///////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below.       //
// Copyright (C) 1998, 1999, 2000, 2001, 2002, 2003, 2004, 2005, 2006,       //
// 2007, 2008, 2009, 2010, 2014, 2015, 2022 by Peter Spirtes, Richard        //
// Scheines, Joseph Ramsey, and Clark Glymour.                               //
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package edu.cmu.tetrad.study.examples.conditions;

import edu.cmu.tetrad.algcomparison.Comparison;
import edu.cmu.tetrad.algcomparison.algorithm.Algorithms;
import edu.cmu.tetrad.algcomparison.algorithm.external.ExternalAlgorithmPcalgGes;
import edu.cmu.tetrad.algcomparison.algorithm.external.ExternalAlgorithmTetrad;
import edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Fges;
import edu.cmu.tetrad.algcomparison.score.SemBicScore;
import edu.cmu.tetrad.algcomparison.statistic.*;
import edu.cmu.tetrad.util.Parameters;

/**
 * An example script to load in data sets and graphs from files and analyze them. The
 * files loaded must be in the same format as
 * <p>
 * new Comparison().saveDataSetAndGraphs("comparison/save1", simulation, parameters);
 * <p>
 * saves them. For other formats, specialty data loaders can be written to implement the
 * Simulation interface.
 *
 * @author josephramsey
 */
public class Condition1 {
    public void generateTetradResults() {
        Parameters parameters = new Parameters();

        parameters.set("alpha", 0.001);
        parameters.set("numRuns", 10);
//        parameters.set("penaltyDiscount", 4);
        parameters.set("useMaxPOrientationHeuristic", true);
        parameters.set("maxPOrientationMaxPathLength", 3);

        Statistics statistics = new Statistics();

        statistics.add(new ParameterColumn("numMeasures"));
        statistics.add(new ParameterColumn("avgDegree"));
        statistics.add(new ParameterColumn("sampleSize"));
        statistics.add(new AdjacencyPrecision());
        statistics.add(new AdjacencyRecall());
        statistics.add(new ArrowheadPrecision());
        statistics.add(new ArrowheadRecall());
        statistics.add(new ElapsedCpuTime());

        statistics.setWeight("AP", 1.0);
        statistics.setWeight("AR", 0.5);
        statistics.setWeight("AHP", 1.0);
        statistics.setWeight("AHR", 0.5);

        Algorithms algorithms = new Algorithms();

        Comparison comparison = new Comparison();
        comparison.setShowAlgorithmIndices(true);
        comparison.setShowSimulationIndices(true);
        comparison.setSortByUtility(false);
        comparison.setShowUtilities(true);
        comparison.setSaveGraphs(true);

        parameters.set("penaltyDiscount", 4);
//
        algorithms.add(new Fges(new SemBicScore()));

        comparison.compareFromFiles("/Users/user/comparison-data/condition_1",
                "/Users/user/causal-comparisons/condition_1",
                algorithms, statistics, parameters);
    }

    public void compileTable() {
        Parameters parameters = new Parameters();

        parameters.set("numRuns", 10);

        Statistics statistics = new Statistics();

        statistics.add(new ParameterColumn("numMeasures"));
        statistics.add(new ParameterColumn("avgDegree"));
        statistics.add(new ParameterColumn("sampleSize"));
        statistics.add(new AdjacencyPrecision());
        statistics.add(new AdjacencyRecall());
        statistics.add(new ArrowheadPrecision());
        statistics.add(new ArrowheadRecall());
        statistics.add(new F1Adj());
        statistics.add(new F1Arrow());
        statistics.add(new F1All());
        statistics.add(new ElapsedCpuTime());

        statistics.setWeight("AP", 1.0);
        statistics.setWeight("AR", 0.5);
        statistics.setWeight("AHP", 1.0);
        statistics.setWeight("AHR", 0.5);

        Algorithms algorithms = new Algorithms();

        algorithms.add(new ExternalAlgorithmTetrad("FGES_(Fast_Greedy_Equivalence_Search)_using_Sem_BIC_Score,_penaltyDiscount_=_1"));
        algorithms.add(new ExternalAlgorithmTetrad("FGES_(Fast_Greedy_Equivalence_Search)_using_Sem_BIC_Score,_penaltyDiscount_=_2"));
        algorithms.add(new ExternalAlgorithmTetrad("FGES_(Fast_Greedy_Equivalence_Search)_using_Sem_BIC_Score,_penaltyDiscount_=_4"));

        algorithms.add(new ExternalAlgorithmPcalgGes("GES_pcalg_defaults_1.0*log(nrow(data)"));
        algorithms.add(new ExternalAlgorithmPcalgGes("GES_pcalg_defaults_2.0*log(nrow(data)"));

        Comparison comparison = new Comparison();
        comparison.setShowAlgorithmIndices(true);
        comparison.setShowSimulationIndices(true);
        comparison.setSortByUtility(false);
        comparison.setShowUtilities(false);
        comparison.setSaveGraphs(true);
        comparison.setComparisonGraph(Comparison.ComparisonGraph.CPDAG_of_the_true_DAG);

        comparison.generateReportFromExternalAlgorithms("/Users/user/comparison-data/condition_1",
                "/Users/user/causal-comparisons/condition_1",
                algorithms, statistics, parameters);

    }

    public static void main(String... args) {
        new Condition1().compileTable();
    }
}




