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/*
* Copyright (C) 2019 University of Pittsburgh.
*
* This library is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public
* License as published by the Free Software Foundation; either
* version 2.1 of the License, or (at your option) any later version.
*
* This library is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
* Lesser General Public License for more details.
*
* You should have received a copy of the GNU Lesser General Public
* License along with this library; if not, write to the Free Software
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
* MA 02110-1301 USA
*/
package edu.cmu.tetrad.util;
import edu.cmu.tetrad.algcomparison.algorithm.Algorithm;
import edu.cmu.tetrad.algcomparison.utils.TakesIndependenceWrapper;
import edu.cmu.tetrad.algcomparison.utils.UsesScoreWrapper;
import edu.cmu.tetrad.annotation.Bootstrapping;
import java.util.Arrays;
import java.util.Collections;
import java.util.HashSet;
import java.util.Set;
/**
* May 7, 2019 2:53:27 PM
*
* @author Kevin V. Bui ([email protected])
* @version $Id: $Id
*/
public final class Params {
/**
* Constant ADD_ORIGINAL_DATASET="addOriginalDataset"
*/
public static final String ADD_ORIGINAL_DATASET = "addOriginalDataset";
/**
* Constant ALPHA="alpha"
*/
public static final String ALPHA = "alpha";
/**
* Constant APPLY_R1="applyR1"
*/
public static final String APPLY_R1 = "applyR1";
/**
* Constant AVG_DEGREE="avgDegree"
*/
public static final String AVG_DEGREE = "avgDegree";
/**
* Constant BASIS_TYPE="basisType"
*/
public static final String BASIS_TYPE = "basisType";
/**
* Constant CCI_SCORE_ALPHA="cciScoreAlpha"
*/
public static final String CCI_SCORE_ALPHA = "cciScoreAlpha";
/**
* Constant CG_EXACT="cgExact"
*/
public static final String CG_EXACT = "cgExact";
/**
* Constant COEF_HIGH="coefHigh"
*/
public static final String COEF_HIGH = "coefHigh";
/**
* Constant COEF_LOW="coefLow"
*/
public static final String COEF_LOW = "coefLow";
/**
* Constant COEF_SYMMETRIC="coefSymmetric"
*/
public static final String COEF_SYMMETRIC = "coefSymmetric";
/**
* Constant COLLIDER_DISCOVERY_RULE="colliderDiscoveryRule"
*/
public static final String COLLIDER_DISCOVERY_RULE = "colliderDiscoveryRule";
/**
* Constant COMPLETE_RULE_SET_USED="completeRuleSetUsed"
*/
public static final String COMPLETE_RULE_SET_USED = "completeRuleSetUsed";
/**
* Constant SEPSET_FINDER_METHOD="sepsetFinderMethod"
*/
public static final String SEPSET_FINDER_METHOD = "sepsetFinderMethod";
/**
* Constant DO_DISCRIMINATING_PATH_COLLIDER_RULE="doDiscriminatingPathColliderRule"
*/
public static final String DO_DISCRIMINATING_PATH_COLLIDER_RULE = "doDiscriminatingPathColliderRule";
/**
* Constant DO_DISCRIMINATING_PATH_TAIL_RULE="doDiscriminatingPathTailRule"
*/
public static final String DO_DISCRIMINATING_PATH_TAIL_RULE = "doDiscriminatingPathTailRule";
/**
* Constant CONCURRENT_FAS="concurrentFAS"
*/
public static final String CONCURRENT_FAS = "concurrentFAS";
/**
* Constant CONFLICT_RULE="conflictRule"
*/
public static final String CONFLICT_RULE = "conflictRule";
/**
* Constant GUARANTEE_CPDAG="guaranteeCpdag"
*/
public static final String GUARANTEE_CPDAG = "guaranteeCpdag";
/**
* Constant CONNECTED="connected"
*/
public static final String CONNECTED = "connected";
/**
* Constant COV_HIGH="covHigh"
*/
public static final String COV_HIGH = "covHigh";
/**
* Constant COV_LOW="covLow"
*/
public static final String COV_LOW = "covLow";
/**
* Constant COV_SYMMETRIC="covSymmetric"
*/
public static final String COV_SYMMETRIC = "covSymmetric";
/**
* Constant CUTOFF_CONSTRAIN_SEARCH="cutoffConstrainSearch"
*/
public static final String CUTOFF_CONSTRAIN_SEARCH = "cutoffConstrainSearch";
/**
* Constant CUTOFF_DATA_SEARCH="cutoffDataSearch"
*/
public static final String CUTOFF_DATA_SEARCH = "cutoffDataSearch";
/**
* Constant CUTOFF_IND_TEST="cutoffIndTest"
*/
public static final String CUTOFF_IND_TEST = "cutoffIndTest";
/**
* Constant DATA_TYPE="dataType"
*/
public static final String DATA_TYPE = "dataType";
/**
* Constant DEPTH="depth"
*/
public static final String DEPTH = "depth";
/**
* Constant DETERMINISM_THRESHOLD="determinismThreshold"
*/
