All Classes and Interfaces
Class
Description
Sep 20, 2017 10:59:43 AM
Base class for variable specifications for DataSet.
Adds Javabean property change events so that it can be used in a MVC type
architecture.
A confusion matrix for adjacencies--i.e.
The adjacency precision.
The adjacency precision.
The adjacency true positive rate.
The adjacency precision.
The adjacency recall.
The adjacency precision.
The adjacency precision.
The adjacency true positive rate.
Constructs and AD leaf tree on the fly.
An implementation of a static AD tree based on Moore and Lee 1998 (mostly)
Stores AD trees for data sets for reuse.
Author : Jeremy Espino MD
Created 6/24/15 3:32 PM
Interface that algorithm must implement.
Sep 5, 2017 10:47:30 AM
Sep 26, 2017 12:19:41 AM
Aug 30, 2017 3:14:40 PM
A list of algorithm to be compared.
Author : Jeremy Espino MD Created 6/30/17 10:36 AM
Calculates the F1 statistic for adjacencies.
The bidirected true positives.
The bidirected true positives.
Implements the Anderson-Darling test for normality, with P values calculated
as in R's ad.test method (in package nortest).
Sep 5, 2017 11:02:14 AM
Sep 6, 2017 11:11:38 AM
Calculates updated marginals for a Bayes net by simulating data and
calculating likelihood ratios.
A confusion matrix for arrows--i.e.
The arrow precision.
The arrow precision.
The adjacency true positive rate.
The arrow precision.
The arrow precision.
The arrow recall.
The arrow recall.
The arrow precision.
The arrow precision.
The adjacency precision.
The adjacency precision.
Initializes a history array by setting the value of each variable to basal
if it is unregulated (has no parents other than itself one time step back)
and to a random value chosen from a N(basal, initStDev) distribution
otherwise.
Basic functionality that all graph-derived classes should provide.
Stores a time series in the "update" (rather than, say, the "repeated")
form--that is, for a given set of factors (the word "factor" is being used
here to avoid ambiguity), only lags behind the getModel time step are recorded
temporally, with causal edges extending from lagged factors with lags >= 1 to
factors in the getModel time step (lag = 0) only.
Implements a space-efficient Lower Triangular Matrix of
elements of type
shortBasic functionality of a Matrix
Feb 22, 2014 3:26:17 PM
Feb 22, 2014 3:35:38 PM
Interface implemented by Bayes instantiated models.
Calculates cell probabilities from conditional BayesIm probabilities on the
fly without constructing the entire table.
Implements a discrete Bayes parametric model--that is, a DAG together with a
map from the nodes in the graph to a set of discrete variables, specifying
the number of categories for each variable and the name of each category for
each variable.
Calculates some scores for Bayes nets as a whole.
Interface for a discrete Bayes updating algorithm.
This class contains a method classify which uses an instantiated Bayes net (BayesIm) provided in the constructor.
Parses Bayes elements back to objects.
Renders Bayes nets and related models in XML.
This is a thread-safe version of BCInference.
Feb 26, 2014 8:07:20 PM
Implements the BOSS DC Experimental algorithm.
BOSS-DC (Best Order Score Search Divide and Conquer Experimental)
Provides a method for computing the score of a model, called the BDe
metric (Bayesian Dirchlet likelihood equivalence), given a dataset (assumes
no missing values) and a Bayes parameterized network (assumes no latent
variables).> 0
Calculates the BDe score.
Wrapper for Fisher Z test.
Calculates the BDeu score.
Implements the continuous BIC score for FGES.
Wrapper for Fisher Z test.
Implements the backward equivalence search of FGES.
Implements a Beta distribution for purposes of drawing random numbers.
J.M.
Adjusts GFCI to use a permutation algorithm (such as BOSS-Tuck) to do the initial
steps of finding adjacencies and unshielded colliders.
Adjusts GFCI to use a permutation algorithm (such as BOSS-Tuck) to do the initial
steps of finding adjacencies and unshielded colliders.
Does BOSS + retain unshielded colliders + final FCI orientation rules
Does an FCI-style latent variable search using permutation-based reasoning.
Adjusts GFCI to use a permutation algorithm (such as BOSS-Tuck) to do the initial
steps of finding adjacencies and unshielded colliders.
Difference between the true and estiamted BIC scores.
Difference between the true and estiamted BIC scores.
Estimated BIC score.
Calculates the discrete BIC score.
True BIC score.
A confusion matrix for bidireced edges--i.e.
The bidirected true positives.
The bidirected false negatives.
The bidirected true positives.
The bidirected edge precision.
The bidirected edge precision.
The bidirected true positives.
The bidirected true positives.
Implements an algorithm for revising regulatory models with expression data.
Implements a digraph to be used by the Biolingua algorithm.
Client of the Biolingua class, can be used to easily
run the algorithm with different inputs.
Stores a boolean function from a set of boolean-valued parents to a single
boolean-valued column.
Updates a gene given a history using the formula Gi.0 = max(Gi.1 -
decayRate * -Gi.1 + booleanInfluenceRate * F(Parents(Gi) in the graph \
Gi.1), lowerBound), as described in Edwards and Glass, (2000), "Combinatorial
explosion in model gene networks", American Institute of Physics.
Wraps the MeasurementSimulator class as an instantiated model.
Implements a parametric model for Boolean Glass gene PM's, which in this case
just presents the underlying workbench.
A version of the Lee and Hastic simulation which is guaranteed to generate a discrete
data set.
This class contains as a member variable (cases) the time series data stored
in an int array of microarray measurements.
This class contains as a member variable (cases) the time series data stored
in an int array of microarray measurements.
Indicate algorithm can do bootstrapping.
Provides a static method for sampling with replacement from a dataset to
create a new dataset with a sample size supplied by the user.
Implements the BOSS algorithm.
BOSS (Best Order Score Search)
BOSS-MB.
Implements the BOSS DC algorithm.
BOSS-DC (Best Order Score Search Divide and Conquer)
Implements the GRASP algorithms, with various execution flags.
Implements the GRASP algorithms, with various execution flags.
Wraps a DataBox in such a way that mixed data sets can be stored.
Build Pure Clusters.
An enumeration of the test types for BuildPureClusters, and Purify.
Implements a really simple idea for building pure clusters, just using the Purify algorithm.
GesSearch is an implementation of the GES algorithm, as specified in
Chickering (2002) "Optimal structure identification with greedy search"
Journal of Machine Learning Research.
FGES (the heuristic version).
BRIDGES (experimental algorithm).
GesSearch is an implementation of the GES algorithm, as specified in
Chickering (2002) "Optimal structure identification with greedy search"
Journal of Machine Learning Research.
FGES (the heuristic version).
Implementation of the experimental BRIDGES algorithm
An example script to simulate data and run a comparison analysis on it.
BuildPureClusters is an implementation of the automated clustering and purification methods
described on the report "Learning Measurement Models" CMU-CALD-03-100.
Stores a 2D array of byte data.
Makes a new data set in which cases in the given data set that have been
assigned multiplicies other than n = 1 are copied out n times.
This class provides the data structures and methods for carrying out the Cyclic Causal Discovery algorithm (CCD)
described by Thomas Richardson and Peter Spirtes in Chapter 7 of Computation, Causation, and Discovery by Glymour and
Cooper eds.
CCD (Cyclic Causal Discovery)
FGES (the heuristic version).
This is an optimization of the CCD (Cyclic Causal Discovery) algorithm by Thomas Richardson.
Requires that the parameter 'randomSelectionSize' be set to indicate how many
datasets should be taken at a time (randomly).
Wrapper for Daudin Conditional Independence test.
Wrapper for Daudin Conditional Independence test.
Searches for a CPDAG representing all of the Markov blankets for a given target T consistent with the given
independence information.
