MANIFEST.in
README
setup.cfg
setup.py
versioneer.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
External/Eigen/src/Core/products/TriangularSolverMatrix_MKL.h
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
External/Eigen/src/Eigen2Support/Geometry/Scaling.h
External/Eigen/src/Eigen2Support/Geometry/Transform.h
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
External/Eigen/src/StlSupport/CMakeLists.txt
External/Eigen/src/StlSupport/StdDeque.h
External/Eigen/src/StlSupport/StdList.h
External/Eigen/src/StlSupport/StdVector.h
External/Eigen/src/StlSupport/details.h
External/Eigen/src/SuperLUSupport/CMakeLists.txt
External/Eigen/src/SuperLUSupport/SuperLUSupport.h
External/Eigen/src/UmfPackSupport/CMakeLists.txt
External/Eigen/src/UmfPackSupport/UmfPackSupport.h
External/Eigen/src/misc/CMakeLists.txt
External/Eigen/src/misc/Image.h
External/Eigen/src/misc/Kernel.h
External/Eigen/src/misc/Solve.h
External/Eigen/src/misc/SparseSolve.h
External/Eigen/src/misc/blas.h
External/Eigen/src/plugins/ArrayCwiseBinaryOps.h
External/Eigen/src/plugins/ArrayCwiseUnaryOps.h
External/Eigen/src/plugins/BlockMethods.h
External/Eigen/src/plugins/CMakeLists.txt
External/Eigen/src/plugins/CommonCwiseBinaryOps.h
External/Eigen/src/plugins/CommonCwiseUnaryOps.h
External/Eigen/src/plugins/MatrixCwiseBinaryOps.h
External/Eigen/src/plugins/MatrixCwiseUnaryOps.h
External/nlopt/.gitignore
External/nlopt/AUTHORS
External/nlopt/BUILD-MINGW32.sh
External/nlopt/BUILD-MINGW64.sh
External/nlopt/CMakeLists.txt
External/nlopt/COPYING
External/nlopt/COPYRIGHT
External/nlopt/ChangeLog
External/nlopt/Makefile.am
External/nlopt/NEWS
External/nlopt/README.md
External/nlopt/SConscript
External/nlopt/TODO
External/nlopt/autogen.sh
External/nlopt/config.cmake.h.in
External/nlopt/config.h
External/nlopt/config.scons.h.in
External/nlopt/configure.ac
External/nlopt/nlopt.pc.in
External/nlopt/api/Makefile.am
External/nlopt/api/deprecated.c
External/nlopt/api/deprecated.cpp
External/nlopt/api/f77api.c
External/nlopt/api/f77api.cpp
External/nlopt/api/f77funcs.h
External/nlopt/api/f77funcs_.h
External/nlopt/api/general.c
External/nlopt/api/general.cpp
External/nlopt/api/nlopt-in.hpp
External/nlopt/api/nlopt-internal.h
External/nlopt/api/nlopt.3
External/nlopt/api/nlopt.h
External/nlopt/api/nlopt_minimize.3
External/nlopt/api/nlopt_minimize_constrained.3
External/nlopt/api/optimize.c
External/nlopt/api/optimize.cpp
External/nlopt/api/options.c
External/nlopt/api/options.cpp
External/nlopt/auglag/Makefile.am
External/nlopt/auglag/README
External/nlopt/auglag/auglag.c
External/nlopt/auglag/auglag.cpp
External/nlopt/auglag/auglag.h
External/nlopt/bobyqa/COPYRIGHT
External/nlopt/bobyqa/Makefile.am
External/nlopt/bobyqa/README
External/nlopt/bobyqa/README.orig
External/nlopt/bobyqa/bobyqa.c
External/nlopt/bobyqa/bobyqa.cpp
External/nlopt/bobyqa/bobyqa.h
