MANIFEST.in
README
setup.py
./External/nlopt/api/deprecated.cpp
./External/nlopt/api/f77api.cpp
./External/nlopt/api/general.cpp
./External/nlopt/api/optimize.cpp
./External/nlopt/api/options.cpp
./External/nlopt/auglag/auglag.cpp
./External/nlopt/bobyqa/bobyqa.cpp
./External/nlopt/cdirect/cdirect.cpp
./External/nlopt/cdirect/hybrid.cpp
./External/nlopt/cobyla/cobyla.cpp
./External/nlopt/crs/crs.cpp
./External/nlopt/direct/DIRect.cpp
./External/nlopt/direct/DIRserial.cpp
./External/nlopt/direct/DIRsubrout.cpp
./External/nlopt/direct/direct_wrap.cpp
./External/nlopt/esch/esch.cpp
./External/nlopt/isres/isres.cpp
./External/nlopt/luksan/mssubs.cpp
./External/nlopt/luksan/plip.cpp
./External/nlopt/luksan/plis.cpp
./External/nlopt/luksan/pnet.cpp
./External/nlopt/luksan/pssubs.cpp
./External/nlopt/mlsl/mlsl.cpp
./External/nlopt/mma/ccsa_quadratic.cpp
./External/nlopt/mma/mma.cpp
./External/nlopt/neldermead/nldrmd.cpp
./External/nlopt/neldermead/sbplx.cpp
./External/nlopt/newuoa/newuoa.cpp
./External/nlopt/praxis/praxis.cpp
./External/nlopt/slsqp/slsqp.cpp
./External/nlopt/stogo/global.cc
./External/nlopt/stogo/linalg.cc
./External/nlopt/stogo/local.cc
./External/nlopt/stogo/stogo.cc
./External/nlopt/stogo/tools.cc
./External/nlopt/util/mt19937ar.cpp
./External/nlopt/util/qsort_r.cpp
./External/nlopt/util/redblack.cpp
./External/nlopt/util/rescale.cpp
./External/nlopt/util/sobolseq.cpp
./External/nlopt/util/stop.cpp
./External/nlopt/util/timer.cpp
./src/limix/LMM/kronecker_lmm.cpp
./src/limix/LMM/lmm.cpp
./src/limix/LMM_forest/lmm_forest.cpp
./src/limix/covar/combinators.cpp
./src/limix/covar/covariance.cpp
./src/limix/covar/dist.cpp
./src/limix/covar/freeform.cpp
./src/limix/covar/linear.cpp
./src/limix/covar/se.cpp
./src/limix/gp/gp_Sum.cpp
./src/limix/gp/gp_base.cpp
./src/limix/gp/gp_kronSum.cpp
./src/limix/gp/gp_kronecker.cpp
./src/limix/gp/gp_opt.cpp
./src/limix/io/dataframe.cpp
./src/limix/io/genotype.cpp
./src/limix/io/split.cpp
./src/limix/likelihood/likelihood.cpp
./src/limix/mean/ADataTerm.cpp
./src/limix/mean/CData.cpp
./src/limix/mean/CKroneckerMean.cpp
./src/limix/mean/CLinearMean.cpp
./src/limix/mean/CSumLinear.cpp
./src/limix/modules/CVarianceDecomposition.cpp
./src/limix/utils/beta.cpp
./src/limix/utils/brentc.cpp
./src/limix/utils/cache.cpp
./src/limix/utils/fisherf.cpp
./src/limix/utils/gamma.cpp
./src/limix/utils/mathfunctions.cpp
./src/limix/utils/matrix_helper.cpp
External/Eigen/Array
External/Eigen/CMakeLists.txt
External/Eigen/Cholesky
External/Eigen/CholmodSupport
External/Eigen/Core
External/Eigen/Dense
External/Eigen/Eigen
External/Eigen/Eigen2Support
External/Eigen/Eigenvalues
External/Eigen/Geometry
External/Eigen/Householder
External/Eigen/IterativeLinearSolvers
External/Eigen/Jacobi
External/Eigen/LU
External/Eigen/LeastSquares
External/Eigen/MetisSupport
External/Eigen/OrderingMethods
External/Eigen/PaStiXSupport
External/Eigen/PardisoSupport
External/Eigen/QR
External/Eigen/QtAlignedMalloc
External/Eigen/SPQRSupport
External/Eigen/SVD
External/Eigen/Sparse
External/Eigen/SparseCholesky
External/Eigen/SparseCore
External/Eigen/SparseLU
External/Eigen/SparseQR
External/Eigen/StdDeque
External/Eigen/StdList
External/Eigen/StdVector
External/Eigen/SuperLUSupport
External/Eigen/UmfPackSupport
