sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
2ead218a3e2f93cc12f2d4ac8500a4757d46f9b0a79678e536fbb6e8c2aa0670 | Java | 21,573 | 490 | package edu.cmu.tetrad.search.harness;
import edu.cmu.tetrad.graph.Graph;
import edu.cmu.tetrad.graph.Node;
import edu.cmu.tetrad.graph.RandomGraph;
import edu.cmu.tetrad.search.RecursiveBlocking;
import edu.cmu.tetrad.search.test.MsepTest;
import edu.cmu.tetrad.util.RandomUtil;
import java.io.FileWriter;
import java... |
7860165912b78f87de8351d8a3eda524b31cff3a04375669e3c67f232d1fb961 | Java | 21,663 | 407 | ///////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// //
// Copyright (C) 2026 by Joseph Ramsey, Peter Spirtes, Clark Glymour, //
... |
447f05e77b823bf5563db9356ce8b9f4ec222f7202d448f6bcfe7dcec05e70cd | Java | 21,678 | 616 | /*-
* #%L
* Fiji distribution of ImageJ for the life sciences.
* %%
* Copyright (C) 2010 - 2026 Fiji developers.
* %%
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as
* published by the Free Software Foundation, either version 3 of ... |
10e91a2c46c5ac5575f6843beb3915101e8e657571f99c06e66b1112ece00aef | Java | 21,697 | 582 | package edu.cmu.tetrad.search.score;
import edu.cmu.tetrad.data.DataSet;
import edu.cmu.tetrad.graph.Node;
import edu.cmu.tetrad.util.TMath;
import org.ejml.data.DMatrixRMaj;
import org.ejml.dense.row.CommonOps_DDRM;
import java.util.*;
/**
* <p>CAM scorer using penalized cubic B-splines (P-splines; Eilers & Ma... |
267410ebf525f26c10bbfc15a74a87086bc36bd68bded9243afa8732669eb2f2 | Java | 21,769 | 570 | ///////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// //
// Copyright (C) 2025 by Joseph Ramsey, Peter Spirtes, Clark Glymour, //
... |
2ce4910ecace0ad3b684e46795bec8746eef5ca81642bacfa46b1b192452b0e6 | Java | 21,856 | 592 | ///////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// //
// Copyright (C) 2025 by Joseph Ramsey, Peter Spirtes, Clark Glymour, //
... |
ec7248d4b8b8fa26e6205b72a85973a53fd9eef1a4dbea0ce7b9210b57b92c35 | Java | 21,867 | 511 | package edu.cmu.tetrad.search.is;
import edu.cmu.tetrad.data.*;
import edu.cmu.tetrad.graph.Node;
import edu.cmu.tetrad.util.TMath;
import java.util.*;
import java.util.stream.IntStream;
/**
* Instance-Specific BIC (IS-BIC) score for discrete data.
*
* <p>Implements {@link IsScore} for discrete variables. Likelih... |
709c84301a4da00a7135ec672634f418df438022a6563df634e644ae043dd05a | Java | 21,881 | 655 | ///////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// //
// Copyright (C) 2025 by Joseph Ramsey, Peter Spirtes, Clark Glymour, //
... |
5a61aa2c5dd63c27c6d77207e27d1b2543b37e27d033f5cac937d5fe3ee58c76 | Java | 21,896 | 521 | /// ////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// //
// Copyright (C) 2025 by Joseph Ramsey, Peter Spirtes, Clark Glymour, //... |
56fed22347c2e7a3da25b1575eb0dceae95dfa6d8f25487880bf4f195b013ae8 | Java | 21,979 | 538 | ///////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// //
// Copyright (C) 2025 by Joseph Ramsey, Peter Spirtes, Clark Glymour, //
... |
9f2501b54de8c2a24ea5fe8f312f764ad5d8ca28f95d248db6cd8dd644c61c7b | Java | 21,996 | 532 | /*-
* #%L
* Fiji distribution of ImageJ for the life sciences.
* %%
* Copyright (C) 2010 - 2026 Fiji developers.
* %%
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as
* published by the Free Software Foundation, either version 3 of ... |
e9aeccdbc2c56308828fc2b44d9c293b6ffc4b6c1c3d5a632280bc4b8dbbd4bb | Java | 22,011 | 673 | ///////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// //
// Copyright (C) 2025 by Joseph Ramsey, Peter Spirtes, Clark Glymour, //
... |
a61bfa451048f6f06f1368ae859d574843fb098eb4b995daa8bdf660ecb036e0 | Java | 22,022 | 626 | /*-
* #%L
* Fiji distribution of ImageJ for the life sciences.