External/nlopt/cdirect/Makefile.am
External/nlopt/cdirect/README
External/nlopt/cdirect/cdirect.c
External/nlopt/cdirect/cdirect.cpp
External/nlopt/cdirect/cdirect.h
External/nlopt/cdirect/hybrid.c
External/nlopt/cdirect/hybrid.cpp
External/nlopt/cobyla/COPYRIGHT
External/nlopt/cobyla/Makefile.am
External/nlopt/cobyla/README
External/nlopt/cobyla/README.orig
External/nlopt/cobyla/cobyla.c
External/nlopt/cobyla/cobyla.cpp
External/nlopt/cobyla/cobyla.h
External/nlopt/cquad/Makefile.am
External/nlopt/cquad/cquad.c
External/nlopt/cquad/cquad.h
External/nlopt/crs/Makefile.am
External/nlopt/crs/README
External/nlopt/crs/crs.c
External/nlopt/crs/crs.cpp
External/nlopt/crs/crs.h
External/nlopt/direct/AUTHORS
External/nlopt/direct/COPYING
External/nlopt/direct/DIRect.c
External/nlopt/direct/DIRect.cpp
External/nlopt/direct/DIRparallel.c
External/nlopt/direct/DIRserial.c
External/nlopt/direct/DIRserial.cpp
External/nlopt/direct/DIRsubrout.c
External/nlopt/direct/DIRsubrout.cpp
External/nlopt/direct/Makefile.am
External/nlopt/direct/README
External/nlopt/direct/direct-internal.h
External/nlopt/direct/direct.h
External/nlopt/direct/direct_wrap.c
External/nlopt/direct/direct_wrap.cpp
External/nlopt/direct/tstc.c
External/nlopt/direct/userguide.pdf
External/nlopt/esch/COPYRIGHT
External/nlopt/esch/Makefile.am
External/nlopt/esch/esch.c
External/nlopt/esch/esch.cpp
External/nlopt/esch/esch.h
External/nlopt/isres/Makefile.am
External/nlopt/isres/README
External/nlopt/isres/isres.c
External/nlopt/isres/isres.cpp
External/nlopt/isres/isres.h
External/nlopt/luksan/COPYRIGHT
External/nlopt/luksan/Makefile.am
External/nlopt/luksan/README
External/nlopt/luksan/luksan.h
External/nlopt/luksan/mssubs.c
External/nlopt/luksan/mssubs.cpp
External/nlopt/luksan/mssubs.for
External/nlopt/luksan/plip.c
External/nlopt/luksan/plip.cpp
External/nlopt/luksan/plip.for
External/nlopt/luksan/plip.txt
External/nlopt/luksan/plis.c
External/nlopt/luksan/plis.cpp
External/nlopt/luksan/plis.for
External/nlopt/luksan/plis.txt
External/nlopt/luksan/pnet.c
External/nlopt/luksan/pnet.cpp
External/nlopt/luksan/pnet.for
External/nlopt/luksan/pnet.txt
External/nlopt/luksan/pssubs.c
External/nlopt/luksan/pssubs.cpp
External/nlopt/luksan/pssubs.for
External/nlopt/luksan/v999-07.pdf
External/nlopt/m4/ax_c_threadlocal.m4
External/nlopt/mlsl/Makefile.am
External/nlopt/mlsl/README
External/nlopt/mlsl/mlsl.c
External/nlopt/mlsl/mlsl.cpp
External/nlopt/mlsl/mlsl.h
External/nlopt/mma/Makefile.am
External/nlopt/mma/README
External/nlopt/mma/ccsa_quadratic.c
External/nlopt/mma/ccsa_quadratic.cpp
External/nlopt/mma/mma.c
External/nlopt/mma/mma.cpp
External/nlopt/mma/mma.h
External/nlopt/neldermead/Makefile.am
External/nlopt/neldermead/README
External/nlopt/neldermead/neldermead.h
External/nlopt/neldermead/nldrmd.c
External/nlopt/neldermead/nldrmd.cpp
External/nlopt/neldermead/sbplx.c