External/Eigen/src/CMakeLists.txt
External/Eigen/src/Cholesky/CMakeLists.txt
External/Eigen/src/Cholesky/LDLT.h
External/Eigen/src/Cholesky/LLT.h
External/Eigen/src/Cholesky/LLT_MKL.h
External/Eigen/src/CholmodSupport/CMakeLists.txt
External/Eigen/src/CholmodSupport/CholmodSupport.h
External/Eigen/src/Core/Array.h
External/Eigen/src/Core/ArrayBase.h
External/Eigen/src/Core/ArrayWrapper.h
External/Eigen/src/Core/Assign.h
External/Eigen/src/Core/Assign_MKL.h
External/Eigen/src/Core/BandMatrix.h
External/Eigen/src/Core/Block.h
External/Eigen/src/Core/BooleanRedux.h
External/Eigen/src/Core/CMakeLists.txt
External/Eigen/src/Core/CommaInitializer.h
External/Eigen/src/Core/CoreIterators.h
External/Eigen/src/Core/CwiseBinaryOp.h
External/Eigen/src/Core/CwiseNullaryOp.h
External/Eigen/src/Core/CwiseUnaryOp.h
External/Eigen/src/Core/CwiseUnaryView.h
External/Eigen/src/Core/DenseBase.h
External/Eigen/src/Core/DenseCoeffsBase.h
External/Eigen/src/Core/DenseStorage.h
External/Eigen/src/Core/Diagonal.h
External/Eigen/src/Core/DiagonalMatrix.h
External/Eigen/src/Core/DiagonalProduct.h
External/Eigen/src/Core/Dot.h
External/Eigen/src/Core/EigenBase.h
External/Eigen/src/Core/Flagged.h
External/Eigen/src/Core/ForceAlignedAccess.h
External/Eigen/src/Core/Functors.h
External/Eigen/src/Core/Fuzzy.h
External/Eigen/src/Core/GeneralProduct.h
External/Eigen/src/Core/GenericPacketMath.h
External/Eigen/src/Core/GlobalFunctions.h
External/Eigen/src/Core/IO.h
External/Eigen/src/Core/Map.h
External/Eigen/src/Core/MapBase.h
External/Eigen/src/Core/MathFunctions.h
External/Eigen/src/Core/Matrix.h
External/Eigen/src/Core/MatrixBase.h
External/Eigen/src/Core/NestByValue.h
External/Eigen/src/Core/NoAlias.h
External/Eigen/src/Core/NumTraits.h
External/Eigen/src/Core/PermutationMatrix.h
External/Eigen/src/Core/PlainObjectBase.h
External/Eigen/src/Core/ProductBase.h
External/Eigen/src/Core/Random.h
External/Eigen/src/Core/Redux.h
External/Eigen/src/Core/Ref.h
External/Eigen/src/Core/Replicate.h
External/Eigen/src/Core/ReturnByValue.h
External/Eigen/src/Core/Reverse.h
External/Eigen/src/Core/Select.h
External/Eigen/src/Core/SelfAdjointView.h
External/Eigen/src/Core/SelfCwiseBinaryOp.h
External/Eigen/src/Core/SolveTriangular.h
External/Eigen/src/Core/StableNorm.h
External/Eigen/src/Core/Stride.h
External/Eigen/src/Core/Swap.h
External/Eigen/src/Core/Transpose.h
External/Eigen/src/Core/Transpositions.h
External/Eigen/src/Core/TriangularMatrix.h
External/Eigen/src/Core/VectorBlock.h
External/Eigen/src/Core/VectorwiseOp.h
External/Eigen/src/Core/Visitor.h
External/Eigen/src/Core/arch/CMakeLists.txt
External/Eigen/src/Core/arch/AltiVec/CMakeLists.txt
External/Eigen/src/Core/arch/AltiVec/Complex.h
External/Eigen/src/Core/arch/AltiVec/PacketMath.h
External/Eigen/src/Core/arch/Default/CMakeLists.txt
External/Eigen/src/Core/arch/Default/Settings.h
External/Eigen/src/Core/arch/NEON/CMakeLists.txt
External/Eigen/src/Core/arch/NEON/Complex.h
External/Eigen/src/Core/arch/NEON/PacketMath.h
External/Eigen/src/Core/arch/SSE/CMakeLists.txt
External/Eigen/src/Core/arch/SSE/Complex.h
External/Eigen/src/Core/arch/SSE/MathFunctions.h
External/Eigen/src/Core/arch/SSE/PacketMath.h
External/Eigen/src/Core/products/CMakeLists.txt
External/Eigen/src/Core/products/CoeffBasedProduct.h