public static final String DETERMINISM_THRESHOLD = "determinismThreshold";
/**
* Constant DIFFERENT_GRAPHS="differentGraphs"
*/
public static final String DIFFERENT_GRAPHS = "differentGraphs";
/**
* Constant DISCRETIZE="discretize"
*/
public static final String DISCRETIZE = "discretize";
/**
* Constant DO_COLLIDER_ORIENTATION="doColliderOrientation"
*/
public static final String DO_COLLIDER_ORIENTATION = "doColliderOrientation";
/**
* Constant ERRORS_NORMAL="errorsNormal"
*/
public static final String ERRORS_NORMAL = "errorsNormal";
/**
* Constant SKEW_EDGE_THRESHOLD="skewEdgeThreshold"
*/
public static final String SKEW_EDGE_THRESHOLD = "skewEdgeThreshold";
/**
* Constant TWO_CYCLE_SCREENING_THRESHOLD="twoCycleScreeningThreshold"
*/
public static final String TWO_CYCLE_SCREENING_THRESHOLD = "twoCycleScreeningThreshold";
/**
* Constant FASK_DELTA="faskDelta"
*/
public static final String FASK_DELTA = "faskDelta";
/**
* Constant FASK_LEFT_RIGHT_RULE="faskLeftRightRule"
*/
public static final String FASK_LEFT_RIGHT_RULE = "faskLeftRightRule";
/**
* Constant FASK_ADJACENCY_METHOD="faskAdjacencyMethod"
*/
public static final String FASK_ADJACENCY_METHOD = "faskAdjacencyMethod";
/**
* Constant FASK_NONEMPIRICAL="faskNonempirical"
*/
public static final String FASK_NONEMPIRICAL = "faskNonempirical";
/**
* Constant FAITHFULNESS_ASSUMED="faithfulnessAssumed"
*/
public static final String FAITHFULNESS_ASSUMED = "faithfulnessAssumed";
/**
* Constant FAS_RULE="fasRule"
*/
public static final String FAS_RULE = "fasRule";
/**
* Constant FAST_ICA_A="fastIcaA"
*/
public static final String FAST_ICA_A = "fastIcaA";
/**
* Constant FAST_ICA_MAX_ITER="fastIcaMaxIter"
*/
public static final String FAST_ICA_MAX_ITER = "fastIcaMaxIter";
/**
* Constant FAST_ICA_TOLERANCE="fastIcaTolerance"
*/
public static final String FAST_ICA_TOLERANCE = "fastIcaTolerance";
/**
* Constant THRESHOLD_B="thresholdBHat"
*/
public static final String THRESHOLD_B = "thresholdBHat";
/**
* Constant GUARANTEE_ACYCLIC="guaranteeAcyclic"
*/
public static final String GUARANTEE_ACYCLIC = "guaranteeAcyclic";
/**
* Constant THRESHOLD_SPINE="thresholdSpine"
*/
public static final String THRESHOLD_W = "thresholdW";
/**
* Constant ORIENTATION_ALPHA="orientationAlpha"
*/
public static final String ORIENTATION_ALPHA = "orientationAlpha";
/**
* Constant FISHER_EPSILON="fisherEpsilon"
*/
public static final String FISHER_EPSILON = "fisherEpsilon";
/**
* Constant GENERAL_SEM_ERROR_TEMPLATE="generalSemErrorTemplate"
*/
public static final String GENERAL_SEM_ERROR_TEMPLATE = "generalSemErrorTemplate";
/**
* Constant GENERAL_SEM_FUNCTION_TEMPLATE_LATENT="generalSemFunctionTemplateLatent"
*/
public static final String GENERAL_SEM_FUNCTION_TEMPLATE_LATENT = "generalSemFunctionTemplateLatent";
/**
* Constant GENERAL_SEM_FUNCTION_TEMPLATE_MEASURED="generalSemFunctionTemplateMeasured"
*/
public static final String GENERAL_SEM_FUNCTION_TEMPLATE_MEASURED = "generalSemFunctionTemplateMeasured";
/**
* Constant GENERAL_SEM_PARAMETER_TEMPLATE="generalSemParameterTemplate"
*/
public static final String GENERAL_SEM_PARAMETER_TEMPLATE = "generalSemParameterTemplate";
/**
* Constant GUARANTEE_IID="guaranteeIid"
*/
public static final String GUARANTEE_IID = "guaranteeIid";
/**
* Constant IA="ia"
*/
public static final String IA = "ia";
/**
* Constant INCLUDE_NEGATIVE_COEFS="includeNegativeCoefs"
*/
public static final String INCLUDE_NEGATIVE_COEFS = "includeNegativeCoefs";
/**
* Constant INCLUDE_NEGATIVE_SKEWS_FOR_BETA="includeNegativeSkewsForBeta"
*/
public static final String INCLUDE_NEGATIVE_SKEWS_FOR_BETA = "includeNegativeSkewsForBeta";
/**
* Constant INCLUDE_POSITIVE_COEFS="includePositiveCoefs"
*/
public static final String INCLUDE_POSITIVE_COEFS = "includePositiveCoefs";
/**
* Constant INCLUDE_POSITIVE_SKEWS_FOR_BETA="includePositiveSkewsForBeta"
*/
public static final String INCLUDE_POSITIVE_SKEWS_FOR_BETA = "includePositiveSkewsForBeta";
/**
* Constant INCLUDE_STRUCTURE_MODEL="include_structure_model"
*/
public static final String INCLUDE_STRUCTURE_MODEL = "include_structure_model";
/**
* Constant INTERVAL_BETWEEN_RECORDINGS="intervalBetweenRecordings"
*/