* %%
* Copyright (C) 2010 - 2026 Fiji developers.
* %%
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as
* published by the Free Software Foundation, either version 3 of ... |
e821d294d0837949fbf3acafc2d8a7906441a4c68947f680f12475d0924524d3 | Java | 22,055 | 621 | /// ////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// //
// Copyright (C) 2025 by Joseph Ramsey, Peter Spirtes, Clark Glymour, //... |
ba911d5c7675809bb10072d8bc3be141cc9ecf660b5c2f087658c2703aa58826 | Java | 22,081 | 439 | /*-
* #%L
* Fiji distribution of ImageJ for the life sciences.
* %%
* Copyright (C) 2010 - 2026 Fiji developers.
* %%
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as
* published by the Free Software Foundation, either version 3 of ... |
0cd2dfbb278c601a33fd0aefedd25719b1035ccd787c28ac652abc8ce540b51b | Java | 22,127 | 519 | /// ////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// //
// Copyright (C) 2025 by Joseph Ramsey, Peter Spirtes, Clark Glymour, //... |
79588ac01b4270245ac8b5fbb82d294fb5a255206e83c25e4976217f1a6d5d73 | Java | 22,274 | 518 | package edu.cmu.tetradapp.editor;
import edu.cmu.tetrad.data.DataSet;
import edu.cmu.tetrad.data.SimpleDataLoader;
import edu.cmu.tetrad.graph.GraphUtils;
import edu.cmu.tetrad.graph.Node;
import edu.cmu.tetradapp.model.DataWrapper;
import edu.cmu.tetradapp.model.EditorUtils;
import edu.cmu.tetradapp.model.HybridCgEst... |
83754f66cc34ab9c591c24981cfa9f1f7f5c186fed584b3d9fd973a31ebd5dcb | Java | 22,305 | 365 | /// ////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// //
// Copyright (C) 2025 by Joseph Ramsey, Peter Spirtes, Clark Glymour, //... |
7a5307b4475edaec8583bf4ad5c31097f92c9e931c46492edf9830b49e0553b5 | Java | 22,342 | 670 | /// ////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// //
// Copyright (C) 2025 by Joseph Ramsey, Peter Spirtes, Clark Glymour, //... |
b90ae7b4d9798bc2606d795051145012086b3a0a179c7b2a78ef59bed7d863ee | Java | 22,417 | 584 | /// ////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// //
// Copyright (C) 2025 by Joseph Ramsey, Peter Spirtes, Clark Glymour, //... |
1447aedab2cd08ba9bb5c18058ad704465a849a5ccfba41ee43fca63d97a25ec | Java | 22,420 | 706 | /// ////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// //
// Copyright (C) 2025 by Joseph Ramsey, Peter Spirtes, Clark Glymour, //... |
bf718f9c90d621d0071a84519ee33f247dc7aa4847268c3802ac9afcee1c3173 | Java | 22,421 | 797 | /*-
* #%L
* Fiji distribution of ImageJ for the life sciences.
* %%
* Copyright (C) 2010 - 2026 Fiji developers.
* %%
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as
* published by the Free Software Foundation, either version 3 of ... |
911b526c2a76354ad273e78c2da8387810e4cf0d79497b7a496134ffc35850bf | Java | 22,508 | 476 | ///////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// //
// Copyright (C) 2025 by Joseph Ramsey, Peter Spirtes, Clark Glymour, //
... |
eeae0452c30a04327a72cfd53f097110993f262f4db2fdc4989f4ca58359d249 | Java | 22,518 | 620 | /*-
* #%L
* Fiji distribution of ImageJ for the life sciences.
* %%
* Copyright (C) 2010 - 2026 Fiji developers.
