Utilities for Learning Sparse Bayesian Networks

A set of tools for representing and estimating sparse Bayesian networks from continuous and discrete data, as described in Aragam, Gu, and Zhou (2017) .

A set of tools for representing and estimating sparse Bayesian networks from continuous and discrete data.

Overview

This package provides various S3 classes for making it easy to estimate graphical models from data:

sparsebnData for managing experimental data with interventions.
sparsebnFit for representing the output of a DAG learning algorithm.
sparsebnPath for representing a solution path of estimates.

The package also provides methods for manipulating these objects and for estimating parameters in graphical models:

estimate.parameters for directed graphs.
get.precision for undirected graphs.
get.covariance for covariance matrices.

News

sparsebnUtils 0.0.6

Features

Added nchar argument to improve output of show.parents with long node names (#13)
openCytoscape now accepts title argument -- allows multiple cytoscape networks with different names to be open at the same time

sparsebnUtils 0.0.5

Features

openCytoscape method added for compatibility with Cytoscape app (sparsebn #4)
select.parameter now works with discrete data
Added summary generics for sparsebnPath, sparsebnFit, sparsebnData, and edgeList objects
Added plot generic for sparsebnData objects
Added specify.prior method to simplify construction of black lists
Improve output when estimate.parameters is singular (#9)

Bug fixes

Fixed bug which caused permute.nodes to throw an error when passing in a user-specified node ordering
Correct error message for mixed data (#8)
Update documentation for conversion methods (#11)

sparsebnUtils 0.0.4

Features

Added new random.graph method to generate random edgeLists

Notes

Conversion to and from sparse matrices using as.sparse is now significantly faster and supports Matrix input

sparsebnUtils 0.0.3

Major changes

get.solution() has been renamed select() (for consistency with select.parameter())

Features

Added a NEWS.md file to track changes to the package
select() now uses fuzzy matching by default
Added new method get.nodes() to return node names from a sparsebn object
Improved output and print method for estimate.parameters() when using discrete data