External/nlopt/neldermead/sbplx.cpp
External/nlopt/newuoa/COPYRIGHT
External/nlopt/newuoa/Makefile.am
External/nlopt/newuoa/README
External/nlopt/newuoa/README.orig
External/nlopt/newuoa/newuoa.c
External/nlopt/newuoa/newuoa.cpp
External/nlopt/newuoa/newuoa.h
External/nlopt/octave/Makefile.am
External/nlopt/octave/NLOPT_AUGLAG.m
External/nlopt/octave/NLOPT_AUGLAG_EQ.m
External/nlopt/octave/NLOPT_GD_MLSL.m
External/nlopt/octave/NLOPT_GD_MLSL_LDS.m
External/nlopt/octave/NLOPT_GD_STOGO.m
External/nlopt/octave/NLOPT_GD_STOGO_RAND.m
External/nlopt/octave/NLOPT_GN_CRS2_LM.m
External/nlopt/octave/NLOPT_GN_DIRECT.m
External/nlopt/octave/NLOPT_GN_DIRECT_L.m
External/nlopt/octave/NLOPT_GN_DIRECT_L_NOSCAL.m
External/nlopt/octave/NLOPT_GN_DIRECT_L_RAND.m
External/nlopt/octave/NLOPT_GN_DIRECT_L_RAND_NOSCAL.m
External/nlopt/octave/NLOPT_GN_DIRECT_NOSCAL.m
External/nlopt/octave/NLOPT_GN_ESCH.m
External/nlopt/octave/NLOPT_GN_ISRES.m
External/nlopt/octave/NLOPT_GN_MLSL.m
External/nlopt/octave/NLOPT_GN_MLSL_LDS.m
External/nlopt/octave/NLOPT_GN_ORIG_DIRECT.m
External/nlopt/octave/NLOPT_GN_ORIG_DIRECT_L.m
External/nlopt/octave/NLOPT_G_MLSL.m
External/nlopt/octave/NLOPT_G_MLSL_LDS.m
External/nlopt/octave/NLOPT_LD_AUGLAG.m
External/nlopt/octave/NLOPT_LD_AUGLAG_EQ.m
External/nlopt/octave/NLOPT_LD_CCSAQ.m
External/nlopt/octave/NLOPT_LD_LBFGS.m
External/nlopt/octave/NLOPT_LD_LBFGS_NOCEDAL.m
External/nlopt/octave/NLOPT_LD_MMA.m
External/nlopt/octave/NLOPT_LD_SLSQP.m
External/nlopt/octave/NLOPT_LD_TNEWTON.m
External/nlopt/octave/NLOPT_LD_TNEWTON_PRECOND.m
External/nlopt/octave/NLOPT_LD_TNEWTON_PRECOND_RESTART.m
External/nlopt/octave/NLOPT_LD_TNEWTON_RESTART.m
External/nlopt/octave/NLOPT_LD_VAR1.m
External/nlopt/octave/NLOPT_LD_VAR2.m
External/nlopt/octave/NLOPT_LN_AUGLAG.m
External/nlopt/octave/NLOPT_LN_AUGLAG_EQ.m
External/nlopt/octave/NLOPT_LN_BOBYQA.m
External/nlopt/octave/NLOPT_LN_COBYLA.m
External/nlopt/octave/NLOPT_LN_NELDERMEAD.m
External/nlopt/octave/NLOPT_LN_NEWUOA.m
External/nlopt/octave/NLOPT_LN_NEWUOA_BOUND.m
External/nlopt/octave/NLOPT_LN_PRAXIS.m
External/nlopt/octave/NLOPT_LN_SBPLX.m
External/nlopt/octave/dummy.c
External/nlopt/octave/mkconstants.sh
External/nlopt/octave/nlopt_minimize.m
External/nlopt/octave/nlopt_minimize_constrained.m
External/nlopt/octave/nlopt_optimize-mex.c
External/nlopt/octave/nlopt_optimize-oct.cc
External/nlopt/octave/nlopt_optimize.m
External/nlopt/praxis/Makefile.am
External/nlopt/praxis/README
External/nlopt/praxis/praxis.c
External/nlopt/praxis/praxis.cpp
External/nlopt/praxis/praxis.h
External/nlopt/slsqp/COPYRIGHT
External/nlopt/slsqp/Makefile.am
External/nlopt/slsqp/README
External/nlopt/slsqp/slsqp.c
External/nlopt/slsqp/slsqp.cpp
External/nlopt/slsqp/slsqp.h
External/nlopt/stogo/COPYRIGHT
External/nlopt/stogo/Makefile.am
External/nlopt/stogo/README
External/nlopt/stogo/global.cc
External/nlopt/stogo/global.h