Stores a cell count table of arbitrary dimension.
Estimates probabilities from data by constructing the entire cell count table
for the data.
Conserative FCI.
Extends Erin Korber's implementation of the Fast Causal Inference algorithm (found in FCI.java) with Jiji Zhang's
Augmented FCI rules (found in sec.
Wrapper for Fisher Z test.
Wraps a chi square distribution for purposes of drawing random samples.
Calculates marginal chi square test results for a discrete dataset.
Simple class to store the parameters of the result returned by the G Square test.
Generates (nonrecursively) all of the combinations of a choose b, where a, b
are nonnegative integers and a >= b.
Tags an algorithm that generates clusters.
Represents a clustering algorithm to cluster some data.
Stores clusters of variables for MimBuild, Purify, etc.
Some methods to check significance of clusters for clustering algroithms.
Some general utilities for dealing with clustering input and output.
Wrapper for Fisher Z test.
Generates (nonrecursively) all of the combinations of objects, where the
number of objects in each dimension is specified.
Iterates through all the posible combinations for a set of variables (each
with a different number of possible values).
The bidirected true positives.
The bidirected true positives.
The bidirected true positives.
The bidirected true positives.
An example script to load in data sets and graphs from files and analyze them.
Script to do a comparison of a list of algorithms using a list of statistics
and a list of parameters and their values.
Does a comparison of algorithm results across algorithm type, sample sizes, etc.
Does a comparison of algorithm results across algorithm type, sample sizes,
etc.
Created by jdramsey on 3/24/16.
.
Runs algorithm on data set (simulation is OK), printing out error statistics.
An example script to load in data sets and graphs from files and analyze them.
An example script to load in data sets and graphs from files and analyze them.
Checks conditional independence of variable in a continuous data set using Daudin's method.
Checks conditional independence of variable in a continuous data set using Daudin's method.
Wrapper for Fisher Z test.
Implements a conditional Gaussian likelihood.
A return value for a likelihood--returns a likelihood value and the degrees of freedom
for it.
Wrapper for Fisher Z test.
Wrapper for Fisher Z test.
Implements a conditional Gaussian likelihood.
A return value for a likelihood--returns a likelihood value and the degrees of freedom
for it.
Implements a conditional Gaussian BIC score for FGS.
Implements a conditional Gaussian BIC score for FGS.
A simulation method based on the conditional Gaussian assumption.
Created by IntelliJ IDEA.
Represents a constant expression, that is an expression that always evaluates to the same value.
Looks up the value of a variable.
Specifies how a column (continuous or discrete) should be discretized.
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.
Represents a real-valued variable.
This interface should be used for non-differentiable convex functions that are decomposable such that
f(x) = g(x) + h(x) where g(x) is a differentiable convex function (i.e.
Outputs 1 if the skeleton is correct, 0 if not..
Stores a correlation matrix together with variable names and sample size;
intended as a representation of a data set.
Stores a covariance matrix together with variable names and sample size,
intended as a representation of a data set.
Indicates that a model could not be created.
Interface for computing covariances.
Stores a covariance matrix together with variable names and sample size,
intended as a representation of a data set.
Jan 25, 2016 2:13:26 PM
Stores a covariance matrix together with variable names and sample size,
intended as a representation of a data set.
Some comemon methods for the various covariance implementations.
Computes covariances using the standard calculation.
Linear covariance function with Automatic Relevance Determination (ARD).
Linear covariance function with a single hyperparameter.
Neural network covariance function with a single parameter for the distance
measure.
Neural network covariance function with a single parameter for the distance
measure and white noise.
Independent covariance function, ie "white noise", with specified variance.
Squared Exponential covariance function with Automatic Relevance Detemination
(ARD) distance measure.
Squared Exponential covariance function with isotropic distance measure.
Composes a covariance function as the sum of other covariance
functions.
Implements a convervative version of PC, in which the Markov condition is assumed but faithfulness is tested
locally.
CPC.
Reorients edges in the getModel graph as CPC would orient them.
PC.
Implements a convervative version of PC, in which the Markov condition is assumed but faithfulness is tested
locally.
Calculates marginals of the form P(V=v') for an updated Bayes net for
purposes of the CPT Invariant Updater.
Calculates updated probabilities for variables conditional on their parents
as well as single-variable updated marginals for a Bayes IM using an
algorithm that restricts expensive updating summations only to conditional
probabilities of variables with respect to their parents that change from
non-updated to updated values.
An adaptation of the CStaR algorithm (Steckoven et al., 2012).
Simple Class to load the example data from files straight into Matrices.
Provides a static method for finding the cutoff value for a symmetric
probability distribution function about the origin.
Returns a cyclic graph build up from small cyclic graph components.
Represents a directed acyclic graph--that is, a graph containing only
directed edges, with no cycles.
Given a pattern, lists all of the DAGs in that pattern.
Given a graph, lists all DAGs that result from directing the undirected edges in that graph every possible way.
Estimates a SemIm given a CovarianceMatrix and a SemPm.
Determines sepsets, collider, and noncolliders by examining d-separation facts in
a DAG.
Extends Erin Korber's implementation of the Fast Causal Inference algorithm (found in FCI.java) with Jiji Zhang's
Augmented FCI rules (found in sec.
Stores a 2D array of data.
Dec 15, 2018 11:10:30 AM
Interface implemented by classes whose purpose is to generate modifications
of data sets.
Created by ajsedgewick on 9/4/15.
Sundry graph utils that need to be located in the data package to
avoid package cycles.
Interface implemented by classes, instantiations of which can serve as data
models in Tetrad.
Stores a list of data models and keeps track of which one is selected.
Implements a rectangular data set, in the sense of being a dataset with
a fixed number of columns and a fixed number of rows, the length of each
column being constant.
Estimates maximum likelihood probabilities directly from data on the fly.
The type of the data set--continuous if all continuous variables, discrete if
all discrete variables; otherwise, mixed.
Fast data loader for continuous or discrete data.
Some static utility methods for dealing with data sets.
Provides static methods for saving data to files.
Implements the DCI (Distributed Causal Inference) algorithm for learning causal structure over a set of variable from
multiple datasets that each may only measure proper overlapping subsets subsets of that sets, or datasets with some
variables in common and others not.
Logger configuration.
The bidirected true positives.
The bidirected true positives.
Wrapper for degenerate Gaussian BIC score
Wrapper for DG LRT.
Implements a degenerate Gaussian BIC score for FGES.
An interface for editors that delegate their editing responsibilities.
Type-safe enum of delimiter types for parsing data.
Jun 20, 2017 12:09:05 PM
Implements a test for simultaneously zero sextads in the style of Bollen, K.
Implements a test for simultaneously zero tetrads in Bollen, K.
The adjacency precision.
The adjacency precision.
Simple implementation of a directed Graph.
Stores Dirichlet pseudocounts for the distributions of each variable
conditional on particular combinations of its parent values and, together
with Bayes Pm and Dag, provides methods to manipulate these tables.
Estimates probabilities directly from data on the fly using maximum
likelihood method.
Estimates a DirichletBayesIm from a DirichletBayesIm (the prior) and a data
set.
Calculates the BDeu score.
Wraps a chi square distribution for purposes of drawing random samples.
Wrapper for Discrete BIC test.
Wrapper for Fisher Z test.
Interface implemented by classes that do discrete classification.
Specifies how a column (continuous or discrete) should be discretized.
Wrapper for Fisher Z test.
Implements a conditional Gaussian likelihood.
A return value for a likelihood--returns a likelihood value and the degrees of freedom
for it.
Implements a conditional Gaussian BIC score for FGS.
Implementation of a test of tetrad constraints with discrete variables.
Represents a discrete variable as a range of integer-valued categories 0, 1,
..., m - 1, where m is the number of categories for the variable.
