ILSM (version 1.0.3.2)

poc: Proportion of interconnection

Description

Calculating the proportion of species sharing with other species of two subnetworks in intermediate layer.

Usage

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

Value

Print a "poc= ;" and Return a numeric value representing the proportion of sharing species in intermediate layer.

Arguments

network.or.subnet_mat1

Either a multilayer(tripartite) network of 'igraph' class which contains three groups of species and interactions within layers without interactions between each group of species, or a numeric matrix(or data.frame) representing interactions between two groups of species. Each row and column of matrix represents single species in the second and first groups of the tripartite network respectively. Elements of matrix are non-zero numbers if two groups of species are connected, and 0 otherwise.

subnet_mat2

A numeric matrix(or data.frame) representing interactions between two groups of species. Each row and column of matrix represents single species in the second and third groups of the tripartite network respectively. Elements of matrix are non-zero numbers if the two groups of species are connected, and 0 otherwise. If network.or.subnet_mat1 is "igraph", subnet_mat2 defaults to NULL.

Details

network.or.subnet_mat1 and subnet_mat2

There are two types of network.or.subnet_mat1 that can be processed:

• (1). Input in a network of type "igraph" alone.

• (2). Must be entered as data frame or matrix with subnet_mat2.

If the type of inputting is data frame or matrix, please make sure the row of network.or.subnet_mat1 and subnet_mat2 correspond with the second group of species that both belong to two subnetworks and interact with other groups of species.

• Try to make the rows of both matrices have the same attributes. Or we default:

• (1). If both matrices have row names, then the function counts all row names to produce two new matrices with the same row names.

• (2). If at most one matrix has row names, the function assigns new row names to both matrices on a row-to-row basis (any extra row names are assigned a new value) and then counts all row names to produce two new matrices with the same row names.

• The two matrices can have different numbers of rows, but read our default handling carefully to make sure the calculation is accurate when using this function!!!

About a network of type "igraph", It can be obtained from the connection matrices of subnetworks by the function igraph_from_matrices.

References

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

Domínguez-García, V., & Kéfi, 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

set.seed(15)
d <- build_net(11,15,17,0.2)
poc(d)

md1<-matrix(sample(c(0,1),80,replace=TRUE),8,10)
md2<-matrix(sample(c(0,1),120,replace=TRUE),10,12)
poc(md1,md2)

mdw1<-matrix(sample(c(rep(0,40),runif(60,0,1))),10,10)
mdw2<-matrix(sample(c(rep(0,40),runif(80,0,1))),10,12)
poc(mdw1,mdw2)

mdw1<-matrix(sample(c(rep(0,60),runif(60,0,1))),12,10)
mdw2<-matrix(sample(c(rep(0,40),runif(80,0,1))),10,12)
poc(mdw1,mdw2)