External/Eigen/src/Core/products/GeneralBlockPanelKernel.h
External/Eigen/src/Core/products/GeneralMatrixMatrix.h
External/Eigen/src/Core/products/GeneralMatrixMatrixTriangular.h
External/Eigen/src/Core/products/GeneralMatrixMatrixTriangular_MKL.h
External/Eigen/src/Core/products/GeneralMatrixMatrix_MKL.h
External/Eigen/src/Core/products/GeneralMatrixVector.h
External/Eigen/src/Core/products/GeneralMatrixVector_MKL.h
External/Eigen/src/Core/products/Parallelizer.h
External/Eigen/src/Core/products/SelfadjointMatrixMatrix.h
External/Eigen/src/Core/products/SelfadjointMatrixMatrix_MKL.h
External/Eigen/src/Core/products/SelfadjointMatrixVector.h
External/Eigen/src/Core/products/SelfadjointMatrixVector_MKL.h
External/Eigen/src/Core/products/SelfadjointProduct.h
External/Eigen/src/Core/products/SelfadjointRank2Update.h
External/Eigen/src/Core/products/TriangularMatrixMatrix.h
External/Eigen/src/Core/products/TriangularMatrixMatrix_MKL.h
External/Eigen/src/Core/products/TriangularMatrixVector.h
External/Eigen/src/Core/products/TriangularMatrixVector_MKL.h
External/Eigen/src/Core/products/TriangularSolverMatrix.h
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External/Eigen/src/Core/products/TriangularSolverVector.h
External/Eigen/src/Core/util/BlasUtil.h
External/Eigen/src/Core/util/CMakeLists.txt
External/Eigen/src/Core/util/Constants.h
External/Eigen/src/Core/util/DisableStupidWarnings.h
External/Eigen/src/Core/util/ForwardDeclarations.h
External/Eigen/src/Core/util/MKL_support.h
External/Eigen/src/Core/util/Macros.h
External/Eigen/src/Core/util/Memory.h
External/Eigen/src/Core/util/Meta.h
External/Eigen/src/Core/util/NonMPL2.h
External/Eigen/src/Core/util/ReenableStupidWarnings.h
External/Eigen/src/Core/util/StaticAssert.h
External/Eigen/src/Core/util/XprHelper.h
External/Eigen/src/Eigen2Support/Block.h
External/Eigen/src/Eigen2Support/CMakeLists.txt
External/Eigen/src/Eigen2Support/Cwise.h
External/Eigen/src/Eigen2Support/CwiseOperators.h
External/Eigen/src/Eigen2Support/LU.h
External/Eigen/src/Eigen2Support/Lazy.h
External/Eigen/src/Eigen2Support/LeastSquares.h
External/Eigen/src/Eigen2Support/Macros.h
External/Eigen/src/Eigen2Support/MathFunctions.h
External/Eigen/src/Eigen2Support/Memory.h
External/Eigen/src/Eigen2Support/Meta.h
External/Eigen/src/Eigen2Support/Minor.h
External/Eigen/src/Eigen2Support/QR.h
External/Eigen/src/Eigen2Support/SVD.h
External/Eigen/src/Eigen2Support/TriangularSolver.h
External/Eigen/src/Eigen2Support/VectorBlock.h
External/Eigen/src/Eigen2Support/Geometry/AlignedBox.h
External/Eigen/src/Eigen2Support/Geometry/All.h
External/Eigen/src/Eigen2Support/Geometry/AngleAxis.h
External/Eigen/src/Eigen2Support/Geometry/CMakeLists.txt
External/Eigen/src/Eigen2Support/Geometry/Hyperplane.h
External/Eigen/src/Eigen2Support/Geometry/ParametrizedLine.h
External/Eigen/src/Eigen2Support/Geometry/Quaternion.h
External/Eigen/src/Eigen2Support/Geometry/Rotation2D.h
External/Eigen/src/Eigen2Support/Geometry/RotationBase.h
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External/Eigen/src/Eigen2Support/Geometry/Translation.h
External/Eigen/src/Eigenvalues/CMakeLists.txt
External/Eigen/src/Eigenvalues/ComplexEigenSolver.h
External/Eigen/src/Eigenvalues/ComplexSchur.h