Type-safe enum of discrete variable types.
A continuous or discrete discretization spec (see).
Discretizes individual columns of discrete or continuous data.
Models the manner in which gene models are initialized differentially
depending on the dishes that the cells are in.
Translates display names of lagged variables (e.g.
Interface for a dissilimarity metric.
Interface for a statistical distribution from which random values can
be drawn.
Implements the DM search.
Tags session nodes that should not be passed on as old models to
new models.
Stores a 2D array of double data.
Wrapper for Fisher Z test.
Wrapper for D-separation test.
EB.
Wrapper for linear, Gaussian Extended BIC score (Chen and Chen).
Implements the extended BIC score (Chen and Chen)..
Represents an edge node1 *-# node2 where * and # are endpoints of type
Endpoint--that is, Endpoint.TAIL, Endpoint.ARROW, or Endpoint.CIRCLE.
Stores a graph a list of lists of edges adjacent to each node in the graph,
with an additional list storing all of the edges in the graph.
This factory class produces edges of the types commonly used for Tetrad-style
graphs.
Apr 13, 2017 3:56:46 PM
Calculates the eigen decomposition of a real matrix.
Records the elapsed time of the algorithm in seconds.
Estimates parameters of the given Bayes net from the given data using maximum
likelihood method.
Calculates some scores for Bayes nets as a whole.
Only the cumulativeProbability, density, setShift methods are implemented.
Returns a sample empirical distribution for a particular expression.
A typesafe enumeration of the types of endpoints that are permitted in
Tetrad-style graphs: null (-), arrow (->), circle (-o), start (-*),
and null (no endpoint).
Represents an equation of the form Variable = Expression, where the Variable represents
a column in some dataset.
Creates a random graph by the Erdos-Renyi method (probabiliy of edge fixed, # edges not).
Estimates the rank of a matrix.
An equation expression.
Stores information for a variable source about evidence we have for each variable as
well as whether each variable has been manipulated.
An example script to load in data sets and graphs from files and analyze them.
An example script to load in data sets and graphs from files and analyze them.
An example script to simulate data and run a comparison analysis on it.
An example script to simulate data and run a comparison analysis on it.
An example script to simulate data and run a comparison analysis on it.
An example script to simulate data and run a comparison analysis on it.
An example script to simulate time series data and run a comparison analysis on it.
An example script to simulate data and run a comparison analysis on it.
Created by ajsedgewick on 8/18/15.
An example script to save out data files and graphs from a simulation.
An example script to save out data files and graphs from a simulation.
An example script to save out data files and graphs from a simulation.
An example script to simulate data and run a comparison analysis on it.
Interface indicating that a class can be executed as an algorithm.
Interface indicating that a parameter object can and should be reinitialized
at each new execution in a simulation edu.cmu.tetrad.study.
Oct 17, 2017 11:40:50 AM
Tags a file as experimental so it's not listed in the configuration.
Runs algorithm on data set (simulation is OK), printing out error statistics.
Created by ajsedgewick on 9/10/15.
Wraps a chi square distribution for purposes of drawing random samples.
Represents a mathematical expression.
Represents a definition for some expression.
Thrown if the expression can't be parsed, for instance, if it has the
wrong number of arguments.
Parses the tokens of an expression.
Manager for expressions, this includes all implementations of expression
descriptors for the calculator.
Parses a string into a tree-like expression.
The type of restriction on parameters.
Represents the signature of the expression, for example sqrt(number).
Tags an an algorithm that loads up external graphs for inclusion in reports.
An API to allow results from external algorithms to be included in a report through the algrorithm
comparison tool.
An API to allow results from external algorithms to be included in a report through the algrorithm
comparison tool.
An API to allow results from external algorithms to be included in a report through the algrorithm
comparison tool.
An API to allow results from external algorithms to be included in a report through the algrorithm
comparison tool.
An API to allow results from external algorithms to be included in a report through the algrorithm
comparison tool.
An API to allow results from external algorithms to be included in a report through the algrorithm
comparison tool.
Returns a data set in variables for columns with missing values are augmented
with an extra category that represents the missing values, with missing
values being reported as belong this category.
Calculates the F1 statistic for adjacencies.
Calculates the F1 statistic for adjacencies.
Calculates the F1 statistic for arrowheads.
Useful references: "Factor Analysis of Data Matrices" - Paul Horst (1965) This work has good specifications and
explanations of factor analysis algorithm and methods of communality estimation.
Implements the procedure Factored-Bayesian-SEM found on page 6 of "The
Bayesian Structural EM Algorithm" by Nir Friedman.> 0
The bidirected true positives.
The bidirected true positives.
Implements the "fast adjacency search" used in several causal algorithm in this package.
FAS.
Implements the "fast adjacency search" used in several causal algorithm in this package.
Implements a modified version of the the "fast adjacency search" for use in the Distributed Causal Inference (DCI)
algorithm.
Implements the "fast adjacency search" used in several causal algorithm in this package.
Implements the "fast adjacency search" used in several causal algorithm in this package.
Runs the FASK (Fast Adjacency Skewness) algorithm.
Wraps the IMaGES algorithm for continuous variables.
Wraps the IMaGES algorithm for continuous variables.
FASK-PW (pairwise).
Wraps the MultiFask algorithm for continuous variables.
Wraps the IMaGES algorithm for continuous variables.
Fast adjacency search followed by robust skew orientation.
Wraps the IMaGES algorithm for continuous variables.
Implements the "fast adjacency search" used in several causal algorithm in this package.
A Java implementation of FastIca following the R package fastICA.
A list containing the following components
Implements the "fast adjacency search" used in several causal algorithm in this package.
FCI.
Extends Erin Korber's implementation of the Fast Causal Inference algorithm (found in FCI.java) with Jiji Zhang's
Augmented FCI rules (found in sec.
FCI.
Extends Erin Korber's implementation of the Fast Causal Inference algorithm (found in FCI.java) with Jiji Zhang's
Augmented FCI rules (found in sec.
Extends Erin Korber's implementation of the Fast Causal Inference algorithm
(found in FCI.java) with Jiji Zhang's Augmented FCI rules (found in sec.
FGES (the heuristic version).
GesSearch is an implementation of the GES algorithm, as specified in
Chickering (2002) "Optimal structure identification with greedy search"
Journal of Machine Learning Research.
Requires that the parameter 'randomSelectionSize' be set to indicate how many
datasets should be taken at a time (randomly).
FGES (the heuristic version).
GesSearch is an implementation of the GES algorithm, as specified in
Chickering (2002) "Optimal structure identification with greedy search"
Journal of Machine Learning Research.
FGES (the heuristic version).
GesSearch is an implementation of the GES algorithm, as specified in Chickering (2002) "Optimal structure
identification with greedy search" Journal of Machine Learning Research.
Implements FindOneFactorCluster by Erich Kummerfeld (adaptation of a two factor
quartet algorithm to a one factor tetrad algorithm).
Implements FindOneFactorCluster by Erich Kummerfeld (adaptation of a two factor
sextet algorithm to a one factor IntSextad algorithm).
First inflection point.
Wrapper for Fisher Z test.
Wrapper for Fisher Z test.
Stores a 2D array of float data.
Find One Factor Clusters.
Static instance of a ForkJoinPool.
FTFC.
Interface for a single-argument, double-valued function that can be passed to
mathematical routines.
Wraps a chi square distribution for purposes of drawing random samples.
Data are normal distributed.
Main class of the package, contains the objects that constitutes a Gaussian Process as well
as the algorithm to train the Hyperparameters and to do predictions.
Created by Erich on 7/3/2016.
Created by Erich on 7/14/2016.
Created by Erich on 8/6/2016.
Created by Erich on 8/6/2016.
Created by Erich on 7/6/2016.
Created by Erich on 8/11/2016.
