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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