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Merging 7.6.0 to master #1704

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merged 141 commits into from
Oct 31, 2023
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151dbff
Update README.md
jdramsey Aug 3, 2023
640c62c
Update README.md
jdramsey Aug 4, 2023
f0961ee
Updated to 7.5.0.
jdramsey Aug 6, 2023
933fd42
Pushing FX examples to my brnach.
jdramsey Aug 7, 2023
b6e0522
Pushing FX examples to my brnach.
jdramsey Aug 7, 2023
d782495
Pushing FX examples to my brnach.
jdramsey Aug 7, 2023
60680fd
Pushing FX examples to my brnach.
jdramsey Aug 7, 2023
579e8f9
Pushing FX examples to my brnach.
jdramsey Aug 7, 2023
edb0267
Pushing FX examples to my brnach.
jdramsey Aug 7, 2023
3fc2280
Pushing FX examples to my brnach.
jdramsey Aug 7, 2023
5160c55
Pushing FX examples to my brnach.
jdramsey Aug 7, 2023
aacba8c
Pushing FX examples to my brnach.
jdramsey Aug 7, 2023
1fdd595
Pushing FX examples to my brnach.
jdramsey Aug 7, 2023
098967d
Pushing FX examples to my brnach.
jdramsey Aug 7, 2023
aa31354
Pushing FX examples to my brnach.
jdramsey Aug 7, 2023
8f80c9b
Adjusted circle layout so that it automatically adjusts the size of t…
jdramsey Aug 8, 2023
4f07b41
Adjusted circle layout so that it automatically adjusts the size of t…
jdramsey Aug 8, 2023
48c8a26
Added threshold option to bootstrapping.
jdramsey Aug 9, 2023
d819ff3
Merge remote-tracking branch 'origin/joe-work-2023-8-4' into joe-work…
jdramsey Aug 9, 2023
28383cf
Adjusted circle layout so that it automatically adjusts the size of t…
jdramsey Aug 9, 2023
6f923a7
Fixed usedataorder for BOSS.
jdramsey Aug 11, 2023
5bf37c0
Merge remote-tracking branch 'origin/joe-work-2023-8-4' into joe-work…
jdramsey Aug 11, 2023
5b6226d
Fixed usedataorder for BOSS.
jdramsey Aug 11, 2023
b361e70
Reverting Matrix.
jdramsey Aug 12, 2023
b261a7d
added gst synchronization
bja43 Aug 15, 2023
456a419
switched to atomic booleans and got rid of the allow randomness withi…
bja43 Aug 15, 2023
b81f344
doesnt work, dont know why
bja43 Aug 16, 2023
c9fcc77
switched to fjp and now it works!
bja43 Aug 16, 2023
79ccd91
Joe's adjustments.
jdramsey Aug 17, 2023
146e0ef
Joe's adjustments.
jdramsey Aug 17, 2023
72da77a
made the pool a class variable
bja43 Aug 17, 2023
5b398b1
Joe's adjustments.
jdramsey Aug 17, 2023
df2162a
Merge remote-tracking branch 'origin/boss_parallel' into boss_parallel
jdramsey Aug 17, 2023
934d0e7
Joe's adjustments.
jdramsey Aug 17, 2023
3bd81ab
Reverted to working version, put pool back to class level.
jdramsey Aug 17, 2023
8f4e6d2
Working version that doesn't scale to 2000:10:1000 pd 8.
jdramsey Aug 18, 2023
89528d8
Working version that doesn't scale to 2000:10:1000 pd 8.
jdramsey Aug 18, 2023
76aafa3
Streamlined graph display in the interface.
jdramsey Aug 22, 2023
c959210
fixed make valid knowledge order
bja43 Aug 23, 2023
5d17003
Merge pull request #1679 from cmu-phil/required_knowledge_fix
jdramsey Aug 23, 2023
f9aa227
Merge branch 'development' of https://github.com/cmu-phil/tetrad into…
jdramsey Aug 23, 2023
a7254cc
modified boss parallel and fixed required edge code
bja43 Aug 24, 2023
f1d2f9d
Added NUM_THREADS parameter for BOSS and tested required knowledge fo…
jdramsey Aug 24, 2023
20423b7
Changed name of GRASP_USE_DATA_ORDER to USE_DATA_ORDER throughout and…
jdramsey Aug 24, 2023
e029775
Merge pull request #1682 from cmu-phil/boss_parallel
bja43 Aug 24, 2023
6f8a007
Merge branch 'development' of https://github.com/cmu-phil/tetrad into…
jdramsey Aug 24, 2023
755fba3
Changed name of GRASP_USE_DATA_ORDER to USE_DATA_ORDER throughout and…
jdramsey Aug 24, 2023
385ac36