Implements the basic machinery used by all history objects.
Implements a parametric gene model.
Data with variables of general distribution.
Implements the Anderson-Darling test against the given CDF, with P values calculated
as in R's ad.test method (in package nortest).
Estimates a Generalized SEM I'M given a Generalized SEM PM and a data set.
Represents a generalized SEM instantiated model.
Parametric model for Generalized SEM model.
Sep 7, 2018 1:38:50 PM
Mar 19, 2017 9:45:44 PM
Created by mahdi on 1/16/17.
This was used for a simulation to test the FTFC and FOFC algorithm and contains
some carefully selected functions to test nonlinearity and non-Gaussianity.
FGES (the heuristic version).
J.M.
GFCI.
A translation from Tibshirani's 2008 Fortran implementation of glasso.
Return value of the algorithm.
Implements a graph capable of storing edges of type N1 *-# N2 where * and
# are endpoints of type Endpoint.
**************************************************************************************
Return a 1 if the graph is exactly right, 0 otherwise.
Modifies the UniformGraphGenerator to generate random DAGs (not assuming
connectivity) with number of edges in given range, min to max.
I couldn't find a mechanism in place to manage algorithm that return
potentially more than 1 graph.
Instantiations of this interface know how to randomize lag graphs in
particular ways.
Implements a basic node in a graph--that is, a node that is not itself a
variable.
Checks the graphoid axioms for a set of Independence Model statements.
Methods to load or save graphs.
Instantiations of this interface know how to randomize update graphs in
particular ways.
Implements Chickering and Meek's (2002) locally consistent score criterion.
Interface for a method that scores a DAG.
Interface for a search method that returns a graph.
A utility class containing graph function from graph theory.
A utility for computing frequency probabilities.
Jun 4, 2019 3:21:47 PM
Basic graph utilities.
Dag plus edge weights.
Implements the GRASP algorithms, with various execution flags.
GRaSP (Greedy Relaxations of Sparsest Permutation)
Adjusts GFCI to use a permutation algorithm (such as BOSS-Tuck) to do the initial
steps of finding adjacencies and unshielded colliders.
J.M.
Implements the GRASP algorithms, with various execution flags.
GRaSP (Greedy Relaxations of Sparsest Permutation)
Implements the Grow-Shrink algorithm of Margaritis and Thrun.
Wrapper for Fisher Z test.
Performs conditional independence tests of discrete data using the G Square method.
Simple class to store the parameters of the result returned by the G Square test.
The purpose of this class is to store evaluation results.
Loss function for PC: * for adjacency errors, 1 pt (i.e.
The purpose of this little converter is to convert "effect" files into
"cause" (BasicLagGraph) files.
Stores a knowledge object.
Tags a gadget as having parameters
Tags a gadget as having parameters values.
Best Fit Finder using a beam search.
Interface for Bff (Best Fit Finder) algorithm.
Best Fit Finder using the GES algorithm.
Model for a conditional histogram for mixed continuous and discrete variables.
Created by Erich on 3/28/2016.
Created by Erich on 3/28/2016.
Created by Erich on 7/15/2016.
Created by Erich on 3/27/2016.
Created by ekummerfeld on 1/26/2017.
Created by Erich on 4/29/2016.
Created by Erich on 3/28/2016.
Created by Erich on 4/29/2016.
generate data from random graph, generated from parameters.
Created by Erich on 3/28/2016.
Created by Erich on 4/29/2016.
Created by Erich on 3/28/2016.
Created by Erich on 3/28/2016.
Created by Erich on 4/22/2016.
The Hungarian algorithm for solving the N-Queens problem.
Implements IAMB.
Created by IntelliJ IDEA.
Created by jdramsey on 2/21/16.
Interface for covariance matrices.
Implements the IDA algorithm, Maathuis, Marloes H., Markus Kalisch, and Peter Bühlmann.
A list of nodes and corresponding minimum effects.
Identifiability, based on RowSummingExactUpdater
An interface for fast adjacency searches (i.e.
Tagging interface for instantiated models.
Wraps the IMaGES algorithm for continuous variables.
Wraps the IMaGES algorithm for discrete variables.
Wraps the IMaGES algorithm for continuous variables.
Implements a score to average results over multiple scores.
Wraps the IMaGES algorithm for continuous variables.
Adds any orientations implied by the given orientation.
Stores a triple (x, y, z) of nodes.
Stores a list of independence facts.
Interface implemented by classes that do conditional independence testing.
May 14, 2019 11:25:02 AM
Interface that algorithm must implement.
Stores a "shapshot" of the indexedConnectivity of a lag graph, using
indices rather than Strings to refer to factors.
Stores a "shapshot" of the indexedLagGraph of a lag graph, using indices
rather than Strings to refer to factors.
Holds an ordered pair (index, lag) to represent a causal parent of a factor,
where the factor at the given index is independently known.
Created by IntelliJ IDEA.
Checks the conditional independence X _||_ Y | S, where S is a set of discrete variable, and X and Y are discrete
variable not in S, by applying a conditional Chi Square test.
Checks conditional independence of variable in a continuous data set using Fisher's Z test.
Checks conditional independence of variable in a continuous data set using a conditional correlation test
for the nonlinear nonGaussian case.
Checks conditional independence of variable in a continuous data set using a conditional correlation test
for the nonlinear nonGaussian case.
Performs a test of conditional independence X _||_ Y | Z1...Zn where all searchVariables are either continuous or discrete.
Checks conditional independence for continuous variables using Cramer's T-test formula (Cramer, Mathematical Methods
of Statistics (1951), page 413).
A return value for a likelihood--returns a likelihood value and the degrees of freedom
for it.
Checks independence facts for variables associated with the nodes in a given graph by checking d-separation facts on
the underlying nodes.
Checks conditional independence of variable in a continuous data set using Fisher's Z test.
Calculates independence from pooled residuals.
Calculates independence from pooled residuals.
Checks independence of X _||_ Y | Z for variables X and Y and list Z of variables.
Calculates independence from pooled residuals.
Checks conditional independence of variable in a continuous data set using Fisher's Z test.
Checks the conditional independence X _||_ Y | S, where S is a set of discrete variable, and X and Y are discrete
variable not in S, by applying a conditional G Square test.
Checks the conditional independence X _||_ Y | S, where S is a set of continuous variable, and X and Y are discrete
variable not in S, using the Hilbert-Schmidth Independence Criterion (HSIC), a kernel based nonparametric test for
conditional independence.
Checks conditional independence against a list of conditional independence facts, manually entered.
Performs a test of conditional independence X _||_ Y | Z1...Zn where all searchVariables are either continuous or discrete.
Performs a test of conditional independence X _||_ Y | Z1...Zn where all searchVariables are either continuous or discrete.
Pools together a set of independence tests using a specified methods
Performs a test of conditional independence X _||_ Y | Z1...Zn where all searchVariables are either continuous or discrete.
Performs a test of conditional independence X _||_ Y | Z1...Zn where all searchVariables are either continuous or discrete.
Performs a test of conditional independence X _||_ Y | Z1...Zn where all searchVariables are either continuous or discrete.
Checks conditional independence of variable in a continuous data set using Fisher's Z test.
Uses BCInference by Cooper and Bui to calculate probabilistic conditional independence judgments.
Checks independence of X _||_ Y | Z for variables X and Y and list Z of variables.
Interface implemented by classes that do conditional independence testing.
Checks independence facts for variables associated associated with a sepset by simply querying the sepset
Checks conditional independence of variable in a continuous data set using Fisher's Z test.
Checks d-separations in structural model using t-separations over indicators.
A typesafe enumeration of the types of independence tests that are used for basic search algorithm in this package.
Initializes a history array.
