Java Code Examples for org.apache.commons.math3.stat.regression.OLSMultipleLinearRegression#newSampleData()

/**
 * Implements ordinary least squares (OLS) to estimate the parameters of a 
 * multiple linear regression model.
 * @param y Y sample data - one dimension array
 * @param x X sample data - two dimension array
 * @param noIntercept No intercept
 * @return Estimated regression parameters and residuals
 */
public static Array[] multipleLineRegress_OLS(Array y, Array x, boolean noIntercept) {
    OLSMultipleLinearRegression regression = new OLSMultipleLinearRegression();
    regression.setNoIntercept(noIntercept);
    double[] yy = (double[])ArrayUtil.copyToNDJavaArray_Double(y);
    double[][] xx = (double[][])ArrayUtil.copyToNDJavaArray_Double(x);
    regression.newSampleData(yy, xx);
    double[] para = regression.estimateRegressionParameters();
    double[] residuals = regression.estimateResiduals();
    int k = para.length;
    int n = residuals.length;
    Array aPara = Array.factory(DataType.DOUBLE, new int[]{k});
    Array aResiduals = Array.factory(DataType.DOUBLE, new int[]{n});
    for (int i = 0; i < k; i++){
        aPara.setDouble(i, para[i]);
    }
    for (int i = 0; i < k; i++){
        aResiduals.setDouble(i, residuals[i]);
    }
    
    return new Array[]{aPara, aResiduals};
}
 

@Test(dataProvider = "thresholds")
public void testMLR(double threshold) {
    final Range<String> rowKeys = Range.of(0, 5000).map(i -> "R" + i);
    final DataFrame<String,String> frame = DataFrame.of(rowKeys, String.class, columns -> {
        columns.add("Y", Double.class).applyDoubles(v -> v.rowOrdinal() + 1d + (Math.random() * 2));
        columns.add("X1", Double.class).applyDoubles(v -> v.rowOrdinal() + 1d + (Math.random() * 3));
        columns.add("X2", Double.class).applyDoubles(v -> v.rowOrdinal() + 1d + (Math.random() * 4));
        columns.add("X3", Double.class).applyDoubles(v -> v.rowOrdinal() + 1d + (Math.random() * 5));
        columns.add("X4", Double.class).applyDoubles(v -> v.rowOrdinal() + 1d + (Math.random() * 6));
    });

    final OLSMultipleLinearRegression model = new OLSMultipleLinearRegression(threshold);
    final double[] dependent = frame.col("Y").toDoubleStream().toArray();
    final double[][] independent = new double[frame.rows().count()][3];
    frame.rows().forEach(row -> {
        independent[row.ordinal()][0] = row.getDouble("X1");
        independent[row.ordinal()][1] = row.getDouble("X2");
        independent[row.ordinal()][2] = row.getDouble("X3");
    });
    model.newSampleData(dependent, independent);
    frame.regress().ols("Y", Arrays.asList("X1", "X2", "X3"), true, mlr -> {
        System.out.println(mlr);
        assertResultsMatch(mlr, model);
        return Optional.empty();
    });
}
 

@Override
public void setValues(double[] y, double[] x) {
    if (x.length != y.length) {
        throw new IllegalArgumentException(String.format("The numbers of y and x values must be equal (%d != %d)", y.length, x.length));
    }
    double[][] xData = new double[x.length][];
    for (int i = 0; i < x.length; i++) {
        // the implementation determines how to produce a vector of predictors from a single x
        xData[i] = xVector(x[i]);
    }
    if (logY()) { // in some models we are predicting ln y, so we replace each y with ln y
        y = Arrays.copyOf(y, y.length); // user might not be finished with the array we were given
        for (int i = 0; i < x.length; i++) {
            y[i] = Math.log(y[i]);
        }
    }
    final OLSMultipleLinearRegression ols = new OLSMultipleLinearRegression();
    ols.setNoIntercept(true); // let the implementation include a constant in xVector if desired
    ols.newSampleData(y, xData); // provide the data to the model
    coef = MatrixUtils.createColumnRealMatrix(ols.estimateRegressionParameters()); // get our coefs
    last_error_rate = ols.estimateErrorVariance();
    Log.d(TAG, getClass().getSimpleName() + " Forecast Error rate: errorvar:"
            + JoH.qs(last_error_rate, 4)
            + " regssionvar:" + JoH.qs(ols.estimateRegressandVariance(), 4)
            + "  stderror:" + JoH.qs(ols.estimateRegressionStandardError(), 4));
}
 