* %%
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as
* published by the Free Software Foundation, either version 3 of ... |
8fc6795e70bb9345ed940f4e9e581dbd8abb4878498d0d7592c74f8df208de83 | Java | 22,670 | 459 | ///////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// //
// Copyright (C) 2025 by Joseph Ramsey, Peter Spirtes, Clark Glymour, //
... |
37f9eb528247bfda08eab64f21608bd4c92d4ee46e009972ca65dcb54b0b6a53 | Java | 22,690 | 572 | ///////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// //
// Copyright (C) 2025 by Joseph Ramsey, Peter Spirtes, Clark Glymour, //
... |
1a59d9217ae70de4d6dd830907fb86e4609c386408b6e2645b68ea6043b4d3c0 | Java | 22,779 | 489 | ///////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// //
// Copyright (C) 2025 by Joseph Ramsey, Peter Spirtes, Clark Glymour, //
... |
9e5820b9c94766f7feba77552f49d4ea8f9e5778b26ab260ca8dd017087e004b | Java | 22,815 | 598 | /// ////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// //
// Copyright (C) 2025 by Joseph Ramsey, Peter Spirtes, Clark Glymour, //... |
43050755167f87da41a5c2c2bb53057b12a190da89de875ef21763c89fc4c79c | Java | 22,840 | 556 | /// ////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// //
// Copyright (C) 2025 by Joseph Ramsey, Peter Spirtes, Clark Glymour, //... |
6383488ba53fe7bf49c25c08f366a661d48b05060b3fe020137203c4e4b93a3e | Java | 22,865 | 692 | ///////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// //
// Copyright (C) 2025 by Joseph Ramsey, Peter Spirtes, Clark Glymour, //
... |
1efbb7943544f62420371c5895a2dc6e6b1ccd30b23ed8a64fb3af9f07ee320c | Java | 22,873 | 595 | /// ////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// //
// Copyright (C) 2025 by Joseph Ramsey, Peter Spirtes, Clark Glymour, //... |
71d9e48353f057375f37dfcd98d974cce085c1240d8684ec264cee2393d84571 | Java | 22,873 | 593 | ///////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// //
// Copyright (C) 2025 by Joseph Ramsey, Peter Spirtes, Clark Glymour, //
... |
0d9df252950817b8d1c54cf0c4c65abccbacc80c6112a8bb044669419fdea75b | Java | 22,904 | 719 | ///////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// //
// Copyright (C) 2025 by Joseph Ramsey, Peter Spirtes, Clark Glymour, //
... |
881f07ae814ff4e1b5dac1aad9015c4ff99d5f0ab4cf801f9a334248966f9cbc | Java | 22,939 | 639 | ///////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// //
// Copyright (C) 2025 by Joseph Ramsey, Peter Spirtes, Clark Glymour, //
... |
ca60820ba1656f50146541a7825c7a5869170c3db707338bb0ec90807f5516fa | Java | 22,995 | 521 | ///////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// //
// Copyright (C) 2025 by Joseph Ramsey, Peter Spirtes, Clark Glymour, //
... |
b68580e85969860f4ba542b4d083d8f041e3c16a98a65eea0577059e0b6d30b7 | Java | 23,039 | 678 | ///////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// //
// Copyright (C) 2025 by Joseph Ramsey, Peter Spirtes, Clark Glymour, //
... |
e38a353217df8ed373e8360b1c675a2cca75242c70d88430d4648ce2f124db49 | Java | 23,048 | 607 | /// ////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// //
// Copyright (C) 2025 by Joseph Ramsey, Peter Spirtes, Clark Glymour, //... |
f2d65adcd97969a882458063218ca3c8480ac53a166793594775f25618ab54ee | Java | 23,082 | 490 | /// ////////////////////////////////////////////////////////////////////////////
// VertexRepairBattery2.java //
// //
// Updated battery sweeping conditioning types as well as scenarios, //
... |
a6b5bf7edf6d7a5a39d32254021bbb49a5a3cd3959328d76757a5d6ee77fe39e | Java | 23,103 | 555 | package edu.cmu.tetrad.search.is;
import edu.cmu.tetrad.data.*;
import edu.cmu.tetrad.graph.Node;
import org.apache.commons.math3.special.Gamma;
import edu.cmu.tetrad.util.TMath;
import java.util.*;
import java.util.stream.Collectors;
import java.util.stream.IntStream;
/**
* Instance‑Specific BDeu (IS‑BDeu) score.
... |
1a43bf1256d36fd3c0d2d38cd5e15dc89ac75199da5d9f2159f5ab278f0c42ac | Java | 23,194 | 617 | ///////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// //
// Copyright (C) 2025 by Joseph Ramsey, Peter Spirtes, Clark Glymour, //
... |
18a226e56c9ea07c07017d51982ce6afaad3a038693dda17e9987baca2cfade3 | Java | 23,336 | 655 | /*-
* #%L
* Fiji distribution of ImageJ for the life sciences.