Estimates probabilities directly from data on the fly using maximum
likelihood method, with the exception that if rows do not exist in the data
satisfying a required condition because certain values are unattested, an
attempt is made to remove each relevant column in turn, record the estimated
probability with column removed from the condition (if it is defined), and
then return the average over the estimated probabilities calculated this
way.
Stores a 2D array of integer data.
Integrates under a function from one endpoint to another.
Implements the Inter-IAMB algorithm.
Returns edges whose entries in the precision matrix exceed a certain threshold.
Implements the ION (Integration of Overlapping Networks) algorithm for distributed causal inference.
Implements the ION (Integration of Overlapping Networks) algorithm for distributed causal inference.
**************************************************************************
An interface for Purify algorithm.
Created by jdramsey on 2/21/16.
An interface for SemIM's; see implementations.
This class contains methods which implement the algorithm described in the
paper " " by Ideker, Thorsen and Karp.
Stores some utility items for displaying JOptionPane messages.
Dec 9, 2016 5:43:47 PM
Junction Tree Algorithm.
Jan 21, 2020 11:03:09 AM
Wrapper for KCI test.
Kernal Independence Test (KCI).
Interface implemented by classes that evaluate scalar valued kernels
Gaussian kernel for a given bandwidth.
Various kernel utilities
Wrapper for linear, Gaussian Extended BIC score (Chen and Chen).
Implements the continuous BIC score for FGES.
Wrapper for Fisher Z test.
Implements the "batch" version of the K Means clustering algorithm-- that is,
in one sweep, assign each point to its nearest center, and then in a second
sweep, reset each center to the mean of the cluster for that center,
repeating until convergence.
Stores information about required and forbidden edges and common causes for
use in algorithm.
Tags classes that can yield graphs as input to knowledge.
Implements a knowledge edge X-->Y as a simple ordered pair of strings.
Represents a "Other Group" in Knowledge, which can be understood as: Group1 -> Group2 where there are
edges between all members of Group1 to Group2.
Interface implemented by classes that are capable of participating in the
transfer of knowledge objects.
Kernelized PC algorithm.
wrapper class for passing factor+edge via a propertyChange event
Identifies a particular factor (by name) at a particular lag (integer).
Implements a graph allowing nodes in the getModel time lag to have parents
taken from previous time lags.
Stores a SEM model, pared down, for purposes of simulating data sets with
large numbers of variables and sample sizes.
The bidirected true positives.
The bidirected true positives.
The bidirected true positives.
The bidirected true positives.
Lays out a graph by linearly summing repulsive force between all nodes and
attractive force between adjacent nodes.
Lays out a graph by placing springs between the nodes and letting the system
settle (one node at a time).
A version of the Lee and Hastic simulation which is guaranteed ot generate a
discrete data set.
Legal PAG
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.
Implements a linear update function, Gi.0 = L(Parents(G0.0)) + ei, where P
is a polynomial function and ei is a random noise term.
Data with Gaussian variables that have linear relationships.
Implements a particular simulation for experimental purposes.
A simulation method based on the mixed variable polynomial assumption.
LiNGAM.
The code used within this class is largely Gustave Lacerda's, which corresponds to his essay, Discovering Cyclic
Causal Models by Independent Components Analysis.
This small class is used to store graph permutations.
LiNGAM.
Implements the LiNGAM algorithm in Shimizu, Hoyer, Hyvarinen, and Kerminen, A linear nongaussian acyclic model for
causal discovery, JMLR 7 (2006).
Implements the Lingam CPDAG algorithm as specified in Hoyer et al., "Causal discovery of linear acyclic models with
arbitrary distributions," UAI 2008.
Implements the Lingam CPDAG algorithm as specified in Hoyer et al., "Causal discovery of linear acyclic models with
arbitrary distributions," UAI 2008.
An example script to simulate data and run a comparison analysis on it.
Sundry utilities for the Ling algorithm.
Created by IntelliJ IDEA.
LOFS = Ling Orientation Fixed Structure.
LOFS = Ling Orientation Fixed Structure.
Sundry methods for logging data.
Implements a logistic regression algorithm based on a Javascript
implementation by John Pezzullo.
Represents a lognormal distribution for purposes of sampling.
Sets up streams for logging via the Java logging API.
Stores a 2D array of long data.
This is merely a main program used to read a binarized measurement data set
and to instantiate a BoolSearch and run one or more search methods of that
instance.
This is merely a main program used to read a binarized measurement data set
and to instantiate a BoolSearch and run one or more search methods of that
instance.
Class that makes some very simple tests
on the classes LtMatrix, Graph, and Biolingua
This is merely a main program used to read a binarized measurement data set
and to instantiate a RevealSearch and run one or more search methods of that
instance.
This is merely a main program used to read a binarized measurement data set
and to instantiate a RevealSearch and run one or more search methods of that
instance.
Implements a space-efficient Lower Triangular Matrix of
elements of type
shortImplements a space-efficient Lower Triangular Matrix of
elements of type
floatImplements the backward equivalence search of FGES.
Does BOSS2, followed by two swap rules, then final FCI orientation.
Does BOSS, followed by the swap rule, then final orientation.
Does BOSS, followed by the swap rule, then final orientation.
Does BOSS, followed by the swap rule, then final orientation.
Wrapper for linear, Gaussian SEM BIC score.
Wrapper for Fisher Z test.
Interface for a Bayes updating algorithm that's capable of doing
manipulation.
Stores information for a variable source about evidence we have for each variable as
well as whether each variable has been manipulated.
Constructs as a (manual) update graph.
Constructs as a (manual) update graph.
Stores the parameters needed to generate a new lag graph, whether randomized
or manually constructed.
Maps a parameter to the matrix element where its value is stored in the
model.
Calculates the Matthew's correlation coefficient for adjacencies.
Calculates the Matthew's correlation coefficient for adjacencies.
Some extra mathematical functions not contained in org.apache.commons.math3.util.FastMath.
Implements a Matrix of elements of type
shortWraps the Apache math3 linear algebra library for most uses in Tetrad.
Implements a Matrix of elements of type
floatSome useful operations defined over Matrices
Class Matrix includes several public static functions performing matrix
operations.
Performs a Bayesian classification of a test set based on a given training set.
An interface for Markov blanket searches.
Some useful utilities for dealing with Markov blankets and Markov blanket DAGs.
Returns a data set in which missing values in each column are filled using
the mean of that column.
Simulates measurement genetic data using an underlying GeneHistory object
to generate individual cell data.
Wraps MeasurementSimulator so that it may be used as a parameter object.
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.
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.
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.
Tags a session node as "memorable", so that it won't be forgotten when a model
is destroyed.
Implementation of Lee and Hastie's (2012) pseudolikelihood method for learning
Mixed Gaussian-Categorical Graphical Models
Created by ajsedgewick on 7/15/15.
Reports elapsed time in wall time, user time, and CPU time
in milliseconds.
An implemetation of Mimbuild based on the Fgsl score.
An implemetation of Mimbuild based on the treks and ranks.
Holds some utility methods for Purify, Build Clusters, and Mimbuild.
Some utilities for generating misclassification tables for graphs.
Data with variables that have linear relationship.
Stores a 2D array of double continuousData.
Created by ajsedgewick on 7/29/15.
Wraps a chi square distribution for purposes of drawing random samples.
Estimates parameters of the given Bayes net from the given data using maximum
likelihood method.
Stores a table of probabilities for a Bayes net and, together with BayesPm
and Dag, provides methods to manipulate this table.
Stores a table of probabilities for a Bayes net and, together with BayesPm
and Dag, provides methods to manipulate this table.
Implements the MMHC algorithm.
Implements the Min-Max Markov Blanks (MMMB) algorithm as defined in Tsamardinos, Aliferis, and Statnikov, Time and
Sample Efficient Discovery of Markov Blankets and Direct Causal Relations (KDD 2003).
