Crustal Geophysics and Geochemistry Science Center

Aqueous Geochemistry Research and Development
Modeling Applications and Reaction Pathways

Geochemical Modeling and Data Analysis Tools

Lopaka (Rob) Lee

The purpose of this activity is to develop data, analytical tools, and methodologies, that will aid geochemical modeling and data analysis activities.

Current work on the development of data analysis tools is focused on statistical analysis methods and software that are capable of analyzing geochemical data with one to many censored values, or nondetects (i.e. "less-thans"). Such data are routinely generated in chemistry labs. However, robust methods for appropriately handling these data have not been widely employed. This is largely due to the fact that software implementing these methods is unavailable to the general public. Currently a library for the R environment for statistics and graphics has been developed and distributed. R is a freely available package that popular in academia and is rapidly gaining popularity in the environmental science community.

Current work on geochemical modeling tools and methodologies is focused on developing software tools that allow researchers to easily compute and manipulate thermodynamic constants, and transform data between different database formats. These tools will aid in the task of compiling and evaluating thermodynamic datasets by eliminating much of the drudgery of text parsing and re-writing reactions. The new tools will be able to translate between popular thermodynamic database formats used in the geosciences such as PHREEQC, The Geochemist's Workbench® (GWB), EQ3/6, and SUPCRT. The software will be distributed as stand-alone applications that run on users' personal computers and also as a web-based service that will allow users to transform data via a web-browser interface.


Journal Articles, Review Volumes, Reports, and Theses

  • Lee, Lopaka, and Helsel, Dennis, 2005, Baseline models of trace elements in major aquifers of the United States: Applied Geochemistry, v. 20, no. 8, p. 1560-1570.
  • Lee, Lopaka, and Helsel, Dennis, 2005, Statistical analysis of water-quality data containing multiple detection limits: S-language software for regression on order statistics: Computers and Geosciences, v. 31, p. 1241-1248.
  • Lee, L., and Helsel, D.R., (submitted), Statistical Analysis of Water-Quality Data Containing Multiple Detection Limits II: S-language Software for Nonparametric distribution Modeling and Hypothesis Testing. Computers and Geosciences.

Abstracts, Presentations, and Posters for Professional Technical Meetings

Lee, L., 2004, Geochemical modeling of soils: a soil-component approach [abs.]: American Geophysical Union (AGU) Fall Meeting, San Francisco, California, December 13-17, 2004: Eos Trans. AGU, v. 85, no. 47, Fall Meet. Suppl., Abstract H43C-0384. (Abstract and poster) Available online at

Lee, Lopaka, and Helsel, Dennis, 2004, Trace elements in ground waters of the United States: a new statistical summary [abs.]: National Water Quality Monitoring Council, National Monitoring Conference 2004, Chattanooga Tennessee, May 17-20, 2004, session block F, abstract 122. (Abstract and presentation) Available online at [PDF file, 288 KB].

Lee, Lopaka, Helsel, D.R., and Goldhaber, M.B., 2002, A formalism for geochemical reaction modeling using combined mass-balance, reaction-path, and stochastic methods: application to the Ozark aquifer system [abs.]: Geological Society of America 2002 Annual Meeting, Denver, Colorado, October 27-30, 2002, Abstracts with Programs, v. 34, no. 6, p. 193. (Abstract and poster) Available online at

Databases and Computer Programs

  • NADA for R: Nondetects and data analysis for the R statistical computing environment: Water Resources Applications Software, U.S. Geological Survey website ( (Lee and Helsel)
  • NADA for R - Nondetects and Data Analysis - Statistics for censored environmental data, a software package for the R environment for data analysis and graphics: Data Analysis Software for the Earth and Environmental Sciences, EnviroR website ( (Lee and Helsel)
  • Lee, Lopaka, and Helsel, Dennis, Nondetects and Data Analysis for R: Software for statistics of censored geochemical data

Contact Information

Lopaka (Rob) Lee
P.O. Box 51 Crater Rim Road
Hawaii National Park, HI 96718-0051
Phone: (808) 967-8883
Email: rclee

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Mineral Resources Program
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