Implements Diego Vazquez proposal of a null model for pollination networks
Number of desired null model webs.
An interaction matrix.
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).
A list of N randomised matrices with the same dimensions and connectivity as the initial web.
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.
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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
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