bipartite (version 2.05)

nested: Calculates any of several measures of nestedness

Description

Wrapper function calling one, several or all currently implemented nestedness measures

Usage

nested(web, method = "binmatnest2", rescale=FALSE, normalised=TRUE)

Arguments

web

A matrix with elements of a set (e.g., plants) as rows, elements of a second set (e.g., pollinators) as columns and number of interactions as entries.

method

One or more of the following: discrepancy, discrepancy2, binmatnest, binmatnest2, NODF, NODF2, C.score, checker,

rescale

Should all measures be rescaled so that higher values mean higher nestedness? Defaults to FALSE, i.e. the standard interpretation of each measure is maintained.

normalised

Logical, defaulting to TRUE. Should C-scores be normalised to a value between 0 and 1? See C.score for details.

Value

• A vector with values for each of the selected nestedness measures.

encoding

UTF-8

Details

There are five different measures currently available: [object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

References

Almeida-Neto, M., Guimaraes, P., Guimaraes, P.R., Loyola, R.D. and Ulrich, W. 2008. A consistent metric for nestedness analysis in ecological systems: reconciling concept and measurement. Oikos 117, 1227--1239. Almeida-Neto, M. and Ulrich, W. (2011) A straightforward computational approach for measuring nestedness using quantitative matrices. Environmental Modelling & Software, 26, 173--178

Blüthgen, N., J. Fründ, D. P. Vazquez, and F. Menzel. 2008. What do interaction network metrics tell us about specialisation and biological traits? Ecology 89, 3387--3399.

Brualdi, R.A. and Sanderson, J.G. 1999. Nested species subsets, gaps, and discrepancy. Oecologia 119, 256--264. Galeano, J., Pastor, J.M., Iriondo and J.M. 2008. Weighted-Interaction Nestedness Estimator (WINE): A new estimator to calculate over frequency matrices. arXiv 0808.3397v2 [physics.bio-ph] Rodríguez-Gironés, M.A. and Santamaría, L. 2006. A new algorithm to calculate the nestedness temperature of presence-absence matrices. J. Biogeogr. 33, 924--935.

Stone, L. and Roberts, A. 1990. The checkerboard score and species distributions. Oecologia 85, 74--79.

Almeida-Neto, M. and Ulrich, W. 2010. A straightforward computational approach for measuring nestedness using quantitative matrices. Environmental Modelling & Software, in press.

See Also

C.score, wine, nestedness, discrepancy; and, within vegan: nestedtemp, nestedchecker, nesteddisc, nestednodf

Examples

data(Safariland)
nested(Safariland, "ALL")
nested(Safariland, "ALL", rescale=TRUE)
# illustration that non-normalised C.score and checker are the same:
nested(Safariland, c("C.score", "checker"), normalise=FALSE)