External/nlopt/stogo/linalg.cc
External/nlopt/stogo/linalg.h
External/nlopt/stogo/local.cc
External/nlopt/stogo/local.h
External/nlopt/stogo/paper.pdf
External/nlopt/stogo/prog.cc
External/nlopt/stogo/rosen.h
External/nlopt/stogo/stogo.cc
External/nlopt/stogo/stogo.h
External/nlopt/stogo/stogo_config.h
External/nlopt/stogo/techreport.pdf
External/nlopt/stogo/testfun.h
External/nlopt/stogo/testros.cc
External/nlopt/stogo/tools.cc
External/nlopt/stogo/tools.h
External/nlopt/stogo/tst.cc
External/nlopt/stogo/tstc.c
External/nlopt/subplex/Makefile.am
External/nlopt/subplex/subplex.c
External/nlopt/subplex/subplex.h
External/nlopt/swig/Makefile.am
External/nlopt/swig/nlopt-exceptions.i
External/nlopt/swig/nlopt-guile.i
External/nlopt/swig/nlopt-python.i
External/nlopt/swig/nlopt.i
External/nlopt/swig/numpy.i
External/nlopt/tensor/COPYRIGHT
External/nlopt/tensor/tensor.c
External/nlopt/test/Makefile.am
External/nlopt/test/box.c
External/nlopt/test/lorentzfit.c
External/nlopt/test/test_std.py
External/nlopt/test/testfuncs.c
External/nlopt/test/testfuncs.h
External/nlopt/test/testopt.cpp
External/nlopt/util/Makefile.am
External/nlopt/util/mt19937ar.c
External/nlopt/util/mt19937ar.cpp
External/nlopt/util/nlopt-util.h
External/nlopt/util/qsort_r.c
External/nlopt/util/qsort_r.cpp
External/nlopt/util/redblack.c
External/nlopt/util/redblack.cpp
External/nlopt/util/redblack.h
External/nlopt/util/redblack_test.c
External/nlopt/util/rescale.c
External/nlopt/util/rescale.cpp
External/nlopt/util/soboldata.h
External/nlopt/util/sobolseq.c
External/nlopt/util/sobolseq.cpp
External/nlopt/util/stop.c
External/nlopt/util/stop.cpp
External/nlopt/util/timer.c
External/nlopt/util/timer.cpp
cython/lmm_forest/.gitignore
cython/lmm_forest/SplittingCore.cpp
cython/lmm_forest/SplittingCore.h
cython/lmm_forest/SplittingCore.pyx
cython/lmm_forest/types.h
limix/__init__.py
limix/_version.py
limix.egg-info/PKG-INFO
limix.egg-info/SOURCES.txt
limix.egg-info/dependency_links.txt
limix.egg-info/pbr.json
limix.egg-info/requires.txt
limix.egg-info/top_level.txt
limix/core/__init__.py
limix/core/association/__init__.py
limix/core/association/lmm_kronecker-LARC3550935.py
limix/core/association/lmm_kronecker.py
limix/core/covar/__init__.py
limix/core/covar/acombinators.py
limix/core/covar/combinators.py
limix/core/covar/cov2kronSum.py
limix/core/covar/cov2kronSumLR.py
limix/core/covar/cov3kronSumLR.py
limix/core/covar/cov_reml.py
limix/core/covar/covar_base.py
limix/core/covar/dirIndirCov.py
limix/core/covar/fixed.py
limix/core/covar/freeform.py
limix/core/covar/kronecker.py
limix/core/covar/lowrank.py
limix/core/covar/sqexp.py
limix/core/covar/test/__init__.py
limix/core/covar/test/test_combinators.py
limix/core/covar/test/test_cov2kronSum.py
limix/core/covar/test/test_cov2kronSumLR.py
limix/core/covar/test/test_cov3kronSumLR.py
limix/core/covar/test/test_dirIndirCov.py