External/Eigen/src/Eigenvalues/ComplexSchur_MKL.h
External/Eigen/src/Eigenvalues/EigenSolver.h
External/Eigen/src/Eigenvalues/GeneralizedEigenSolver.h
External/Eigen/src/Eigenvalues/GeneralizedSelfAdjointEigenSolver.h
External/Eigen/src/Eigenvalues/HessenbergDecomposition.h
External/Eigen/src/Eigenvalues/MatrixBaseEigenvalues.h
External/Eigen/src/Eigenvalues/RealQZ.h
External/Eigen/src/Eigenvalues/RealSchur.h
External/Eigen/src/Eigenvalues/RealSchur_MKL.h
External/Eigen/src/Eigenvalues/SelfAdjointEigenSolver.h
External/Eigen/src/Eigenvalues/SelfAdjointEigenSolver_MKL.h
External/Eigen/src/Eigenvalues/Tridiagonalization.h
External/Eigen/src/Geometry/AlignedBox.h
External/Eigen/src/Geometry/AngleAxis.h
External/Eigen/src/Geometry/CMakeLists.txt
External/Eigen/src/Geometry/EulerAngles.h
External/Eigen/src/Geometry/Homogeneous.h
External/Eigen/src/Geometry/Hyperplane.h
External/Eigen/src/Geometry/OrthoMethods.h
External/Eigen/src/Geometry/ParametrizedLine.h
External/Eigen/src/Geometry/Quaternion.h
External/Eigen/src/Geometry/Rotation2D.h
External/Eigen/src/Geometry/RotationBase.h
External/Eigen/src/Geometry/Scaling.h
External/Eigen/src/Geometry/Transform.h
External/Eigen/src/Geometry/Translation.h
External/Eigen/src/Geometry/Umeyama.h
External/Eigen/src/Geometry/arch/CMakeLists.txt
External/Eigen/src/Geometry/arch/Geometry_SSE.h
External/Eigen/src/Householder/BlockHouseholder.h
External/Eigen/src/Householder/CMakeLists.txt
External/Eigen/src/Householder/Householder.h
External/Eigen/src/Householder/HouseholderSequence.h
External/Eigen/src/IterativeLinearSolvers/BasicPreconditioners.h
External/Eigen/src/IterativeLinearSolvers/BiCGSTAB.h
External/Eigen/src/IterativeLinearSolvers/CMakeLists.txt
External/Eigen/src/IterativeLinearSolvers/ConjugateGradient.h
External/Eigen/src/IterativeLinearSolvers/IncompleteLUT.h
External/Eigen/src/IterativeLinearSolvers/IterativeSolverBase.h
External/Eigen/src/Jacobi/CMakeLists.txt
External/Eigen/src/Jacobi/Jacobi.h
External/Eigen/src/LU/CMakeLists.txt
External/Eigen/src/LU/Determinant.h
External/Eigen/src/LU/FullPivLU.h
External/Eigen/src/LU/Inverse.h
External/Eigen/src/LU/PartialPivLU.h
External/Eigen/src/LU/PartialPivLU_MKL.h
External/Eigen/src/LU/arch/CMakeLists.txt
External/Eigen/src/LU/arch/Inverse_SSE.h
External/Eigen/src/MetisSupport/CMakeLists.txt
External/Eigen/src/MetisSupport/MetisSupport.h
External/Eigen/src/OrderingMethods/Amd.h
External/Eigen/src/OrderingMethods/CMakeLists.txt
External/Eigen/src/OrderingMethods/Eigen_Colamd.h
External/Eigen/src/OrderingMethods/Ordering.h
External/Eigen/src/PaStiXSupport/CMakeLists.txt
External/Eigen/src/PaStiXSupport/PaStiXSupport.h
External/Eigen/src/PardisoSupport/CMakeLists.txt
External/Eigen/src/PardisoSupport/PardisoSupport.h
External/Eigen/src/QR/CMakeLists.txt
External/Eigen/src/QR/ColPivHouseholderQR.h
External/Eigen/src/QR/ColPivHouseholderQR_MKL.h
External/Eigen/src/QR/FullPivHouseholderQR.h
External/Eigen/src/QR/HouseholderQR.h
External/Eigen/src/QR/HouseholderQR_MKL.h
External/Eigen/src/SPQRSupport/CMakeLists.txt
External/Eigen/src/SPQRSupport/SuiteSparseQRSupport.h
External/Eigen/src/SVD/CMakeLists.txt
External/Eigen/src/SVD/JacobiSVD.h
External/Eigen/src/SVD/JacobiSVD_MKL.h
External/Eigen/src/SVD/UpperBidiagonalization.h
