Deprecated API
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Deprecated ClassesClassDescriptionLegacy shell over
StarFciOriginal; extendStarFciinstead.The knowledge handling of this class has been consolidated intoStarFci(formerly StarFciGuaranteePag); with empty knowledge the two already coincided. This standalone copy is retained only for the hand-run comparison harness (TestStarFciKeepKnowledgeOrientations) and receives no further changes; extendStarFciinstead.Use IndTestBlocksTs instead.
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Deprecated FieldsFieldDescriptionThis name covered both the Gaussian and the non-Gaussian linear SEM simulations, which was confusing. It is kept so that scripts and saved selections using the old name still resolve (to the Linear Gaussian SEM); use
SimulationTypes.LINEAR_GAUSSIAN_SEMorSimulationTypes.LINEAR_NON_GAUSSIAN_SEMinstead.
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Deprecated MethodsMethodDescriptionThis does NOT compute the nonparanormal (Gaussian copula) correlation estimator, despite the name. It stores raw Kendall's tau, omitting the inversion sin(pi * tau / 2) that maps a rank correlation back to the latent Gaussian correlation. Raw tau is severely attenuated relative to the correlation it is standing in for -- a latent rho of 0.9 returns about 0.71, and 0.5 returns about 0.34 -- so anything scored from this matrix systematically under-detects edges. It also uses tau-a rather than tau-b, so ties attenuate it further, and it is O(n^2) per variable pair. Use
DataTransforms.covarianceGaussianCopula(DataSet)instead, which corrects all three. Retained only because removing a public method is a breaking change; nothing in Tetrad calls it.UseCdnod.Builder.alpha(double)instead.This parameter is unused in CdnodBoss and will be removed.Contexts are now determined from Knowledge tier 0, not from column position. UseCdnodBoss.setData(DataSet)instead.OverrideStarFci.getMarkovCpdag(boolean)onStarFciinstead.This reflects thread-local per-call state. PreferIndTestFisherZ.getResult(Node, Node, Set)andIndTestFisherZ.Result.bic(), or the pureIndTestFisherZ.bic(double, int).This reflects thread-local per-call state. PreferIndTestFisherZ.getResult(Node, Node, Set)andIndTestFisherZ.Result.r().This reflects thread-local per-call state. PreferIndTestFisherZ.getResult(Node, Node, Set)andIndTestFisherZ.Result.r().useMinimaxCITest.setQMinimax(double)with q = 1.0 for max aggregation.This method is deprecated and will be removed in a future release.This method is deprecated and will be removed in a future release.This method is deprecated and will be removed in a future release.Use setErrVar(x, value) for variances, or setErrCovar(x, y, value) for covariances.