R/dist.bin.3col.r

In iCAMP: Infer Community Assembly Mechanisms by Phylogenetic-Bin-Based Null Model Analysis

dist.bin.3col<-function(dist.bin,obj.name=NULL)
{
  dist.3col<-function(dist)
  {
    dist=as.matrix(dist)
    rowname=rownames(dist)
    colname=colnames(dist)
    rown=row(dist)
    coln=col(dist)
    dist.v=as.vector(stats::as.dist(dist))
    rown.v=as.vector(stats::as.dist(rown))
    coln.v=as.vector(stats::as.dist(coln))
    res=data.frame(name1=rowname[rown.v],name2=colname[coln.v],dis=dist.v)
    res
  }
  dist.3col=cbind(dist.3col(dist.bin[[1]]),sapply(2:length(dist.bin),function(i){dist.3col(dist.bin[[i]])[,3]}))
  colnames(dist.3col)[3:ncol(dist.3col)]<-paste0(paste(c(obj.name,"bin"),collapse = "."),1:length(dist.bin))
  dist.3col
}