Wrapper for MVP BIC Score.
Calculates Mixed Variables Polynomial likelihood.
Wrapper for Fisher Z test.
Implements a mixed variable polynomial BIC score for fGES.
Creates a data set in which missing values in each column are filled using
the mode of that column.
Provides static methods for generating variants of an input graph.
Allows editors launched for session nodes to register that relevant changes
have been made that will require models downstream to be reconstructed.
Implements an algorithm that takes multiple data sets as input.
Aug 7, 2018 10:21:59 AM
Stores a table of cells with int values of arbitrary dimension.
Wraps the MultiFask algorithm for continuous variables.
Created by user on 3/29/18.
Implements the Anderson-Darling test against the given CDF, with P values calculated
as in R's ad.test method (in package nortest).
Wrapper for Fisher Z test.
Wrapper for MVP BIC Score.
An example script to load in data sets and graphs from files and analyze them.
Calculates Mixed Variables Polynomial likelihood.
Wrapper for Fisher Z test.
Implements a mixed variable polynomial BIC score for fGES.
Specifies the protocol used in Tetrad for variable names.
Represents an object with a name, node type, and position that can serve as a
node in a graph.
Sets whether nodes are compared by the equals method or by object
identity.
An unordered pair of nodes.
The adjacency precision.
The adjacency precision.
A typesafe enum of the types of the types of nodes in a graph (MEASURED,
LATENT, ERROR).
Indicates an algorithm is nonexecutable.
A normal distribution that allows its parameters to be set and allows
random sampling.
Calculates the F1 statistic for adjacencies.
The bidirected true positives.
The bidirected true positives.
The adjacency precision.
Provides an application-wide "memory" of the number format to be used.
Wraps a 2D array of Number objects in such a way that mixed data sets can be
stored.
Prints the number of edges in the true graph.
Prints the number of edges in the true graph.
The bidirected edge precision.
The adjacency precision.
The adjacency precision.
The bidirected true positives.
The bidirected true positives.
The bidirected true positives.
The bidirected true positives.
The bidirected true positives.
The bidirected true positives.
The bidirected true positives.
The bidirected true positives.
The bidirected true positives.
The bidirected true positives.
The bidirected true positives.
The bidirected true positives.
The bidirected true positives.
The bidirected true positives.
The bidirected true positives.
The bidirected true positives.
The bidirected true positives.
The bidirected true positives.
The bidirected true positives.
The bidirected true positives.
The bidirected true positives.
The bidirected true positives.
The bidirected true positives.
The bidirected true positives.
The bidirected true positives.
The bidirected true positives.
The bidirected true positives.
The bidirected true positives.
The bidirected true positives.
The bidirected true positives.
The bidirected true positives.
An ordered pair of objects.
This is an optimization of the CCD (Cyclic Causal Discovery) algorithm by Thomas Richardson.
Implements various permutation algorithms, including BOSS and GASP.
Represents a graph that's output by a genetic search algorithm.
The adjacency precision.
The adjacency recall.
Jan 29, 2023 3:45:09 PM
Jan 29, 2023 4:10:52 PM
This class contains methods which can be used to determine whether a directed graph is in the equivalence class
determined by the given PAG.
A typesafe enum of the types of the various comparisons parameter may have
with respect to one another for SEM estimation.
A class for implementing constraints on the values of the freeParameters of of
instances of the SemIm class.
A typesafe enum of the types of the types of constraints on freeParameters for
SEM models (LT, GT, EQ).
Describes a parameter.
Stores descriptions of the parameters for the simulation box.
Stores information about the identity of a SEM parameter--its name, its type
(COEF, COVAR), and the node(s) it is associated with.
Adds a column to the output table in which values for the given parameter
are listed.
Implements an ordered pair of objects (a, b) suitable for storing in
HashSets.
Stores a list of named parameters with their values.
A utility to create/modify parameters.
Tags a class that can return values for parameters.
May 7, 2019 2:53:27 PM
Tags models whose parameters can be reset.
A typesafe enum of the types of the types of freeParameters for SEM models (COEF,
MEAN, VAR, COVAR).
Frequency function of partial correlation r(12|34...k), assuming that the
true partial correlation is equal to zero.
Implements the PC ("Peter/Clark") algorithm, as specified in Chapter 6 of Spirtes, Glymour, and Scheines, "Causation,
Prediction, and Search," 2nd edition, with a modified rule set in step D due to Chris Meek.
CPC.
PC.
CPC.
Implements a convervative version of PC, in which the Markov condition is assumed but faithfulness is tested
locally.
PC.
Implements the PC ("Peter/Clark") algorithm, as specified in Chapter 6 of Spirtes, Glymour, and Scheines, "Causation,
Prediction, and Search," 2nd edition, with a modified rule set in step D due to Chris Meek.
Implements the PC Local algorithm.
CPC.
Searches for a CPDAG representing all the Markov blankets for a given target T consistent with the given
independence information.
PC-Stable.
Implements the PC ("Peter/Clark") algorithm, as specified in Chapter 6 of Spirtes, Glymour, and Scheines, "Causation,
Prediction, and Search," 2nd edition, with a modified rule set in step D due to Chris Meek.
Implements a modification of the the PC ("Peter/Clark") algorithm, as specified in Chapter 6 of
Spirtes, Glymour, and Scheines, Causation, Prediction, and Search, 2nd edition, using the rule set
in step D due to Chris Meek.
Requires that the parameter 'randomSelectionSize' be set to indicate how many
datasets should be taken at a time (randomly).
The adjacency precision.
The adjacency precision.
Runs some basic performance tests of various algorithm.
Contains some tests for Dan Malinsky, that might be of interest to others.
Generates all of the permutations of [0,..., numObjects - 1], where numObjects is numObjects nonnegative
integer.
Tagging interface for parametric models.
Implements an n-dimensional point.
Stores a (x, y) point without having to use awt classes.
Wraps a chi square distribution for purposes of drawing random samples.
Wrapper for the Poisson prior score (Bryan)
Implements Poisson prior score (Bryan).
Implements a polynomial as a sum of a list of terms whose variables are
identified as integers in the set {0, 1, 2, ...}.
Implements a polynomial update function, Gi.0 = P(Parents(G0.0)) + ei,
where P is a polynomial function and ei is a random noise term.
Implements a term in a polymonial whose variables are mapped to indices in
in the set {0, 1, 2, ...}.
Implements a test of tetrad constraints in a known correlation matrix.
Wrapper for Fisher Z test.
Wrapper for Fisher Z test.
Finds possible d-connecting undirectedPaths for the IonSearch.
This class implements the Possible-D-Sep search step of Spirtes, et al's (1993) FCI algorithm (pp 144-145).
Created by Erich on 8/21/2016.
Initializes a graph by adding the previous time step only of each variable.
Uses BCInference by Cooper and Bui to calculate probabilistic conditional independence judgments.
Dec 17, 2018 3:44:46 PM
Implements a number of important functions from probability and
statistics.> 0
Represents propositions over the variables of a particular BayesIm describing
an event of a fairly general sort--namely, conjunctions of propositions that
particular variables take on values from a particular disjunctive list of
categories.
Implementation of Nesterov's 83 method as described in Beck and Teboulle, 2009
aka Fast Iterative Shrinkage Thresholding Algorithm
Purify is a implementation of the automated purification methods described on CPS and the report "Learning
Measurement Models" CMU-CALD-03-100.
Created by IntelliJ IDEA.
A clean-up of Ricardo's IntSextad-based purify.
A clean-up of Ricardo's tetrad-based purify.
A clean-up of Ricardo's tetrad-based purify.
R1.
R2.
R3.
Constructs as a randomized update workbench.
A distribution from which noise values are drawn.
Creates a random graph by adding forward edges.
