nestedness: Calculates nestedness temperature of presence/absence...

In bipartite: Visualising Bipartite Networks and Calculating Some (Ecological) Indices

Calculates nestedness temperature of presence/absence matrices

Description

Deprecated: Calculates matrix temperature using the binmatnest approach of Miguel Rodríguez-Gironés

Usage

nestedness(m, null.models = TRUE, n.nulls = 100, popsize = 30, 
n.ind = 7, n.gen = 2000, binmatnestout=FALSE)

Arguments

m	m is the matrix object for which the temperature is calculated. m will be converted to a binary matrix as temperature is only based on binary data
null.models	Ignored. Logical; shall the three different null models to check for significance of the matrix temperature be calculated? The null models procedure is quite time consuming and therefore we added this switch. Defaults to null.models=TRUE.
n.nulls	Ignored. How many null models should be calculated. Defaults to n.nulls=100.
popsize	Ignored. For the genetic algorithm some parameters have to be initialised. First is popsize, default is 30
n.ind	Ignored. Second is number of individuals picked for the next generation. Default of n.ind is 7.
n.gen	Ignored. Third is the number of generations until the genetic algorithm stops. Default of n.gen is 2000.
binmatnestout	Ignored. If set to TRUE a file "binmat.out" is saved in the current working directory , which stores the original binmatnest output

Details

This is a note that the original function provided here, and detailed below, has been retired. vegan's nestedtemp is more stable and replaces this call whereever we use it in bipartite. Indeed, calling bipartite's nestedness now simply call's vegan's nestedtemp. The function will eventually disappear, but for now this fix is provided as legacy support for dependent packages.

All arguments except first are ignored.

There are several implementations of nestedness-calculators, most noticeably NTC (nestedness temperature calculator), BINMATNEST and aninhado (check Wikipedia's entry on the subject: https://en.wikipedia.org/wiki/Nestedness). While we used BINMATNEST, this does not disqualify any of the others. Miguel was simply the first we contacted and he was readily willing to share his code.

We used BINMATNEST by calling a tweaked version of the C++ program binmatnest. In principle nestedness temperature is calculated by using a line of perfect order (using a genetic algorithm) to determine the reordering of rows and columns that leads to minimum matrix temperature of given size and fills. The deviation from this minimun temperature is the matrix temperature. In addition nestedness uses different null models to check for statistical significance of the matrix temperature. For details on what BINMATNEST does different, and better, than the original NTC see reference below.

Notice also that the original software BINMATNEST is available as a stand-alone application. Check out Miguel's homepage: http://www.eeza.csic.es/eeza/personales/rgirones.aspx

Value

comm	Returns the input.
u	null model matrix
r	marginal row proportions
c	marginal col proportions
p	??
fill	connectance: proportion of non-zero cells
statistic	nestedness temperature
smooth	??

References

Rodríguez-Gironés M.A., and Santamaría L. 2006. A new algorithm to calculate the nestedness temperature of presence-absence matrices. Journal of Biogeography 33, 924–935

bipartite documentation built on May 29, 2024, 2:23 a.m.