* %%
* Copyright (C) 2010 - 2026 Fiji developers.
* %%
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as
* published by the Free Software Foundation, either version 3 of ... |
8e4d85c29b2ef00537bcb9861485e0fc9a8a06f46bfc9257c386aa954705dd4e | Java | 23,375 | 556 | ///////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// //
// Copyright (C) 2025 by Joseph Ramsey, Peter Spirtes, Clark Glymour, //
... |
bf96396f486a35662e537e0873adafe80c114a6671afcf1178d24fb60521d276 | Java | 23,409 | 654 | package edu.cmu.tetrad.search.score;
import edu.cmu.tetrad.data.DataModel;
import edu.cmu.tetrad.data.DataSet;
import edu.cmu.tetrad.data.DiscreteVariable;
import edu.cmu.tetrad.graph.Node;
import edu.cmu.tetrad.util.EffectiveSampleSizeSettable;
import edu.cmu.tetrad.util.TetradLogger;
import edu.cmu.tetrad.util.TMath... |
db1eaf20ce1009cca88654258a9f9183692aa19fee157fab03ce7cdb8cd6d00e | Java | 23,523 | 537 | /// ////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// //
// Copyright (C) 2025 by Joseph Ramsey, Peter Spirtes, Clark Glymour, //... |
b5593d7a13d6e2d0a3daa433c0dc578a68f1b9034ee9a08730695d955a66b1a3 | Java | 23,540 | 532 | package edu.cmu.tetradapp.editor;
import edu.cmu.tetrad.data.ContinuousVariable;
import edu.cmu.tetrad.data.DataSet;
import edu.cmu.tetrad.data.DiscreteVariable;
import edu.cmu.tetrad.data.Histogram;
import edu.cmu.tetrad.graph.Graph;
import edu.cmu.tetrad.graph.Node;
import edu.cmu.tetrad.util.NaturalSort;
import edu... |
64af80bda30825690c2fbb132ff2383c9d2d745c198c00478bff4104a2f9c76b | Java | 23,598 | 652 | package edu.cmu.tetradapp.model;
import edu.cmu.tetrad.data.DataModel;
import edu.cmu.tetrad.data.DataSet;
import edu.cmu.tetrad.data.DiscreteVariable;
import edu.cmu.tetrad.graph.*;
import edu.cmu.tetrad.search.RecursiveAdjustment;
import edu.cmu.tetrad.search.RecursiveAdjustmentMultiple;
import edu.cmu.tetrad.util.P... |
926578663184f7f1bd0b9f58f97972e75740ffd0576480eeb57587b5bbd0dbc7 | Java | 23,633 | 641 | /// ////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// //
// Copyright (C) 2025 by Joseph Ramsey, Peter Spirtes, Clark Glymour, //... |
632f55f45ef0a3822dc94fd25fc549ac38710654311a6eae90db3cfb72996d9f | Java | 23,687 | 600 | package edu.cmu.tetradapp.model;
import edu.cmu.tetrad.data.*;
import edu.cmu.tetrad.graph.Graph;
import edu.cmu.tetrad.graph.Node;
import edu.cmu.tetrad.util.TetradLogger;
import edu.cmu.tetrad.util.TetradSerializable;
import edu.cmu.tetradapp.session.SessionModel;
import edu.cmu.tetradapp.util.WatchedProcess;
import... |
11c2aa1538b2bcb7f73161ca8078e7559bcd4ab3e3a23304a67098c986bbacbc | Java | 23,733 | 606 | ///////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// //
// Copyright (C) 2025 by Joseph Ramsey, Peter Spirtes, Clark Glymour, //
... |
68df779f2914c78b9e67c15d027876b6969f4f963e9f3ba3ce3c1115342eaf7b | Java | 23,748 | 595 | /*-
* #%L
* Fiji distribution of ImageJ for the life sciences.
* %%
* Copyright (C) 2010 - 2026 Fiji developers.
