#' Convert network matrix to network rank matrix
#'
#' The edge weights in the network matrix will be converted to their ranks. A high rank value indcates a high edge connection.
#'
#' @param adjmatrix A network matrix
#' @param directed Logical. If TRUE, the network is considered as directed. If FALSE, the upper triangular part of the symmetric network matrix is used to calcuate the rank matrix.
#' @return \code{adj2rankadj} returns a network matrix with ranks of the edge weightes.
#' @export
adj2rankadj<-function(adjmatrix,directed=F){
adjmatrix.rank<-adjmatrix-adjmatrix
if(!directed){
values<-rank(adjmatrix[upper.tri(adjmatrix)])
adjmatrix.rank[upper.tri(adjmatrix.rank)]<-values
adjmatrix.rank<-pmax(adjmatrix.rank,t(adjmatrix.rank))
}
if(directed){
diag(adjmatrix)<-NA
values<-rank(adjmatrix)
adjmatrix.rank[]=values
diag(adjmatrix.rank)<-0
}
return(adjmatrix.rank)
}
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