package edu.cmu.tetrad.util; import java.util.HashMap; import java.util.Map; /** * Stores descriptions of the parameters for the simulation box. All parameters * that go into the interface need to be described here. * * @author jdramsey */ public class ParamDescriptions { private static ParamDescriptions instance = new ParamDescriptions(); private Map map = new HashMap<>(); public ParamDescriptions() { put("numMeasures", new ParamDescription("Number of measured variables", 10, 1, Integer.MAX_VALUE)); put("numLatents", new ParamDescription("Number of latent variables", 0, 0, Integer.MAX_VALUE)); put("avgDegree", new ParamDescription("Average degree of graph", 2, 1, Integer.MAX_VALUE)); put("maxDegree", new ParamDescription("The maximum degree of the graph.", 100, -1, Integer.MAX_VALUE)); put("maxIndegree", new ParamDescription("Maximum indegree of graph", 100, 1, Integer.MAX_VALUE)); put("maxOutdegree", new ParamDescription("Maximum outdegree of graph", 100, 1, Integer.MAX_VALUE)); put("connected", new ParamDescription("Yes if graph should be connected", false)); put("sampleSize", new ParamDescription("Sample size", 1000, 1, Integer.MAX_VALUE)); put("numRuns", new ParamDescription("Number of runs", 1, 1, Integer.MAX_VALUE)); put("differentGraphs", new ParamDescription("Yes if a different graph should be used for each run", false)); put("alpha", new ParamDescription("Cutoff for p values (alpha)", 0.01, 0.0, 1.0)); put("penaltyDiscount", new ParamDescription("Penalty discount", 2.0, 0.0, Double.MAX_VALUE)); put("fgesDepth", new ParamDescription("Maximum number of new colliders", 1, 1, Integer.MAX_VALUE)); put("standardize", new ParamDescription("Yes if the data should be standardized", false)); put("measurementVariance", new ParamDescription("Additive measurement noise variance", 0.0, 0, Double.MAX_VALUE)); put("depth", new ParamDescription("Maximum size of conditioning set", -1, -1, Integer.MAX_VALUE)); put("coefLow", new ParamDescription("Low end of coefficient range", 0.5, 0.0, Double.MAX_VALUE)); put("coefHigh", new ParamDescription("High end of coefficient range", 1.5, 0.0, Double.MAX_VALUE)); put("covLow", new ParamDescription("Low end of covariance range", 0.5, 0.0, Double.MAX_VALUE)); put("covHigh", new ParamDescription("High end of covariance range", 1.5, 0.0, Double.MAX_VALUE)); put("varLow", new ParamDescription("Low end of variance range", 1.0, 0.0, Double.MAX_VALUE)); put("varHigh", new ParamDescription("High end of variance range", 3.0, 0.0, Double.MAX_VALUE)); put("printWinners", new ParamDescription("Yes if winning models should be printed", false)); put("printAverages", new ParamDescription("Yes if averages should be printed", false)); put("printAverageTables", new ParamDescription("Yes if average tables should be printed", true)); put("printGraphs", new ParamDescription("Yes if graphs should be printed", false)); put("dataType", new ParamDescription("Categorical or discrete", "categorical")); put("percentDiscrete", new ParamDescription("Percentage of discrete variables (0 - 100) for mixed data", 0.0, 0.0, 100.0)); put("ofInterestCutoff", new ParamDescription("Cutoff for graphs considered to be of interest", 0.05, 0.0, 1.0)); put("numCategories", new ParamDescription("Number of categories for discrete variables", 4, 2, Integer.MAX_VALUE)); put("minCategories", new ParamDescription("Minimum number of categories", 2, 2, Integer.MAX_VALUE)); put("maxCategories", new ParamDescription("Maximum number of categories", 2, 2, Integer.MAX_VALUE)); put("samplePrior", new ParamDescription("Sample prior", 1.0, 1.0, Double.MAX_VALUE)); put("structurePrior", new ParamDescription("Structure prior coefficient", 1.0, 1.0, Double.MAX_VALUE)); put("mgmParam1", new ParamDescription("MGM tuning parameter #1", 0.1, 0.0, Double.MAX_VALUE)); put("mgmParam2", new ParamDescription("MGM tuning parameter #2", 0.1, 0.0, Double.MAX_VALUE)); put("mgmParam3", new ParamDescription("MGM tuning parameter #3", 0.1, 0.0, Double.MAX_VALUE)); put("scaleFreeAlpha", new ParamDescription("For scale-free graphs, the parameter alpha", 0.05, 0.0, 1.0)); put("scaleFreeBeta", new