| org.apache.commons.math3.analysis.FunctionUtils.add(DifferentiableUnivariateFunction...) | 
| org.apache.commons.math3.util.ArithmeticUtils.binomialCoefficient(int, int) | 
| org.apache.commons.math3.util.ArithmeticUtils.binomialCoefficientDouble(int, int) | 
| org.apache.commons.math3.util.ArithmeticUtils.binomialCoefficientLog(int, int) | 
| org.apache.commons.math3.linear.AbstractFieldMatrix.buildArray(Field, int) | 
| org.apache.commons.math3.linear.AbstractFieldMatrix.buildArray(Field, int, int) | 
| org.apache.commons.math3.util.ResizableDoubleArray.checkContractExpand(float, float) | 
| org.apache.commons.math3.analysis.FunctionUtils.compose(DifferentiableUnivariateFunction...) | 
| org.apache.commons.math3.stat.descriptive.rank.Percentile.copy(Percentile, Percentile) | 
| org.apache.commons.math3.distribution.LogNormalDistribution.cumulativeProbability(double, double) | 
| org.apache.commons.math3.distribution.NormalDistribution.cumulativeProbability(double, double) | 
| org.apache.commons.math3.distribution.ParetoDistribution.cumulativeProbability(double, double) | 
| org.apache.commons.math3.distribution.RealDistribution.cumulativeProbability(double, double) As of 3.1. In 4.0, this method will be renamed
 probability(double x0, double x1). | 
| org.apache.commons.math3.distribution.AbstractRealDistribution.cumulativeProbability(double, double) | 
| org.apache.commons.math3.analysis.function.Inverse.derivative() | 
| org.apache.commons.math3.analysis.function.Power.derivative() | 
| org.apache.commons.math3.analysis.function.Cbrt.derivative() | 
| org.apache.commons.math3.analysis.function.Cos.derivative() | 
| org.apache.commons.math3.analysis.function.Asinh.derivative() | 
| org.apache.commons.math3.analysis.function.Minus.derivative() | 
| org.apache.commons.math3.analysis.function.Log1p.derivative() | 
| org.apache.commons.math3.analysis.function.Tanh.derivative() | 
| org.apache.commons.math3.analysis.function.Expm1.derivative() | 
| org.apache.commons.math3.analysis.function.Identity.derivative() | 
| org.apache.commons.math3.analysis.function.Log10.derivative() | 
| org.apache.commons.math3.analysis.function.Logit.derivative() | 
| org.apache.commons.math3.analysis.function.Asin.derivative() | 
| org.apache.commons.math3.analysis.function.Atanh.derivative() | 
| org.apache.commons.math3.analysis.function.Logistic.derivative() | 
| org.apache.commons.math3.analysis.function.Tan.derivative() | 
| org.apache.commons.math3.analysis.function.HarmonicOscillator.derivative() | 
| org.apache.commons.math3.analysis.function.Acos.derivative() | 
| org.apache.commons.math3.analysis.function.Sigmoid.derivative() | 
| org.apache.commons.math3.analysis.function.Cosh.derivative() | 
| org.apache.commons.math3.analysis.function.Sinh.derivative() | 
| org.apache.commons.math3.analysis.function.Sqrt.derivative() | 
| org.apache.commons.math3.analysis.function.Gaussian.derivative() | 
| org.apache.commons.math3.analysis.function.Sin.derivative() | 
| org.apache.commons.math3.analysis.function.Atan.derivative() | 
| org.apache.commons.math3.analysis.function.Constant.derivative() | 
| org.apache.commons.math3.analysis.function.Exp.derivative() | 
| org.apache.commons.math3.analysis.function.Log.derivative() | 
| org.apache.commons.math3.analysis.function.Acosh.derivative() | 
| org.apache.commons.math3.analysis.function.Sinc.derivative() | 
| org.apache.commons.math3.geometry.euclidean.oned.Vector1D.distance(Vector) | 
| org.apache.commons.math3.linear.OpenMapRealVector.dotProduct(OpenMapRealVector) as of 3.1 (to be removed in 4.0). The computation is
 performed by the parent class. The method must be kept to maintain
 backwards compatibility. | 
| org.apache.commons.math3.util.ArithmeticUtils.factorial(int) | 
| org.apache.commons.math3.util.ArithmeticUtils.factorialDouble(int) | 
| org.apache.commons.math3.util.ArithmeticUtils.factorialLog(int) | 
| org.apache.commons.math3.optimization.fitting.PolynomialFitter.fit() | 