External/Eigen/src/SparseCholesky/CMakeLists.txt
External/Eigen/src/SparseCholesky/SimplicialCholesky.h
External/Eigen/src/SparseCholesky/SimplicialCholesky_impl.h
External/Eigen/src/SparseCore/AmbiVector.h
External/Eigen/src/SparseCore/CMakeLists.txt
External/Eigen/src/SparseCore/CompressedStorage.h
External/Eigen/src/SparseCore/ConservativeSparseSparseProduct.h
External/Eigen/src/SparseCore/MappedSparseMatrix.h
External/Eigen/src/SparseCore/SparseBlock.h
External/Eigen/src/SparseCore/SparseColEtree.h
External/Eigen/src/SparseCore/SparseCwiseBinaryOp.h
External/Eigen/src/SparseCore/SparseCwiseUnaryOp.h
External/Eigen/src/SparseCore/SparseDenseProduct.h
External/Eigen/src/SparseCore/SparseDiagonalProduct.h
External/Eigen/src/SparseCore/SparseDot.h
External/Eigen/src/SparseCore/SparseFuzzy.h
External/Eigen/src/SparseCore/SparseMatrix.h
External/Eigen/src/SparseCore/SparseMatrixBase.h
External/Eigen/src/SparseCore/SparsePermutation.h
External/Eigen/src/SparseCore/SparseProduct.h
External/Eigen/src/SparseCore/SparseRedux.h
External/Eigen/src/SparseCore/SparseSelfAdjointView.h
External/Eigen/src/SparseCore/SparseSparseProductWithPruning.h
External/Eigen/src/SparseCore/SparseTranspose.h
External/Eigen/src/SparseCore/SparseTriangularView.h
External/Eigen/src/SparseCore/SparseUtil.h
External/Eigen/src/SparseCore/SparseVector.h
External/Eigen/src/SparseCore/SparseView.h
External/Eigen/src/SparseCore/TriangularSolver.h
External/Eigen/src/SparseLU/CMakeLists.txt
External/Eigen/src/SparseLU/SparseLU.h
External/Eigen/src/SparseLU/SparseLUImpl.h
External/Eigen/src/SparseLU/SparseLU_Memory.h
External/Eigen/src/SparseLU/SparseLU_Structs.h
External/Eigen/src/SparseLU/SparseLU_SupernodalMatrix.h
External/Eigen/src/SparseLU/SparseLU_Utils.h
External/Eigen/src/SparseLU/SparseLU_column_bmod.h
External/Eigen/src/SparseLU/SparseLU_column_dfs.h
External/Eigen/src/SparseLU/SparseLU_copy_to_ucol.h
External/Eigen/src/SparseLU/SparseLU_gemm_kernel.h
External/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h
External/Eigen/src/SparseLU/SparseLU_kernel_bmod.h
External/Eigen/src/SparseLU/SparseLU_panel_bmod.h
External/Eigen/src/SparseLU/SparseLU_panel_dfs.h
External/Eigen/src/SparseLU/SparseLU_pivotL.h
External/Eigen/src/SparseLU/SparseLU_pruneL.h
External/Eigen/src/SparseLU/SparseLU_relax_snode.h
External/Eigen/src/SparseQR/CMakeLists.txt
External/Eigen/src/SparseQR/SparseQR.h
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External/Eigen/src/StlSupport/StdList.h
External/Eigen/src/StlSupport/StdVector.h
External/Eigen/src/StlSupport/details.h
External/Eigen/src/SuperLUSupport/CMakeLists.txt
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External/Eigen/src/plugins/ArrayCwiseBinaryOps.h
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External/Eigen/src/plugins/MatrixCwiseUnaryOps.h
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External/nlopt/BUILD-MINGW32.sh
External/nlopt/BUILD-MINGW64.sh
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External/nlopt/COPYRIGHT
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External/nlopt/README.md
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External/nlopt/config.scons.h.in
External/nlopt/configure.ac
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