@Override
public void setValues(double[] y, double[] x) {
    if (x.length != y.length) {
        throw new IllegalArgumentException(String.format("The numbers of y and x values must be equal (%d != %d)", y.length, x.length));
    }
    double[][] xData = new double[x.length][];
    for (int i = 0; i < x.length; i++) {
        // the implementation determines how to produce a vector of predictors from a single x
        xData[i] = xVector(x[i]);
    }
    if (logY()) { // in some models we are predicting ln y, so we replace each y with ln y
        y = Arrays.copyOf(y, y.length); // user might not be finished with the array we were given
        for (int i = 0; i < x.length; i++) {
            y[i] = Math.log(y[i]);
        }
    }
    final OLSMultipleLinearRegression ols = new OLSMultipleLinearRegression();
    ols.setNoIntercept(true); // let the implementation include a constant in xVector if desired
    ols.newSampleData(y, xData); // provide the data to the model
    coef = MatrixUtils.createColumnRealMatrix(ols.estimateRegressionParameters()); // get our coefs
    last_error_rate = ols.estimateErrorVariance();
    Log.d(TAG, getClass().getSimpleName() + " Forecast Error rate: errorvar:"
            + JoH.qs(last_error_rate, 4)
            + " regssionvar:" + JoH.qs(ols.estimateRegressandVariance(), 4)
            + "  stderror:" + JoH.qs(ols.estimateRegressionStandardError(), 4));
}
 

@Override
public void setValues(double[] y, double[] x) {
    if (x.length != y.length) {
        throw new IllegalArgumentException(String.format("The numbers of y and x values must be equal (%d != %d)", y.length, x.length));
    }
    double[][] xData = new double[x.length][];
    for (int i = 0; i < x.length; i++) {
        // the implementation determines how to produce a vector of predictors from a single x
        xData[i] = xVector(x[i]);
    }
    if (logY()) { // in some models we are predicting ln y, so we replace each y with ln y
        y = Arrays.copyOf(y, y.length); // user might not be finished with the array we were given
        for (int i = 0; i < x.length; i++) {
            y[i] = Math.log(y[i]);
        }
    }
    final OLSMultipleLinearRegression ols = new OLSMultipleLinearRegression();
    ols.setNoIntercept(true); // let the implementation include a constant in xVector if desired
    ols.newSampleData(y, xData); // provide the data to the model
    coef = MatrixUtils.createColumnRealMatrix(ols.estimateRegressionParameters()); // get our coefs
    last_error_rate = ols.estimateErrorVariance();
    Log.d(TAG, getClass().getSimpleName() + " Forecast Error rate: errorvar:"
            + JoH.qs(last_error_rate, 4)
            + " regssionvar:" + JoH.qs(ols.estimateRegressandVariance(), 4)
            + "  stderror:" + JoH.qs(ols.estimateRegressionStandardError(), 4));
}
 

@Override
public void setValues(double[] y, double[] x) {
    if (x.length != y.length) {
        throw new IllegalArgumentException(String.format("The numbers of y and x values must be equal (%d != %d)", y.length, x.length));
    }
    double[][] xData = new double[x.length][];
    for (int i = 0; i < x.length; i++) {
        // the implementation determines how to produce a vector of predictors from a single x
        xData[i] = xVector(x[i]);
    }
    if (logY()) { // in some models we are predicting ln y, so we replace each y with ln y
        y = Arrays.copyOf(y, y.length); // user might not be finished with the array we were given
        for (int i = 0; i < x.length; i++) {
            y[i] = Math.log(y[i]);
        }
    }
    final OLSMultipleLinearRegression ols = new OLSMultipleLinearRegression();
    ols.setNoIntercept(true); // let the implementation include a constant in xVector if desired
    ols.newSampleData(y, xData); // provide the data to the model
    coef = MatrixUtils.createColumnRealMatrix(ols.estimateRegressionParameters()); // get our coefs
    last_error_rate = ols.estimateErrorVariance();
    Log.d(TAG, getClass().getSimpleName() + " Forecast Error rate: errorvar:"
            + JoH.qs(last_error_rate, 4)
            + " regssionvar:" + JoH.qs(ols.estimateRegressandVariance(), 4)
            + "  stderror:" + JoH.qs(ols.estimateRegressionStandardError(), 4));
}
 