ParamDescription("For scale-free graphs, the parameter beta", 0.9, 0.0, 1.0)); put("scaleFreeDeltaIn", new ParamDescription("For scale-free graphs, the parameter delta_in", 3, 0.0, Double.MAX_VALUE)); put("scaleFreeDeltaOut", new ParamDescription("For scale-free graphs, the parameter delta_out", 3, 0.0, Double.MAX_VALUE)); put("generalSemFunctionTemplateMeasured", new ParamDescription("General function template for measured variables", "TSUM(NEW(B)*$)")); put("generalSemFunctionTemplateLatent", new ParamDescription("General function template for latent variables", "TSUM(NEW(B)*$)")); put("generalSemErrorTemplate", new ParamDescription("General function for error terms", "Beta(2, 5)")); put("coefSymmetric", new ParamDescription("Yes if negative coefficient " + "values should be considered", true)); put("covSymmetric", new ParamDescription("Yes if negative covariance " + "values should be considered", true)); put("retainPreviousValues", new ParamDescription("Retain previous values", false)); // Boolean Glass parameters. put("lagGraphVarsPerInd", new ParamDescription("Number of variables per individual", 5, 1, Integer.MAX_VALUE)); put("lagGraphMlag", new ParamDescription("Maximum lag of graph", 1, 1, Integer.MAX_VALUE)); put("lagGraphIndegree", new ParamDescription("Indegree of graph", 2, 1, Integer.MAX_VALUE)); put("numDishes", new ParamDescription("Number of dishes", 1, 1, Integer.MAX_VALUE)); put("numCellsPerDish", new ParamDescription("Number of cells per dish", 10000, 1, Integer.MAX_VALUE)); put("stepsGenerated", new ParamDescription("Number of steps generated", 4, 1, Integer.MAX_VALUE)); put("firstStepStored", new ParamDescription("The index of the first step stored", 1, 1, Integer.MAX_VALUE)); put("interval", new ParamDescription("The interval between steps stored", 1, 1, Integer.MAX_VALUE)); put("rawDataSaved", new ParamDescription("Yes if the raw data should be saved (otherwise tossed)", false)); put("measuredDataSaved", new ParamDescription("Yes if the measured data should be saved (otherwise tossed)", true)); put("initSync", new ParamDescription("Yes if cells should be initialized synchronously, otherwise randomly", true)); put("antilogCalculated", new ParamDescription("Yes if antilogs of data should be calculated", false)); put("dishDishVariability", new ParamDescription("Dish to dish variability", 10.0, 0.0, Double.MAX_VALUE)); put("numChipsPerDish", new ParamDescription("Number of chips per dish", 4, 1, Integer.MAX_VALUE)); put("sampleSampleVariability", new ParamDescription("Sample to sample variability", 0.025, 0.0, Double.MAX_VALUE)); put("chipChipVariability", new ParamDescription("Chip to chip variability", 0.1, 0.0, Double.MAX_VALUE)); put("pixelDigitalization", new ParamDescription("Pixel digitalization", 0.025, 0.0, Double.MAX_VALUE)); put("includeDishAndChipColumns", new ParamDescription("Yes if Dish and Chip columns should be included in output", true)); put("numRuns", new ParamDescription("The number runs", 1)); put("randomSelectionSize", new ParamDescription("The number of datasets that should be taken in each random sample", 1)); put("maxit", new ParamDescription("MAXIT parameter (GLASSO)", 10000, 1, Integer.MAX_VALUE)); put("ia", new ParamDescription("IA parameter (GLASSO)", false)); put("is", new ParamDescription("IS parameter (GLASSO)", false)); put("itr", new ParamDescription("ITR parameter (GLASSO)", false)); put("ipen", new ParamDescription("IPEN parameter (GLASSO)", false)); put("thr", new ParamDescription("THR parameter (GLASSO)", 1e-4, 0.0, Double.MAX_VALUE)); put("targetName", new ParamDescription("Target name", "")); put("verbose", new ParamDescription("Yes if verbose output should be printed or logged", false)); put("faithfulnessAssumed", new ParamDescription("Yes if (one edge) faithfulness should be assumed", false)); put("useWishart", new ParamDescription("Yes if the Wishart test shoud be used. No if the Delta test should be used", false)); put("useGap", new ParamDescription("Yes if the GAP algorithms should be used. No if the SAG algorithm should be used", false)); // Multiple