Updating some versions of plugins in the poms, responding to warnings.
jdramsey Aug 24, 2023
6023db4
Merge pull request #1680 from cmu-phil/joe-work-2023-8-4
bja43 Aug 24, 2023
4d8be74
Update README.md
jdramsey Aug 26, 2023
c9ac3d8
Merge pull request #1684 from cmu-phil/jdramsey-patch-2
jdramsey Aug 26, 2023
7c54842
Update README.md
jdramsey Aug 26, 2023
d559669
Update README.md
jdramsey Aug 27, 2023
4cadfc6
Update README.md
jdramsey Aug 27, 2023
5ca1ebe
Update README.md
jdramsey Aug 27, 2023
a8e9047
Update README.md
jdramsey Aug 27, 2023
fd59303
Merge pull request #1685 from cmu-phil/jdramsey-patch-3
jdramsey Aug 27, 2023
9021c49
Update README.md
jdramsey Aug 27, 2023
e10d9fc
Update README.md
jdramsey Aug 27, 2023
5c0f5a4
Update README.md
jdramsey Aug 27, 2023
e176c42
Update README.md
jdramsey Aug 27, 2023
4f5eff6
Update README.md
jdramsey Aug 27, 2023
e6dc7dd
Update README.md
jdramsey Aug 27, 2023
043c65b
Update README.md
jdramsey Aug 30, 2023
8eee94e
Update README.md
jdramsey Aug 30, 2023
680f5e7
parallel boss + polish
bja43 Sep 9, 2023
e39f98e
parallel boss + polish
bja43 Sep 11, 2023
433872f
fixed a few knowledge bugs for boss and grasp
bja43 Sep 18, 2023
1b696a2
Merge pull request #1691 from cmu-phil/boss-updates
jdramsey Sep 19, 2023
84f117b
Fixed kurtosis centering.
jdramsey Sep 29, 2023
78ca6f5
Fixed an issue Clark found where if you draw a graph in the Graph Edi…
jdramsey Sep 29, 2023
2288016
Fixed the GFCI test issue by copying code over from BFCI into GFCI.
jdramsey Sep 29, 2023
b7c5e3d
Fixed the GFCI test issue by copying code over from BFCI into GFCI.
jdramsey Oct 1, 2023
cbca548
1. Fixed the self-inflicted bug of layout requiring acyclic graphs.
jdramsey Oct 1, 2023
5260d08
Added a note to the bootstrapping section of the manual, in response …
jdramsey Oct 1, 2023
18468a3
Formatted the manual.
jdramsey Oct 2, 2023
0ccc7f1
Formatted the manual.
jdramsey Oct 2, 2023
2956a57
New branch to reconcile other branches.
jdramsey Oct 3, 2023
7fc4fc1
New branch to reconcile other branches.
jdramsey Oct 3, 2023
f386d2f
New branch to reconcile other branches.
jdramsey Oct 3, 2023
ad0f298
Fixed variable orderign 1.2.3... for knowledge required/forbidden edg…
jdramsey Oct 3, 2023
a99fcb9
Fixed variable orderign 1.2.3... for knowledge required/forbidden edg…
jdramsey Oct 3, 2023
cb04147
Collapsed existsSemiDirectedPaths() methods in Paths.
jdramsey Oct 5, 2023
078b0d7
Collapsed existsSemiDirectedPaths() methods in Paths.
jdramsey Oct 5, 2023
2b3dbff
Fixed private static long serialVerUids
jdramsey Oct 5, 2023
a1af3de
Fixed private static long serialVerUids
jdramsey Oct 5, 2023
351a959
Working on the determnistic SEM IM issue.
jdramsey Oct 5, 2023
229c5ba
Working on the determnistic SEM IM issue.
jdramsey Oct 5, 2023
d63102c
Working on the determnistic SEM IM issue.
jdramsey Oct 5, 2023
4095f43
Copyed some layouts from Tetrad-FX.
jdramsey Oct 5, 2023
13b08b2
Substituted continuous and discrete data loader methods from Tetrad-F…
jdramsey Oct 5, 2023
d78c058
Same for mixed data loader.
jdramsey Oct 5, 2023
7329ec6
Copied over the mixed loader and also methods to save and load JSON f…
jdramsey Oct 5, 2023
95f6a2a
Copied data transforms and graph transforms over from tetrad-fx; need…
jdramsey Oct 5, 2023
528aa27
Added a menu item to the PlotMatrix to remove the minimum points per …
jdramsey Oct 6, 2023
b6cb41f
Switched that manu item to remove zeros from the data instead of minima.
jdramsey Oct 6, 2023
6096c6a
Switched that manu item to remove zeros from the data instead of minima.
jdramsey Oct 7, 2023
1def095
Changed the default layout for graphs to circle if # nodes <= 20 and …
jdramsey Oct 12, 2023
0598206
