compute_dis: compute pairwise network dissimilarity indices

In MarcOhlmann/metanetwork: Handling and Representing Trophic Networks in Space and Time

compute pairwise network dissimilarity indices

Description

Function to compute pairwise network dissimilarity indices based on Hill numbers following the method described in Ohlmann et al. 2019

Usage

compute_dis(metanetwork, q = 1, res = NULL, ncores = 4)

Arguments

metanetwork	object of class 'metanetwork'
q	viewpoint parameter controlling the weight given to abundant species/groups and links, default is 1
res	a vector containing the resolutions at which the diversities are computed
ncores	number of cores used for the computation, default is 4

Details

This function compute pairwise dissimilarity indices using Hill numbers on node and link abundances. Importantly, a viewpoint parameters q allows giving more weigth to abundant nodes/links. Given a network, we note p_q the abundance of node q (stored as node attribute ab) and \pi_{ql} interaction probability between nodes q and l (stored as edge attribute weight). The link abundance L_{ql} between nodes q and l is then:

L_{ql} = \pi_{ql}p_q p_l

Node diversity (for q = 1) is then computed as:

D(p) = \exp (\sum_q - p_q \log p_q)

Link diversity is computed as:

D(L) = \exp (\sum_{ql} - \frac{L_{ql}}{C} \log L_{ql}{C})

where C is the weighted connectance

C = \sum_{ql} \pi_{ql}p_q p_l

For q = 1, the pairwise node dissimilarity indices are computed from pairwise diversities as:

\delta_P=\frac{\log(G_P)-log(A_P)}{\log 2}

where G_P is node \gamma-diversity and A_P the node \alpha-diversity

Pairwise link diversity is:

\delta_L=\frac{\log(G_L)-log(A_L)}{\log 2}

where G_P is the link \gamma-diversity and A_P the link \alpha-diversity

For more details on \alpha-,\beta- and \gamma-diversity, see Ohlmann et al. 2019.

Value

a list of data.frame containing node and link pairwise dissimilarities

References

Ohlmann, M., Miele, V., Dray, S., Chalmandrier, L., O'connor, L., & Thuiller, W. (2019). Diversity indices for ecological networks: a unifying framework using Hill numbers. Ecology letters, 22(4), 737-747.

See Also

compute_div()

Examples

library(metanetwork)
library(igraph)

#on angola dataset
data(meta_angola)
compute_dis(meta_angola,q = 1,ncores = 1)

#computing dissimilarities only at Phylum level
compute_dis(meta_angola,q = 1,res = "Phylum",ncores = 1)

MarcOhlmann/metanetwork documentation built on July 1, 2023, 6:27 a.m.