compart: Detects compartments

Description Usage Arguments Details Value Note Author(s) References See Also Examples

Description

Finds number of compartments, based on multivariate ordination techniques, and labels interactions according to the compartment they belong to.

Usage

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compart(web)

Arguments

web

A bipartite interaction web, i.e.~a matrix with higher (cols) and lower (rows) trophic levels.

Details

Internal function, to be called by networklevel.

Value

Returns a list with two entries:

cweb

A matrix similar to web, but now with compartment numbers instead of interaction values.

ncompart

The number of compartments.

Note

Note that up to (and including) version 0.85 we used a code based on correspondence analysis (see Lewinsohn et al. 2006). This is, however, faulty for webs with many same-linked species. Hence we resorted to a brute-force search for compartments, which is orders of magnitude slower, but at least works correctly. Only in version 1.18 Juan M. Barreneche eventually found a solution that is fast and works with ties!

Author(s)

Juan M. Barreneche <jumanbar@gmail.com>, but please co-copy comments/questions to package maintainer: Carsten F. Dormann <carsten.dormann@biom.uni-freiburg.de>

References

Lewinsohn, T. M., P. I. Prado, P. Jordano, J. Bascompte, and J. M. Olesen (2006) Structure in plant-animal interaction assemblages. Oikos 113, 174–184

See Also

See also networklevel.

Examples

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# make a nicely comparted web:
web <- matrix(0, 10,10)
web[1,1:3] <- 1 
web[2,4:5] <- 1 
web[3:7, 6:8] <- 1
web[8:10, 9:10] <- 1
web <- web[-c(4:5),] #oh, and make it asymmetric!
web <- web[,c(1:5, 9,10, 6:8)] #oh, and make it non-diagonal
compart(web)

# or, standard, use Safariland as example:
data(Safariland)
compart(Safariland)

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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