sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
9cf3ccf20eff538cd940e7973a3aa233f1525c0b3832b79074a9d4bd54654310 | Java | 34,897 | 793 | /*-
* #%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 ... |
45a28838140dadc2a244921b2a1867f6c852847550cd58f30f1698a18283f6a7 | Java | 35,114 | 896 | ///////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// //
// Copyright (C) 2025 by Joseph Ramsey, Peter Spirtes, Clark Glymour, //
... |
517c191fda7e7005fe4011b5a785eb722362ca49416dcf529e192809f4f554c6 | Java | 35,388 | 1,111 | ///////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// //
// Copyright (C) 2025 by Joseph Ramsey, Peter Spirtes, Clark Glymour, //
... |
95fab989b64609746708ef4f5f8729ff074acf51bf2ee3ed6cdd2ca237695578 | Java | 35,517 | 1,018 | /*-
* #%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 ... |
c42469b1ccc2539165ec4518a5ef5cfd3832433540724e140db5b5daddba311f | Java | 35,878 | 921 | ///////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// //
// Copyright (C) 2025 by Joseph Ramsey, Peter Spirtes, Clark Glymour, //
... |
1088e6f875ba7151d7416eb5de5d8a72fdb4baec7a40a221430e424f384b9fcc | Java | 35,891 | 1,039 | ///////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// //
// Copyright (C) 2025 by Joseph Ramsey, Peter Spirtes, Clark Glymour, //
... |
f1627ff702a14a396041767a44d37395da40d054557be2e1004d6bb8aa649249 | Java | 35,981 | 1,081 | ///////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// //
// Copyright (C) 2025 by Joseph Ramsey, Peter Spirtes, Clark Glymour, //
... |
b5391edf9885b1d1547a6e5557a2fbf3e75d21dfaaca21da11d9184f5b203c4c | Java | 36,167 | 990 | package edu.cmu.tetrad.search.score;
import edu.cmu.tetrad.data.missing.MissingValueSupport;
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... |
bc13a9d74e75ced193c9d8ef57076d4f6b9e99779427d360b3b1e60261d93732 | Java | 36,371 | 819 | /// ////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// //
// Copyright (C) 2025 by Joseph Ramsey, Peter Spirtes, Clark Glymour, //... |
2d3350b041fcf27848cc83a2c7a15e5e49af0312480efbf124ba382f105081c9 | Java | 37,161 | 942 | /// ////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// //
// Copyright (C) 2025 by Joseph Ramsey, Peter Spirtes, Clark Glymour, //... |
2bc2975989170a0305d0edc566259522ef36c48e7daf628cbc1134cd6ffacb7d | Java | 37,190 | 934 | package edu.cmu.tetrad.search.test;
import edu.cmu.tetrad.data.DataModel;
import edu.cmu.tetrad.graph.IndependenceFact;
import edu.cmu.tetrad.graph.Node;
import edu.cmu.tetrad.util.TMath;
import edu.cmu.tetrad.util.TetradSerializable;
import java.io.Serial;
import java.util.*;
import java.util.concurrent.ConcurrentHa... |
7a95a8ebb6ba0b4e6ec29956907912a93e2b9f51d17a4c4d0d392b3da18ab55c | Java | 37,268 | 1,100 | ///////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// //
// Copyright (C) 2025 by Joseph Ramsey, Peter Spirtes, Clark Glymour, //
... |
31ddca7b16c6ee41be003f814ef9708f44e034156ee2ded7a5effb90944c37ba | Java | 37,517 | 1,121 | ///////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// //
// Copyright (C) 2025 by Joseph Ramsey, Peter Spirtes, Clark Glymour, //
... |
51e4c1acc858dca8c07775c6083b1cd071e58dd768d3cda2fc966ce81add461d | Java | 37,813 | 860 | ///////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// //
// Copyright (C) 2025 by Joseph Ramsey, Peter Spirtes, Clark Glymour, //
... |
68898b277a70d9050b2e3d184b24cc92e241794d914fbbd448dec8e654c5aa74 | Java | 38,010 | 864 | ///////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// //
// Copyright (C) 2026 by Joseph Ramsey, Peter Spirtes, Clark Glymour, //
... |
31807c31fb87097aa2aa6b574f8e31d2fa64d79d0786acd6bbd6fea1675a01e8 | Java | 38,285 | 866 | ///////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// //