limix/core/covar/test/test_fixed.py
limix/core/covar/test/test_freeform.py
limix/core/covar/test/test_kronecker.py
limix/core/covar/test/test_lowrank.py
limix/core/covar/test/test_sqexp.py
limix/core/covar/util/__init__.py
limix/core/gp/__init__.py
limix/core/gp/gp2kronSum.py
limix/core/gp/gp2kronSumLR.py
limix/core/gp/gp3kronSumLR.py
limix/core/gp/gp_base.py
limix/core/gp/relay.py
limix/core/likelihood/__init__.py
limix/core/likelihood/likelihood_base.py
limix/core/linalg/__init__.py
limix/core/linalg/dist.py
limix/core/linalg/linalg_matrix.py
limix/core/mean/__init__.py
limix/core/mean/base.py
limix/core/mean/linear.py
limix/core/mean/mean.py
limix/core/mean/meanKronSum.py
limix/core/mean/mean_base.py
limix/core/mean/mean_efficient.py
limix/core/optimize/__init__.py
limix/core/optimize/optimize_bfgs.py
limix/core/test/__init__.py
limix/core/test/test_gp2kronSum.py
limix/core/test/test_gp2kronSumLR.py
limix/core/test/test_gp3kronSumLR.py
limix/core/test/test_gp_base.py
limix/core/test/test_gp_more.py
limix/core/type/__init__.py
limix/core/type/cached.py
limix/core/type/exception.py
limix/core/type/observed.py
limix/core/utils/__init__.py
limix/deprecated/__init__.py
limix/deprecated/core.py
limix/deprecated/io/__init__.py
limix/deprecated/io/conversion.py
limix/deprecated/io/data.py
limix/deprecated/io/data_util.py
limix/deprecated/io/genotype_reader.py
limix/deprecated/io/output_writer.py
limix/deprecated/io/phenotype_reader.py
limix/deprecated/io/plink.py
limix/deprecated/modules/BLUP.py
limix/deprecated/modules/__init__.py
limix/deprecated/modules/lmm_fast.py
limix/deprecated/modules/lmm_forest.py
limix/deprecated/modules/lmmlasso.py
limix/deprecated/modules/mixedForestUtils.py
limix/deprecated/modules/multiPanama.py
limix/deprecated/modules/panama.py
limix/deprecated/modules/parMixedForest.py
limix/deprecated/modules/pySplittingCore.py
limix/deprecated/modules/qtl.py
limix/deprecated/modules/varDecompSet.py
limix/deprecated/modules/varianceDecomposition.py
limix/deprecated/stats/__init__.py
limix/deprecated/stats/fdr.py
limix/deprecated/stats/geno_summary.py
limix/deprecated/stats/pca.py
limix/deprecated/stats/power.py
limix/deprecated/utils/__init__.py
limix/deprecated/utils/fastlmm.py
limix/deprecated/utils/plot.py
limix/deprecated/utils/preprocess.py
limix/ensemble/__init__.py
limix/ensemble/blup.py
limix/ensemble/lmm_fast.py
limix/ensemble/lmm_forest.py
limix/ensemble/lmm_forest_utils.py
limix/ensemble/par_lmm_forest.py
limix/ensemble/py_splitting_core.py
limix/io/__init__.py
limix/io/conversion.py
limix/io/data.py
limix/io/data_util.py
limix/io/genotype_reader.py
limix/io/output_writer.py
limix/io/phenotype_reader.py
limix/io/plink.py
limix/io_/__init__.py
limix/modules/BLUP.py
limix/modules/__init__.py
limix/modules/lmm_fast.py
limix/modules/lmm_forest.py
limix/modules/lmmlasso.py
limix/modules/mixedForestUtils.py
