'OrderMatrix' ordinates an interaction matrix scores derived from reciprocal
averaging (Gauch et al. 1977). These scores represent a latent environmental
gradient along which species distributions are structured.
logical. Default is to return the ordinated matrix. If
'outputScores' is TRUE, the function returns the site and species scores.
binary
logical argument indicating whether to ordinate the community
matrix based on abundance or binary (default) data.
Value
'OrderMatrix' returns either an ordinated matrix (outputScores =
FALSE) or the site and species scores (outputScores = TRUE) obtained from
reciprocal averaging. This function is already contained within functions
calculating coherence, species turnover & boundary clumping, but may be
useful for visualizations or for hypothesis testing concerning the important
variables associated with the site or species scores.
Note
'OrderMatrix', like many of these functions, relies heavily on the
'vegan' package.
Author(s)
Tad Dallas
References
Gauch, H.G., R.H. Whittaker, and T.R. Wentworth. 1977. A
comparative study of reciprocal averaging and other ordination techniques.
Journal of Ecology 65:157-174.
Leibold, M.A. and G.M. Mikkelson. 2002. Coherence, species turnover, and
boundary clumping: elements of meta-community structure. Oikos 97: 237 -
250.
Oksanen,J., F.G. Blanchet, R. Kindt, P. Legendre, P.R. Minchin, R.B. O'Hara,
G.L. Simpson, P. Solymos, M.H.H. Stevens and H. Wagner (2012). vegan:
Community Ecology Package. R package version 2.0-4.
http://CRAN.R-project.org/package=vegan
Examples
#define an interaction matrix
data(TestMatrices)
pres3c <- TestMatrices[[6]]
#obtain an ordinated interaction matrix
OrderMatrix(pres3c, scores = 1, outputScores = FALSE)
#obtain site and species scores from reciprocal averaging
OrderMatrix(pres3c, scores = 1, outputScores = TRUE)