@Override
public void setValues( double[] y, double[] x ) {
    if (x.length != y.length) {
        throw new IllegalArgumentException(
                String.format("The numbers of y and x values must be equal (%d != %d)", y.length, x.length));
    }
    double[][] xData = new double[x.length][];
    for( int i = 0; i < x.length; i++ ) {
        // the implementation determines how to produce a vector of predictors from a single x
        xData[i] = xVector(x[i]);
    }
    if (logY()) { // in some models we are predicting ln y, so we replace each y with ln y
        y = Arrays.copyOf(y, y.length); // user might not be finished with the array we were
                                        // given
        for( int i = 0; i < x.length; i++ ) {
            y[i] = Math.log(y[i]);
        }
    }
    ols = new OLSMultipleLinearRegression();
    ols.setNoIntercept(true); // let the implementation include a constant in xVector if desired
    ols.newSampleData(y, xData); // provide the data to the model
    coef = MatrixUtils.createColumnRealMatrix(ols.estimateRegressionParameters());
}
 

public void calculateSumOfSquaresOLS(double[] expressionValues) throws IOException, IllegalAccessException {
	// OLS = Ordinary Least Squares
	OLSMultipleLinearRegression regression = new OLSMultipleLinearRegression();
	// if GetIntercept is false, remove the intercept (Beta1) from the linear model
	regression.setNoIntercept(true);
	try{
		regression.newSampleData(expressionValues, this.getObservedValues());
	}
	catch (DimensionMismatchException e){
		DeconvolutionLogger.log.info(String.format("Length of expression and genotype data not the same\nexpression length: %d\nobserved values length: %d\n", 
				expressionValues.length, this.getNumberOfTerms()));
		throw(e);
	}
	this.setSumOfSquares(regression.calculateResidualSumOfSquares());
	this.setDegreesOfFreedom(expressionValues.length - (this.getNumberOfTerms() + 1));
	setResiduals(regression.estimateResiduals());
	setEstimatedRegressionParameters(regression.estimateRegressionParameters());
}
 

@Override
    public void setValues(Array y, Array x) {
        if (x.getSize() != y.getSize()) {
            throw new IllegalArgumentException(String.format("The numbers of y and x values must be equal (%d != %d)",y.getSize(),x.getSize()));
        }

        y = y.copyIfView();
        x = x.copyIfView();

        double[][] xData = new double[(int)x.getSize()][];
        for (int i = 0; i < x.getSize(); i++) {
            // the implementation determines how to produce a vector of predictors from a single x
            xData[i] = xVector(x.getDouble(i));
        }
        double[] yy = new double[(int)y.getSize()];
        if(logY()) { // in some models we are predicting ln y, so we replace each y with ln y
            for (int i = 0; i < yy.length; i++) {
                if (i < x.getSize())
                    yy[i] = Math.log(y.getDouble(i));
                else
                    yy[i] = y.getDouble(i);
            }
        } else {
            for (int i = 0; i < yy.length; i++) {
                yy[i] = y.getDouble(i);
            }
        }
//        double[] yy = (double[])y.copyTo1DJavaArray();
//        if(logY()) { // in some models we are predicting ln y, so we replace each y with ln y
//            yy = Arrays.copyOf(yy, yy.length); // user might not be finished with the array we were given
//            for (int i = 0; i < x.getSize(); i++) {
//                yy[i] = Math.log(yy[i]);
//            }
//        }
        OLSMultipleLinearRegression ols = new OLSMultipleLinearRegression();
        ols.setNoIntercept(true); // let the implementation include a constant in xVector if desired
        ols.newSampleData(yy, xData); // provide the data to the model
        coef = MatrixUtils.createColumnRealMatrix(ols.estimateRegressionParameters()); // get our coefs
        rs = ols.calculateRSquared();
    }
 

