graph-operations2: More advanced operations on undirected and directed acyclic graphs.

Description

Make operations on undirected and directed acyclic graphs.

Usage

mcs(object, root=NULL, index=FALSE)
mcsMAT(amat, vn = colnames(amat), root = NULL, index = FALSE) 
rip(object,root=NULL,nLevels=NULL)
ripMAT(amat, root = NULL, nLevels = NULL) 
moralize(object)
moralizeMAT(amat)
maxCliqueMAT(amat)
jTree(object, method="mcwh", nLevels=rep(2,length(nodes(object))),control=list())

Arguments

object

An undirected graph (of class "graphNEL")

root

Variables to be considered first when doing the orderings

index

If TRUE, then a permutation is returned

nLevels

Number of levels of the nodes in the graph

amat

Adjacency matrix

Nodes in the graph given by adjacency matrix

method

The triangulation method, "mcwh" is a C implementation of a minimum clique weight heuristic, "R" is a corresponding R implementation (experimental)

control

Currently not used

Value

moralize and triangulate returns objects of class "graphsh". MCS and MCSMAT return a vector with a linear ordering (obtained by maximum cardinality search) of the variables or character(0) if such an ordering can not be created. RIP and RIPMAT returns a list with cliques, separators etc. if a RIP ordering can be made and an empty list if not.

Details

The RIP and RIPMAT functions return a RIP ordering of the cliques. This is obtained by first ordering the variables linearly with maximum cardinality search (by MCS). The root argument is transfered to MCS as a way of controlling which clique will be the first in the RIP ordering. The jTree (for "junction tree") is just a wrapper for a call of triangulate followed by a call of RIP.

Examples

Run this code

## Undirected graphs
##
ugr <- ug(~me+ve,~me+al,~ve+al,~al+an,~al+st,~an+st)
ugm <- as.adjMAT(ugr)
edges(ugr)
nodes(ugr)
mcs(ugr)
mcsMAT(ugm)
rip(ugr)
ripMAT(ugm)

maxClique(ugr)
maxCliqueMAT(ugm)

## Directed graphs
##
dagr <- dag(~me+ve,~me+al,~ve+al,~al+an,~al+st,~an+st)
edges(dagr)
nodes(dagr)
moralize(dagr)