An interface to represent a random graph of some sort.
Generates random DAGs uniformly with certain classes of DAGs using variants
of Markov chain algorithm by Malancon, Dutour, and Philippe.
Provides a static method for sampling without replacement from a dataset to
create a new dataset with a sample size supplied by the user.
Creates a random graph by adding forward edges.
Creates a random graph by adding forward edges.
Provides a common random number generator to be used throughout Tetrad, to avoid problems that happen when random
number generators are created more often than once per millisecond.
Jan 27, 2016 4:46:07 PM
Jan 27, 2016 5:35:01 PM
Jan 27, 2016 5:37:40 PM
Feb 9, 2016 3:13:19 PM
Feb 9, 2016 3:14:08 PM
Feb 9, 2016 3:15:29 PM
Created by josephramsey on 4/13/14.
Tokenizes the given input character sequence using the type of delimiter
specified bythe given CPDAG.
Implements a multiple regression model, allowing data to be specified
either as a tabular data set or as a covariance matrix plus list of means.
Implements a regression model from correlations--that is, from a correlation
matrix, a list of standard deviations, and a list of means.
Implements a regression model from tabular continuous data.
Stores the various components of a regression result so they can be passed
around together more easily.
Sundry utilities for regression.
Utility for reidentifying variables for multiple indicator structure searches.
Reorients all or part of the given graph.
Sep 12, 2018 4:07:46 PM
Utilities for resolving inconsistencies that arise between sepsets learned for overlapping datasets.
Provides the methods for computing mutual information between expression
levels between genes and, for a given gene, between points in time determined
by a lag value.
Provides the methods for computing mutual information between expression
levels between genes and, for a given gene, between points in time determined
by a lag value.
This class contains as a member variable (cases) the time series data stored
in an int array of microarray measurements.
This class contains as a member variable (cases) the time series data stored
in an int array of microarray measurements.
RFCI.
Extends Erin Korber's implementation of the Fast Causal Inference algorithm (found in FCI.java) with Jiji Zhang's
Augmented FCI rules (found in sec.
Jan 4, 2019 4:32:05 PM
Dec 17, 2018 3:28:15 PM
Implements ICF as specified in Drton and Richardson (2003), Iterative Conditional Fitting for Gaussian Ancestral
Graph Models, using hints from previous implementations by Drton in the ggm package in R and by Silva in the Purify
class.
Calculates a ROC curve and AUC (area under curve) for a list of scored cases
whose inclusion in category C is known.
Performs updating operations on a BayesIm by summing over cells in the joint
probability table for the BayesIm.
RSkew.
RSkewE.
An example script to save out data files and graphs from a simulation.
Implements a conservative version of PC, in which the Markov condition is assumed but faithfulness is tested
locally.
Implements a conservative version of PC, in which the Markov condition is assumed but faithfulness is tested
locally.
An example script to save out data files and graphs from a simulation.
An example script to save out data files and graphs from a simulation.
Returns a scale free graph.
Sep 1, 2017 10:51:13 AM
Interface for a score suitable for FGES
Sep 26, 2017 1:14:01 AM
May 14, 2019 11:23:54 AM
Stores a graph with a score.
Implements Chickering and Meek's (2002) locally consistent score criterion.
Interface for a class that represents a scoring of a SEM model.
Author : Jeremy Espino MD
Created 1/12/18 2:05 PM
Interface that algorithm must implement.
Graph utilities for search algorithm.
Contains utilities for logging search steps.
Created by ajsedgewick on 9/4/15.
Generates (nonrecursively) all of the selections from a items, where a is
a nonnegative integer.
Wrapper for Fisher Z test.
Wrapper for linear, Gaussian SEM BIC score.
Implements the continuous BIC score for FGES.
Wrapper for Fisher Z test.
Implements the continuous BIC score for FGES.
Implements a degenerate Gaussian BIC score for FGES.
Implements the continuous BIC score for FGES.
Implements the continuous BIC score for FGES.
Wrapper for Fisher Z test.
Estimates a SemIm given a CovarianceMatrix and a SemPm.
Implements the Gibbs sampler apporach to obtain samples of arbitrary size
from the posterior distribution over the freeParameters of a SEM given a
continuous dataset and a SemPm.
Stores the freeParameters for an instance of a SemEstimatorGibbs.
Stores information for a SemIm about evidence we have for each variable as
well as whether each variable has been manipulated.
Represents the graphical structure of a structural equation model.
Calculates the F1 statistic for adjacencies.
The bidirected true positives.
The bidirected true positives.
Stores an instantiated structural equation model (SEM), with error covariance
terms, possibly cyclic, suitable for estimation and simulation.
Stores information for a BayesIm about evidence we have for each variable as
well as whether each variable has been manipulated.
Interface for algorithm that optimize the fitting function of a SemIm model
by adjusting its freeParameters in search of a global maximum.
Optimizes a DAG SEM with hidden variables using expectation-maximization.
Optimizes a SEM using Powell's method from the Apache library.
Optimizes a DAG SEM with no hidden variables using closed formula
regressions.
Optimizes a SEM using RICF (see that class).
Optimizes a SEM by randomly selecting points in cubes of decreasing size about
a given point.
Parametric model for Structural Equation Models.
Represents propositions over the variables of a particular BayesIm describing
and event of a fairly general sort--namely, conjunctions of propositions that
particular variables take on values from a particular disjunctive list of
categories.
Includes methods for estimating the standard errors of the freeParameters of
an estimated SEM.
Calculates updated structural equation models given evidence of the form
X1=x1',...,The main task of such and algorithm is to calculate P(X = x' |
evidence), where evidence takes the form of a Proposition over the variables
in the Bayes net, possibly with additional information about which variables
in the Bayes net have been manipulated.
This class takes an xml element representing a SEM im and converts it to
a SemIM
This class converts a SemIm into xml.
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.
This is the same as the usual SepsetMap described below, but also keeps up with the individual sets of conditioning
nodes for d-separation relations for use with the Distributed Causal Inference (DCI) algorithm.
Created by josephramsey on 3/24/15.
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.
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.
Created by josephramsey on 3/24/15.
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.
Stores a directed graph over models of specific types, where the possible
parent relationships between the models are given in the constructors of the
model classes themselves.
Basic implementation of SessionListener with empty methods.
Notifies a listener that some change has occurred in the session--a node has
been added or removed, an edge has been added or removed, a model has been
created or destroyed.
Listens for SessionEvents on a Session--nodes being added or removed, parents
being added or removed, models being created or destroyed.
Interface implemented by all session models in Tetrad.
Represents a node in a session for a model in a particular class.
Handles firing of SessionSupport events to listeners.
Represents a sextad of variables.
Calculates the structural Hamming distance (SHD) between the estimated graph and
the true graph.
Tries to find a good shifting of variables to minimize average BIC
Stores a 2D array of short data.
Useful for storing very large correlation matrices (space saver).
GRaSP (Greedy Relaxations of Sparsest Permutation)
Randomizes a graph using existing factors by first removing all edges and
then adding for each factor (a) an edge from the same factor at time lag 1
and (b) a given number of factors chosen uniformly from all lagged factors
with lag > 0.
The interface that simulations must implement.
Created by jdramsey on 3/14/16.
Some simulations may wish to implement this interface to specify a simulation
path, which will be printed in the output.
A list of simulations to be compared.
Runs a simulation edu.cmu.tetrad.study for a session which traverses a subtree of the
session graph in depth-first order and executes each node encountered a
specified number of times.
Jun 4, 2019 3:10:49 PM
Jun 4, 2019 5:21:45 PM
Created by jdramsey on 12/22/15.
Stores a single graph for use in simulations, etc.
PC.
A pretend distribution that always returns the given value when
nextRandom() is called.
Skew.
SkewE.