public static final String INTERVAL_BETWEEN_RECORDINGS = "intervalBetweenRecordings";
/**
* Constant INTERVAL_BETWEEN_SHOCKS="intervalBetweenShocks"
*/
public static final String INTERVAL_BETWEEN_SHOCKS = "intervalBetweenShocks";
/**
* Constant IPEN="ipen"
*/
public static final String IPEN = "ipen";
/**
* Constant IS="is"
*/
public static final String IS = "is";
/**
* Constant ITR="itr"
*/
public static final String ITR = "itr";
/**
* Constant KCI_ALPHA="kciAlpha"
*/
public static final String KCI_ALPHA = "kciAlpha";
/**
* Constant KCI_CUTOFF="kciCutoff"
*/
public static final String KCI_CUTOFF = "kciCutoff";
/**
* Constant KCI_EPSILON="kciEpsilon"
*/
public static final String KCI_EPSILON = "kciEpsilon";
/**
* Constant KCI_NUM_BOOTSTRAPS="kciNumBootstraps"
*/
public static final String KCI_NUM_BOOTSTRAPS = "kciNumBootstraps";
/**
* Constant KCI_USE_APPROXIMATION="kciUseApproximation"
*/
public static final String KCI_USE_APPROXIMATION = "kciUseApproximation";
/**
* Constant KERNEL_MULTIPLIER="kernelMultiplier"
*/
public static final String KERNEL_MULTIPLIER = "kernelMultiplier";
/**
* Constant KERNEL_REGRESSION_SAMPLE_SIZE="kernelRegressionSampleSize"
*/
public static final String KERNEL_REGRESSION_SAMPLE_SIZE = "kernelRegressionSampleSize";
/**
* Constant KERNEL_TYPE="kernelType"
*/
public static final String KERNEL_TYPE = "kernelType";
/**
* Constant KERNEL_WIDTH="kernelWidth"
*/
public static final String KERNEL_WIDTH = "kernelWidth";
/**
* Constant LATENT_MEASURED_IMPURE_PARENTS="latentMeasuredImpureParents"
*/
public static final String LATENT_MEASURED_IMPURE_PARENTS = "latentMeasuredImpureParents";
/**
* Constant LOWER_BOUND="lowerBound"
*/
public static final String LOWER_BOUND = "lowerBound";
/**
* Constant MAX_CATEGORIES="maxCategories"
*/
public static final String MAX_CATEGORIES = "maxCategories";
/**
* Constant MAX_DEGREE="maxDegree"
*/
public static final String MAX_DEGREE = "maxDegree";
/**
* Constant MAX_DISTINCT_VALUES_DISCRETE="maxDistinctValuesDiscrete"
*/
public static final String MAX_DISTINCT_VALUES_DISCRETE = "maxDistinctValuesDiscrete";
/**
* Constant MAX_INDEGREE="maxIndegree"
*/
public static final String MAX_INDEGREE = "maxIndegree";
/**
* Constant MAX_ITERATIONS="maxIterations"
*/
public static final String MAX_ITERATIONS = "maxIterations";
/**
* Constant MAX_OUTDEGREE="maxOutdegree"
*/
public static final String MAX_OUTDEGREE = "maxOutdegree";
/**
* Constant MAX_PATH_LENGTH="maxPathLength"
*/
public static final String MAX_PATH_LENGTH = "maxPathLength";
/**
* Constant MAXIT="maxit"
*/
public static final String MAXIT = "maxit";
/**
* Constant MEAN_HIGH="meanHigh"
*/
public static final String MEAN_HIGH = "meanHigh";
/**
* Constant MEAN_LOW="meanLow"
*/
public static final String MEAN_LOW = "meanLow";
/**
* Constant MEASURED_MEASURED_IMPURE_ASSOCIATIONS="measuredMeasuredImpureAssociations"
*/
public static final String MEASURED_MEASURED_IMPURE_ASSOCIATIONS = "measuredMeasuredImpureAssociations";
/**
* Constant MEASURED_MEASURED_IMPURE_PARENTS="measuredMeasuredImpureParents"
*/
public static final String MEASURED_MEASURED_IMPURE_PARENTS = "measuredMeasuredImpureParents";
/**
* Constant MEASUREMENT_MODEL_DEGREE="measurementModelDegree"
*/
public static final String MEASUREMENT_MODEL_DEGREE = "measurementModelDegree";
/**
* Constant MEASUREMENT_VARIANCE="measurementVariance"
*/
public static final String MEASUREMENT_VARIANCE = "measurementVariance";
/**
* Constant MGM_PARAM1="mgmParam1"
*/
public static final String MGM_PARAM1 = "mgmParam1";
/**
* Constant MGM_PARAM2="mgmParam2"
*/
public static final String MGM_PARAM2 = "mgmParam2";
/**
* Constant MGM_PARAM3="mgmParam3"
*/
public static final String MGM_PARAM3 = "mgmParam3";
/**
* Constant MIN_CATEGORIES="minCategories"
*/
public static final String MIN_CATEGORIES = "minCategories";
/**
* Constant NO_RANDOMLY_DETERMINED_INDEPENDENCE="noRandomlyDeterminedIndependence"
*/
public static final String NO_RANDOMLY_DETERMINED_INDEPENDENCE = "noRandomlyDeterminedIndependence";
/**
* Constant NUM_BASIS_FUNCTIONS="numBasisFunctions"
*/
public static final String NUM_BASIS_FUNCTIONS = "numBasisFunctions";
/**
* Constant NUM_BSC_BOOTSTRAP_SAMPLES="numBscBootstrapSamples"
*/
