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graph generation utilities {bnlearn} R Documentation

Generate empty or random graphs

Description

Generate empty or random graphs from a given set of nodes.

Usage

empty.graph(nodes, num = 1)
random.graph(nodes, num = 1, method = "ordered", ...,
  debug = FALSE)

Arguments

nodes a vector of character strings, the labels of the nodes.
num an integer, the number of graphs to be generated.
method a character string, the label of a score. Possible values are ordered (full ordering based generation), ic-dag (Ide's and Cozman's Generating Multi-connected DAGs algorithm), melancon (Melancon's and Philippe's Uniform Random Acyclic Digraphs algorithm) and empty (generates empty graphs).
... additional tuning parameters (see below).
debug a boolean value. If TRUE a lot of debugging output is printed; otherwise the function is completely silent. Ignored in some generation methods.

Details

Available graph generation algorithms are:

  • full ordering based generation (ordered): generates graphs whose node ordering is given by the order of the labels in the nodes parameter. The same algorithm is used in the randomDAG function in package pcalg.
  • Ide's and Cozman's Generating Multi-connected DAGs algorithm (ic-dag): generates graphs with a uniform probability distribution over the set of multiconnected graphs.
  • empty graphs (empty): generates graphs without any arc.

Additional parameters for the random.graph function are:

  • prob: the probability of each arc to be present in a graph generated by the ordered algorithm. The default value is 2 / (length(nodes) - 1), which results in a sparse graph (the number of arcs should be of the same order as the number of nodes).
  • burn.in: the number of iterations for the ic-dag and melancon algorithms to converge to a stationary (and uniform) probability distribution. The default value is 6 * length(nodes)^2.
  • max.degree: the maximum degree for any node in a graph generated by the ic-dag and melancon algorithms. The default value is Inf.
  • max.in.degree: the maximum in-degree for any node in a graph generated by the ic-dag and melancon algorithms. The default value is Inf.
  • max.out.degree: the maximum out-degree for any node in a graph generated by the ic-dag and melancon algorithms. The default value is Inf.

Value

Both empty.graph and random.graph return an object of class bn (if num is equal to 1) or a list of objects of class bn (otherwise).

Author(s)

Marco Scutari

References

Ide JS, Cozman FG (2002). "Random Generation of Bayesian Networks". In "SBIA '02: Proceedings of the 16th Brazilian Symposium on Artificial Intelligence", pp. 366-375. Springer-Verlag.

Melancon G, Dutour I, Bousquet-Melou M (2000). "Random Generation of Dags for Graph Drawing". Technical Report INS-R0005, Centre for Mathematics and Computer Sciences, Amsterdam.

Melancon G, Philippe F (2004). "Generating Connected Acyclic Digraphs Uniformly at Random". Information Processing Letters, 90(4), 209-213.

Examples

empty.graph(LETTERS[1:8])
#
#  Randomly generated Bayesian network
#
#  model:
#    [A][B][C][D][E][F][G][H]
#  nodes:                                 8
#  arcs:                                  0
#    undirected arcs:                     0
#    directed arcs:                       0
#  average markov blanket size:           0.00
#  average neighbourhood size:            0.00
#  average branching factor:              0.00
#
#  generation algorithm:                  Empty
#
random.graph(LETTERS[1:8])
# <insert the description of a random graph here>
plot(random.graph(LETTERS[1:8], method = "ic-dag", max.in.degree = 2))
plot(random.graph(LETTERS[1:8]))
plot(random.graph(LETTERS[1:8], prob = 0.2))
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