/**
 * Trigger the calculation of the model parameters.
 * @return True if the parameters are generated, otherwise false;
 */
public synchronized boolean updateModelCoefficient() {
  if (validBuckets().size() < MIN_CPU_UTIL_OBSERVATION_BUCKETS) {
    return false;
  }
  try {
    OLSMultipleLinearRegression regression = new OLSMultipleLinearRegression();
    regression.setNoIntercept(true);
    boolean ignoreLeaderBytesOut = !isLeaderBytesInAndOutRatioDiverseEnough();
    regression.newSampleData(aggregateSampleCpuUtilData(),
                             aggregateSampleBytesRateData(ignoreLeaderBytesOut));
    double[] parameters = regression.estimateRegressionParameters();
    int leaderBytesInIndex = 0;
    int leaderBytesOutIndex = 1;
    int followerBytesInIndex = ignoreLeaderBytesOut ? 1 : 2;
    _coefficients.put(ModelCoefficient.LEADER_BYTES_IN, parameters[leaderBytesInIndex]);
    if (!ignoreLeaderBytesOut) {
      _coefficients.put(ModelCoefficient.LEADER_BYTES_OUT, parameters[leaderBytesOutIndex]);
    }
    _coefficients.put(ModelCoefficient.FOLLOWER_BYTES_IN, parameters[followerBytesInIndex]);

    LOG.info("Coefficient generated: leader_bytes_in: {}, leader_bytes_out: {}, follower_bytes_in: {}",
             _coefficients.get(ModelCoefficient.LEADER_BYTES_IN),
             _coefficients.get(ModelCoefficient.LEADER_BYTES_OUT),
             _coefficients.get(ModelCoefficient.FOLLOWER_BYTES_IN));
    return true;
  } catch (Exception e) {
    LOG.warn("received exception {}", e);
  }
  return false;
}
 

public void calculateOlsRegression(double[][] x, double[] y){
	OLSMultipleLinearRegression regression = new OLSMultipleLinearRegression();
	regression.newSampleData(y, x);
	
	double[] beta = regression.estimateRegressionParameters();       
	double[] residuals = regression.estimateResiduals();
	double[][] parametersVariance = regression.estimateRegressionParametersVariance();
	double regressandVariance = regression.estimateRegressandVariance();
	double rSquared = regression.calculateRSquared();
	double sigma = regression.estimateRegressionStandardError();
}
 

/**
 * @return Linear regression model state.
 */
public synchronized LinearRegressionModelState modelState() {
  Map<Integer, Double> detailCompleteness = new HashMap<>();
  for (Map.Entry<Integer, AtomicInteger> entry : INDICES.entrySet()) {
    detailCompleteness.put(entry.getKey(),
                           Math.min((double) entry.getValue().get() / NUM_OBSERVATIONS_PER_UTIL_BUCKET, 1.0));
  }
  Map<Integer, Integer> usedLeaderToFollowerRatio = new HashMap<>();
  Map<Integer, Integer> usedLeaderBytesInToBytesOutRatio = new HashMap<>();
  Map<ModelCoefficient, Double> coefficientFromAvailableData = new HashMap<>(_coefficients);
  OLSMultipleLinearRegression regression = new OLSMultipleLinearRegression();
  regression.setNoIntercept(true);
  boolean ignoreLeaderBytesOutRate = !isLeaderBytesInAndOutRatioDiverseEnough();
  double[][] sampleBytesRateData = aggregateSampleBytesRateData(ignoreLeaderBytesOutRate);

  int leaderBytesInIndex = 0;
  int leaderBytesOutIndex = 1;
  int followerBytesInIndex = ignoreLeaderBytesOutRate ? 1 : 2;
  for (int i = 0; i < sampleBytesRateData.length; i++) {
    int leaderToFollowerRatio = sampleBytesRateData[i][followerBytesInIndex] == 0.0 ? 10000000 :
        (int) ((sampleBytesRateData[i][leaderBytesInIndex] / sampleBytesRateData[i][followerBytesInIndex]) * 10);
    int count = usedLeaderToFollowerRatio.getOrDefault(leaderToFollowerRatio, 0);
    usedLeaderToFollowerRatio.put(leaderToFollowerRatio, count + 1);