BOSS (Best Order Score Search).
Implements various permutation algorithms, including BOSS and GASP.
J.M.
Wraps a chi square distribution for purposes of drawing random samples.
Specifies how a column (continuous or discrete) should be discretized.
Adjusts GFCI to use a permutation algorithm (in this case SP) to do the initial
steps of finding adjacencies and unshielded colliders.
Euclidean dissimilarity metric--i.e., the sum of the differences in
corresponding variable values.
Stability selection.
Runs a search algorithm over a N subsamples of size b to asses stability
as in "Stability Selection" and "Stability Approach to Regularization Selection"
A special SEM model in which variances of variables are always 1 and means of variables
are always 0.
Stores a coefficient range--i.e.
StARS
The interface that each statistic needs to implement.
A list of statistics and their utility weights.
Contains a number of basic statistical functions.
Creates a table of stored cell probabilities for the given list of
variables.
Creates a table of stored cell probabilities for the given list of
variables.
Stores a file for reading in a lag graph from a file.
Generates (nonrecursively) all of the sublists of size b from a list of size a,
where a, b are nonnegative integers and a >= b.
SvarFCI.
Extends Erin Korber's implementation of the Fast Causal Inference algorithm (found in FCI.java) with Jiji Zhang's
Augmented FCI rules (found in sec.
Extends Erin Korber's implementation of the Fast Causal Inference algorithm (found in FCI.java) with Jiji Zhang's
Augmented FCI rules (found in sec.
SvarFCI.
Replaces the FAS search in the previous version with GES followed by PC adjacency removals for more accuracy.
Implements a space-efficient symmetric matrix
(of elements of type
short),
storing only the lower triangular portion of itImplements a space-efficient symmetric matrix
(of elements of type
short),
storing only the lower triangular portion of itA confusion matrix for tails--i.e.
The arrow precision.
The arrow recall.
Tags a gadget that takes a data model list as argument to its constructor.
Tags an algorithm that can take an external graph as input.
Author : Jeremy Espino MD
Created 7/13/17 2:25 PM
Tanh.
This cancels all processes that check the TaskManager.getInstance().isCanceled()
method.
Expands templates for the generalized SEM PM.
Implements a conditional Gaussian BIC score for FGES.
Tests the BooleanFunction class.
Test the degenerate Gaussian score.
Test the degenerate Gaussian score.
Tests the IndexedConnectivity class by constructing graphs with randomly
chosen parameters and seeing if they have the required properties.
Tests the IndexedLagGraph class by constructing graphs with randomly chosen
parameters and seeing if they have the required properties.
Tests the MeasurementSimulator class using diagnostics devised by Richard
Scheines.
Aug 31, 2017 4:42:08 PM
Sep 26, 2017 1:18:28 AM
Tests the Polynomial class.
Tests the PolynomialTerm class.
Test the Reveal evaluator.
Tests the SimpleRandomizer class by constructing graphs with randomly chosen
parameters and seeing if they have the required properties.
An enumeration of the test types for BuildPureClusters, and Purify.
Represents a tetrad of variables.
Some algebra methods.
Represents a logging utility used throughout tetrad.
A empty config, where no event is active.
Represents an output stream that can get its own length.
Represents the configuration for the logger.
Represents an event which is just an id and a description.
An event associated with the
TetradLoggerListener.A listener for tetrad's logger.
Nov 10, 2017 4:14:31 PM
Interface to tag a class that is part of the set of serializable classes
in the Tetrad API.
Interface to tag a class that should be exluded from the set of
TetradSerializable classes, even if it implements the TetradSerializable
interface.
Contains methods used by TestSerialization to ensure that previous "stable"
versions of Tetrad will by loadable by later "stable" versions of Tetrad.
Interface implemented by classes that test tetrad constraints.
Stores a 2D array of Strings for printing out tables.
Implements a scorer extending Teyssier, M., and Koller, D.
Implements a scorer extending Teyssier, M., and Koller, D.
Implements a scorer extending Teyssier, M., and Koller, D.
Implements a scorer extending Teyssier, M., and Koller, D.
Implements a scorer extending Teyssier, M., and Koller, D.
Wrapper for Fisher Z test.
Represents a time series graph--that is, a graph with a fixed number S of lags, with edges into initial lags
only--that is, into nodes in the first R lags, for some R.
Nov 14, 2017 12:00:31 PM
Aug 7, 2019 6:17:29 PM
Stores time series data as a list of continuous columns.
Implements a convervative version of PC, in which the Markov condition is assumed but faithfulness is tested
locally.
Contains some utilities for doing autoregression.
Allowable tokens.
Represents a transformation on some dataset.
Stores a triple (x, y, z) of nodes.
Marks a search algorithm as a triad classifier and returns the triad classifications if makes.
The bidirected true positives.
The bidirected true positives.
The bidirected true positives.
The bidirected true positives.
The bidirected true positives.
The bidirected true positives.
The bidirected true positives.
The bidirected true positives.
The bidirected true positives.
The bidirected true positives.
A normal distribution that allows its parameters to be set and allows
random sampling.
Extends Erin Korber's implementation of the Fast Causal Inference algorithm (found in FCI.java) with Jiji Zhang's
Augmented FCI rules (found in sec.
GesSearch is an implementation of the GES algorithm, as specified in Chickering (2002) "Optimal structure
identification with greedy search" Journal of Machine Learning Research.
The 2-cycle precision.
The 2-cycle precision.
The 2-cycle precision.
The 2-cycle recall.
The 2-cycle precision.
A sample class to be wrapped in a SessionNode as a model.
A sample class to be wrapped in a SessionNode as a model.
A sample class to be wrapped in a SessionNode as a model.
A sample class to be wrapped in a SessionNode as a model.
A sample class to be wrapped in a SessionNode as a model.
A sample class to be wrapped in a SessionNode as a model.
A sample class to be wrapped in a SessionNode as a model.
A sample class to be wrapped in a SessionNode as a model.
A sample class to be wrapped in a SessionNode as a model.
A sample class to be wrapped in a SessionNode as a model.
A sample class to be wrapped in a SessionNode as a model.
A sample class to be wrapped in a SessionNode as a model.
For given a, b (a < b), returns a point chosen uniformly from [a, b].
Interface to tag classes that should not be cloned by marshalling.> 0
Sep 19, 2017 1:56:20 PM
Represents a Bayes IM in which all of the conditional probability tables have
been updated to take into account evidence.
Implements a function from the previous time steps of a history array to
the getModel time step.
Author : Jeremy Espino MD
Created 7/6/17 2:19 PM
Interface implemented by classes, instantiations of which are capable of
serving as variables for columns in a DataSet.
An Expression for a variable.
Inteface implemented by classes, instantiations of which are associated with
lists of variables.
Feb 9, 2016 3:18:03 PM
Feb 9, 2016 3:18:44 PM
Feb 9, 2016 3:19:52 PM
Implements the "fast adjacency search" used in several causal algorithm in this package.
Implements a convervative version of PC, in which the Markov condition is assumed but faithfulness is tested
locally.
Implements a convervative version of PC, in which the Markov condition is assumed but faithfulness is tested
locally.
Implements a convervative version of PC, in which the Markov condition is assumed but faithfulness is tested
locally.
Vector wrapping matrix library.
Represents the getModel Tetrad version.
Stores a 2D array of double data.
Stores a 2D array of int data.
This version of Vicinity finds nearby nodes by searching with an expanding cube
Prior to Vicinity4, versions of Vicinity looked at the 3 axis independently instead of collectively.
Implements the Washdown algorithm,
This class takes an xml element representing a bayes im and converts it to
a BayesIM
Wrapper for linear, Gaussian Extended BIC score (Chen and Chen).
Implements the Zhang-Shen bound score.
Implements the continuous BIC score for FGES.