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#' Functions for loading and writing Pajek files
#'
#' Functions for reading/loading and writing Pajek files:
#'
#'
#' @name Pajek
NULL
#' @rdname Pajek
#' @description \code{loadnetwork} - Loads a Pajek ".net" filename as a matrix. For now, only simple one and two-mode networks are supported (eg. only single relations, no time information).
#'
#' @aliases Pajek loadnetwork loadnetwork2 loadnetwork3 loadnetwork4 savevector savenetwork savematrix loadmatrix loadvector loadvector2 loadpajek
#'
#' @param filename The name of the file to be loaded or saved to or an open file object.
#' @param useSparseMatrix Should a sparse matrix be use instead of the ordinary one? Sparse matrices can only be used if package Matrix is installed. The default \code{NULL} uses sparse matrices for networks with more that \code{minN} vertices.
#' @param minN The minimal number of units in the network to use sparse matrices.
#'
#' @return NULL, a matrix or a vector.
#'
#' @references
#' Batagelj, V., & Mrvar. A. (1999). Pajek - Program for Large Network Analysis. Retrieved from http://vlado.fmf.uni-lj.si/pub/networks/pajek/.
#'
#' de Nooy, W., Mrvar, A., & Batagelj. V. (2005). Exploratory Social Network Analysis with Pajek. London: SAGE Publications.
#'
#' @author Vladimir Batagelj & Andrej Mrvar (most functions), \enc{Aleš Žiberna}{Ales Ziberna} (\code{loadnetwork}, \code{loadpajek} and modification of others)
#' @seealso \code{\link{plot.mat}}, \code{\link{critFunC}}, \code{\link{optRandomParC}}
#' @keywords graphs file
#' @import Matrix
#' @importFrom utils read.table
#'
#' @export
"loadnetwork" <-
function(filename,useSparseMatrix=NULL,minN=50){
trim.trailing <- function (x) sub("\\s+$", "", x)
n<-c("%")
i=0
repeat {
n<-read.table(file=filename,nrows=1,as.is=TRUE,skip = i)
if(substr(n[1],1,1)!="%") break
print(paste(n,collapse=" "))
i=i+1
}
if(length(n)==2){
n<-as.numeric(n[2])
n
rLines<-readLines(con=filename)
nl<-length(rLines)
#ind.stars<-which(regexpr(pattern="*", text=rLines,fixed=TRUE)>0)
ind.stars<-which(substr(rLines,1,1)=="*")
nstars<-length(ind.stars)
stars<-rLines[ind.stars]
stars<-trim.trailing(stars)
rm(rLines)
vnames1<-read.table(file=filename,skip=ind.stars[1],nrows=ind.stars[2]-ind.stars[1]-1,as.is =TRUE)
vnames<-character(n)
vnames[vnames1[,1]]<-vnames1[,2]
if(all(is.na(vnames))){
vnames<-NULL
} else vnames[is.na(vnames)]<-""
if(is.null(useSparseMatrix)){
useSparseMatrix<- n>=50
}
if(useSparseMatrix){
if(requireNamespace("Matrix")){
M<-Matrix::Matrix(0,nrow=n,ncol=n,sparse=TRUE)
}else{
warning("Matrix package is not installed. Ordanary (dense) matrices will be used instead of sparse onse")
M<-matrix(0,nrow=n,ncol=n)
}
}else{
M<-matrix(0,nrow=n,ncol=n)
}
if(useSparseMatrix){
if(requireNamespace("Matrix")){
M<-Matrix::Matrix(0,nrow=n,ncol=n,sparse=TRUE)
}else{
M<-matrix(0,nrow=n,ncol=n)
warning("Matrix package is not installed. Ordanary (dense) matrices will be used instead of sparse onse")
}
} else{
M<-matrix(0,nrow=n,ncol=n)
}
for(i in 2:nstars){
nrows<-ifelse(i==nstars,-1,ind.stars[i+1]-ind.stars[i]-1)
ties<-read.table(file=filename,skip=ind.stars[i],nrows=nrows)
ncols<-dim(ties)[2]
if(ncols==2){
ties<-cbind(ties,1)
} else if(ncols>3){
ties<-ties[,1:3]
}
ties<-apply(ties,2,as.numeric)
if(stars[i]=="*Arcs"|stars[i]=="*arcs"){
M[ties[,1:2]]<-ties[,3]
} else if(stars[i]=="*Edges"|stars[i]=="*edges"){
M[ties[,1:2]]<-ties[,3]
M[ties[,2:1]]<-ties[,3]
}
}
dimnames(M)<-list(vnames,vnames)
} else{
n12<-as.numeric(n[2])
n1<-as.numeric(n[3])
n2<-n12-n1
rLines<-readLines(con=filename)
nl<-length(rLines)
#ind.stars<-which(regexpr(pattern="*", text=rLines,fixed=TRUE)>0)
ind.stars<-which(substr(rLines,1,1)=="*")
nstars<-length(ind.stars)
stars<-rLines[ind.stars]
rm(rLines)
vnames1<-read.table(file=filename,skip=ind.stars[1],nrows=ind.stars[2]-ind.stars[1]-1,as.is =TRUE)
vnames<-character(n12)
vnames[vnames1[,1]]<-vnames1[,2]
if(all(is.na(vnames))){
vnames<-NULL
} else vnames[is.na(vnames)]<-""
if(is.null(useSparseMatrix)){
useSparseMatrix<- n12>50
}
if(useSparseMatrix){
if(requireNamespace("Matrix")){
M<-Matrix::Matrix(0,nrow=n12,ncol=n12,sparse=TRUE)
}else{
warning("Matrix package is not installed. Ordanary (dense) matrices will be used instead of sparse onse")
M<-matrix(0,nrow=n12,ncol=n12)
}
}else{
M<-matrix(0,nrow=n12,ncol=n12)
}
for(i in 2:nstars){
nrows<-ifelse(i==nstars,-1,ind.stars[i+1]-ind.stars[i]-1)
ties<-read.table(file=filename,skip=ind.stars[i],nrows=nrows)
ncols<-dim(ties)[2]
if(ncols==2){
ties<-cbind(ties,1)
} else if(ncols>3){
ties<-ties[,1:3]
}
ties<-apply(ties,2,as.numeric)
M[ties[,1:2]]<-ties[,3]
M[ties[,2:1]]<-ties[,3]
}
dimnames(M)<-list(vnames,vnames)
M<-M[1:n1,(n1+1):n12]
}
return(M)
}
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