// Copyright (C) 2025 by Joseph Ramsey, Peter Spirtes, Clark Glymour, //
... |
8e61000259ce118c9b32924eb431f9aa30cf42355b11dc09946ab6fae3b95ecb | Java | 38,349 | 845 | /// ////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// //
// Copyright (C) 2025 by Joseph Ramsey, Peter Spirtes, Clark Glymour, //... |
6fd0adb97b094deda3dc126d2f3b1788989de5ee6389c5c8d529fd638ccaee44 | Java | 38,437 | 1,062 | ///////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// //
// Copyright (C) 2025 by Joseph Ramsey, Peter Spirtes, Clark Glymour, //
... |
67c75510a6f2df6d8519b04b62a2e39aaf9e0d00893550c005a78675c6e2a967 | Java | 38,507 | 884 | ///////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// //
// Copyright (C) 2025 by Joseph Ramsey, Peter Spirtes, Clark Glymour, //
... |
9502c41d281009679525361657239783dd9ed771daec4cac90300e24fca4eb49 | Java | 38,766 | 879 | package edu.cmu.tetrad.search.utils;
import edu.cmu.tetrad.data.Knowledge;
import edu.cmu.tetrad.graph.*;
import edu.cmu.tetrad.util.TetradLogger;
import java.util.*;
import java.util.concurrent.*;
/**
* The PagLegalityCheck class provides utility methods for validating the legality of Partial Ancestral Graphs (PAG... |
4ab3659db737ea75c3c19a87feaf45b41c7e18ed789ef5c78ec2fa017435ed19 | Java | 38,944 | 945 | ///////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// //
// Copyright (C) 2025 by Joseph Ramsey, Peter Spirtes, Clark Glymour, //
... |
ea6f7725790afe8fc14aff05d5e4d16decc925bc0e7326991886614497f6d917 | Java | 39,220 | 1,144 | package edu.cmu.tetrad.search.test;
import edu.cmu.tetrad.data.*;
import edu.cmu.tetrad.graph.IndependenceFact;
import edu.cmu.tetrad.graph.Node;
import edu.cmu.tetrad.search.RawMarginalIndependenceTest;
import edu.cmu.tetrad.util.Parameters;
import edu.cmu.tetrad.util.RandomUtil;
import edu.cmu.tetrad.util.TMath;
imp... |
c50d22500eb6175bf970625604403f0449e50d1cc29a7e56a37f5aaba31a98bf | Java | 39,308 | 1,128 | package edu.cmu.tetrad.search.mimic;
import edu.cmu.tetrad.data.CorrelationMatrix;
import edu.cmu.tetrad.data.DataSet;
import edu.cmu.tetrad.data.DataTransforms;
import edu.cmu.tetrad.data.Knowledge;
import edu.cmu.tetrad.graph.*;
import edu.cmu.tetrad.search.blocks.BlockSpec;
import edu.cmu.tetrad.util.ChoiceGenerato... |
604650838bf515751faeaf098c5b23d34b6075c675f6d1d018d4ecb08b45120c | Java | 39,469 | 808 | /*-
* #%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 ... |
827b6878f71484965c88228805855aa7fe902c2cc461d2dd251615e7f12c8223 | Java | 39,583 | 1,262 | /*-
* #%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 ... |
a4ee5de44de5bbd6613051dddb2e7272ed4872d7b46e996741f8db0c8aa241ca | Java | 39,647 | 958 | /*-
* #%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 ... |
4200fb617930d9922db5c25ba1e78cd549591c669706038dd31d81451b5a28b4 | Java | 39,717 | 1,078 | /// ////////////////////////////////////////////////////////////////////////////
// Copyright (C) 2025 by Joseph Ramsey, Peter Spirtes, Clark Glymour, //
// and Richard Scheines. //
// //... |
b0435cdae159dce0ed16670ec536b018ca5b28fded5848b23e0a176efcc0a35b | Java | 39,759 | 935 | /*-
* #%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 ... |
95937705dda0b2ace9b4b5fc02244f6c8ba786bf4798add57c2efa6679cf8b66 | Java | 39,884 | 911 | /*-
* #%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 ... |
169974f0a903641f24c75c489c7a004c81d4e8b6d5c23ef140900f017b323f37 | Java | 39,933 | 861 | /// ////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// //
// Copyright (C) 2025 by Joseph Ramsey, Peter Spirtes, Clark Glymour, //... |
3a3d66de4d930dabf0556d35f91dfc7b499b60cd720e125521b7866cd88b5ede | Java | 40,056 | 981 | ///////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// //