public static final String NUM_BSC_BOOTSTRAP_SAMPLES = "numBscBootstrapSamples";
/**
* Constant NUM_CATEGORIES="numCategories"
*/
public static final String NUM_CATEGORIES = "numCategories";
/**
* Constant NUM_CATEGORIES_TO_DISCRETIZE="numCategoriesToDiscretize"
*/
public static final String NUM_CATEGORIES_TO_DISCRETIZE = "numCategoriesToDiscretize";
/**
* Constant NUM_LAGS="numLags"
*/
public static final String NUM_LAGS = "numLags";
/**
* Constant NUM_LATENTS="numLatents"
*/
public static final String NUM_LATENTS = "numLatents";
/**
* Constant NUM_MEASURES="numMeasures"
*/
public static final String NUM_MEASURES = "numMeasures";
/**
* Constant PROBABILITY_OF_EDGE="probabilityOfEdge"
*/
public static final String PROBABILITY_OF_EDGE = "probabilityOfEdge";
/**
* Constant NUM_RANDOMIZED_SEARCH_MODELS="numRandomizedSearchModels"
*/
public static final String NUM_RANDOMIZED_SEARCH_MODELS = "numRandomizedSearchModels";
/**
* Constant NUM_RUNS="numRuns"
*/
public static final String NUM_RUNS = "numRuns";
/**
* Constant NUM_STRUCTURAL_EDGES="numStructuralEdges"
*/
public static final String NUM_STRUCTURAL_EDGES = "numStructuralEdges";
/**
* Constant NUM_STRUCTURAL_NODES="numStructuralNodes"
*/
public static final String NUM_STRUCTURAL_NODES = "numStructuralNodes";
/**
* Constant NUMBER_RESAMPLING="numberResampling"
*/
public static final String NUMBER_RESAMPLING = "numberResampling";
/**
* Constant ORIENT_TOWARD_DCONNECTIONS="orientTowardDConnections"
*/
public static final String ORIENT_TOWARD_DCONNECTIONS = "orientTowardDConnections";
/**
* Constant ORIENT_VISIBLE_FEEDBACK_LOOPS="orientVisibleFeedbackLoops"
*/
public static final String ORIENT_VISIBLE_FEEDBACK_LOOPS = "orientVisibleFeedbackLoops";
/**
* Constant OUTPUT_RBD="outputRBD"
*/
public static final String OUTPUT_RBD = "outputRBD";
/**
* Constant PARALLELIZED="parallelized"
*/
public static final String PARALLELIZED = "parallelized";
/**
* Constant PENALTY_DISCOUNT="penaltyDiscount"
*/
public static final String PENALTY_DISCOUNT = "penaltyDiscount";
/**
* Constant PENALTY_DISCOUNT_ZS="penaltyDiscountZs"
*/
public static final String PENALTY_DISCOUNT_ZS = "penaltyDiscountZs";
/**
* Constant EBIC_GAMMA="ebicGamma"
*/
public static final String EBIC_GAMMA = "ebicGamma";
/**
* Constant PERCENT_DISCRETE="percentDiscrete"
*/
public static final String PERCENT_DISCRETE = "percentDiscrete";
/**
* Constant PERCENT_RESAMPLE_SIZE="percentResampleSize"
*/
public static final String PERCENT_RESAMPLE_SIZE = "percentResampleSize";
/**
* Constant POSSIBLE_MSEP_DONE="possibleMsepDone"
*/
public static final String POSSIBLE_MSEP_DONE = "possibleMsepDone";
/**
* Constant PROB_CYCLE="probCycle"
*/
public static final String PROB_CYCLE = "probCycle";
/**
* Constant PROB_TWO_CYCLE="probTwoCycle"
*/
public static final String PROB_TWO_CYCLE = "probTwoCycle";
/**
* Constant RANDOM_SELECTION_SIZE="randomSelectionSize"
*/
public static final String RANDOM_SELECTION_SIZE = "randomSelectionSize";
/**
* Constant RANDOMIZE_COLUMNS="randomizeColumns"
*/
public static final String RANDOMIZE_COLUMNS = "randomizeColumns";
/**
* Constant RCIT_NUM_FEATURES="rcitNumFeatures"
*/
public static final String RCIT_NUM_FEATURES = "rcitNumFeatures";
/**
* Constant RESAMPLING_ENSEMBLE="resamplingEnsemble"
*/
public static final String RESAMPLING_ENSEMBLE = "resamplingEnsemble";
/**
* Constant RESAMPLING_WITH_REPLACEMENT="resamplingWithReplacement"
*/
public static final String RESAMPLING_WITH_REPLACEMENT = "resamplingWithReplacement";
/**
* Constant PRIOR_EQUIVALENT_SAMPLE_SIZE="priorEquivalentSampleSize"
*/
public static final String PRIOR_EQUIVALENT_SAMPLE_SIZE = "priorEquivalentSampleSize";
/**
* Constant SAMPLE_SIZE="sampleSize"
*/
public static final String SAMPLE_SIZE = "sampleSize";
/**
* Constant SAVE_LATENT_VARS="saveLatentVars"
*/
public static final String SAVE_LATENT_VARS = "saveLatentVars";
/**
* Constant SCALE_FREE_ALPHA="scaleFreeAlpha"
*/
public static final String SCALE_FREE_ALPHA = "scaleFreeAlpha";
/**
* Constant SCALE_FREE_BETA="scaleFreeBeta"
*/
public static final String SCALE_FREE_BETA = "scaleFreeBeta";
/**
* Constant SCALE_FREE_DELTA_IN="scaleFreeDeltaIn"
*/
public static final String SCALE_FREE_DELTA_IN = "scaleFreeDeltaIn";
