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Function to calculate weighted network indices

Source: R/calcFunctionalIndices.r
calc_weighted_topological_indices.Rd

This function calculates weighted topological indices for ecological networks, including: weighted linkage density, connectance, generality and vulnerability and the SDs of the last two based on [1] and the level of omnivory, mean and maximum trophic level based on [2] using NetIndices::TrophInd() function. The igraph networks must have the weight attribute.

Usage

calc_weighted_topological_indices(ig, ncores = 0)

Arguments

ig

An igraph object with the weight attribute representing fluxes

ncores

number of cores used to compute in parallel, if 0 sequential processing is used.

Value

a data.frame with the following fields:

  • LD: linkage density

  • Connectance: directed Connectance

  • TLmean: mean trophic level

  • TLmax: maximum trophic level

  • LOmnivory: Level of omnivory, quantifies mean of the variety in trophic levels of the preys of a consumer

  • Vulnerability: mean of number of consumers per prey

  • VulSD: the standard deviation of normalized Vulnerability

  • Generality: mean number of prey per consumer

  • GenSD: the standard deviation of normalized Generality

References

  1. Bersier, LF. et al. (2002). Quantitative Descriptors Of Food-web Matrices. Ecology, 83(9), 2394–2407.

  2. Kones, JK. et al. (2009). Are network indices robust indicators of food web functioning? A Monte Carlo approach. Ecological Modelling, 220, 370–382.

Examples


# Generate a test network

g <-   graph_from_literal( 1 -+ 4 -+ 7,2 -+ 5 -+7, 3-+6-+7, 7-+7, 4+-3, simplify = FALSE)

# Add weight

E(g)$weight <- sample(c(.1,.2,.8,.9),gsize(g),replace=TRUE)

calc_weighted_topological_indices(g)
#>        wLD wConnectance  wTLmean   wTLmax wLOmnivory wVulnerability    wVulSD
#> 1 1.839137    0.2627338 1.626374 2.384615 0.08140971       1.083482 0.5894277
#>   wGenerality   wGenSD
#> 1    2.594791 2.067256