// Copyright (C) 2025 by Joseph Ramsey, Peter Spirtes, Clark Glymour, //
... |
d4f34d8bcc59068db46870e000ae1fe0c2f3fd1522d8983c491b3cbc0485f803 | Java | 40,067 | 811 | ///////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// //
// Copyright (C) 2025 by Joseph Ramsey, Peter Spirtes, Clark Glymour, //
... |
6527302c7fdeb405fbd4c6db81ca8dea1edcbcdd749b19764160655c1a5c4461 | Java | 40,304 | 777 | /*-
* #%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 ... |
bf27102ebe57cfa82ac699761dd32421694404a47c688afef2749d754411839a | Java | 40,419 | 934 | ///////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// //
// Copyright (C) 2025 by Joseph Ramsey, Peter Spirtes, Clark Glymour, //
... |
93db13ce1573e4ac6430e786e6188f9663acfdcacce4f23579552ce005e67e2c | Java | 40,715 | 1,151 | ///////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// //
// Copyright (C) 2025 by Joseph Ramsey, Peter Spirtes, Clark Glymour, //
... |
6e2328dd20a1bef69e96d37f5016e953de69f705d70b15f26f76707bb5167e1c | Java | 40,868 | 1,001 | /*-
* #%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 ... |
4ed02ae3ee62e1afef0687ea70c6c82fcc7c55ddf3a2fb8f89c1eb700ac7d162 | Java | 40,889 | 1,073 | /*-
* #%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 ... |
1513e801ee4bc61718c123ed47f93edcc594726eaf745c0d5057c914a744573f | Java | 40,924 | 1,117 | /// ////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// //
// Copyright (C) 2025 by Joseph Ramsey, Peter Spirtes, Clark Glymour, //... |
eee3582f4b2dd1288c79dfefd228a7068c269b4c2fae2cea1393ffa18986ae06 | Java | 41,025 | 815 | /*-
* #%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 ... |
519b384dc8bfac91bf629d5e3357cf02a1284b07d5662cf5ed2369f825ff3a5f | Java | 41,052 | 1,064 | /*-
* #%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 ... |
529abaf15f7b90c7fd841668c58e0f6e51361481fc90b166dca430bdf9a5e84c | Java | 41,159 | 1,009 | /*-
* #%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 ... |
038fe4809f88afe323067aa3b35db0ed99e8b5ddf0bdce6f05824fc5a03259b4 | Java | 41,297 | 1,113 | /*-
* #%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 ... |
9721c65e4bcbb97949ba1ad0ee66bd48174dde58731565e4f15d7b3733079d22 | Java | 41,470 | 1,107 | ///////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// //
// Copyright (C) 2025 by Joseph Ramsey, Peter Spirtes, Clark Glymour, //
... |
d43c8501281ab6c05607f7af3c33d7bd833a7ab663b85f18eed71c51a5cc8ff2 | Java | 41,573 | 1,070 | package edu.cmu.tetrad.search.test;
import edu.cmu.tetrad.data.missing.MissingValueSupport;
import edu.cmu.tetrad.data.DataSet;
import edu.cmu.tetrad.data.DataTransforms;
import edu.cmu.tetrad.graph.IndependenceFact;
import edu.cmu.tetrad.graph.Node;
import edu.cmu.tetrad.search.utils.LogUtilsSearch;
import edu.cmu.te... |
fafa8118734c38c206b6d776f72f7dcf0bb01d060692cbd3bea1fbd4dac9ade5 | Java | 42,718 | 1,188 | ///////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// //
// Copyright (C) 2025 by Joseph Ramsey, Peter Spirtes, Clark Glymour, //
... |
c19080f28c44854c0e4bbf9058032c88a5b9512751ef3998b4ffc341076727dd | Java | 42,809 | 975 | package edu.cmu.tetrad.search;
import edu.cmu.tetrad.graph.Edge;
import edu.cmu.tetrad.graph.Edges;
import edu.cmu.tetrad.graph.Endpoint;
import edu.cmu.tetrad.graph.Graph;
import edu.cmu.tetrad.graph.Node;
import edu.cmu.tetrad.search.test.IndependenceResult;
import edu.cmu.tetrad.search.test.MsepTest;
import edu.cmu... |
25f17d08e5a00cce8227a294cd5faa20b2c2cb57e00291b2013c07b6421a1cce | Java | 42,897 | 1,218 | ///////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// //
// Copyright (C) 2025 by Joseph Ramsey, Peter Spirtes, Clark Glymour, //
... |
8210d5aa8913b6ab461cf005fa475802ab011ba616b016b2f182aabe02c2c18e | Java | 43,030 | 866 | /// ////////////////////////////////////////////////////////////////////////////