/**
* Constant SCALE_FREE_DELTA_OUT="scaleFreeDeltaOut"
*/
public static final String SCALE_FREE_DELTA_OUT = "scaleFreeDeltaOut";
/**
* Constant SELF_LOOP_COEF="selfLoopCoef"
*/
public static final String SELF_LOOP_COEF = "selfLoopCoef";
/**
* Constant SKIP_NUM_RECORDS="skipNumRecords"
*/
public static final String SKIP_NUM_RECORDS = "skipNumRecords";
/**
* Constant STABLE_FAS="stableFAS"
*/
public static final String STABLE_FAS = "stableFAS";
/**
* Constant STANDARDIZE="standardize"
*/
public static final String STANDARDIZE = "standardize";
/**
* Constant STRUCTURE_PRIOR="structurePrior"
*/
public static final String STRUCTURE_PRIOR = "structurePrior";
/**
* Constant SYMMETRIC_FIRST_STEP="symmetricFirstStep"
*/
public static final String SYMMETRIC_FIRST_STEP = "symmetricFirstStep";
/**
* Constant TARGET_NAME="targetName"
*/
public static final String TARGET_NAME = "targetName";
/**
* Constant THR="thr"
*/
public static final String THR = "thr";
/**
* Constant THRESHOLD_FOR_NUM_EIGENVALUES="thresholdForNumEigenvalues"
*/
public static final String THRESHOLD_FOR_NUM_EIGENVALUES = "thresholdForNumEigenvalues";
/**
* Constant THRESHOLD_NO_RANDOM_CONSTRAIN_SEARCH="thresholdNoRandomConstrainSearch"
*/
public static final String THRESHOLD_NO_RANDOM_CONSTRAIN_SEARCH = "thresholdNoRandomConstrainSearch";
/**
* Constant THRESHOLD_NO_RANDOM_DATA_SEARCH="thresholdNoRandomDataSearch"
*/
public static final String THRESHOLD_NO_RANDOM_DATA_SEARCH = "thresholdNoRandomDataSearch";
/**
* Constant TWO_CYCLE_ALPHA="twoCycleAlpha"
*/
public static final String TWO_CYCLE_ALPHA = "twoCycleAlpha";
/**
* Constant UPPER_BOUND="upperBound"
*/
public static final String UPPER_BOUND = "upperBound";
/**
* Constant USE_CORR_DIFF_ADJACENCIES="useCorrDiffAdjacencies"
*/
public static final String USE_CORR_DIFF_ADJACENCIES = "useCorrDiffAdjacencies";
/**
* Constant USE_FAS_ADJACENCIES="useFasAdjacencies"
*/
public static final String USE_FAS_ADJACENCIES = "useFasAdjacencies";
/**
* Constant USE_GAP="useGap"
*/
public static final String USE_GAP = "useGap";
/**
* Constant USE_MAX_P_HEURISTIC="useMaxPHeuristic"
*/
public static final String USE_MAX_P_HEURISTIC = "useMaxPHeuristic";
/**
* Constant USE_MAX_P_ORIENTATION_HEURISTIC="useMaxPOrientationHeuristic"
*/
public static final String USE_MAX_P_ORIENTATION_HEURISTIC = "useMaxPOrientationHeuristic";
/**
* Constant USE_SKEW_ADJACENCIES="useSkewAdjacencies"
*/
public static final String USE_SKEW_ADJACENCIES = "useSkewAdjacencies";
/**
* Constant USE_WISHART="useWishart"
*/
public static final String USE_WISHART = "useWishart";
/**
* Constant CHECK_TYPE="checkType"
*/
public static final String CHECK_TYPE = "checkType";
/**
* Constant VAR_HIGH="varHigh"
*/
public static final String VAR_HIGH = "varHigh";
/**
* Constant VAR_LOW="varLow"
*/
public static final String VAR_LOW = "varLow";
/**
* Constant VERBOSE="verbose"
*/
public static final String VERBOSE = "verbose";
/**
* Constant MEEK_VERBOSE="meekVerbose"
*/
public static final String MEEK_VERBOSE = "meekVerbose";
/**
* Constant SEM_BIC_RULE="semBicRule"
*/
public static final String SEM_BIC_RULE = "semBicRule";
/**
* Constant SEM_GIC_RULE="semGicRule"
*/
public static final String SEM_GIC_RULE = "semGicRule";
/**
* Constant SEM_BIC_STRUCTURE_PRIOR="semBicStructurePrior"
*/
public static final String SEM_BIC_STRUCTURE_PRIOR = "semBicStructurePrior";
/**
* Constant POISSON_LAMBDA="poissonLambda"
*/
public static final String POISSON_LAMBDA = "poissonLambda";
/**
* Constant USE_BES="useBes"
*/
public static final String USE_BES = "useBes";
/**
* Constant NUM_STARTS="numStarts"
*/
public static final String NUM_STARTS = "numStarts";
/**
* Constant CACHE_SCORES="cacheScores"
*/
public static final String CACHE_SCORES = "cacheScores";
/**
* Constant BOSS_ALG="bossAlg"
*/
public static final String BOSS_ALG = "bossAlg";
/**
* Constant OUTPUT_CPDAG="outputCpdag"
*/
public static final String OUTPUT_CPDAG = "outputCpdag";
/**
* Constant ZS_RISK_BOUND="zSRiskBound"
*/
public static final String ZS_RISK_BOUND = "zSRiskBound";
/**
* Constant NUM_ROUNDS="numRounds"
*/
public static final String NUM_ROUNDS = "numRounds";
// GRASP parameters and flags.
