the GNU General Public License.

New testers and contributors to the software package, especially those in the food or dermal exposure areas, are most welcome. If you are interested, please send email to Dr. Klepeis using the contact form at http://neil.klepeis.net. Make sure to include some information on your background in exposure research.

The current component packages of heR are as follows:

  • heR.Misc -- Miscellaneous basic functions for plotting, statistics, and analysis
  • heR.IndoorAir -- Indoor air quality modeling
  • heR.Activities -- Human activity pattern analysis
  • heR.ActivityData -- Human activity pattern databases
  • heR.Inhalation -- Inhalation modeling and databases
  • heR.Simulation -- Routines for simulating individual and population exposure
  • heR.SurveyData -- Exposure monitoring survey databases
  • heR.MonitoringData -- Pollutant monitoring databases

You can download and view the documentation for each package using the links in the table below.

Why R?

The following are some advantages of using the R environment as a platform for heR:

  • R is very similar to the well-known S-plus commercial statistics package.
  • R is a complete programming language optimized for statistical computation, incorporating
    vectorized calculations, simulation, and object-oriented programming
  • A multitude of available add-on statistical packages are available, including time series, regression, optimization, bootstrap, and spatial statistics.
  • R has built-in low and high level plotting and graphic functions, including Trellis graphics similar
    to those in S-plus
  • R has good inter-operability with other software, such as C, C++, FORTRAN, Perl, Python, Java, and Excel-style spreadsheets
  • R has been ported to multiple computing architectures, including MacOS X, Windows, Unix, and GNU/Linux
  • R has growing support for menu and dialog-driven graphical user interfaces
  • R has growing data-base connectivity, currently including MySQL, PostgreSQL, netCDF, HDF, Oracle, XML, ArcInfo, SPSS, SAS

The heR Packages

Online HTML documentation is available for each heR component sub-package (module) by following the "[Docs]" links in the following table. Some packages you can download directly using the "[Download]" link, others you need to request the package files by using the "[Request Package]" link.

Note: When you install a heR package all of the documentation is included in your local installation.

If you use a heR package in your research, please cite the listed paper(s) as appropriate, or the ExposureScience.Org website, in any of your publications.

Module Links Description Reference(s)
heR.Misc [Docs]
[Download]
Miscellaneous Plotting and Statistics Klepeis, N.E. Exposure Science Website. http://ExposureScience.Org, 2004.
heR.Activities [Docs]
[Request Package]
Time-Activity Pattern Analysis Klepeis, N.E. Exposure Science Website. http://ExposureScience.Org, 2004.
heR.ActivityData [Docs]
[Download]
Human Activity Pattern Data [[Nodetitle:The National Human Activity Pattern Survey (NHAPS): A Resource for Assessing Exposure to Environmental Pollutants|Klepeis et al. 2001]].
heR.Inhalation [Docs]
[Request Package]
Inhalation Data and Modeling Klepeis, N.E. Exposure Science Website. http://ExposureScience.Org, 2004.
heR.IndoorAir [Docs]
[Request Package]
Indoor Air Modeling Klepeis, N.E. Exposure Science Website. http://ExposureScience.Org, 2004.
heR.Simulation [Docs]
[Request Package]
Exposure Simulation Klepeis, N.E. Exposure Science Website. http://ExposureScience.Org, 2004.
heR.SurveyData [Docs]
[Download]
Exposure Survey Data Klepeis, N.E. Exposure Science Website. http://ExposureScience.Org, 2004.
heR.MonitoringData [Docs]
[Request Package]
Pollutant Monitoring Data Klepeis, N.E. Exposure Science Website. http://ExposureScience.Org, 2004.

In addition to the online HTML heR documentation available by following the links in the above table, you may wish to view the online HTML documentation for the current standard version of R, although it is typically included on local machines where R is installed.

Installation of the Packages

Before installing heR from source-code package files, you must first install R itself. Binary packages of R are available from the Comprehensive R Archive Network (CRAN).

After installing R, download each desired heR sub-package archive. Note that there are dependencies among the packages, so the easiest approach is to install everything.

Once downloaded, the packages are installed on GNU/Linux or Unix-like systems by using the following command when logged in as root: R INSTALL package-file-name

Unfortunately, pre-compiled packages are not currently available for Windows. However, the source-code packages available here may be used to port each package to other platforms.

Important Note

heR is intended to be a collaborative free software project among exposure science researchers. The heR source code is available through this website to members of the research community. Although it has been tested and used extensively as part of the PhD research of Neil Klepeis, heR is currently in an early state of development and is not yet ready for an official public release. This website will serve as a focal point for the future development of heR.

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