moduleWeb-class: Class "moduleWeb"

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

Class "moduleWeb"

Description

This class is the output of an application of the function computeModules to a graph. It consists of the matrix representing the original graph which has been passed to computeModules in order to compute modules, a matrix representing the same graph but permutated according to the identified modules, two vectors indicating the permutation of row and column indices, respectively, and information about the modules themselves.

Objects from the class

Objects from the class should only be created by using the function computeModules.

Slots

likelihood:

Contains a number with the likelihood-equivalent of the final proposed module structure. This value is the same value as Q (or M), the modularity as given by Newman or Guimerà & Amaral (2005).

originalWeb:

Object of class "matrix" representing the original bipartite graph in which modules have been computed.

moduleWeb:

Object of class "matrix" representing the original bipartite graph but reordered such that plotting modules is possible.

orderA:

Object of class "vector" representing the permutation of the rows of the original graph.

orderB:

Object of class "vector" representing the permutation of the columns of the original graph.

modules:

Object of class "matrix" containing for each module the information about its depth and involved nodes. The first row is just a consecutive number, so of no information; the first two columns can also be ignored. This matrix shows ALL network players (in the sequence of the original matrix, starting with rows), so first rows, then columns. There are as many rows as modules. Each row writes a number if a species is in that module, or a 0 if it isn't. For the modules of Safariland (mod <- computeModules(Safariland); mod@modules[-1, -c(1,2) ]), the third module are species 3 and 24, i.e. Schinus patagonicus (third row) and Ichneumonidae4 (24 - 9 column).

Methods

Objects of this class are used in following functions:

listModuleInformation(moduleWebObject)

printoutModuleInformation(moduleWebObject)

plotModuleWeb(moduleWebObject, plotModules=TRUE, rank=FALSE, weighted=TRUE, displayAlabels=TRUE, displayBlabels=TRUE, labsize=1, plotsize=12, xlabel="", ylabel="", square.border="white", fromDepth=0, upToDepth=-1)

Author(s)

Rouven Strauss

Examples

showClass("moduleWeb")

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