/**
* Constant GRASP_CHECK_COVERING="graspCheckCovering"
*/
public static final String GRASP_CHECK_COVERING = "graspCheckCovering";
/**
* Constant GRASP_FORWARD_TUCK_ONLY="graspForwardTuckOnly"
*/
public static final String GRASP_FORWARD_TUCK_ONLY = "graspForwardTuckOnly";
/**
* Constant GRASP_BREAK_AFTER_IMPROVEMENT="graspBreakAFterImprovement"
*/
public static final String GRASP_BREAK_AFTER_IMPROVEMENT = "graspBreakAFterImprovement";
/**
* Constant GRASP_ORDERED_ALG="graspOrderedAlg"
*/
public static final String GRASP_ORDERED_ALG = "graspOrderedAlg";
/**
* Constant GRASP_USE_SCORE="graspUseScore"
*/
public static final String GRASP_USE_SCORE = "graspUseScore";
/**
* Constant GRASP_USE_RASKUTTI_UHLER="graspUseRaskuttiUhler"
*/
public static final String GRASP_USE_RASKUTTI_UHLER = "graspUseRaskuttiUhler";
/**
* Constant USE_DATA_ORDER="useDataOrder"
*/
public static final String USE_DATA_ORDER = "useDataOrder";
/**
* Constant ALLOW_INTERNAL_RANDOMNESS="allowInternalRandomness"
*/
public static final String ALLOW_INTERNAL_RANDOMNESS = "allowInternalRandomness";
/**
* Constant GRASP_DEPTH="graspDepth"
*/
public static final String GRASP_DEPTH = "graspDepth";
/**
* Constant GRASP_SINGULAR_DEPTH="graspSingularDepth"
*/
public static final String GRASP_SINGULAR_DEPTH = "graspSingularDepth";
/**
* Constant GRASP_NONSINGULAR_DEPTH="graspNonSingularDepth"
*/
public static final String GRASP_NONSINGULAR_DEPTH = "graspNonSingularDepth";
/**
* Constant GRASP_TOLERANCE_DEPTH="graspToleranceDepth"
*/
public static final String GRASP_TOLERANCE_DEPTH = "graspToleranceDepth";
/**
* Constant GRASP_ALG="graspAlg"
*/
public static final String GRASP_ALG = "graspAlg";
/**
* Constant TIMEOUT="timeout"
*/
public static final String TIMEOUT = "timeout"; /**
* Constant TEST_TIMEOUT="testTimeout"
*/
public static final String TEST_TIMEOUT = "testTimeout";
/**
* Constant GRASP_USE_VP_SCORING="graspUseVpScoring"
*/
public static final String GRASP_USE_VP_SCORING = "graspUseVpScoring";
/**
* Constant SIMULATION_ERROR_TYPE="simulationErrorType"
*/
public static final String SIMULATION_ERROR_TYPE = "simulationErrorType";
/**
* Constant SIMULATION_PARAM1="simulationParam1"
*/
public static final String SIMULATION_PARAM1 = "simulationParam1";
/**
* Constant SIMULATION_PARAM2="simulationParam2"
*/
public static final String SIMULATION_PARAM2 = "simulationParam2";
/**
* Constant SELECTION_MIN_EFFECT="selectionMinEffect"
*/
public static final String SELECTION_MIN_EFFECT = "selectionMinEffect";
/**
* Constant NUM_SUBSAMPLES="numSubsamples"
*/
public static final String NUM_SUBSAMPLES = "numSubsamples";
/**
* Constant TARGETS="targets"
*/
public static final String TARGETS = "targets";
/**
* Constant MB="mb"
*/
public static final String MB = "mb";
/**
* Constant TOP_BRACKET="topBracket"
*/
public static final String TOP_BRACKET = "topBracket";
/**
* Constant TIME_LAG="timeLag"
*/
public static final String TIME_LAG = "timeLag";
/**
* Constant PRECOMPUTE_COVARIANCES="precomputeCovariances"
*/
public static final String PRECOMPUTE_COVARIANCES = "precomputeCovariances";
/**
* Constant IMAGES_META_ALG="imagesMetaAlg"
*/
public static final String IMAGES_META_ALG = "imagesMetaAlg";
/**
* Constant SEED="seed"
*/
public static final String SEED = "seed";
/**
* Constant SIGNIFICANCE_CHECKED="significanceChecked"
*/
public static final String SIGNIFICANCE_CHECKED = "significanceChecked";
/**
* Constant PROB_REMOVE_COLUMN="probRemoveColumn"
*/
public static final String PROB_REMOVE_COLUMN = "probRemoveColumn";
/**
* Constant SAVE_BOOTSTRAP_GRAPHS="saveBootstrapGraphs"
*/
public static final String SAVE_BOOTSTRAP_GRAPHS = "saveBootstrapGraphs";
/**
* Constant LAMBDA1="lambda1"
*/
public static final String LAMBDA1 = "lambda1";
/**
* Constant W_THRESHOLD="wThreshold"
*/
public static final String W_THRESHOLD = "wThreshold";
/**
* Constant CPDAG="cpdag"
*/
public static final String CPDAG = "cpdag";
/**
* Constant TRIMMING_STYLE="trimmingStyle"
*/
public static final String TRIMMING_STYLE = "trimmingStyle";
/**
* Constant NUMBER_OF_EXPANSIONS="numberOfExpansions"
*/