// PhantomKernelEnumerator8.java (parallel, deduplicated, checkpointed) //
// //
// PKE8 answers the complement of PKE7's question. PKE7 audited FCIT-SL's ... |
a7a8137c9689f6380a9d0a423eeb77790593f09d186fdbf036845d40c741352d | Java | 43,052 | 958 | /// ////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// //
// Copyright (C) 2025 by Joseph Ramsey, Peter Spirtes, Clark Glymour, //... |
0651a0d0d0508f2dfc696c86ade7efc0ae4f96fac8d540e99da2ed3b5a3ca0bd | Java | 43,184 | 1,131 | ///////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// //
// Copyright (C) 2025 by Joseph Ramsey, Peter Spirtes, Clark Glymour, //
... |
a17c76d4aff92123421f1c13e56241f05fed7c73aa2afe30da7fe4ec8f9be950 | Java | 43,478 | 1,189 | /*-
* #%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 ... |
f1a697e6d629f5f834cd0bc65faae9244eb610237437b99544df978035819f7d | Java | 43,502 | 855 | /*-
* #%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 ... |
a1cd9007ed595068cdd1e74c7902fe74a18b138bf8054a81ac4976b671afa1ee | Java | 43,578 | 1,008 | ///////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// //
// Copyright (C) 2025 by Joseph Ramsey, Peter Spirtes, Clark Glymour, //
... |
8d180078c08ff085ade86557e8b1f0b69c00bfffd0dd54baa068cee35b28988b | Java | 43,718 | 1,080 | /*-
* #%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 ... |
b7f082f098f9c18d35dc3b1bba684e32582e60b336f3bf93fab3211b3f2550a3 | Java | 43,784 | 1,212 | ///////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// //
// Copyright (C) 2025 by Joseph Ramsey, Peter Spirtes, Clark Glymour, //
... |
fb3cadc64b18045598ae80e48ff4e8a5d5dd350b707f3e719ca57bd9ee47ff68 | Java | 44,016 | 1,160 | /// ////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// //
// Copyright (C) 2025 by Joseph Ramsey, Peter Spirtes, Clark Glymour, //... |
c9b5c9e5f8a153eb928b45b170911a34841dc664f485f268e4d999404ac83f12 | Java | 44,045 | 1,382 | ///////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// //
// Copyright (C) 2025 by Joseph Ramsey, Peter Spirtes, Clark Glymour, //
... |
839a40c71b3dfdd539addcb828362ba805a962b9a4c199699c2d6e691a41ec56 | Java | 44,219 | 892 | ///////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// Copyright (C) 1998, 1999, 2000, 2001, 2002, 2003, 2004, 2005, 2006, //
// 2007, 2008, 2009, 2010, 2014, 2015, 2022 by Peter Spirtes, Richard //
... |
3ba4631b79bb65e5b8a70d12052eda0984be8e48946a4744545a0ae9169bb83c | Java | 44,643 | 1,134 | /// ////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// //
// Copyright (C) 2026 by Joseph Ramsey, Peter Spirtes, Clark Glymour, //... |
609069f7b44659b5566432a19baaa0e69dceba7a76df4b8432cb6e870d006978 | Java | 45,164 | 961 | package edu.cmu.tetrad.search.harness;
import edu.cmu.tetrad.algcomparison.graph.SingleGraph;
import edu.cmu.tetrad.algcomparison.independence.*;
import edu.cmu.tetrad.algcomparison.simulation.Simulation;
import edu.cmu.tetrad.data.ContinuousVariable;
import edu.cmu.tetrad.data.DataSet;
import edu.cmu.tetrad.data.Gene... |
a1c9e7ad25cb35f0a062f9ba770f371964c456e94c560bd9af64de2b61451bf0 | Java | 45,229 | 1,095 | /// ////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// //
// Copyright (C) 2025 by Joseph Ramsey, Peter Spirtes, Clark Glymour, //... |
92690b67feab582ddc36e99362ee975073deacdcd2382fdf9f700b0d895ce101 | Java | 45,329 | 1,329 | package edu.cmu.tetrad.search.score;
import edu.cmu.tetrad.data.missing.MissingValueSupport;
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... |
affd0832c7b9977b80eeeb24b12b2033f174740d353d9a5849be105961e5f3d8 | Java | 45,773 | 1,168 | // v1: Drop-in skeleton for adjustment-based effect estimation on mixed (continuous+discrete) data.