* %%
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as
* published by the Free Software Foundation, either version 3 of ... |
57cf3e92115787e3c04dd2811110e179a1cf31e0b2bae38db51c09cc4b97099d | Java | 23,765 | 623 | package edu.cmu.tetrad.search.score;
import edu.cmu.tetrad.data.CorrelationMatrix;
import edu.cmu.tetrad.graph.Node;
import edu.cmu.tetrad.search.blocks.BlockSpec;
import edu.cmu.tetrad.util.EffectiveSampleSizeSettable;
import edu.cmu.tetrad.util.RankTests;
import edu.cmu.tetrad.util.TMath;
import org.ejml.simple.Simp... |
661d413affde15515e7d3c91e8627dc5836d67a83c8d689d4a4a219982d6ac95 | Java | 23,822 | 720 | package edu.cmu.tetrad.search.score;
import edu.cmu.tetrad.data.DataModel;
import edu.cmu.tetrad.data.DataSet;
import edu.cmu.tetrad.graph.Node;
import edu.cmu.tetrad.util.EffectiveSampleSizeSettable;
import edu.cmu.tetrad.util.TetradLogger;
import edu.cmu.tetrad.util.TMath;
import org.ejml.data.DMatrixRMaj;
import or... |
1699f6cc5552cd9afedbaef95405f222416fde651aab286fe98a30e55ee8baba | Java | 23,859 | 535 | package edu.cmu.tetrad.search.test;
import java.util.*;
/**
* Standalone validation harness for the CORD port. No Tetrad dependencies: operates on
* double[][] / double[]. Contains the histogram gradient-boosted regression tree learner
* (Gbrt), the threshold-CDF estimator, and the CORD score. main() reproduces th... |
892a98c640bc52683d2ff12d149bc26c8e0f7559f4c1cd84f4aed9e54b32bd10 | Java | 23,860 | 640 | package edu.cmu.tetrad.search.test;
import edu.cmu.tetrad.data.DataSet;
import edu.cmu.tetrad.graph.IndependenceFact;
import edu.cmu.tetrad.graph.Node;
import edu.cmu.tetrad.util.Parameters;
import edu.cmu.tetrad.util.TetradLogger;
import org.apache.commons.math3.distribution.ChiSquaredDistribution;
import edu.cmu.tet... |
aad4c525519da3aeb81ab911e2e5c3aca902b455071670241debd5d050e00ec1 | Java | 23,920 | 668 | /*-
* #%L
* Fiji distribution of ImageJ for the life sciences.
* %%
* Copyright (C) 2010 - 2026 Fiji developers.
* %%
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as
* published by the Free Software Foundation, either version 3 of ... |
60b0ef4a664d617fab6779333706b10b5187f46eb000a33bae942ccedf9d2233 | Java | 24,077 | 528 | /*-
* #%L
* Fiji distribution of ImageJ for the life sciences.
* %%
* Copyright (C) 2010 - 2026 Fiji developers.
* %%
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as
* published by the Free Software Foundation, either version 3 of ... |
d388e7f8996bdab9edd101222af2c1ef9196e3f9f1de13def4e8675030e51ab8 | Java | 24,092 | 761 | ///////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// //
// Copyright (C) 2025 by Joseph Ramsey, Peter Spirtes, Clark Glymour, //
... |
56b078e0ff9bd51d46491263a04317fddc970c17438ed5f617eeeb44056c25fa | Java | 24,109 | 597 | /*-
* #%L
* Fiji distribution of ImageJ for the life sciences.
* %%
* Copyright (C) 2010 - 2026 Fiji developers.
* %%
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as
* published by the Free Software Foundation, either version 3 of ... |
ab38f35ef982967eb0060f41a0ae452f1e78dd9fdc09b3151be5daa2d09c2eff | Java | 24,137 | 685 | ///////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// //
// Copyright (C) 2025 by Joseph Ramsey, Peter Spirtes, Clark Glymour, //
... |
141325f5aad19a1d36738ab6a401c17a585d4fa59c1879380e6749ef5f6a59f3 | Java | 24,168 | 609 | package edu.cmu.tetrad.search.score;
import edu.cmu.tetrad.data.CorrelationMatrix;
import edu.cmu.tetrad.graph.Node;
import edu.cmu.tetrad.search.blocks.BlockSpec;
import edu.cmu.tetrad.util.EffectiveSampleSizeSettable;
import edu.cmu.tetrad.util.RankTests;
import edu.cmu.tetrad.util.TMath;
import org.ejml.simple.Simp... |
245e1f9db7af941b52d37b97cb60ed347b24117280cc2eb49c000eb378cb1c0f | Java | 24,189 | 723 | /*-
* #%L
* Fiji distribution of ImageJ for the life sciences.