limix/modules/multiPanama.py
limix/modules/panama.py
limix/modules/parMixedForest.py
limix/modules/pySplittingCore.py
limix/modules/qtl.py
limix/modules/varDecompSet.py
limix/modules/varianceDecomposition.py
limix/mtSet/__init__.py
limix/mtSet/mtset.py
limix/mtSet/core/__init__.py
limix/mtSet/core/analyzeCore.py
limix/mtSet/core/plink_reader.py
limix/mtSet/core/postprocessCore.py
limix/mtSet/core/preprocessCore.py
limix/mtSet/core/read_utils.py
limix/mtSet/core/simPhenoCore.py
limix/mtSet/core/simulator.py
limix/mtSet/core/splitter.py
limix/mtSet/core/splitter_bed.py
limix/stats/__init__.py
limix/stats/chi2mixture.py
limix/stats/fdr.py
limix/stats/geno_summary.py
limix/stats/pca.py
limix/stats/power.py
limix/utils/__init__.py
limix/utils/check_grad.py
limix/utils/eigen.py
limix/utils/plot.py
limix/utils/preprocess.py
limix/utils/psd_solve.py
limix/utils/svd_utils.py
limix/utils/util_functions.py
scripts/limix_converter
scripts/limix_runner
scripts/mtSet_analyze
scripts/mtSet_postprocess
scripts/mtSet_preprocess
scripts/mtSet_simPheno
src/interfaces/python/limix_wrap.cpp
src/limix/types.h
src/limix/LMM/kronecker_lmm.cpp
src/limix/LMM/kronecker_lmm.h
src/limix/LMM/lmm.cpp
src/limix/LMM/lmm.h
src/limix/LMM_forest/SplittingCore.h
src/limix/LMM_forest/lmm_forest.cpp
src/limix/LMM_forest/lmm_forest.h
src/limix/covar/combinators.cpp
src/limix/covar/combinators.h
src/limix/covar/covariance.cpp
src/limix/covar/covariance.h
src/limix/covar/dist.cpp
src/limix/covar/dist.h
src/limix/covar/freeform.cpp
src/limix/covar/freeform.h
src/limix/covar/linear.cpp
src/limix/covar/linear.h
src/limix/covar/se.cpp
src/limix/covar/se.h
src/limix/gp/gp_Sum.cpp
src/limix/gp/gp_Sum.h
src/limix/gp/gp_base.cpp
src/limix/gp/gp_base.h
src/limix/gp/gp_kronSum.cpp
src/limix/gp/gp_kronSum.h
src/limix/gp/gp_kronecker.cpp
src/limix/gp/gp_kronecker.h
src/limix/gp/gp_opt.cpp
src/limix/gp/gp_opt.h
src/limix/io/dataframe.cpp
src/limix/io/dataframe.h
src/limix/io/genotype.cpp
src/limix/io/genotype.h
src/limix/io/split.cpp
src/limix/io/split.h
src/limix/likelihood/likelihood.cpp
src/limix/likelihood/likelihood.h
src/limix/mean/ADataTerm.cpp
src/limix/mean/ADataTerm.h
src/limix/mean/CData.cpp
src/limix/mean/CData.h
src/limix/mean/CKroneckerMean.cpp
src/limix/mean/CKroneckerMean.h
src/limix/mean/CLinearMean.cpp
src/limix/mean/CLinearMean.h
src/limix/mean/CSumLinear.cpp
src/limix/mean/CSumLinear.h
src/limix/modules/CVarianceDecomposition.cpp
src/limix/modules/CVarianceDecomposition.h
src/limix/utils/beta.cpp
src/limix/utils/beta.h
src/limix/utils/brentc.cpp
src/limix/utils/brentc.h
src/limix/utils/cache.cpp
src/limix/utils/cache.h
src/limix/utils/fisherf.cpp
src/limix/utils/fisherf.h
src/limix/utils/gamma.cpp
src/limix/utils/gamma.h
src/limix/utils/mathfunctions.cpp
src/limix/utils/mathfunctions.h
src/limix/utils/matrix_helper.cpp
src/limix/utils/matrix_helper.h