// v1: Binary treatment X (2-category discrete) and continuous outcome Y.
// v1: Outcome model = OLS with mixed-feature basis + X*features interactions.
// v1: Propensity model = logistic regression via IRLS on mixed-fea... |
e41e01c0e7bca740e76c5cfa4ba5ccf892d572a658173be99c5d8c33e79f1694 | Java | 45,874 | 1,376 | package edu.cmu.tetrad.search.score;
import edu.cmu.tetrad.data.missing.MissingValueSupport;
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... |
da2ece88388d93cea136defd13f9e8621f8016ab7e19d748a26d31571f7dc24d | Java | 45,977 | 1,140 | /*-
* #%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 ... |
fb30d000fdd61310664f8ed9a688bc588d7ca86f992b074621260ec2f9cb17d8 | Java | 46,862 | 1,202 | /// ////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// //
// Copyright (C) 2025 by Joseph Ramsey, Peter Spirtes, Clark Glymour, //... |
3da208e30c9ec1ae6901f27e1eb421ba1dd656bd94fedb5a7428daa7948608c1 | Java | 46,932 | 1,316 | package edu.cmu.tetrad.search.test;
import edu.cmu.tetrad.data.DataSet;
import edu.cmu.tetrad.data.DiscreteVariable;
import edu.cmu.tetrad.graph.IndependenceFact;
import edu.cmu.tetrad.graph.Node;
import edu.cmu.tetrad.search.utils.LogUtilsSearch;
import edu.cmu.tetrad.util.RandomUtil;
import edu.cmu.tetrad.util.TMath... |
ac8056128232a89e6b24b29471724c9112d3f9af48ebb37cbf89f97cdf062409 | Java | 47,541 | 888 | /*-
* #%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 ... |
54d87840c980e656e3cb6944da0a45a668c2f3a03439e5cdcf92b833f37bfb01 | Java | 47,863 | 1,112 | /// ////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// //
// Copyright (C) 2025 by Joseph Ramsey, Peter Spirtes, Clark Glymour, //... |
563738c75c099a58cf5cacbcd6bc33e558b93a301a5ca8811027e36d8a614148 | Java | 47,930 | 1,072 | package edu.cmu.tetradapp.editor;
import edu.cmu.tetrad.data.DataSet;
import edu.cmu.tetrad.graph.Node;
import edu.cmu.tetrad.search.utils.NonlinearityTests;
import edu.cmu.tetradapp.util.DesktopController;
import edu.cmu.tetradapp.util.WatchedProcess;
import edu.cmu.tetrad.util.TMath;
import javax.swing.*;
import ja... |
5de92fc1ebb723956e6c846411524e246fd2596e79e14570db29117867846df6 | Java | 48,072 | 1,202 | /*-
* #%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 ... |
33c7a6f38131d7659de5534f0232e75beb9ad735921a7c2bf1a5ca12c22f6d39 | Java | 48,173 | 931 | ///////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// //
// Copyright (C) 2025 by Joseph Ramsey, Peter Spirtes, Clark Glymour, //
... |
806bcdce22095e7752808e6d1ca4999261267f0c369378e7a317203b3c2a8e0e | Java | 48,600 | 1,110 | package edu.cmu.tetrad.search;
import edu.cmu.tetrad.data.*;
import edu.cmu.tetrad.graph.EdgeListGraph;
import edu.cmu.tetrad.graph.Graph;
import edu.cmu.tetrad.graph.GraphUtils;
import edu.cmu.tetrad.graph.Node;
import edu.cmu.tetrad.search.score.Score;
import edu.cmu.tetrad.search.score.SemBicScore;
import edu.cmu.t... |
08c47c3cd4f6d35415818194887802bb7a16451be940488323a6d0ed18506514 | Java | 48,993 | 1,329 | /*
* #%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 t... |
fc8a5faa150452f7229aa641af8408a760b2a82cfec2105ca24b9975ff6139fa | Java | 49,292 | 1,505 | ///////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// //
// Copyright (C) 2025 by Joseph Ramsey, Peter Spirtes, Clark Glymour, //
... |
12913a3e5a5e37ef0e5870df9ec7669f9918ed117b0ab145fbae7b1c9cface13 | Java | 49,448 | 1,117 | package edu.cmu.tetrad.search;
/*
* Cord.java -- Faithful single-file Java port of CORD (Orthogonal Rank-Score
* Conditional Independence Test) for H0: Y _||_ Z | X.
