calc_modularity_swness_zscore: Calculation of Modularity and Small-world-ness z-scores

In lsaravia/EcoNetwork: Ecological network analyses including multiplex networks

Calculation of Modularity and Small-world-ness z-scores

Description

The function calculates modularity, number of groups and small-world-ness z-scores and 99\ using as null model the list of networks in the nullDist parameters. Modularity is calculated using the igraph::cluster_spinglass() if the parameter weights is NULL the atribute "weigths" is used, or if it has the name of an network attribute, that is used as a weigth to build the modules, when this parameter is NA then no weigth is used. Only works for one component networks

Usage

calc_modularity_swness_zscore(
  g,
  nullDist,
  sLevel = 0.01,
  ncores = 0,
  weights = NA
)

Arguments

g	igraph object
nullDist	list of igraph object with the null model simulations
sLevel	significance level to calculate CI (two tails)
ncores	number of cores to use paralell computation, if 0 sequential processing is used.
weights	The weights of the edges. Either a numeric vector or NULL or NA. If it is null and the input graph has a ‘weight’ edge attribute then that will be used. If NULL and no such attribute is present then the edges will have equal weights. Set this to NA if the graph was a ‘weight’ edge attribute, but you don't want to use it for community detection.

Value

a list with two data frames: one with indices z-scores and CI

Clustering	Clustering coefficient, measures the average fraction of pairs of neighbors of a node that are also neighbors of each other
PathLength	Mean of the shortest paths between all pair of vertices
Modularity	modularity measures how separated are different groups from each other, the algorithm cluster_spinglass was used to obtain the groups
zCC, zCP, zMO	Z-scores of Clustering,PathLength and Modularity with respect to a random Erdos-Renyi null model
CClow, CChigh, CPlow, CPhigh, MOlow, MOhigh	sLevel confidence intervals
SWness, SWnessCI	Small-world-ness and it CI value
isSW, isSWness	Logical variable signalling if the network is Small-world by the method of Marina 2018 or the method of Humprhies & Gurney 2008

Another data.frame with the values calculated for the nullDist.

References

Marina, T. I., Saravia, L. A., Cordone, G., Salinas, V., Doyle, S. R., & Momo, F. R. (2018). Architecture of marine food webs: To be or not be a ‘small-world.’ PLoS ONE, 13(5), 1–13. https://doi.org/10.1371/journal.pone.0198217

Examples

## Not run: 
nullg <- generateERbasal(netData[[1]],10)
calcModularitySWnessZScore(netData[[1]],nullg)

## End(Not run)

lsaravia/EcoNetwork documentation built on March 20, 2024, 3:27 p.m.