vaznull: Null model with constrained connectance and moderately...

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

View source: R/vaznull.r

Description

Implements Diego Vazquez proposal of a null model for pollination networks

Usage

1
 vaznull(N, web) 

Arguments

N

Number of desired null model webs.

web

An interaction matrix.

Details

This function produces a null model network with the main constraint of a connectance that is the same as in the original network. In the process of producing this null model, marginal totals will turn out to be different from the original network, less so for large, dense webs than for small, sparse webs. vaznull is our implementation of the algorithm propose by Diego Vazquez, hence its name. vaznull differs from swap.web in that marginal totals are not strictly constraint! The algorithm used as well as the null model it outputs are different.

The algorithm was described as follows: "The algorithm randomized the total number of individual interactions observed in the original interaction matrix, F. To this end, the algorithm first created a binary matrix, assigning interspecific interactions according to species-specific probabilities, requiring that each species had at least one interaction. As in Vazquez et al. (2005b), the species-specific probabilities were proportional to species' relative abundances (probabilities are in fact approximately proportional and not equal to relative abundances because of the requirement that each species receives at least one interaction; this requirement causes probabilities to deviate from relative abundances, especially for rare species). Once the number of filled cells in the original matrix was reached, the remaining interactions were distributed among the filled cells, so that connectance in the original and randomized matrices was the same." (Vazquez et al. 2007, page 1122-1123).

Value

A list of N randomised matrices with the same dimensions and connectivity as the initial web.

Author(s)

Bernd Gruber <[email protected]> & Carsten F. Dormann <[email protected]>

References

Vázquez, D. P., C. J. Melian, N. M. Williams, N. Blüthgen, B. R. Krasnov, and R. Poulin. 2007. Species abundance and asymmetric interaction strength in ecological networks. Oikos 116: 1120-1127.

See Also

r2dtable, swap.web

Examples

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	## Not run: 
		data(Safariland)
		networklevel(Safariland, index="info")
		networklevel(vaznull(1, Safariland)[[1]], index="info")
		system.time(vaznull(10, Safariland))
		system.time(swap.web(10, Safariland))
	
## End(Not run)

Example output

Loading required package: vegan
Loading required package: permute
Loading required package: lattice
This is vegan 2.4-3
Loading required package: sna
Loading required package: statnet.common
Loading required package: network
network: Classes for Relational Data
Version 1.13.0 created on 2015-08-31.
copyright (c) 2005, Carter T. Butts, University of California-Irvine
                    Mark S. Handcock, University of California -- Los Angeles
                    David R. Hunter, Penn State University
                    Martina Morris, University of Washington
                    Skye Bender-deMoll, University of Washington
 For citation information, type citation("network").
 Type help("network-package") to get started.

sna: Tools for Social Network Analysis
Version 2.4 created on 2016-07-23.
copyright (c) 2005, Carter T. Butts, University of California-Irvine
 For citation information, type citation("sna").
 Type help(package="sna") to get started.

 This is bipartite 2.08
 For latest changes see versionlog in  ?"bipartite-package".
 For citation see: citation("bipartite").
 Have a nice time plotting and analysing two-mode networks.


Attaching package: 'bipartite'

The following object is masked from 'package:vegan':

    nullmodel

           connectance          web asymmetry      links per species 
             0.1604938              0.5000000              1.0833333 
number of compartments   number.of.species.HL   number.of.species.LL 
             2.0000000             27.0000000              9.0000000 
           connectance          web asymmetry      links per species 
             0.1604938              0.5000000              1.0833333 
number of compartments   number.of.species.HL   number.of.species.LL 
             1.0000000             27.0000000              9.0000000 
   user  system elapsed 
  0.281   0.004   0.289 
   user  system elapsed 
  0.093   0.004   0.097 

bipartite documentation built on May 30, 2017, 1:25 a.m.