indicator random graphs put("numStructuralNodes", new ParamDescription("Number of structural nodes", 3)); put("numStructuralEdges", new ParamDescription("Number of structural edges", 3)); put("measurementModelDegree", new ParamDescription("Number of measurements per Latent", 5)); put("latentMeasuredImpureParents", new ParamDescription("Number of Latent --> Measured impure edges", 0)); put("measuredMeasuredImpureParents", new ParamDescription("Number of Measured --> Measured impure edges", 0)); put("measuredMeasuredImpureAssociations", new ParamDescription("Number of Measured <-> Measured impure edges", 0)); // put("useRuleC", new ParamDescription("Yes if rule C for CCD should be used", false)); put("applyR1", new ParamDescription("Yes if the orient away from arrow rule should be applied", true)); put("probCycle", new ParamDescription("The probability of adding a cycle to the graph", 1.0, 0.0, 1.0)); put("intervalBetweenShocks", new ParamDescription("Interval beween shocks (R. A. Fisher simulation model)", 10, 1, Integer.MAX_VALUE)); put("intervalBetweenRecordings", new ParamDescription( "Interval between data recordings for the linear Fisher model", 10, 1, Integer.MAX_VALUE)); put("skipNumRecords", new ParamDescription("Number of records that should be skipped between recordings", 0, 0, Integer.MAX_VALUE)); put("fisherEpsilon", new ParamDescription("Epsilon where |xi.t - xi.t-1| < epsilon, criterion for convergence", .001, Double.MIN_VALUE, Double.MAX_VALUE)); put("useMaxPOrientationHeuristic", new ParamDescription( "Yes if the heuristic for orienting unshielded colliders for max P should be used", true)); put("maxPOrientationMaxPathLength", new ParamDescription( "Maximum path length for the unshielded collider heuristic for max P", 3, 0, Integer.MAX_VALUE)); put("orientTowardDConnections", new ParamDescription( "Yes if Richardson's step C (orient toward d-connection) should be used", true)); put("orientVisibleFeedbackLoops", new ParamDescription( "Yes if visible feedback loops should be oriented", true)); put("doColliderOrientation", new ParamDescription( "Yes if unshielded collider orientation should be done", true)); put("completeRuleSetUsed", new ParamDescription( "Yes if the complete FCI rule set should be used", false)); put("maxDistinctValuesDiscrete", new ParamDescription( "The maximum number of distinct values in a column for discrete variables", 0, 0, Integer.MAX_VALUE)); put("ngAlpha", new ParamDescription( "Alpha for testing non-Gaussianity", 0.05, 0.0, 1.0)); put("twoCycleAlpha", new ParamDescription( "Alpha orienting 2-cycles", 1e-6, 0.0, 1.0)); put("symmetricFirstStep", new ParamDescription( "Yes if the first step step for FGES should do scoring for both X->Y and Y->X", false)); put("discretize", new ParamDescription( "Yes if continuous variables should be discretized when child is discrete", true)); put("determinismThreshold", new ParamDescription( "Threshold for judging a regression of a variable onto its parents to be deternimistic", 0.1, 0.0, Double.POSITIVE_INFINITY)); put("cgExact", new ParamDescription( "Yes if the exact algorithm should be used for continuous parents and discrete children", false)); put("numCategoriesToDiscretize", new ParamDescription( "The number of categories used to discretize continuous variables, if necessary", 3, 2, Integer.MAX_VALUE)); put("maxPathLength", new ParamDescription( "The maximum length for any discriminating path. -1 if unlimited", -1, -1, Integer.MAX_VALUE)); put("thresholdForReversing", new ParamDescription( "Variables with skewnesses less than this value will be reversed in sign", 0.0, Double.NEGATIVE_INFINITY, Double.POSITIVE_INFINITY)); } public static ParamDescriptions instance() { return instance; } public ParamDescription get(String name) { if (!map.containsKey(name)) { return new ParamDescription("Please add a description to ParamDescriptions for " + name, 0); // throw new IllegalArgumentException("Expecting a default value for " + name); } return map.get(name); } public void put(String name, ParamDescription paramDescription) { map.put(name, paramDescription); } }