*
* This is a dependency-free (pure JDK, Java 8+) port of the Python reference
* `cord.py` (numpy + scipy + scikit-learn). It reproduces the CORD al... |
14baf8c30f0abb487092d16a452af7bd2a8fe8644d9d189141c85dc337118c51 | Java | 49,564 | 1,094 | /// ////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// //
// Copyright (C) 2025 by Joseph Ramsey, Peter Spirtes, Clark Glymour, //... |
556ef4fcbeab1da01df2ad82c69f0e3e3db58cd6551956c78feeddcf3d028027 | Java | 49,581 | 1,508 | ///////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// //
// Copyright (C) 2025 by Joseph Ramsey, Peter Spirtes, Clark Glymour, //
... |
291a12b6621e1a17faa7a38c7cf9a2191ebb19a585dae38130c0eb6bb9dfbdd5 | Java | 49,911 | 1,308 | package edu.cmu.tetrad.search.score;
import edu.cmu.tetrad.data.missing.MissingValueSupport;
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... |
9b2fc9361f742d3daa9ac5f75978750fd3e8582a3cf852ff643cea7d0fa34a88 | Java | 50,522 | 1,204 | package edu.cmu.tetrad.search;
import edu.cmu.tetrad.data.DataSet;
import edu.cmu.tetrad.graph.Edge;
import edu.cmu.tetrad.graph.EdgeListGraph;
import edu.cmu.tetrad.graph.Graph;
import edu.cmu.tetrad.graph.Node;
import edu.cmu.tetrad.util.Matrix;
import edu.cmu.tetrad.util.TMath;
import org.ejml.simple.SimpleEVD;
imp... |
578afd24606e929c336a325d12879527b88f645a8370026cbb531fff3caf068e | Java | 51,216 | 1,110 | /*-
* #%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 ... |
971584b990c36667ee9090ff558ffbf082b2472c59c5000b159edc39142df87a | Java | 51,222 | 1,267 | /*
* Copyright (C) 2026
*
* Exact inference for discrete Bayes nets using a Junction Tree (Clique Tree).
*
* This implementation follows standard junction-tree theory:
* 1) Moralize the DAG
* 2) Triangulate (chordalize) via elimination order with fill-in edges
* 3) Form cliques induced by elimination (each e... |
ea0c3250baef1efb0913a8ad0f331241376f5e897744a1daa5ab90df963ac49c | Java | 51,350 | 1,721 | ///////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// //
// Copyright (C) 2025 by Joseph Ramsey, Peter Spirtes, Clark Glymour, //
... |
7667c08ba65d665ef58f9e8cffa176a6444b907402f93ff9500f7a4edec9ace6 | Java | 51,733 | 1,042 | /// ////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// //
// Copyright (C) 2025 by Joseph Ramsey, Peter Spirtes, Clark Glymour, //... |
a03c6c651de776ca4a6223a0eaa4eb8790fb5bd7b07a3e71b7a78a49a6ae68f6 | Java | 51,857 | 1,112 | /// ////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// //
// Copyright (C) 2025 by Joseph Ramsey, Peter Spirtes, Clark Glymour, //... |
2e7a404baa6382255c6e9ab449e656466e6e58e8635e649fd221ba6bd3f90993 | Java | 52,172 | 1,212 | /*-
* #%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 ... |
42f4760eda350f4660f1b05e017d9efe7474bbd38e15c8214614debc68a42d82 | Java | 52,310 | 1,372 | package edu.cmu.tetrad.search.test;
import edu.cmu.tetrad.data.DataSet;
import edu.cmu.tetrad.data.DataTransforms;
import edu.cmu.tetrad.data.missing.MissingDataPolicy;
import edu.cmu.tetrad.data.missing.MissingDataSpec;
import edu.cmu.tetrad.data.missing.MissingDataUtils;
import edu.cmu.tetrad.data.missing.MissingVal... |
2fc078d09d8b1f805e679f22d828b93998532f0510a64dfe1d4427feb89ac5cd | Java | 52,618 | 1,474 | ///////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// //
// Copyright (C) 2025 by Joseph Ramsey, Peter Spirtes, Clark Glymour, //
... |
d912b87d0ab0741545d4c68528017f318c6b370819d07743db041b20f5a93b51 | Java | 52,742 | 1,063 | package edu.cmu.tetrad.search;
import edu.cmu.tetrad.data.DataSet;
import edu.cmu.tetrad.graph.Graph;
import edu.cmu.tetrad.graph.IndependenceFact;
import edu.cmu.tetrad.graph.Node;
import java.util.*;
/**
* Joint, dependence-aware Markov check for a DAG or CPDAG.
