Package edu.cmu.tetrad.search.utils
package edu.cmu.tetrad.search.utils
Contains some utility classes for search algorithms.
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ClassDescriptionConstructs and AD leaf tree on the fly.Takes an xml element representing a bayes im and converts it to a BayesIMExtracts the backward step of GES for use GES but also in other algorithms.An arrow in the search.Implements a version of the BES (Best Equivalent Search) algorithm that takes a permutation as input and yields a permtuation as output, where the related DAG or CPDAG models are implied by the ordering or variables in these permutations.Enumerates the algorithm types for BuildPureClusters, and Purify.Enumerates the test types for BuildPureClusters, and Purify.Provides some methods to check significance of clusters for clustering algroithms.Gives the options for checking significance of clusters--could check the significance using a regression model, or could check to see if the cluster is a clique, or could not do the check.Provides some general utilities for dealing with clustering input and output.Given a CPDAG, lists all the DAGs in that DPCAG.Given a graph, lists all DAGs that result from directing the undirected edges in that graph every possible way.Interface for a method that scores a DAG.Determines sepsets, collider, and noncolliders by examining d-separation facts in a DAG.Converts a DAG (Directed acyclic graph) into the PAG (partial ancestral graph) which it is in the equivalence class of.Implements a test for simultaneously zero sextads in the style of Bollen, K.Implements a test for simultaneously zero tetrads in Bollen, K.Estimates the rank of a matrix.Performs the final orientation steps of the FCI algorithms, which is a useful tool to use in a variety of FCI-like algorithms.This Orients a given undirected graph such that the edges in the graph are a superset of the edges in the oriented graph, using FGES method.Contains methods which can be used to determine whether a directed graph is in the equivalence class determined by the given PAG.Checks the graphoid axioms for a set of Independence Model statements.Represents a graphoid independence fact--i.e., a fact in a general independence model (IM) X _||_Y | Z.Provides some graph utilities for search algorithm.Gives the options for triple type for a conservative unshielded collider orientation, which may be "collider" or "noncollider" or "ambiguous".Stores a result for checking whether a graph is a legal MAG--(a) whether it is (a boolean), and (b) the reason why it is not, if it is not (a String).Stores a result for checking whether a graph is a legal PAG--(a) whether it is (a boolean), and (b) the reason why it is not, if it is not (a String).GrowShrinkTree class.Provides an interface for an algorithm can can get/set a value for penalty disoucnt.Provides an implemetation of the Kuhn–Munkres assignment algorithm of the year 1957.Provides an interface for Purify algorithm.Gives an implemented that is implemented by classes that evaluate scalar valued kernelsSoces the Gaussian kernel for a given bandwidth.Provides various kernel utilities.Determines whether nodes indexed as (n1, center, n2) form a legal pair of edges in a graph for purposes of some algorithm that uses this information.Contains utilities for logging search steps.Performs a Max-P orientation of unshielded triples in a graph.Provides some useful utilities for dealing with Markov blankets and Markov blanket DAGs.Implements Meek's complete orientation rule set for PC (Chris Meek (1995), "Causal inference and causal explanation with background knowledge"), modified for Conservative PC to check noncolliders against recorded noncolliders before orienting.Provides some utility methods for Purify, Build Clusters, and Mimbuild.Returns row positions for placing rooks for an n x n matrix so the rooks cannot attach each other, with a given boolean[][] specification of where rooks are allowed to be placed.Calculates partial correlation using the recursive method.Provides some common implementation pieces of various PC-like algorithms, with options for collider discovery type, FAS type, and conflict rule.Give the options for the collider discovery algorithm to use--FAS with sepsets reasoning, FAS with conservative reasoning, or FAS with Max P reasoning.Gives the type of conflict to be used, priority (when there is a conflict, keep the orientation that has already been made), bidirected (when there is a conflict, orient a bidirected edge), or overwrite (when there is a conflict, use the new orientation).Gives the type of FAS used, regular or stable.The PC heuristic type, where this is taken from Causation, Prediction, and Search.Stores a matrix together with a row and column permutation.Finds possible d-connecting undirectedPaths for the IonSearch.Implements the Possible-M-Sep search step of Spirtes, et al's (1993) FCI algorithm (pp 144-145).Implements the Purify algorithm, which is a implementation of the automated purification methods described on CPS and the report "Learning Measurement Models" CMU-CALD-03-100.Implements a score-based Purify method.Implments a sextad-based Purify method.Implements a tetrad-based purify method.Provides some utilities for resolving inconsistencies that arise between sepsets learned for overlapping datasets.Gives the method to be used to resolve sepsets when they conflict.Stores a map from pairs of nodes to separating sets--that is, for each unordered pair of nodes {node1, node2} in a graph, stores a set of nodes conditional on which node1 and node2 are independent (where the nodes are considered as variables) or stores null if the pair was not judged to be independent.Provides a covenience interface for classes that can generate and keep track of sepsets.Provides a SepsetProcuder that selects the first sepset it comes to from among the extra sepsets or the adjacents of i or k, or null if none is found.Provides a SepsetProcuder that selects the first sepset it comes to from among the extra sepsets or the adjacents of i or k, or null if none is found.Provides a SepsetProcuder that selects the first sepset it comes to from among the extra sepsets or the adjacents of i or k, or null if none is found.Provides a sepset producer using conditional independence tests to generate the Sepset map, for the case where possible msep sets are required.Provides a sepset producer using conditional independence tests to generate the Sepset map.Represents an ordered sextad of nodes.Tries to find a good shifting of variables to minimize average BIC for time-series data.Adapts FciOrient for the SvarFCI algorithm.Represents a ordered tetrad of variables, (i, j, k, l).Provides an interface for classes that test tetrad constraints.Implements different tests of tetrad constraints: using Wishart's test (CPS, Wishart 1928); Bollen's test (Bollen, 1990) or a more computationally intensive test that fits one/two factor Gaussian models.Implements a test of tetrad constraints with discrete variables.Implements a test of tetrad constraints in a known correlation matrix.Implements and extends a scorer extending Teyssier, M., and Koller, D.Finds the PAG to which a DAG belongs, for a time series model.Contains some utilities for doing autoregression.Gives a result consisting of the residuals and collapsed var graphs.