nestedcontribution: Calculates the per-species contribution to nestedness...

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

View source: R/nestedcontribution.R

Description

Estimates the degree to which the interactions of each row and column species increase or decrease community nestedness.

Usage

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nestedcontribution(web, nsimul = 99)

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. Non-binary matrices will be converted to 0/1 data.

nsimul

Number of randomizations to use as the basis for each comparison.

Details

The idea behind nestedness contribution is to determine how individual species' interactions change community nestedness compared to a random null model that is designed to control for the effect of differences in degree. For each row and column species, this function compares observed nestedness to an ensemble of nestedness values generated by randomizing the interactions of just that focal species. Nestedness contributions are the z-scores from this comparison. Therefore, a positive contributor to community nestedness (i.e., a species whose interactions increase overall nestedness) will obtain values greater than 0 and negative contributors to nestedness will obtain values less than 0.

Value

For both the “higher trophic level” and the “lower trophic level”, this function returns a data frame with the per-species nestedness contributions.

Note

This function calculates per-species nestedness contributions as described in Saavedra et al. 2011—namely it is based on the metric NODF to measure nestedness and employs a probabilistic null model to randomize interactions (that is described in Bascompte et al. 2003). The underlying methodology is amenable to other choices in both of these cases; however, this is not implemented at present.

The currently implemented null model replaces the observed vector of 0/1s by a probabalistic draw of 0/1s as given by the mean of mean degree in the higher trophic level (rowSums(web)/ncol(web)) and the mean degree for the target higher trophic level species i (colSums(web)[i]/nrow(web)).

Author(s)

Daniel B. Stouffer [email protected]

References

Bascompte, J., Jordano, P., Melián, C.J., and Olesen, J.M. 2003. The nested assembly of plant-animal mutualistic networks. Proceedings of the National Academy of Sciences of the USA 100, 9383–9387

Saavedra, S., Stouffer, D.B., Uzzi, B., and Bascompte, J. 2011. Strong contributors to network persistence are the most vulnerable to extinction. Nature 478, 233–235

Examples

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  data(Safariland)
  ## Not run: 
    nestedcontribution(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

Aristotelia chilensis
Alstroemeria aurea
Schinus patagonicus
Berberis darwinii
Rosa eglanteria
Cynanchum diemii
Ribes magellanicum
Mutisia decurrens
Calceolaria crenatiflora
Policana albopilosa
Bombus dahlbomii
Ruizantheda mutabilis
Trichophthalma amoena
Syrphus octomaculatus
Manuelia gayi
Allograpta.Toxomerus
Trichophthalma jaffueli
Phthiria
Platycheirus1
Sapromyza.Minettia
Formicidae3
Nitidulidae
Staphilinidae
Ichneumonidae4
Braconidae3
Chalepogenus caeruleus
Vespula germanica
Torymidae2
Phthiria1
Svastrides melanura
Sphecidae
Thomisidae
Corynura prothysteres
Ichneumonidae2
Ruizantheda proxima
Braconidae2
$`higher level`
                        nestedcontribution
Policana albopilosa             -0.1153531
Bombus dahlbomii                 0.5859491
Ruizantheda mutabilis           -0.4593660
Trichophthalma amoena           -1.1149470
Syrphus octomaculatus            0.9430449
Manuelia gayi                    0.6062842
Allograpta.Toxomerus             1.0546365
Trichophthalma jaffueli          0.2858216
Phthiria                         0.7967057
Platycheirus1                    0.7752536
Sapromyza.Minettia               0.3048672
Formicidae3                     -0.8575450
Nitidulidae                     -0.8877459
Staphilinidae                    0.6725511
Ichneumonidae4                  -0.6973507
Braconidae3                     -0.8849903
Chalepogenus caeruleus          -1.0535915
Vespula germanica                0.5543586
Torymidae2                      -0.9074764
Phthiria1                        0.6900327
Svastrides melanura              0.3085028
Sphecidae                        0.4831139
Thomisidae                       0.4000538
Corynura prothysteres            1.0009616
Ichneumonidae2                   0.6178060
Ruizantheda proxima              0.2672394
Braconidae2                     -0.1994650

$`lower level`
                         nestedcontribution
Aristotelia chilensis             0.2442554
Alstroemeria aurea                2.3621969
Schinus patagonicus              -1.5136854
Berberis darwinii                -0.1068592
Rosa eglanteria                  -0.1412871
Cynanchum diemii                 -1.5941621
Ribes magellanicum               -1.2492716
Mutisia decurrens                -0.2519333
Calceolaria crenatiflora         -1.1980554

bipartite documentation built on May 22, 2019, 1:02 a.m.