essentialGraph: Construct the essential graph

View source: R/abn-toolbox.R

essentialGraphR Documentation

Construct the essential graph


Constructs different versions of the essential graph from a given DAG


essentialGraph(dag, node.names = NULL, PDAG = "minimal")



a matrix or a formula statement (see ‘Details’ for format) defining the network structure, a directed acyclic graph (DAG).


a vector of names if the DAG is given via formula, see ‘Details’.


a character value that can be: minimal or complete, see ‘Details’.


This function returns an essential graph from a DAG, aka acyclic partially directed graph (PDAG). This can be useful if the learning procedure is defined up to a Markov class of equivalence. A minimal PDAG is defined as only directed edges are those who participate in v-structure. Whereas the completed PDAG: every directed edge corresponds to a compelled edge, and every undirected edge corresponds to a reversible edge.

The dag can be provided using a formula statement (similar to glm). A typical formula is ~ node1|parent1:parent2 + node2:node3|parent3. The formula statement have to start with ~. In this example, node1 has two parents (parent1 and parent2). node2 and node3 have the same parent3. The parents names have to exactly match those given in node.names. : is the separator between either children or parents, | separates children (left side) and parents (right side), + separates terms, . replaces all the variables in node.names.


A matrix giving the PDAG.


Gilles Kratzer


West, D. B. (2001). Introduction to Graph Theory. Vol. 2. Upper Saddle River: Prentice Hall.

Chickering, D. M. (2013) A Transformational Characterization of Equivalent Bayesian Network Structures, arXiv:1302.4938.

Further information about abn can be found at:


dag <- matrix(c(0,0,0, 1,0,0, 1,1,0), nrow = 3, ncol = 3)
dist <- list(a="gaussian", b="gaussian", c="gaussian")
colnames(dag) <- rownames(dag) <- names(dist)


abn documentation built on April 25, 2022, 9:06 a.m.