R/del.node.R

In bomeara/phybase: Basic functions for phylogenetic analysis

`del.node` <-
function(inode,name,nodematrix)
{

    nodes<-nodematrix
    root<-rootoftree(nodematrix)
    if(inode == root)
        stop("Delete the whole tree!")
    if(nodes[inode,1] == root){
        if(nodes[root,3] == inode)
            newroot <- nodes[root,2]
        if(nodes[root,2] == inode)
            newroot <- nodes[root,3]
    }  else{
        newroot <- root
        father<-nodes[inode,1]
        grandfather<-nodes[father,1]
        if(nodes[father,3] == inode)
            son <- nodes[father,2]
        if(nodes[father,2] == inode)
            son <- nodes[father,3]
        nodes[inode,4] <- nodes[inode,4] + nodes[father,4]
        nodes[son,1] <- grandfather
        nodes[son,4]<-nodes[son,4]+nodes[father,4]

        if(nodes[grandfather,3] == father)
            nodes[grandfather,3]<-son
        if(nodes[grandfather,2] == father)
            nodes[grandfather,2]<-son
    }
    
    z <- list(nodes = matrix(0, dim(nodes)[1], 5), treestr="")

    z$nodes<-nodes
    z$treestr<-write.subtree(newroot,nodes,name,newroot)
    z
}