Code

Several fixes, updates.#1699

Code

Merged

jdramsey merged 46 commits intodevelopmentcmu-phil/tetrad:developmentfrom joe-work-2023-10-2cmu-phil/tetrad:joe-work-2023-10-2Copy head branch name to clipboardOct 31, 2023

+5,286-3,600

Commits

Commits on Oct 3, 2023

• New branch to reconcile other branches.

  jdramsey

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  2956a57

• New branch to reconcile other branches.

  jdramsey

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  7fc4fc1

• New branch to reconcile other branches.

  jdramsey

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  f386d2f

• Fixed variable orderign 1.2.3... for knowledge required/forbidden edge editor.

  jdramsey

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  ad0f298

• Fixed variable orderign 1.2.3... for knowledge required/forbidden edge editor.

  jdramsey

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  a99fcb9

Commits on Oct 5, 2023

• Collapsed existsSemiDirectedPaths() methods in Paths.

  jdramsey

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  cb04147

• Collapsed existsSemiDirectedPaths() methods in Paths.

  jdramsey

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  078b0d7

• Fixed private static long serialVerUids

  jdramsey

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  2b3dbff

• Fixed private static long serialVerUids

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  a1af3de

• Working on the determnistic SEM IM issue.

  jdramsey

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  351a959

• Working on the determnistic SEM IM issue.

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  229c5ba

• Working on the determnistic SEM IM issue.

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  d63102c

• Copyed some layouts from Tetrad-FX.

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  4095f43

• Substituted continuous and discrete data loader methods from Tetrad-FX in SimpleDataLoader.

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  13b08b2

• Same for mixed data loader.

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  d78c058

• Copied over the mixed loader and also methods to save and load JSON files.

  jdramsey

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  7329ec6

• Copied data transforms and graph transforms over from tetrad-fx; need to inline the uses of these methods at some point. Some stuff from the Changed class I put in the Utils in Tetrad-FX instead.

  jdramsey

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  95f6a2a

Commits on Oct 6, 2023

• Added a menu item to the PlotMatrix to remove the minimum points per plot. This does not work for regressions though.

  jdramsey

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  528aa27

• Switched that manu item to remove zeros from the data instead of minima.

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  b6cb41f

Commits on Oct 7, 2023

• Switched that manu item to remove zeros from the data instead of minima.

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  6096c6a

Commits on Oct 12, 2023

• Changed the default layout for graphs to circle if # nodes <= 20 and square otherwise.

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  1def095

• Added remove zero points per plot feature for Histogram.

  Show description for 0598206
  jdramsey

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  0598206

• Inlined DataTransforms methods in DataUtils.

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  65105c8

• For all tests, throwing an exception if singularities, undefined p-values, or undefined score bumps are encountered. These should be handled by the calling algorithm.

  jdramsey

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  78a3dc6

• Fixed this issues:

  Show description for 640cd00
  jdramsey

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  640cd00

Commits on Oct 13, 2023

• Fixed PC-LiNGAM and added it back into the interface.

  jdramsey

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  79cbf87

• Factored out the method in Markov Check that generates all of the independence facts to check for the all-subsets case.

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  d74d125

• Factored out the method in Markov Check that generates all of the independence facts to check for the all-subsets case.

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  6e22d4b

• Fixed tests.

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  9e886e7

• Fixing some javadoc errors insisted on by the new Javadoc builder.

  jdramsey

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  6a199a6

• Fixing some javadoc errors insisted on by the new Javadoc builder.

  jdramsey

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  e77e8f6

• Fixing some javadoc errors insisted on by the new Javadoc builder.

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  a2729a5

Commits on Oct 15, 2023

• Trying to fix a persistent bug in knowledge where when you delete required edges in the interface, and toggle show explicitly required only, the edges reappear.

  jdramsey

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  1f3d6ba

Commits on Oct 19, 2023

• Trying to fix a persistent bug in knowledge where when you delete required edges in the interface, and toggle show explicitly required only, the edges reappear.

  jdramsey

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  90a0272

Commits on Oct 20, 2023

• Trying to fix a bug in FCI-like algorithms where with R1 or R9 directed edges could be oriented against knowledge. Also, putting CFCI back in the interface.

  jdramsey

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  3bd738e

• Actually fixed the FCI knowledge but this time. The issue was that the forbidden edges iterator was wrong.

  jdramsey

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  8e6b52a

• Actually fixed the FCI knowledge but this time. The issue was that the forbidden edges iterator was wrong.

  jdramsey

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  559f803

Commits on Oct 21, 2023

• Actually fixed the FCI knowledge but this time. The issue was that the forbidden edges iterator was wrong.

  jdramsey

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  e0c1cec

• Actually fixed the FCI knowledge but this time. The issue was that the forbidden edges iterator was wrong.

  jdramsey

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  91e62f6

• Fixed some unit tests.

  jdramsey

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  3e00658

Commits on Oct 24, 2023

• Fixed some unit tests.

  jdramsey

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  18fa2ab

Commits on Oct 27, 2023

• Fixed some knowledge issues.

  jdramsey

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  8dc9855

• Fixed some knowledge issues.

  jdramsey

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  3aecff1

• Fixed some knowledge issues.

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  6aaca9c

Commits on Oct 30, 2023

• Fixed some knowledge issues.

  jdramsey

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  66b920b

Commits on Oct 31, 2023

• Fixed a problem with Fisher Z with testwise deletion.

  jdramsey

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  43c260d