Analysis of ecological networks

The EcologicalNetwork package offers a convenient interface to analyse several types of ecological networks. Rather than providing multiple measures of the same property, we selected measures that have been demonstrated to work and be robust.

The structure of this documentation is trying to match (as much as possible) the structure of Delmas et al. (2017), where most of the measures presented here are reviewed.

Overview of methods

This table gives an overview of the currently available methods, as a function of the network type. In the Quantitative column, a D means that the method exists but works on the Deterministic part of the network (i.e. the information about interaction weight is removed).

Measure type Measure Deterministic Quantitative Probabilistic
degree yes yes yes
specificity PDI yes
RR yes
connectance yes D yes
link density yes
nestedness $\eta$ bipartite bipartite
NODF bipartite
WNODF bipartite
modularity $Q$ yes yes yes
$Q'_R$ yes yes yes
label propagation yes yes yes
motif counting yes D yes
null models 1 (connectance) yes
2 (degree) yes
3in (columns) yes
3out (rows) yes
swap fill yes
generality yes
vulnerability yes
degre distribution yes
centrality Katz yes yes
Closeness yes
paths number yes yes
shortest yes yes
trophic level fractional unipartite
weighted unipartite