Added remove zero points per plot feature for Histogram.
jdramsey Oct 12, 2023
65105c8
Inlined DataTransforms methods in DataUtils.
jdramsey Oct 12, 2023
78a3dc6
For all tests, throwing an exception if singularities, undefined p-va…
jdramsey Oct 12, 2023
640cd00
Fixed this issues:
jdramsey Oct 12, 2023
79cbf87
Fixed PC-LiNGAM and added it back into the interface.
jdramsey Oct 13, 2023
d74d125
Factored out the method in Markov Check that generates all of the ind…
jdramsey Oct 13, 2023
6e22d4b
Factored out the method in Markov Check that generates all of the ind…
jdramsey Oct 13, 2023
9e886e7
Fixed tests.
jdramsey Oct 13, 2023
6a199a6
Fixing some javadoc errors insisted on by the new Javadoc builder.
jdramsey Oct 13, 2023
e77e8f6
Fixing some javadoc errors insisted on by the new Javadoc builder.
jdramsey Oct 13, 2023
a2729a5
Fixing some javadoc errors insisted on by the new Javadoc builder.
jdramsey Oct 13, 2023
1f3d6ba
Trying to fix a persistent bug in knowledge where when you delete req…
jdramsey Oct 15, 2023
90a0272
Trying to fix a persistent bug in knowledge where when you delete req…
jdramsey Oct 19, 2023
3bd738e
Trying to fix a bug in FCI-like algorithms where with R1 or R9 direct…
jdramsey Oct 20, 2023
8e6b52a
Actually fixed the FCI knowledge but this time. The issue was that th…
jdramsey Oct 20, 2023
559f803
Actually fixed the FCI knowledge but this time. The issue was that th…
jdramsey Oct 20, 2023
e0c1cec
Actually fixed the FCI knowledge but this time. The issue was that th…
jdramsey Oct 21, 2023
91e62f6
Actually fixed the FCI knowledge but this time. The issue was that th…
jdramsey Oct 21, 2023
3e00658
Fixed some unit tests.
jdramsey Oct 21, 2023
ba2531d
Update README.md
jdramsey Oct 23, 2023
9234705
Create InstallApplication.md
jdramsey Oct 23, 2023
8003854
Rename InstallApplication.md to INSTALL_APPLICATION.md
jdramsey Oct 23, 2023
2e91c11
Update README.md
jdramsey Oct 23, 2023
483cdbb
Update README.md
jdramsey Oct 23, 2023
1a2ef42
Fixed a typing error in README.md
daulatojha17 Oct 23, 2023
987815a
Update INSTALL_APPLICATION.md
jdramsey Oct 23, 2023
4c14763
Update INSTALL_APPLICATION.md
jdramsey Oct 23, 2023
f0ff6d1
Update README.md
jdramsey Oct 23, 2023
09df9bd
Merge pull request #1700 from daulatojha17/development
jdramsey Oct 23, 2023
321df68
Update README.md
jdramsey Oct 23, 2023
af4e626
Merge pull request #1702 from cmu-phil/jdramsey-patch-8
jdramsey Oct 23, 2023
b107e6c
Update README.md
jdramsey Oct 23, 2023
547f04a
Update README.md
jdramsey Oct 23, 2023
d81dd7d
Update README.md
jdramsey Oct 23, 2023
18fa2ab
Fixed some unit tests.
jdramsey Oct 24, 2023
8dc9855
Fixed some knowledge issues.
jdramsey Oct 27, 2023
3aecff1
Fixed some knowledge issues.
jdramsey Oct 27, 2023
6aaca9c
Fixed some knowledge issues.
jdramsey Oct 27, 2023
66b920b
Fixed some knowledge issues.
jdramsey Oct 30, 2023
43c260d
Fixed a problem with Fisher Z with testwise deletion.
jdramsey Oct 31, 2023
dccf96d
Merge pull request #1699 from cmu-phil/joe-work-2023-10-2
jdramsey Oct 31, 2023
7161428
Changing version to 7.6.0-SNAPSHOT
jdramsey Oct 31, 2023
9ff1c39
Merge remote-tracking branch 'origin/development' into development
jdramsey Oct 31, 2023
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Fixed the GFCI test issue by copying code over from BFCI into GFCI.
  • Loading branch information
jdramsey committed Sep 29, 2023
commit 22880163727b3b4e46ea06348a691321cc64adb3
20 changes: 7 additions & 13 deletions tetrad-lib/src/main/java/edu/cmu/tetrad/search/GFci.java
Original file line number Diff line number Diff line change
@@ -124,29 +124,23 @@ public Graph search() {
fges.setOut(this.out);
graph = fges.search();