| org.apache.commons.math3.distribution.GammaDistribution.getAlpha() | 
| org.apache.commons.math3.geometry.euclidean.threed.FieldRotation.getAngles(RotationOrder) | 
| org.apache.commons.math3.geometry.euclidean.threed.Rotation.getAngles(RotationOrder) | 
| org.apache.commons.math3.geometry.euclidean.threed.FieldRotation.getAxis() | 
| org.apache.commons.math3.geometry.euclidean.threed.Rotation.getAxis() | 
| org.apache.commons.math3.distribution.GammaDistribution.getBeta() | 
| org.apache.commons.math3.geometry.partitioning.BSPTree.getCell(Vector ) | 
| org.apache.commons.math3.util.ResizableDoubleArray.getContractionCriteria() | 
| org.apache.commons.math3.optimization.general.AbstractLeastSquaresOptimizer.getCovariances() | 
| org.apache.commons.math3.optimization.general.AbstractLeastSquaresOptimizer.getCovariances(double) | 
| org.apache.commons.math3.linear.FieldVector.getData() | 
| org.apache.commons.math3.linear.SparseFieldVector.getData() | 
| org.apache.commons.math3.ode.AbstractIntegrator.getEvaluationsCounter() | 
| org.apache.commons.math3.util.ResizableDoubleArray.getExpansionFactor() As of 3.1. Return type will be changed to "double" in 4.0. | 
| org.apache.commons.math3.util.ResizableDoubleArray.getExpansionMode() | 
| org.apache.commons.math3.util.ResizableDoubleArray.getInternalValues() As of 3.1. | 
| org.apache.commons.math3.geometry.euclidean.oned.Interval.getLength() | 
| org.apache.commons.math3.geometry.euclidean.oned.Interval.getLower() | 
| org.apache.commons.math3.geometry.euclidean.oned.Interval.getMidPoint() | 
| org.apache.commons.math3.ode.nonstiff.AdamsNordsieckTransformer.getNSteps() as of 3.6, this method is not used anymore | 
| org.apache.commons.math3.optimization.direct.BaseAbstractMultivariateVectorOptimizer.getTargetRef() As of 3.1. | 
| org.apache.commons.math3.geometry.euclidean.twod.Line.getTransform(AffineTransform) | 
| org.apache.commons.math3.geometry.euclidean.oned.Interval.getUpper() | 
| org.apache.commons.math3.optimization.direct.BaseAbstractMultivariateVectorOptimizer.getWeightRef() As of 3.1. | 
| org.apache.commons.math3.optimization.general.AbstractLeastSquaresOptimizer.guessParametersErrors() | 
| org.apache.commons.math3.geometry.partitioning.BSPTree.insertInTree(BSPTree , boolean) | 
| org.apache.commons.math3.distribution.RealDistribution.isSupportLowerBoundInclusive() to be removed in 4.0 | 
| org.apache.commons.math3.distribution.RealDistribution.isSupportUpperBoundInclusive() to be removed in 4.0 | 
| org.apache.commons.math3.analysis.solvers.LaguerreSolver.laguerre(double, double, double, double) This method should not be part of the public API: It will
 be made private in version 4.0. | 
| org.apache.commons.math3.dfp.Dfp.log10() as of 3.2, replaced by Dfp.intLog10(), in 4.0 the return type
  will be changed to Dfp | 
| org.apache.commons.math3.special.Beta.logBeta(double, double, double, int) as of version 3.1, this method is deprecated as the
 computation of the beta function is no longer iterative; it will be
 removed in version 4.0. Current implementation of this method
 internally calls Beta.logBeta(double, double). | 
| org.apache.commons.math3.transform.FastFourierTransformer.mdfft(Object, TransformType) see MATH-736 | 
| org.apache.commons.math3.analysis.FunctionUtils.multiply(DifferentiableUnivariateFunction...) | 
| org.apache.commons.math3.random.RandomDataImpl.nextInversionDeviate(IntegerDistribution) use the distribution's sample() method | 
| org.apache.commons.math3.random.RandomDataImpl.nextInversionDeviate(RealDistribution) use the distribution's sample() method | 
| org.apache.commons.math3.optimization.general.AbstractLeastSquaresOptimizer.optimize(int, DifferentiableMultivariateVectorFunction, double[], double[], double[]) | 
| org.apache.commons.math3.optimization.BaseMultivariateVectorOptimizer.optimize(int, FUNC, double[], double[], double[]) As of 3.1. In 4.0, this will be replaced by the declaration