    if (!ignoreLeaderBytesOutRate) {
      int leaderBytesInToBytesOutRatio = sampleBytesRateData[i][leaderBytesOutIndex] == 0.0 ? 10000000 :
          (int) ((sampleBytesRateData[i][leaderBytesInIndex] / sampleBytesRateData[i][leaderBytesOutIndex]) * 10);
      count = usedLeaderBytesInToBytesOutRatio.getOrDefault(leaderBytesInToBytesOutRatio, 0);
      usedLeaderBytesInToBytesOutRatio.put(leaderBytesInToBytesOutRatio, count + 1);
    }
  }
  regression.newSampleData(aggregateSampleCpuUtilData(), sampleBytesRateData);
  double[] parameters = regression.estimateRegressionParameters();
  coefficientFromAvailableData.put(ModelCoefficient.LEADER_BYTES_IN, parameters[leaderBytesInIndex]);
  if (ignoreLeaderBytesOutRate) {
    coefficientFromAvailableData.put(ModelCoefficient.FOLLOWER_BYTES_IN, parameters[followerBytesInIndex]);
  } else {
    coefficientFromAvailableData.put(ModelCoefficient.LEADER_BYTES_OUT, parameters[leaderBytesOutIndex]);
    coefficientFromAvailableData.put(ModelCoefficient.FOLLOWER_BYTES_IN, parameters[followerBytesInIndex]);
  }
  return new LinearRegressionModelState(detailCompleteness, coefficientFromAvailableData,
                                        OBSERVED_LEADER_TO_FOLLOWER_BYTES_RATIO,
                                        OBSERVED_LEADER_BYTES_IN_TO_BYTES_OUT_RATIO,
                                        usedLeaderToFollowerRatio, usedLeaderBytesInToBytesOutRatio,
                                        CPU_UTIL_ESTIMATION_ERROR_STATS);
}
 

public static void main(String[] args) {
    OLSMultipleLinearRegression mlr = new OLSMultipleLinearRegression();
    mlr.newSampleData(y, x);
    double[] b = mlr.estimateRegressionParameters();
    printResults(b);
}
 

protected MultipleLinearRegression regress(double[][] observations, double[] outcomes) {
  OLSMultipleLinearRegression olsMultipleLinearRegression = new OLSMultipleLinearRegression();
  olsMultipleLinearRegression.newSampleData(outcomes, observations);
  return olsMultipleLinearRegression;
}
 

public DoubleMatrixDataset<String, String> vifCorrect(DoubleMatrixDataset<String, String> finalCovariates, double threshold) throws Exception {

		System.out.println("VIF: " + finalCovariates.rows() + " x " + finalCovariates.columns());

		// determine variance inflation factor
		System.out.println("Checking variance inflation factor...");
		HashSet<Integer> skipCol = new HashSet<>();
		boolean inflated = true;
		int iter = 0;
		while (inflated) {
			skipCol = new HashSet<>();

			for (int col = 0; col < finalCovariates.columns(); col++) {
				OLSMultipleLinearRegression ols = new OLSMultipleLinearRegression();
				double[] y = finalCovariates.getCol(col).toArray(); //[row];
				// check if variance is >0
				double[][] otherCovariates = new double[finalCovariates.rows()][finalCovariates.columns() - 1];
				int colctr = 0;
				for (int col2 = 0; col2 < finalCovariates.columns(); col2++) {
					if (col != col2) {
						for (int row = 0; row < finalCovariates.rows(); row++) {
							otherCovariates[row][colctr] = finalCovariates.getElementQuick(row, col2);
						}
						colctr++;
					}
				}
				ols.newSampleData(y, otherCovariates);

				double rsq = ols.calculateRSquared();
				double vif = 1 / (1 - rsq);
				boolean alias = false;

				if (rsq > threshold) {
					alias = true;
					skipCol.add(col);
					System.out.println("Iteration: " + iter + "\tCovariate: " + finalCovariates.getColObjects().get(col) + "\tRSq: " + rsq + "\tVIF: " + vif + "\tAliased: " + alias);
					break;
				} else {
					System.out.println("Iteration: " + iter + "\tCovariate: " + finalCovariates.getColObjects().get(col) + "\tRSq: " + rsq + "\tVIF: " + vif + "\tAliased: " + alias);
				}
			}

			if (skipCol.isEmpty()) {
				System.out.println("There are no more collinear covariates.");
				inflated = false;
			} else {
				finalCovariates = excludeCols(finalCovariates, skipCol);
				inflated = true;
			}
			iter++;


		}

		return finalCovariates;
	}