R/role_sim.R

In ILSM: Analyze Interconnection Structure of Tripartite Interaction Networks

#' Similarity of roles of interconnecting species
#'
#' The average of Similarity of 65 roles of interconnecting species of
#'   tripartite network.
#'
#' @param spe_role_mat A matrix of 70 columns representing the roles of
#'   interconnecting species in the motifs. Columns names are Role1, Role2,
#'   Role3 ... Role70.
#'
#' @details
#'
#' \strong{spe_role_mat}
#'
#' Should acquire from function \code{motif_role}.
#'
#' @return
#' Return a numeric value.
#'
#' @export
#'
#'
#' @examples
#'
#' ## generate a random tripartite network
#' set.seed(12)
#' Net <- build_toy_net(11,15,16,0.2)
#' role_sim(icmotif_role(Net))
#'
#' data(PPH_Coltparkmeadow)
#' Net <- PPH_Coltparkmeadow
#' role_sim(icmotif_role(Net))
#'
#'
#'
#'
role_sim<-function(spe_role_mat){
  logi<-(rowSums(spe_role_mat)!=0)
  spe_role_mat<-spe_role_mat[logi,]
  role_sim<-NULL
  for(i in 1:(nrow(spe_role_mat)-1)){
    for(j in (i+1):nrow(spe_role_mat)){
      mat<-spe_role_mat[c(i,j),]
      role_sim<-c(role_sim,sum(apply(mat,2,min))/sum(apply(mat,2,max)))
    }
  }
  return(mean(role_sim))
}