 corresponding to this method. | 
| org.apache.commons.math3.optimization.direct.BaseAbstractMultivariateVectorOptimizer.optimize(int, FUNC, double[], double[], double[]) | 
| org.apache.commons.math3.optimization.BaseMultivariateOptimizer.optimize(int, FUNC, GoalType, double[]) As of 3.1. In 4.0, it will be replaced by the declaration
 corresponding to this method. | 
| org.apache.commons.math3.optimization.direct.BaseAbstractMultivariateOptimizer.optimize(int, FUNC, GoalType, double[]) | 
| org.apache.commons.math3.optimization.general.AbstractLeastSquaresOptimizer.optimize(int, MultivariateDifferentiableVectorFunction, double[], double[], double[]) | 
| org.apache.commons.math3.optimization.direct.BaseAbstractMultivariateVectorOptimizer.optimizeInternal(int, FUNC, double[], double[], double[]) | 
| org.apache.commons.math3.optimization.direct.BaseAbstractMultivariateOptimizer.optimizeInternal(int, FUNC, GoalType, double[]) | 
| org.apache.commons.math3.optimization.general.AbstractDifferentiableOptimizer.optimizeInternal(int, MultivariateDifferentiableFunction, GoalType, double[]) | 
| org.apache.commons.math3.optimization.general.AbstractLeastSquaresOptimizer.optimizeInternal(int, MultivariateDifferentiableVectorFunction, OptimizationData...) As of 3.1. Override is necessary only until this class's generic
 argument is changed to MultivariateDifferentiableVectorFunction. | 
| org.apache.commons.math3.util.ArithmeticUtils.pow(int, long) | 
| org.apache.commons.math3.util.ArithmeticUtils.pow(long, long) | 
| org.apache.commons.math3.genetics.ListPopulation.setChromosomes(List) | 
| org.apache.commons.math3.util.ResizableDoubleArray.setContractionCriteria(float) As of 3.1 (to be removed in 4.0 as field will become "final"). | 
| org.apache.commons.math3.util.ResizableDoubleArray.setExpansionFactor(float) As of 3.1 (to be removed in 4.0 as field will become "final"). | 
| org.apache.commons.math3.util.ResizableDoubleArray.setExpansionMode(int) | 
| org.apache.commons.math3.util.ResizableDoubleArray.setExpansionMode(ResizableDoubleArray.ExpansionMode) As of 3.1 (to be removed in 4.0 as field will become "final"). | 
| org.apache.commons.math3.util.ResizableDoubleArray.setInitialCapacity(int) As of 3.1, this is a no-op. | 
| org.apache.commons.math3.optimization.direct.SimplexOptimizer.setSimplex(AbstractSimplex) | 
| org.apache.commons.math3.geometry.spherical.oned.ArcsSet.side(Arc) | 
| org.apache.commons.math3.geometry.partitioning.AbstractSubHyperplane.side(Hyperplane ) | 
| org.apache.commons.math3.geometry.partitioning.Region.side(Hyperplane )as of 3.6, this method which was only intended for
 internal use is not used anymore | 
| org.apache.commons.math3.geometry.partitioning.SubHyperplane.side(Hyperplane ) | 
| org.apache.commons.math3.geometry.partitioning.AbstractRegion.side(Hyperplane ) | 
| org.apache.commons.math3.util.ResizableDoubleArray.start() As of 3.1. | 
| org.apache.commons.math3.util.ArithmeticUtils.stirlingS2(int, int) | 
| org.apache.commons.math3.analysis.FunctionUtils.toDifferentiableMultivariateFunction(MultivariateDifferentiableFunction) | 
| org.apache.commons.math3.analysis.FunctionUtils.toDifferentiableMultivariateVectorFunction(MultivariateDifferentiableVectorFunction) | 
| org.apache.commons.math3.analysis.FunctionUtils.toDifferentiableUnivariateFunction(UnivariateDifferentiableFunction) | 
| org.apache.commons.math3.analysis.FunctionUtils.toMultivariateDifferentiableFunction(DifferentiableMultivariateFunction) | 
| org.apache.commons.math3.analysis.FunctionUtils.toMultivariateDifferentiableVectorFunction(DifferentiableMultivariateVectorFunction) | 
| org.apache.commons.math3.analysis.FunctionUtils.toUnivariateDifferential(DifferentiableUnivariateFunction) | 
| org.apache.commons.math3.optimization.general.AbstractLeastSquaresOptimizer.updateJacobian() | 
| org.apache.commons.math3.optimization.general.AbstractLeastSquaresOptimizer.updateResidualsAndCost() |