OrderMatrix {metacom}

Ordinates interaction matrix

Description

'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.

Usage

OrderMatrix(comm, scores = 1, outputScores = FALSE, binary = TRUE)

Arguments

comm

community data in the form of a presence absence matrix

scores

axis scores to ordinate matrix. 1: primary axis scores (default) 2: secondary axis scores

outputScores

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)