Description Usage Arguments Details Value Author(s) References Examples

Computation of the cpness measure for a bipartite graph/network

1 |

`web` |
A |

`type` |
Type of matrix. This should be (an unambiguous
abbreviation of) one of |

`plot` |
Plot the matrix reordered according to the core-periphery
partitioning. |

`fastplot` |
If |

In a matrix displaying a core-periphery structure, there is a species ordering (i.e. an ordering in rows and columns) such that interactions are distributed in an L-shape. This L-shape is composed by four blocks of varying connectance: block C11 represents the core; blocks C12 and C21 include the interactions between core and periphery; block C22 includes the interactions that occur between peripheral species.

This fonction computes the core-peripheriness (CPness), as
CPness=(E11+E12+E21)/E, where Eij is the number of interactions
(edges) or the sum of weights for each block (Eij for block ij) or
for the entire network (E). Here, we rely on a stochastic block model
(SBM) to detect the four groups/blocks C11, C12, C21 and C22 when they
actually exist. However, the SBM can fail in finding these blocks: in
these cases, there is no core-periphery partition and the CPness value is set to `NA`

.

This function can deal with binary and weighted networks with the appropriate statistical distribution (Bernouilli for `binary`

data, Poisson for `integer`

weights, and Gaussian for `float`

weights). Note that it is often advisable to log-transform float data before running the `cpness`

function.

`cpness`

returns an object of class `list`

with the following components:

`cpness` |
The value of the core-peripheriness measure. |

`rowmembership` |
An integer |

`colmembership` |
Same as |

Authors: Vincent Miele Maintainer: Vincent Miele <vincent.miele@univ-lyon1.fr>

Ana M. Martin Gonzalez, Diego P. Vazquez, Rodrigo Ramos-Jiliberto, Sang Hoon Lee & Vincent Miele, Core-periphery structure in mutualistic networks: an epitaph for nestedness? BiorXiv (2020) <doi:10.1101/2020.04.02.021691>

1 2 3 4 5 6 7 8 9 10 |

```
Loading required package: vegan
Loading required package: permute
Loading required package: lattice
This is vegan 2.5-7
Loading required package: sna
Loading required package: statnet.common
Attaching package: ‘statnet.common’
The following object is masked from ‘package:base’:
order
Loading required package: network
network: Classes for Relational Data
Version 1.16.1 created on 2020-10-06.
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 2.6 created on 2020-10-5.
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 2.15.
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
$cpness
[1] 0.9179104
$rowmembership
Cerastium.alpinum Caltha.palustris Papaver.radicatum Potentilla.vahliana
2 2 2 1
Dryas.integrifolia Geum.rossii Astragalus.alpinus Oxytropis.arctica
1 2 1 2
Petasites.frigidus Arnica.alpina Taraxacum.sp.
2 2 2
$colmembership
Boloria.improba Colias.hecla
2 1
Colias.nastes Anarta.richardsoni
2 2
Rhamphomyia.sp. Boreellus.atriceps
2 2
Protocalliphora.sp. Spilogona.aesturium
2 2
Spilogona.almquistii Spilogona.dorsata
1 2
Spilogona.hurdiana Spilogona.latilamina
2 2
Spilogona.melanosoma Spilogona.projecta
2 2
Spilogona.sanctipauli Eupogonomyia.probilofensis
1 1
Pogonomyiodes.segnis Bombus.polaris
2 1
[1] 0.7572879
1 2
5 51
1 2
8 249
```

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