EPA: RIVPACS
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Title
| RIVPACS-type predictive modeling |
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Author
| Van Sickle, J. |
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Abstract/Summary Statement
| A RIVPACS-type predictive model predicts the taxonomic assemblage of macroinvertebrates, fish, or periphyton that one would expect to find in an aquatic ecosystem, if that ecosystem were in a minimally-disturbed "reference" condition. The expected assemblage is then compared with the assemblage that is observed by sampling the ecosystem. Discrepancies between the two assemblages indicate the degree of ecosystem stress or impairment. |
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Table of Contents
| Features include: 1. Creation and manipulation of site-by-taxa data matrices, including random subsampling to a fixed count. 2. Options for different dissimilarity measures and clustering algorithms, including flexible-beta clustering and options for dendrogram pruning. 3. Options for all subsets or stepwise discriminant function analysis. 4. Predictions for new sites, including assessment of site outlier status. 5. Save final model as an R object and export to users, with a stand-alone script for assessing new sites. 6. Export your custom model for submission to the Western Center for Monitoring's web-accessible modeling system. 7. Calibration and predictions for null models. 8. O/E and BC indices. 9. Detailed comparisons of expected and observed taxa at user-selected sites. 10. Use a Random Forest model, rather than discriminant functions, to predict site group membership. |
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Citation
| Van Sickle, J., 2011, R-language scripts for RIVPACS-type predictive modeling, Version 4.2. U.S. Environmental Agency, last accessed March 15, 2012 at http://www.epa.gov/wed/pages/models/rivpacs/rivpacs.htm |
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Method Source
| EPA |
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Source Organization Country
| USA |
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Publication Year
| 2011 |
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Special Notes
| Version 4.2 (January 1, 2011); Version 4.0 (2008) The scripts are written for use by experienced R programmers. Users will need to modify some scripts to suit their particular data sets. Related article: Van Sickle, J., 2008, An index of compositional dissimilarity between observed and expected assemblages. Journal of the North American Benthological Society 27, 227-235. |
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Item Type
| Downloadable Software |
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Publication Source Type
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Government Agency (Federal, USA) |
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Purpose
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Data analysis |
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Design or Data Analysis Objectives
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Communities & populations |
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Complexity
| High |
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Media Emphasized
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Biological |
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Media Subcategory
| |
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Special Topics
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