Graph fgesGraph = new EdgeListGraph(graph);
Knowledge knowledge2 = new Knowledge(knowledge);
Graph referenceDag = new EdgeListGraph(graph);

// GFCI extra edge removal step...
SepsetProducer sepsets = new SepsetsGreedy(graph, this.independenceTest, null, this.depth, knowledge);
gfciExtraEdgeRemovalStep(graph, fgesGraph, nodes, sepsets);
GraphUtils.gfciR0(graph, fgesGraph, sepsets, knowledge);

if (this.possibleMsepSearchDone) {
graph.paths().removeByPossibleMsep(independenceTest, null);
}
gfciExtraEdgeRemovalStep(graph, referenceDag, nodes, sepsets);
GraphUtils.gfciR0(graph, referenceDag, sepsets, knowledge);

FciOrient fciOrient = new FciOrient(sepsets);

fciOrient.setCompleteRuleSetUsed(this.completeRuleSetUsed);
fciOrient.setMaxPathLength(this.maxPathLength);
fciOrient.setDoDiscriminatingPathColliderRule(this.doDiscriminatingPathRule);
fciOrient.setDoDiscriminatingPathTailRule(this.doDiscriminatingPathRule);
fciOrient.setVerbose(this.verbose);
fciOrient.setKnowledge(this.knowledge);
fciOrient.setVerbose(verbose);
fciOrient.setKnowledge(knowledge2);

fciOrient.doFinalOrientation(graph);

GraphUtils.replaceNodes(graph, this.independenceTest.getVariables());

return graph;
}

2 changes: 1 addition & 1 deletion tetrad-lib/src/test/java/edu/cmu/tetrad/test/TestGFci.java
Original file line number Diff line number Diff line change
@@ -188,7 +188,7 @@ public void testFromGraph() {
10, 10, 10, false);

// Fci gfci = new Fci(new MsepTest(dag));
BFci gfci = new BFci(new MsepTest(dag), new GraphScore(dag));
GFci gfci = new GFci(new MsepTest(dag), new GraphScore(dag));
gfci.setCompleteRuleSetUsed(true);
// gfci.setFaithfulnessAssumed(false);
Graph pag1 = gfci.search();