*
* <p>Fo... |
f89feaf526782ebcd8045a14a4b0e9893aaf2c5de6832b9df506f19a1d8760f4 | Java | 52,885 | 1,174 | package edu.cmu.tetradapp.editor;
import edu.cmu.tetrad.data.Knowledge;
import edu.cmu.tetrad.graph.*;
import edu.cmu.tetrad.search.VertexRepairSearch;
import edu.cmu.tetrad.search.VertexRepairSearch.AdjustmentGraphType;
import edu.cmu.tetrad.search.VertexRepairSearch.CandidateEdit;
import edu.cmu.tetrad.search.Vertex... |
e09ccf3abad35f9837ca724f377fdd45665f780fcb2304e5b790cb83c51c04f2 | Java | 54,183 | 1,379 | /// ////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// //
// Copyright (C) 2025 by Joseph Ramsey, Peter Spirtes, Clark Glymour, //... |
2606b4d7964871f38739e50ec2a99103c367eb99ceaa62b69a3c6bc4b8cc1f39 | Java | 54,293 | 931 | /// ////////////////////////////////////////////////////////////////////////////
// PhantomKernelEnumerator.java (parallel) //
// //
// EXHAUSTIVE companion to PhantomCounterexampleHarness. Enumerates EVERY DA... |
555b033abebb34320335cde3ca2d470a477bb422d47747ee309931a6b785e4a8 | Java | 54,760 | 1,248 | /*-
* #%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 ... |
95b5342c043f220d01eb4b1ee2b0cc1786b92a456b5bdbd59666e2ba9fd78f23 | Java | 54,941 | 1,336 | ///////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// //
// Copyright (C) 2025 by Joseph Ramsey, Peter Spirtes, Clark Glymour, //
... |
001cb0df986f3d927b3303a1475909c63cf508b074f8ffac84b056da06cd0ec9 | Java | 55,288 | 1,340 | /// ////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// //
// Copyright (C) 2025 by Joseph Ramsey, Peter Spirtes, Clark Glymour, //... |
73f5cbc8839afb521f3a1715fb305d57f744861729a8de835739329357f834d7 | Java | 55,402 | 1,422 | /// ////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// //
// Copyright (C) 2025 by Joseph Ramsey, Peter Spirtes, Clark Glymour, //... |
82f08ae038c8cbe3d444cc0124190d9444aa41e941d974770f7aafc56913d08e | Java | 55,509 | 1,636 | /// ////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// //
// Copyright (C) 2025 by Joseph Ramsey, Peter Spirtes, Clark Glymour, //... |
e8c744ca90bb5fefe950bd2c1db8e51a37415782bb3bf9e8ac4a90a18cb881e7 | Java | 55,737 | 1,448 | ///////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// //
// Copyright (C) 2025 by Joseph Ramsey, Peter Spirtes, Clark Glymour, //
... |
218d6a13690e1b4dd4cb0229c00d4ec26322231673ceed3b979b71c5fbb050ce | Java | 56,703 | 1,388 | /// ////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// //
// Copyright (C) 2025 by Joseph Ramsey, Peter Spirtes, Clark Glymour, //... |
ae9335e8bbf519fed1d34c2238284769666645a2099425f5a175065b0c0c4697 | Java | 56,994 | 1,322 | /*-
* #%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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