poc: Proportion of connector nodes

In ILSM: Analyze Interconnection Structure of Tripartite Interaction Networks

Proportion of connector nodes

Description

Calculating the proportion of connector nodes in the shared set of nodes.

Usage

poc(network.or.subnet_mat1, subnet_mat2 = NULL)

Arguments

network.or.subnet_mat1	An igraph object or matrix. An "igraph" object with node attribute 'level' or a matrix representing one subnetwork. See details.
subnet_mat2	A matrix representing one subnetwork.

Details

In this package, a tripartite network contains three groups of nodes (a-nodes,b-nodes,c-nodes) and two subnetworks (P includes the links between a-nodes and b-nodes, Q includes the links between b-nodes and c-nodes). Connector nodes belong to b-nodes.

Two types of inputs network.or.subnet_mat1 can be processed:

• An "igraph" object with node attribute 'level' (0 for a-nodes, 1 for b-nodes,2 for c-nodes).

• Or a matrix representing subnetwork P, and must be input with subnet_mat2 representing subnetwork Q.

If the inputs are two matrices, please make sure the rows of network.or.subnet_mat1 and subnet_mat2 both represent the groups of connector species,i.e, the b-group species. If both matrices have row names, then the function matches row names to produce connector nodes. Otherwise, row numbers are assigned to row names and matched. Within the two matrices (P and Q), columns represents a-group nodes and c-group nodes respectively. Elements in matrices are non-zero values if two nodes are linked with or without weights, and 0 otherwise.

Value

Return a vector of POC (proportion of connector nodes), number of connector nodes and number of shared species set.

References

Battiston, F., Nicosia, V. & Latora, V. (2014) Structural measures for multiplex networks. Physical Review E, 89, 032804.

Dominguez-Garcia, V. and Kefi, S. (2024). The structure and robustness of ecological networks with two interaction types. PLOS Computational Biology, 20(1), e1011770.

Guimera, R. & Amaral, L.A.N. (2005) Cartography of complex networks: modules and universal roles. Journal of Statistical Mechanics: Theory and Experiment, 2005, P02001.

Examples

## generate a random binary tripartite network
set.seed(12)
Net <- build_toy_net(11,15,16,0.2)
poc(Net)

## empirical network
data(PPH_Coltparkmeadow)
Net <- PPH_Coltparkmeadow
poc(Net)

##input as binary matrices,with row names.
md1 <- matrix(sample(c(0,1),8*11,replace=TRUE),8,11)
dimnames(md1) = list(paste0("b",1:8),paste0("c",1:11))
md2 <- matrix(sample(c(0,1),10*12,replace=TRUE),10,12)
dimnames(md2) = list(paste0("b",1:10),paste0("a",1:12))
poc(md1,md2)

##input as weighted matrices,with row numbers as row names.
mdw1 <- matrix(sample(c(rep(0,40),runif(48,0,1))),8,11)
mdw2 <- matrix(sample(c(rep(0,40),runif(80,0,1))),10,12)
poc(mdw1,mdw2)

ILSM documentation built on Aug. 8, 2025, 7:42 p.m.