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Open-File Report 2005–1353

User Manual for Blossom Statistical Package for R

By Marian K. Talbert and Brian S. Cade

Thumbnail of and link to report PDF (2.83 MB)Abstract

Blossom is an R package with functions for making statistical comparisons with distance-function based permutation tests developed by P.W. Mielke, Jr. and colleagues at Colorado State University (Mielke and Berry, 2001) and for testing parameters estimated in linear models with permutation procedures developed by B. S. Cade and colleagues at the Fort Collins Science Center, U.S. Geological Survey. This manual is intended to provide identical documentation of the statistical methods and interpretations as the manual by Cade and Richards (2005) does for the original Fortran program, but with changes made with respect to command inputs and outputs to reflect the new implementation as a package for R (R Development Core Team, 2012). This implementation in R has allowed for numerous improvements not supported by the Cade and Richards (2005) Fortran implementation, including use of categorical predictor variables in most routines.

First posted 2005

Revised August 8, 2013

For additional information contact:
Director, Fort Collins Science Center
U.S. Geological Survey
2150 Centre Ave., Bldg. C
Fort Collins, CO 80526-8118
http://www.fort.usgs.gov/

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Suggested citation:

Talbert, M.K., and Cade, B.S., 2013, (revised August 8, 2013) User manual for Blossom statistical package for R: U.S. Geological Survey Open-File Report 2005–1353, 81 p., http://pubs.usgs.gov/of/2005/1353/.



Contents

Introduction

Overview of Statistical Concepts

Statistical Commands

Appendix 1. Common Statistical Tests Embraced by the MRPP Command

Appendix 2. Compilation of the internal Blossom code

Appendix 3. Blossom Statistics Program Installation, Configuration, Requirements

Appendix 4. Blossom Development and Testing

Appendix 5. Acknowledgments

References Cited


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