ig_icmotif_role: Count the roles of connector nodes defined by interconnection...

In ILSM: Analyze Interconnection Structure of Tripartite Interaction Networks

Count the roles of connector nodes defined by interconnection motifs with intra-guild interactions

Description

Count the roles of connector nodes defined by interconnection motifs in a tripartite network with intra-guild interactions.

Usage

ig_icmotif_role(mat, guilds, weighted = FALSE)

Arguments

mat	A square block interaction matrix representing a tripartite network including intra-guild and inter-guild interactions. See details.
guilds	A character vector matching rows of mat to indicate the guilds using ('a','b' and 'c'). See details.
weighted	Logical. Default to FALSE. If TRUE, a weighted measure is provided. See details.

Details

This function is designed for tripartite networks with intra-guild interactions. The input network should be nput as a block matrix (M) to represent three groups of nodes (a-nodes, b-nodes and c-nodes): three intra-guild interaction matrices (m_{aa},m_{bb},m_{cc}), two inter-guild matrices of a and b-nodes (m_{ab},m_{ba}), and two inter-guild matrices of b- and c-nodes(m_{bc},m_{cb}).

\left( \begin{array}{ccc} m_{aa} & m_{ab} & 0 \\ m_{ba} & m_{bb} & m_{bc} \\ 0 & m_{cb} & m_{cc} \end{array} \right)

guilds should be a vector of the same length as the row of mat like c("a","a"..."b","b"..."c","c"..)

Interconnection motifs in tripartite networks with intra-guild interactions
An interconnection motif is defined to comprise three sets of connected nodes: the connector nodes (belonging to b-nodes), the nodes in one subnetwork (belonging to a-nodes in the P subnetwork), and the nodes in the other subnetwork (belonging to c-nodes in the Q subnetwork). Each guild has two nodes at most, resulting in a total of 107 distinct motif forms. The algorithm for counting interconnection motifs is designed by extending the fast approach from Simmons et al.(2019). Currently, only the roles in first 35 motifs are provided (see ). For interconnection motifs in tripartite networks without intra-guild interactions, please see icmotif_count and icmotif_role.

Weighted networks
For weighted tripartite networks, the mean weight of the motif occurrence (i.e., a motif occurrence isomorphic to a particular motif form) is provided for a given node with a given role, following Mora et al. (2018) and Simmons et al. (2019).

Value

For binary networks, return a matrix with elements representing the number of times each connector node plays for each unique role within interconnection motifs; for weighted networks, the matrix element represents the mean weight of the motif occurrences where the node exists.

References

Garcia-Callejas, D., Godoy, O., Buche, L., Hurtado, M., Lanuza, J.B., Allen-Perkins, A. et al. (2023) Non-random interactions within and across guilds shape the potential to coexist in multi-trophic ecological communities. Ecology Letters, 26, 831-842.

Pilosof, S., Porter, M. A., Pascual, M., & KC)fi, S. (2017). The multilayer nature of ecological networks. Nature Ecology & Evolution, 1(4), 0101.

Mora, B.B., Cirtwill, A.R. and Stouffer, D.B. (2018). pymfinder: a tool for the motif analysis of binary and quantitative complex networks. bioRxiv, 364703.

Simmons, B. I., Sweering, M. J., Schillinger, M., Dicks, L. V., Sutherland, W. J., & Di Clemente, R. (2019). bmotif: A package for motif analyses of bipartite networks. Methods in Ecology and Evolution, 10(5), 695-701.

Examples

##A toy tripartite network with intra-guild negative interactions:
##Inter-guild mutualistic interactions and inter-guild antagonistic interactions.
set.seed(12)
##4 a-nodes, 5 b-nodes, and 3 c-nodes

##Intra-guild interaction matrices
mat_aa<-matrix(runif(16,-0.8,-0.2),4,4)
mat_aa <- mat_aa + t(mat_aa); diag(mat_aa) <- 0
mat_bb<-matrix(runif(25,-0.8,-0.2),5,5)
mat_bb <- mat_bb + t(mat_bb); diag(mat_bb) <- 0
mat_cc<-matrix(runif(9,-0.8,-0.2),3,3)
mat_cc <- mat_cc + t(mat_cc); diag(mat_cc) <- 0

##Inter-guild interaction matrices between a- and b-nodes.
mat_ab<-mat_ba<-matrix(sample(c(rep(0,8),runif(12,0,0.5))),4,5,byrow=TRUE)
mat_ba<-t(mat_ba)

##Inter-guild interaction matrices between b- and c-nodes.
mat_cb<-mat_bc<-matrix(sample(c(rep(0,8),runif(7,0,0.5))),3,5,byrow=TRUE)
mat_bc<--t(mat_bc)
mat<-rbind(cbind(mat_aa,mat_ab,matrix(0,4,3)),cbind(mat_ba,mat_bb,mat_bc))
mat<-rbind(mat,cbind(matrix(0,3,4),mat_cb,mat_cc))

##Set the node names
rownames(mat)<-c(paste0("a",1:4),paste0("b",1:5),paste0("c",1:3))
colnames(mat)<-c(paste0("a",1:4),paste0("b",1:5),paste0("c",1:3))

myguilds=c(rep("a",4),rep("b",5),rep("c",3))
ig_icmotif_role(mat,guilds=myguilds)
ig_icmotif_role(mat,guilds=myguilds,TRUE)

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