* %%
* Copyright (C) 2010 - 2026 Fiji developers.
* %%
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as
* published by the Free Software Foundation, either version 3 of ... |
1ee1b7f29ca1b8bf508a985328090fd00ac0ffc0b1d712efa4d32f44b7c356b3 | Java | 24,197 | 535 | ///////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// //
// Copyright (C) 2026 by Joseph Ramsey, Peter Spirtes, Clark Glymour, //
... |
57e21c69dff9b55ad8964ca07f241428331f6a2696f5cda9f1ab97bed32822da | Java | 24,199 | 701 | ///////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// //
// Copyright (C) 2025 by Joseph Ramsey, Peter Spirtes, Clark Glymour, //
... |
4af855ef69997eecef39e087ae5ec01995beb3ca05cd2000832729a4e0c54608 | Java | 24,274 | 612 | /// ////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// //
// Copyright (C) 2025 by Joseph Ramsey, Peter Spirtes, Clark Glymour, //... |
d55082981067f2ded2e6c94fb03c0f14564c0ea6a3b8d60fe90f185668a701af | Java | 24,305 | 669 | ///////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// //
// Copyright (C) 2025 by Joseph Ramsey, Peter Spirtes, Clark Glymour, //
... |
b80d8024e77f34f00a9bd5f045d0b8157dbb7fbb0c1b1baea2b3d9ce77457262 | Java | 24,338 | 676 | ///////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// //
// Copyright (C) 2025 by Joseph Ramsey, Peter Spirtes, Clark Glymour, //
... |
b1961f29cc4bac36c58376b9ec5b776d2b06613c0ad5205f2c532804d48e7cf7 | Java | 24,440 | 754 | ///////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// //
// Copyright (C) 2025 by Joseph Ramsey, Peter Spirtes, Clark Glymour, //
... |
e32f03f2865ef0c1305d7dad8ad5d58ca3e73d786a2583de8af344dda7244274 | Java | 24,443 | 712 | ///////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// //
// Copyright (C) 2025 by Joseph Ramsey, Peter Spirtes, Clark Glymour, //
... |
0d4b97a0abd1e2569bae6e5184c3e8a2f0c727c9a3e8f499407c7934a9fae067 | Java | 24,546 | 689 | ///////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// //
// Copyright (C) 2025 by Joseph Ramsey, Peter Spirtes, Clark Glymour, //
... |
62c167bff76135936189d29ce485cf24c4e593513d11f9e2817d4087ea215f2d | Java | 24,550 | 677 | package edu.cmu.tetradapp.editor;
import edu.cmu.tetrad.graph.Graph;
import edu.cmu.tetrad.graph.GraphNode;
import edu.cmu.tetrad.graph.Node;
import edu.cmu.tetrad.util.NaturalSort;
import edu.cmu.tetrad.util.NumberFormatUtil;
import edu.cmu.tetradapp.model.DoublyRobustEstModelV2;
import edu.cmu.tetradapp.model.Doubly... |
b348654e26e108c096ac405c70f6852711caee70a63285597c2f033bef66848d | Java | 24,581 | 687 | /*-
* #%L
* Fiji distribution of ImageJ for the life sciences.
* %%
* Copyright (C) 2010 - 2026 Fiji developers.
* %%
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as
* published by the Free Software Foundation, either version 3 of ... |
97d43d4c5427be88e3ec80d3c46b477b2d2288c599fad38f2182da8322774183 | Java | 24,637 | 745 | ///////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// //
// Copyright (C) 2025 by Joseph Ramsey, Peter Spirtes, Clark Glymour, //
... |
8f570904ed76007e2357049b5a1009f08b2143181c7018c25f078264d1adb6ab | Java | 24,789 | 805 | ///////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// //
// Copyright (C) 2025 by Joseph Ramsey, Peter Spirtes, Clark Glymour, //
... |
cf8b224f7afd9d9bc7b716ddd58b2471c1b989263c7452d805896859fa0d3828 | Java | 24,877 | 620 | /// ////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// //
// Copyright (C) 2025 by Joseph Ramsey, Peter Spirtes, Clark Glymour, //... |
c192422f103681aa45b8ff67543ddd70d813ad476e2bcbc624b61b2dc637cead | Java | 24,892 | 577 | ///////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// //
// Copyright (C) 2025 by Joseph Ramsey, Peter Spirtes, Clark Glymour, //
... |
226eca74d60154901a494485bb7afa6d171a7417c1e052cb439f2082fb5c8300 | Java | 24,979 | 554 | /*-
* #%L
* Fiji distribution of ImageJ for the life sciences.
