User manual for Blossom Statistical Software

Blossom is an interactive program 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 (known as the Midcontinent Ecological Science Center prior to
2002). This manual is intended to update and replace earlier versions by B. S. Cade and J. D.
Richards dated 2000 and 1999 and by W. B. Slauson, B. S. Cade, and J. D. Richards dated 1991
and 1994. We have expanded on material in earlier versions and provide documentation on new
routines added since 2000. Routines added since 2000 are: double permutation (HYP/DP)
procedures for linear model tests (OLS, LAD regression, and quantile rank score tests) when null
models are either implicitly or explicitly constrained through the origin, i.e., no intercept models
(Cade 2003, Cade et al. 2005, Cade et al. In press); dropping all but a single zero residual in LAD
(and quantile) regression permutation tests of subsets of variables in multiple regression models
(Cade 2005, Cade and Richards In press); and computation of all quantile regression estimates
(LAD/ QUANT = ALL). In addition, we now offer the option of saving output to a terse
formatted file that is useful for summarizing results of multiple simulations (OUTPUT /TERSE
or VERBOSE), and the option to store (SAVETEST = file name) the vector of permuted test
statistic values from Monte Carlo resampling approximations of probabilities. The computer
code has been made more efficient where possible and was compiled with Lahey Fortran 95 to
dynamically allocate memory.