public static final String NUMBER_OF_EXPANSIONS = "numberOfExpansions";
/**
* Constant CSTAR_CPDAG_ALGORITHM="cstarCpdagAlgorithm"
*/
public static final String CSTAR_CPDAG_ALGORITHM = "cstarCpdagAlgorithm";
/**
* Constant FILE_OUT_PATH="fileOutPath"
*/
public static final String FILE_OUT_PATH = "fileOutPath";
/**
* Constant REMOVE_EFFECT_NODES="removeEffectNodes"
*/
public static final String REMOVE_EFFECT_NODES = "removeEffectNodes";
/**
* Constant SAMPLE_STYLE="sampleStyle"
*/
public static final String SAMPLE_STYLE = "sampleStyle";
/**
* Constant NUM_THREADS="numThreads"
*/
public static final String NUM_THREADS = "numThreads";
/**
* Constant BOOTSTRAPPING_NUM_THEADS="bootstrappingNumThreads"
*/
public static final String BOOTSTRAPPING_NUM_THREADS = "bootstrappingNumThreads";
/**
* Constant USE_PSEUDOINVERSE="usePseudoinverse"
*/
public static final String USE_PSEUDOINVERSE = "usePseudoinverse";
/**
* Constant USE_PSEUDOINVERSE_FOR_LATENT="usePseudoinverseForLatent"
*/
public static final String COMPARE_GRAPH_ALGCOMP = "compareGraphAlgcomp";
/**
* Constant COMPARE_GRAPH_ALGCOMP="compareGraphAlgcomp"
*/
public static final String MIN_SAMPLE_SIZE_PER_CELL = "minSampleSizePerCell";
/**
* Constant ABLATION_LEAVE_OUT_TUCKING_STEP="ablationLeaveOutTuckingStep"
*/
public static final String ABLATION_LEAVE_OUT_TUCKING_STEP = "ablationLeaveOutTuckingStep";
/**
* Constant ALLOW_TESTING="ABLATION_LEAVE_OUT_SCORING_STEP = "ablationLeaveOutScoringStep""
*/
public static final String ABLATION_LEAVE_OUT_SCORING_STEP = "ablationLeaveOutScoringStep";
/**
* Constant ALLOW_TESTING="ABLATION_LEAVE_OUT_TESTING_STEPS = "ablationLeaveOutTestingSteps""
*/
public static final String ABLATION_LEAVE_OUT_TESTING_STEPS = "ablationLeaveOutTestingSteps";
/**
* Constant MAX_SCORE_DROP="maxScoreDrop"
*/
public static final String MAX_SCORE_DROP = "maxScoreDrop";
/**
* Constant GUARANTEE_PAG="guaranteePag"
*/
public static final String GUARANTEE_PAG = "guaranteePag";
/**
* Constant REMOVE_ALMOST_CYCLES="removeAlmostCycles"
*/
public static final String REMOVE_ALMOST_CYCLES = "removeAlmostCycles";
/**
* Constant MIN_COUNT_PER_CELL="minCountPerCell"
*/
public static String MIN_COUNT_PER_CELL = "minCountPerCell";
/**
* Constant PC_HEURISTIC="pcHeuristic"
*/
public static String PC_HEURISTIC = "pcHeuristic";
/**
* Constant LV_LITE_STARTS_WITGH="LvLiteStartsWith"
*/
public static String LV_LITE_STARTS_WITH = "lvLiteStartsWith";
/**
* Constant EXTRA_EDGE_REMOVAL_STEP="extraEdgeRemovalStep"
*/
public static String EXTRA_EDGE_REMOVAL_STEP = "extraEdgeRemovalStep";
/**
* Constant LV_LITE_MAX_PATH_LENGTH="lvLiteMaxPathLength"
*/
public static final String MAX_BLOCKING_PATH_LENGTH = "maxBlockingPathLength";
/**
* Constant MAX_SEPSET_SIZE="maxSepsetSize"
*/
public static final String MAX_SEPSET_SIZE = "maxSepsetSize";
private Params() {
}
// All parameters that are found in HTML manual documentation
private static final Set ALL_PARAMS_IN_HTML_MANUAL = new HashSet<>(Arrays.asList(
Params.ADD_ORIGINAL_DATASET, Params.ALPHA, Params.APPLY_R1, Params.AVG_DEGREE, Params.BASIS_TYPE,
Params.CCI_SCORE_ALPHA, Params.CG_EXACT, Params.COEF_HIGH, Params.COEF_LOW, Params.COEF_SYMMETRIC,
Params.COLLIDER_DISCOVERY_RULE, Params.COMPLETE_RULE_SET_USED, Params.CONCURRENT_FAS,
Params.CONFLICT_RULE, Params.CONNECTED, Params.COV_HIGH, Params.COV_LOW, Params.COV_SYMMETRIC,
Params.CUTOFF_CONSTRAIN_SEARCH, Params.CUTOFF_DATA_SEARCH, Params.CUTOFF_IND_TEST,
Params.DATA_TYPE, Params.DEPTH, Params.DETERMINISM_THRESHOLD, Params.DIFFERENT_GRAPHS, Params.DISCRETIZE,
Params.DO_COLLIDER_ORIENTATION, Params.ERRORS_NORMAL, Params.SKEW_EDGE_THRESHOLD,
Params.FAITHFULNESS_ASSUMED, Params.FAS_RULE, Params.FISHER_EPSILON, Params.GENERAL_SEM_ERROR_TEMPLATE,
Params.GENERAL_SEM_FUNCTION_TEMPLATE_LATENT, Params.GENERAL_SEM_FUNCTION_TEMPLATE_MEASURED,
Params.GENERAL_SEM_PARAMETER_TEMPLATE, Params.IA, Params.INCLUDE_NEGATIVE_COEFS,
Params.INCLUDE_NEGATIVE_SKEWS_FOR_BETA, Params.INCLUDE_POSITIVE_COEFS,
Params.INCLUDE_POSITIVE_SKEWS_FOR_BETA, Params.INCLUDE_STRUCTURE_MODEL,