* %%
* Copyright (C) 2010 - 2026 Fiji developers.
* %%
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as
* published by the Free Software Foundation, either version 3 of ... |
63432c7b35efb65094b071d7e5a204fe52d140026a1c5271c663009a2aa06955 | Java | 25,003 | 705 | /*
* Copyright (C) 2026
*
* Exact inference for discrete Bayes nets using Variable Elimination (VE).
* This class provides the API expected by JunctionTreeUpdater.
*
* NOTE:
* - Despite the name, this implementation does NOT build a junction tree;
* it performs exact inference by factor multiplication + eli... |
1d2046090584a5e9036a6aa99836085650ebb1a78bad486432aff7a0a95f8bca | Java | 25,125 | 664 | /// ////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// //
// Copyright (C) 2025 by Joseph Ramsey, Peter Spirtes, Clark Glymour, //... |
925a58474370c566ab63a9307fdbca1e59519872e673aad4c923b11853e4e3fd | Java | 25,192 | 681 | /*-
* #%L
* Fiji distribution of ImageJ for the life sciences.
* %%
* Copyright (C) 2010 - 2026 Fiji developers.
* %%
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as
* published by the Free Software Foundation, either version 3 of ... |
cb64ada9e4ac44470031b976a06597554d021b4e3e571f669bc132703f98a4c9 | Java | 25,301 | 590 | /*-
* #%L
* Fiji distribution of ImageJ for the life sciences.
* %%
* Copyright (C) 2010 - 2026 Fiji developers.
* %%
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as
* published by the Free Software Foundation, either version 3 of ... |
19b33d23f917ac8b169360a9ed082acfdbac3e16a51b483affd7a9395fdd1583 | Java | 25,422 | 757 | /*-
* #%L
* Fiji distribution of ImageJ for the life sciences.
* %%
* Copyright (C) 2010 - 2026 Fiji developers.
* %%
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as
* published by the Free Software Foundation, either version 3 of ... |
d4a0cd07cb0504c54f4501e257cf88577458fa37152d825d3d4b16f620548c34 | Java | 25,625 | 578 | /*-
* #%L
* Fiji distribution of ImageJ for the life sciences.
* %%
* Copyright (C) 2010 - 2026 Fiji developers.
* %%
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as
* published by the Free Software Foundation, either version 3 of ... |
7eb7cb97da1255cda2f18924756fa415bbd3335624f478c83d45e32aa6ff83d1 | Java | 25,637 | 733 | /*-
* #%L
* Fiji distribution of ImageJ for the life sciences.
* %%
* Copyright (C) 2010 - 2026 Fiji developers.
* %%
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as
* published by the Free Software Foundation, either version 3 of ... |
15f926fb8a6599e2a2bbf89e25d117df3f7974f2bec8c9e3cef7fa930ffdd07e | Java | 25,717 | 753 | /*-
* #%L
* Fiji distribution of ImageJ for the life sciences.
* %%
* Copyright (C) 2010 - 2026 Fiji developers.
* %%
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as
* published by the Free Software Foundation, either version 3 of ... |
b65fb4d90c870bded18022936476bc533a3e7472dc3f1600c9dfc9aa5616dba6 | Java | 25,801 | 488 | ///////////////////////////////////////////////////////////////////////////////
// FcitBenchmarkHarness.java //
// //
// Serial benchmark harness for comparing seven causal-discovery algorithms: //
... |
38f25d3a892ba19d772ee9843afe13a683dd23a4c72c9e0dec63741694a1186a | Java | 26,001 | 737 | /// ////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// //
// Copyright (C) 2025 by Joseph Ramsey, Peter Spirtes, Clark Glymour, //... |
817516da8e8eb27451c97ba5b8953cbd311a73fd1c9620a0c7f209ac319216ba | Java | 26,041 | 902 | ///////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// //
// Copyright (C) 2025 by Joseph Ramsey, Peter Spirtes, Clark Glymour, //
... |
237b177cb47fd224e515c39cc9df6bffec0ab753d928779fc1477813482e0a95 | Java | 26,087 | 764 | /*-
* #%L
* Fiji distribution of ImageJ for the life sciences.
* %%
* Copyright (C) 2010 - 2026 Fiji developers.
* %%
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as
* published by the Free Software Foundation, either version 3 of ... |
9933aa6406210c4b9e15999acf84436e792223fcbce0f82a0f9b9e3fa857dee6 | Java | 26,090 | 873 | ///////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// //
// Copyright (C) 2025 by Joseph Ramsey, Peter Spirtes, Clark Glymour, //
... |
119d53fb117ec26fe87c18288cf65b71a5b6060a34b9e3da2edcc7db94668933 | Java | 26,157 | 722 | /// ////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// //
// Copyright (C) 2025 by Joseph Ramsey, Peter Spirtes, Clark Glymour, //... |
5f8ac9215358287a5887c39d2aa8c81492dfe7b3507dc78d220c52c07c54ecb7 | Java | 26,168 | 653 | ///////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// //
// Copyright (C) 2026 by Joseph Ramsey, Peter Spirtes, Clark Glymour, //
... |
ffd3c637196c8c30e570a911744be49f115515354a60414ae975803369f66b1f | Java | 26,227 | 805 | package edu.cmu.tetradapp.workbench;
import edu.cmu.tetrad.graph.Edge;
import edu.cmu.tetrad.graph.Endpoint;
import edu.cmu.tetrad.util.TMath;
import javax.swing.*;
import java.awt.*;
import java.awt.geom.Ellipse2D;
import java.awt.geom.Path2D;
import java.awt.event.ComponentAdapter;
import java.awt.event.ComponentEv... |
0bbcca3a1dda3437c1c7473d1ab2309c47a8505b7f33fa530aaec7f173ab5146 | Java | 26,305 | 696 | /*-
* #%L
* Fiji distribution of ImageJ for the life sciences.
* %%
* Copyright (C) 2010 - 2026 Fiji developers.
* %%
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as
* published by the Free Software Foundation, either version 3 of ... |
26ed178b653c2b72f0ad28b425ecb84e926a7570204ef113e6082042d4224fad | Java | 26,318 | 475 | ///////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// //
// Copyright (C) 2026 by Joseph Ramsey, Peter Spirtes, Clark Glymour, //
... |
61cb84e8a98147df3ab76e598510908db5db2708082f436553210da126fa08e0 | Java | 26,438 | 641 | ///////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// //
// Copyright (C) 2025 by Joseph Ramsey, Peter Spirtes, Clark Glymour, //
... |
08ef39f48460b3d2924e095c151b8f0df64a0328dd8cdd912c02c102cf0d5d03 | Java | 26,620 | 774 | package edu.cmu.tetrad.search.mimic;
import edu.cmu.tetrad.data.Knowledge;
import edu.cmu.tetrad.graph.*;
import edu.cmu.tetrad.search.IGraphSearch;
import edu.cmu.tetrad.search.Pc;
import edu.cmu.tetrad.search.test.IndependenceTest;
import java.util.*;
/**
* A more robust detect-mimic heuristic for MIMIC-like stru... |
3f9f90169996364e7a8637c26567d589f4f84827b6d6a1ad344487489dc3014f | Java | 26,696 | 771 | ///////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// //
// Copyright (C) 2025 by Joseph Ramsey, Peter Spirtes, Clark Glymour, //
... |
e5e4f2e96d9983879ad2a7a0fd4b874da8ec54122fcfd25530d06de2538d3ad3 | Java | 26,789 | 766 | /*-
* #%L
* Fiji distribution of ImageJ for the life sciences.
* %%
* Copyright (C) 2010 - 2026 Fiji developers.
* %%
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as
* published by the Free Software Foundation, either version 3 of ... |
a179b3d30aab1464b97084bea0833634283332ba8173c17278fb8c2cc57ca231 | Java | 26,806 | 890 | ///////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// //
// Copyright (C) 2025 by Joseph Ramsey, Peter Spirtes, Clark Glymour, //
... |
fa95e772188bb5e12927b1bd568f42a844b4ff8b607a944b6e966e55d8a65fc2 | Java | 26,832 | 606 | /*-
* #%L
* Fiji distribution of ImageJ for the life sciences.
* %%
* Copyright (C) 2010 - 2026 Fiji developers.
* %%
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as
* published by the Free Software Foundation, either version 3 of ... |
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