Params.INTERVAL_BETWEEN_RECORDINGS, Params.INTERVAL_BETWEEN_SHOCKS, Params.IPEN, Params.IS, Params.ITR,
Params.KCI_ALPHA, Params.KCI_CUTOFF, Params.KCI_EPSILON, Params.KCI_NUM_BOOTSTRAPS, Params.KCI_USE_APPROXIMATION,
Params.KERNEL_MULTIPLIER, Params.KERNEL_REGRESSION_SAMPLE_SIZE, Params.KERNEL_TYPE, Params.KERNEL_WIDTH,
Params.LATENT_MEASURED_IMPURE_PARENTS, Params.LOWER_BOUND, Params.MAX_CATEGORIES, Params.MAX_DEGREE,
Params.MAX_DISTINCT_VALUES_DISCRETE, Params.MAX_INDEGREE, Params.MAX_ITERATIONS, Params.MAX_OUTDEGREE,
Params.MEAN_LOW, Params.MEASURED_MEASURED_IMPURE_ASSOCIATIONS, Params.MEASURED_MEASURED_IMPURE_PARENTS,
Params.MEASUREMENT_MODEL_DEGREE, Params.MEASUREMENT_VARIANCE, Params.MGM_PARAM1, Params.MGM_PARAM2, Params.MGM_PARAM3,
Params.MIN_CATEGORIES, Params.NO_RANDOMLY_DETERMINED_INDEPENDENCE, Params.NUM_BASIS_FUNCTIONS,
Params.NUM_BSC_BOOTSTRAP_SAMPLES, Params.NUM_CATEGORIES, Params.NUM_CATEGORIES_TO_DISCRETIZE, Params.NUM_LAGS,
Params.NUM_LATENTS, Params.NUM_MEASURES, Params.NUM_RANDOMIZED_SEARCH_MODELS, Params.NUM_RUNS,
Params.NUM_STRUCTURAL_EDGES, Params.NUM_STRUCTURAL_NODES, Params.NUMBER_RESAMPLING,
Params.ORIENT_TOWARD_DCONNECTIONS, Params.ORIENT_VISIBLE_FEEDBACK_LOOPS, Params.OUTPUT_RBD,
Params.PENALTY_DISCOUNT, Params.PERCENT_DISCRETE, Params.PERCENT_RESAMPLE_SIZE, Params.POSSIBLE_MSEP_DONE,
Params.PROB_CYCLE, Params.PROB_TWO_CYCLE, Params.RANDOM_SELECTION_SIZE, Params.RANDOMIZE_COLUMNS,
Params.RCIT_NUM_FEATURES, Params.RESAMPLING_ENSEMBLE, Params.RESAMPLING_WITH_REPLACEMENT, Params.PRIOR_EQUIVALENT_SAMPLE_SIZE,
Params.SAMPLE_SIZE, Params.SAVE_LATENT_VARS, Params.SCALE_FREE_ALPHA, Params.SCALE_FREE_BETA, Params.SCALE_FREE_DELTA_IN,
Params.SCALE_FREE_DELTA_OUT, Params.SELF_LOOP_COEF, Params.SKIP_NUM_RECORDS, Params.STABLE_FAS, Params.STANDARDIZE,
Params.STRUCTURE_PRIOR, Params.SYMMETRIC_FIRST_STEP, Params.TARGET_NAME, Params.THR, Params.THRESHOLD_FOR_NUM_EIGENVALUES,
Params.THRESHOLD_NO_RANDOM_CONSTRAIN_SEARCH, Params.THRESHOLD_NO_RANDOM_DATA_SEARCH, Params.TWO_CYCLE_ALPHA,
Params.UPPER_BOUND, Params.USE_CORR_DIFF_ADJACENCIES, Params.USE_FAS_ADJACENCIES, Params.USE_GAP,
Params.USE_MAX_P_ORIENTATION_HEURISTIC, Params.USE_SKEW_ADJACENCIES, Params.USE_WISHART, Params.VAR_HIGH,
Params.VAR_LOW, Params.VERBOSE
));
private static final Set BOOTSTRAPPING_PARAMS = new HashSet<>(Arrays.asList(
Params.ADD_ORIGINAL_DATASET,
Params.NUMBER_RESAMPLING,
Params.PERCENT_RESAMPLE_SIZE,
// Params.RESAMPLING_ENSEMBLE,
Params.RESAMPLING_WITH_REPLACEMENT,
Params.BOOTSTRAPPING_NUM_THREADS,
Params.SAVE_BOOTSTRAP_GRAPHS,
Params.SEED
));
/**
* getAlgorithmParameters.
*
* @param algorithm a {@link edu.cmu.tetrad.algcomparison.algorithm.Algorithm} object
* @return a {@link java.util.Set} object
*/
public static Set getAlgorithmParameters(Algorithm algorithm) {
return new HashSet<>(algorithm.getParameters());
}
/**
* getTestParameters.
*
* @param algorithm a {@link edu.cmu.tetrad.algcomparison.algorithm.Algorithm} object
* @return a {@link java.util.Set} object
*/
public static Set getTestParameters(Algorithm algorithm) {
return (algorithm instanceof TakesIndependenceWrapper)
? new HashSet<>(((TakesIndependenceWrapper) algorithm).getIndependenceWrapper().getParameters())
: Collections.emptySet();
}
/**
* getScoreParameters.
*
* @param algorithm a {@link edu.cmu.tetrad.algcomparison.algorithm.Algorithm} object
* @return a {@link java.util.Set} object
*/
public static Set getScoreParameters(Algorithm algorithm) {
return (algorithm instanceof UsesScoreWrapper)
? new HashSet<>(((UsesScoreWrapper) algorithm).getScoreWrapper().getParameters())
: Collections.emptySet();
}
/**
* getBootstrappingParameters.
*
* @param algorithm a {@link edu.cmu.tetrad.algcomparison.algorithm.Algorithm} object
* @return a {@link java.util.Set} object
*/
public static Set getBootstrappingParameters(Algorithm algorithm) {
return (algorithm.getClass().isAnnotationPresent(Bootstrapping.class))
? Params.BOOTSTRAPPING_PARAMS
: Collections.emptySet();
}
/**
* getParameters.
*
* @return a {@link java.util.Set} object
*/
public static Set getParameters() {
return Params.ALL_PARAMS_IN_HTML_MANUAL;
}
}