├── .gitignore ├── .travis.yml ├── External ├── Eigen │ ├── Array │ ├── CMakeLists.txt │ ├── Cholesky │ ├── CholmodSupport │ ├── Core │ ├── Dense │ ├── Eigen │ ├── Eigen2Support │ ├── Eigenvalues │ ├── Geometry │ ├── Householder │ ├── IterativeLinearSolvers │ ├── Jacobi │ ├── LU │ ├── LeastSquares │ ├── MetisSupport │ ├── OrderingMethods │ ├── PaStiXSupport │ ├── PardisoSupport │ ├── QR │ ├── QtAlignedMalloc │ ├── SPQRSupport │ ├── SVD │ ├── Sparse │ ├── SparseCholesky │ ├── SparseCore │ ├── SparseLU │ ├── SparseQR │ ├── StdDeque │ ├── StdList │ ├── StdVector │ ├── SuperLUSupport │ ├── UmfPackSupport │ └── src │ │ ├── CMakeLists.txt │ │ ├── Cholesky │ │ ├── CMakeLists.txt │ │ ├── LDLT.h │ │ ├── LLT.h │ │ └── LLT_MKL.h │ │ ├── CholmodSupport │ │ ├── CMakeLists.txt │ │ └── CholmodSupport.h │ │ ├── Core │ │ ├── Array.h │ │ ├── ArrayBase.h │ │ ├── ArrayWrapper.h │ │ ├── Assign.h │ │ ├── Assign_MKL.h │ │ ├── BandMatrix.h │ │ ├── Block.h │ │ ├── BooleanRedux.h │ │ ├── CMakeLists.txt │ │ ├── CommaInitializer.h │ │ ├── CoreIterators.h │ │ ├── CwiseBinaryOp.h │ │ ├── CwiseNullaryOp.h │ │ ├── CwiseUnaryOp.h │ │ ├── CwiseUnaryView.h │ │ ├── DenseBase.h │ │ ├── DenseCoeffsBase.h │ │ ├── DenseStorage.h │ │ ├── Diagonal.h │ │ ├── DiagonalMatrix.h │ │ ├── DiagonalProduct.h │ │ ├── Dot.h │ │ ├── EigenBase.h │ │ ├── Flagged.h │ │ ├── ForceAlignedAccess.h │ │ ├── Functors.h │ │ ├── Fuzzy.h │ │ ├── GeneralProduct.h │ │ ├── GenericPacketMath.h │ │ ├── GlobalFunctions.h │ │ ├── IO.h │ │ ├── Map.h │ │ ├── MapBase.h │ │ ├── MathFunctions.h │ │ ├── Matrix.h │ │ ├── MatrixBase.h │ │ ├── NestByValue.h │ │ ├── NoAlias.h │ │ ├── NumTraits.h │ │ ├── PermutationMatrix.h │ │ ├── PlainObjectBase.h │ │ ├── ProductBase.h │ │ ├── Random.h │ │ ├── Redux.h │ │ ├── Ref.h │ │ ├── Replicate.h │ │ ├── ReturnByValue.h │ │ ├── Reverse.h │ │ ├── Select.h │ │ ├── SelfAdjointView.h │ │ ├── SelfCwiseBinaryOp.h │ │ ├── SolveTriangular.h │ │ ├── StableNorm.h │ │ ├── Stride.h │ │ ├── Swap.h │ │ ├── Transpose.h │ │ ├── Transpositions.h │ │ ├── TriangularMatrix.h │ │ ├── VectorBlock.h │ │ ├── VectorwiseOp.h │ │ ├── Visitor.h │ │ ├── arch │ │ │ ├── AltiVec │ │ │ │ ├── CMakeLists.txt │ │ │ │ ├── Complex.h │ │ │ │ └── PacketMath.h │ │ │ ├── CMakeLists.txt │ │ │ ├── Default │ │ │ │ ├── CMakeLists.txt │ │ │ │ └── Settings.h │ │ │ ├── NEON │ │ │ │ ├── CMakeLists.txt │ │ │ │ ├── Complex.h │ │ │ │ └── PacketMath.h │ │ │ └── SSE │ │ │ │ ├── CMakeLists.txt │ │ │ │ ├── Complex.h │ │ │ │ ├── MathFunctions.h │ │ │ │ └── PacketMath.h │ │ ├── products │ │ │ ├── CMakeLists.txt │ │ │ ├── CoeffBasedProduct.h │ │ │ ├── GeneralBlockPanelKernel.h │ │ │ ├── GeneralMatrixMatrix.h │ │ │ ├── GeneralMatrixMatrixTriangular.h │ │ │ ├── GeneralMatrixMatrixTriangular_MKL.h │ │ │ ├── GeneralMatrixMatrix_MKL.h │ │ │ ├── GeneralMatrixVector.h │ │ │ ├── GeneralMatrixVector_MKL.h │ │ │ ├── Parallelizer.h │ │ │ ├── SelfadjointMatrixMatrix.h │ │ │ ├── SelfadjointMatrixMatrix_MKL.h │ │ │ ├── SelfadjointMatrixVector.h │ │ │ ├── SelfadjointMatrixVector_MKL.h │ │ │ ├── SelfadjointProduct.h │ │ │ ├── SelfadjointRank2Update.h │ │ │ ├── TriangularMatrixMatrix.h │ │ │ ├── TriangularMatrixMatrix_MKL.h │ │ │ ├── TriangularMatrixVector.h │ │ │ ├── TriangularMatrixVector_MKL.h │ │ │ ├── TriangularSolverMatrix.h │ │ │ ├── TriangularSolverMatrix_MKL.h │ │ │ └── TriangularSolverVector.h │ │ └── util │ │ │ ├── BlasUtil.h │ │ │ ├── CMakeLists.txt │ │ │ ├── Constants.h │ │ │ ├── DisableStupidWarnings.h │ │ │ ├── ForwardDeclarations.h │ │ │ ├── MKL_support.h │ │ │ ├── Macros.h │ │ │ ├── Memory.h │ │ │ ├── Meta.h │ │ │ ├── NonMPL2.h │ │ │ ├── ReenableStupidWarnings.h │ │ │ ├── StaticAssert.h │ │ │ └── XprHelper.h │ │ ├── Eigen2Support │ │ ├── Block.h │ │ ├── CMakeLists.txt │ │ ├── Cwise.h │ │ ├── CwiseOperators.h │ │ ├── Geometry │ │ │ ├── AlignedBox.h │ │ │ ├── All.h │ │ │ ├── AngleAxis.h │ │ │ ├── CMakeLists.txt │ │ │ ├── Hyperplane.h │ │ │ ├── ParametrizedLine.h │ │ │ ├── Quaternion.h │ │ │ ├── Rotation2D.h │ │ │ ├── RotationBase.h │ │ │ ├── Scaling.h │ │ │ ├── Transform.h │ │ │ └── Translation.h │ │ ├── LU.h │ │ ├── Lazy.h │ │ ├── LeastSquares.h │ │ ├── Macros.h │ │ ├── MathFunctions.h │ │ ├── Memory.h │ │ ├── Meta.h │ │ ├── Minor.h │ │ ├── QR.h │ │ ├── SVD.h │ │ ├── TriangularSolver.h │ │ └── VectorBlock.h │ │ ├── Eigenvalues │ │ ├── CMakeLists.txt │ │ ├── ComplexEigenSolver.h │ │ ├── ComplexSchur.h │ │ ├── ComplexSchur_MKL.h │ │ ├── EigenSolver.h │ │ ├── GeneralizedEigenSolver.h │ │ ├── GeneralizedSelfAdjointEigenSolver.h │ │ ├── HessenbergDecomposition.h │ │ ├── MatrixBaseEigenvalues.h │ │ ├── RealQZ.h │ │ ├── RealSchur.h │ │ ├── RealSchur_MKL.h │ │ ├── SelfAdjointEigenSolver.h │ │ ├── SelfAdjointEigenSolver_MKL.h │ │ └── Tridiagonalization.h │ │ ├── Geometry │ │ ├── AlignedBox.h │ │ ├── AngleAxis.h │ │ ├── CMakeLists.txt │ │ ├── EulerAngles.h │ │ ├── Homogeneous.h │ │ ├── Hyperplane.h │ │ ├── OrthoMethods.h │ │ ├── ParametrizedLine.h │ │ ├── Quaternion.h │ │ ├── Rotation2D.h │ │ ├── RotationBase.h │ │ ├── Scaling.h │ │ ├── Transform.h │ │ ├── Translation.h │ │ ├── Umeyama.h │ │ └── arch │ │ │ ├── CMakeLists.txt │ │ │ └── Geometry_SSE.h │ │ ├── Householder │ │ ├── BlockHouseholder.h │ │ ├── CMakeLists.txt │ │ ├── Householder.h │ │ └── HouseholderSequence.h │ │ ├── IterativeLinearSolvers │ │ ├── BasicPreconditioners.h │ │ ├── BiCGSTAB.h │ │ ├── CMakeLists.txt │ │ ├── ConjugateGradient.h │ │ ├── IncompleteLUT.h │ │ └── IterativeSolverBase.h │ │ ├── Jacobi │ │ ├── CMakeLists.txt │ │ └── Jacobi.h │ │ ├── LU │ │ ├── CMakeLists.txt │ │ ├── Determinant.h │ │ ├── FullPivLU.h │ │ ├── Inverse.h │ │ ├── PartialPivLU.h │ │ ├── PartialPivLU_MKL.h │ │ └── arch │ │ │ ├── CMakeLists.txt │ │ │ └── Inverse_SSE.h │ │ ├── MetisSupport │ │ ├── CMakeLists.txt │ │ └── MetisSupport.h │ │ ├── OrderingMethods │ │ ├── Amd.h │ │ ├── CMakeLists.txt │ │ ├── Eigen_Colamd.h │ │ └── Ordering.h │ │ ├── PaStiXSupport │ │ ├── CMakeLists.txt │ │ └── PaStiXSupport.h │ │ ├── PardisoSupport │ │ ├── CMakeLists.txt │ │ └── PardisoSupport.h │ │ ├── QR │ │ ├── CMakeLists.txt │ │ ├── ColPivHouseholderQR.h │ │ ├── ColPivHouseholderQR_MKL.h │ │ ├── FullPivHouseholderQR.h │ │ ├── HouseholderQR.h │ │ └── HouseholderQR_MKL.h │ │ ├── SPQRSupport │ │ ├── CMakeLists.txt │ │ └── SuiteSparseQRSupport.h │ │ ├── SVD │ │ ├── CMakeLists.txt │ │ ├── JacobiSVD.h │ │ ├── JacobiSVD_MKL.h │ │ └── UpperBidiagonalization.h │ │ ├── SparseCholesky │ │ ├── CMakeLists.txt │ │ ├── SimplicialCholesky.h │ │ └── SimplicialCholesky_impl.h │ │ ├── SparseCore │ │ ├── AmbiVector.h │ │ ├── CMakeLists.txt │ │ ├── CompressedStorage.h │ │ ├── ConservativeSparseSparseProduct.h │ │ ├── MappedSparseMatrix.h │ │ ├── SparseBlock.h │ │ ├── SparseColEtree.h │ │ ├── SparseCwiseBinaryOp.h │ │ ├── SparseCwiseUnaryOp.h │ │ ├── SparseDenseProduct.h │ │ ├── SparseDiagonalProduct.h │ │ ├── SparseDot.h │ │ ├── SparseFuzzy.h │ │ ├── SparseMatrix.h │ │ ├── SparseMatrixBase.h │ │ ├── SparsePermutation.h │ │ ├── SparseProduct.h │ │ ├── SparseRedux.h │ │ ├── SparseSelfAdjointView.h │ │ ├── SparseSparseProductWithPruning.h │ │ ├── SparseTranspose.h │ │ ├── SparseTriangularView.h │ │ ├── SparseUtil.h │ │ ├── SparseVector.h │ │ ├── SparseView.h │ │ └── TriangularSolver.h │ │ ├── SparseLU │ │ ├── CMakeLists.txt │ │ ├── SparseLU.h │ │ ├── SparseLUImpl.h │ │ ├── SparseLU_Memory.h │ │ ├── SparseLU_Structs.h │ │ ├── SparseLU_SupernodalMatrix.h │ │ ├── SparseLU_Utils.h │ │ ├── SparseLU_column_bmod.h │ │ ├── SparseLU_column_dfs.h │ │ ├── SparseLU_copy_to_ucol.h │ │ ├── SparseLU_gemm_kernel.h │ │ ├── SparseLU_heap_relax_snode.h │ │ ├── SparseLU_kernel_bmod.h │ │ ├── SparseLU_panel_bmod.h │ │ ├── SparseLU_panel_dfs.h │ │ ├── SparseLU_pivotL.h │ │ ├── SparseLU_pruneL.h │ │ └── SparseLU_relax_snode.h │ │ ├── SparseQR │ │ ├── CMakeLists.txt │ │ └── SparseQR.h │ │ ├── StlSupport │ │ ├── CMakeLists.txt │ │ ├── StdDeque.h │ │ ├── StdList.h │ │ ├── StdVector.h │ │ └── details.h │ │ ├── SuperLUSupport │ │ ├── CMakeLists.txt │ │ └── SuperLUSupport.h │ │ ├── UmfPackSupport │ │ ├── CMakeLists.txt │ │ └── UmfPackSupport.h │ │ ├── misc │ │ ├── CMakeLists.txt │ │ ├── Image.h │ │ ├── Kernel.h │ │ ├── Solve.h │ │ ├── SparseSolve.h │ │ └── blas.h │ │ └── plugins │ │ ├── ArrayCwiseBinaryOps.h │ │ ├── ArrayCwiseUnaryOps.h │ │ ├── BlockMethods.h │ │ ├── CMakeLists.txt │ │ ├── CommonCwiseBinaryOps.h │ │ ├── CommonCwiseUnaryOps.h │ │ ├── MatrixCwiseBinaryOps.h │ │ └── MatrixCwiseUnaryOps.h ├── msinttypes-r26 │ ├── changelog.txt │ ├── inttypes.h │ └── stdint.h ├── nlopt │ ├── .gitignore │ ├── AUTHORS │ ├── BUILD-MINGW32.sh │ ├── BUILD-MINGW64.sh │ ├── CMakeLists.txt │ ├── COPYING │ ├── COPYRIGHT │ ├── ChangeLog │ ├── Makefile.am │ ├── NEWS │ ├── README.md │ ├── SConscript │ ├── TODO │ ├── api │ │ ├── Makefile.am │ │ ├── deprecated.c │ │ ├── deprecated.cpp │ │ ├── f77api.c │ │ ├── f77api.cpp │ │ ├── f77funcs.h │ │ ├── f77funcs_.h │ │ ├── general.c │ │ ├── general.cpp │ │ ├── nlopt-in.hpp │ │ ├── nlopt-internal.h │ │ ├── nlopt.3 │ │ ├── nlopt.h │ │ ├── nlopt_minimize.3 │ │ ├── nlopt_minimize_constrained.3 │ │ ├── optimize.c │ │ ├── optimize.cpp │ │ ├── options.c │ │ └── options.cpp │ ├── auglag │ │ ├── Makefile.am │ │ ├── auglag.c │ │ ├── auglag.cpp │ │ └── auglag.h │ ├── autogen.sh │ ├── bobyqa │ │ ├── COPYRIGHT │ │ ├── Makefile.am │ │ ├── README.orig │ │ ├── bobyqa.c │ │ ├── bobyqa.cpp │ │ └── bobyqa.h │ ├── cdirect │ │ ├── Makefile.am │ │ ├── cdirect.c │ │ ├── cdirect.cpp │ │ ├── cdirect.h │ │ ├── hybrid.c │ │ └── hybrid.cpp │ ├── cobyla │ │ ├── COPYRIGHT │ │ ├── Makefile.am │ │ ├── README.orig │ │ ├── cobyla.c │ │ ├── cobyla.cpp │ │ └── cobyla.h │ ├── config.cmake.h.in │ ├── config.h │ ├── config.scons.h.in │ ├── configure.ac │ ├── cquad │ │ ├── Makefile.am │ │ ├── cquad.c │ │ └── cquad.h │ ├── crs │ │ ├── Makefile.am │ │ ├── crs.c │ │ ├── crs.cpp │ │ └── crs.h │ ├── direct │ │ ├── AUTHORS │ │ ├── COPYING │ │ ├── DIRect.c │ │ ├── DIRect.cpp │ │ ├── DIRparallel.c │ │ ├── DIRserial.c │ │ ├── DIRserial.cpp │ │ ├── DIRsubrout.c │ │ ├── DIRsubrout.cpp │ │ ├── Makefile.am │ │ ├── direct-internal.h │ │ ├── direct.h │ │ ├── direct_wrap.c │ │ ├── direct_wrap.cpp │ │ └── tstc.c │ ├── esch │ │ ├── COPYRIGHT │ │ ├── Makefile.am │ │ ├── esch.c │ │ ├── esch.cpp │ │ └── esch.h │ ├── isres │ │ ├── Makefile.am │ │ ├── isres.c │ │ ├── isres.cpp │ │ └── isres.h │ ├── luksan │ │ ├── COPYRIGHT │ │ ├── Makefile.am │ │ ├── luksan.h │ │ ├── mssubs.c │ │ ├── mssubs.cpp │ │ ├── mssubs.for │ │ ├── plip.c │ │ ├── plip.cpp │ │ ├── plip.for │ │ ├── plip.txt │ │ ├── plis.c │ │ ├── plis.cpp │ │ ├── plis.for │ │ ├── plis.txt │ │ ├── pnet.c │ │ ├── pnet.cpp │ │ ├── pnet.for │ │ ├── pnet.txt │ │ ├── pssubs.c │ │ ├── pssubs.cpp │ │ └── pssubs.for │ ├── m4 │ │ └── ax_c_threadlocal.m4 │ ├── mlsl │ │ ├── Makefile.am │ │ ├── mlsl.c │ │ ├── mlsl.cpp │ │ └── mlsl.h │ ├── mma │ │ ├── Makefile.am │ │ ├── ccsa_quadratic.c │ │ ├── ccsa_quadratic.cpp │ │ ├── mma.c │ │ ├── mma.cpp │ │ └── mma.h │ ├── neldermead │ │ ├── Makefile.am │ │ ├── neldermead.h │ │ ├── nldrmd.c │ │ ├── nldrmd.cpp │ │ ├── sbplx.c │ │ └── sbplx.cpp │ ├── newuoa │ │ ├── COPYRIGHT │ │ ├── Makefile.am │ │ ├── README.orig │ │ ├── newuoa.c │ │ ├── newuoa.cpp │ │ └── newuoa.h │ ├── nlopt.pc.in │ ├── octave │ │ ├── Makefile.am │ │ ├── NLOPT_AUGLAG.m │ │ ├── NLOPT_AUGLAG_EQ.m │ │ ├── NLOPT_GD_MLSL.m │ │ ├── NLOPT_GD_MLSL_LDS.m │ │ ├── NLOPT_GD_STOGO.m │ │ ├── NLOPT_GD_STOGO_RAND.m │ │ ├── NLOPT_GN_CRS2_LM.m │ │ ├── NLOPT_GN_DIRECT.m │ │ ├── NLOPT_GN_DIRECT_L.m │ │ ├── NLOPT_GN_DIRECT_L_NOSCAL.m │ │ ├── NLOPT_GN_DIRECT_L_RAND.m │ │ ├── NLOPT_GN_DIRECT_L_RAND_NOSCAL.m │ │ ├── NLOPT_GN_DIRECT_NOSCAL.m │ │ ├── NLOPT_GN_ESCH.m │ │ ├── NLOPT_GN_ISRES.m │ │ ├── NLOPT_GN_MLSL.m │ │ ├── NLOPT_GN_MLSL_LDS.m │ │ ├── NLOPT_GN_ORIG_DIRECT.m │ │ ├── NLOPT_GN_ORIG_DIRECT_L.m │ │ ├── NLOPT_G_MLSL.m │ │ ├── NLOPT_G_MLSL_LDS.m │ │ ├── NLOPT_LD_AUGLAG.m │ │ ├── NLOPT_LD_AUGLAG_EQ.m │ │ ├── NLOPT_LD_CCSAQ.m │ │ ├── NLOPT_LD_LBFGS.m │ │ ├── NLOPT_LD_LBFGS_NOCEDAL.m │ │ ├── NLOPT_LD_MMA.m │ │ ├── NLOPT_LD_SLSQP.m │ │ ├── NLOPT_LD_TNEWTON.m │ │ ├── NLOPT_LD_TNEWTON_PRECOND.m │ │ ├── NLOPT_LD_TNEWTON_PRECOND_RESTART.m │ │ ├── NLOPT_LD_TNEWTON_RESTART.m │ │ ├── NLOPT_LD_VAR1.m │ │ ├── NLOPT_LD_VAR2.m │ │ ├── NLOPT_LN_AUGLAG.m │ │ ├── NLOPT_LN_AUGLAG_EQ.m │ │ ├── NLOPT_LN_BOBYQA.m │ │ ├── NLOPT_LN_COBYLA.m │ │ ├── NLOPT_LN_NELDERMEAD.m │ │ ├── NLOPT_LN_NEWUOA.m │ │ ├── NLOPT_LN_NEWUOA_BOUND.m │ │ ├── NLOPT_LN_PRAXIS.m │ │ ├── NLOPT_LN_SBPLX.m │ │ ├── dummy.c │ │ ├── mkconstants.sh │ │ ├── nlopt_minimize.m │ │ ├── nlopt_minimize_constrained.m │ │ ├── nlopt_optimize-mex.c │ │ ├── nlopt_optimize-oct.cc │ │ └── nlopt_optimize.m │ ├── praxis │ │ ├── Makefile.am │ │ ├── praxis.c │ │ ├── praxis.cpp │ │ └── praxis.h │ ├── slsqp │ │ ├── COPYRIGHT │ │ ├── Makefile.am │ │ ├── slsqp.c │ │ ├── slsqp.cpp │ │ └── slsqp.h │ ├── stogo │ │ ├── COPYRIGHT │ │ ├── Makefile.am │ │ ├── global.cc │ │ ├── global.h │ │ ├── linalg.cc │ │ ├── linalg.h │ │ ├── local.cc │ │ ├── local.h │ │ ├── prog.cc │ │ ├── rosen.h │ │ ├── stogo.cc │ │ ├── stogo.h │ │ ├── stogo_config.h │ │ ├── testfun.h │ │ ├── testros.cc │ │ ├── tools.cc │ │ ├── tools.h │ │ ├── tst.cc │ │ └── tstc.c │ ├── subplex │ │ ├── Makefile.am │ │ ├── subplex.c │ │ └── subplex.h │ ├── swig │ │ ├── Makefile.am │ │ ├── nlopt-exceptions.i │ │ ├── nlopt-guile.i │ │ ├── nlopt-python.i │ │ ├── nlopt.i │ │ └── numpy.i │ ├── tensor │ │ ├── COPYRIGHT │ │ └── tensor.c │ ├── test │ │ ├── Makefile.am │ │ ├── box.c │ │ ├── lorentzfit.c │ │ ├── test_std.py │ │ ├── testfuncs.c │ │ ├── testfuncs.h │ │ └── testopt.cpp │ └── util │ │ ├── Makefile.am │ │ ├── mt19937ar.c │ │ ├── mt19937ar.cpp │ │ ├── nlopt-util.h │ │ ├── qsort_r.c │ │ ├── qsort_r.cpp │ │ ├── redblack.c │ │ ├── redblack.cpp │ │ ├── redblack.h │ │ ├── redblack_test.c │ │ ├── rescale.c │ │ ├── rescale.cpp │ │ ├── soboldata.h │ │ ├── sobolseq.c │ │ ├── sobolseq.cpp │ │ ├── stop.c │ │ ├── stop.cpp │ │ ├── timer.c │ │ └── timer.cpp └── nlopt_src.files ├── LICENSE ├── MANIFEST.in ├── README.md ├── cython └── lmm_forest │ ├── .gitignore │ ├── SplittingCore.h │ ├── SplittingCore.pyx │ └── types.h ├── demos ├── demo_gp2kronSum.py ├── demo_gp2kronSumLR.py ├── demo_gp3kronSumLR.py ├── demo_gp_regression.py ├── run_mtSet.sh └── run_mtSetPC.sh ├── deploy ├── appveyor.miniconda.install.ps1 ├── appveyor.run_with_env.cmd ├── apt_limix_install ├── conda ├── conda.step ├── dnf_limix_install ├── github ├── github.step ├── pypi ├── pypi.step ├── test.pypi.apt ├── test.pypi.dnf ├── test.pypi.zypper ├── travis_conda ├── version └── zypper_limix_install ├── derivations ├── 2kronSum_reml │ ├── notes.tex │ └── utils.tex ├── derivations.tex └── utils.tex ├── doc ├── doxy.cfg ├── pages │ ├── authors.page │ ├── documentation.page │ ├── faq.page │ ├── installation.page │ ├── license.page │ ├── limix_html_footer.html │ └── tutorials.page ├── py_filter └── update_doc.sh ├── limix ├── __init__.py ├── core │ ├── __init__.py │ ├── covar │ │ ├── __init__.py │ │ ├── acombinators.py │ │ ├── categorical.py │ │ ├── categoricalLR.py │ │ ├── combinators.py │ │ ├── cov2kronSum.py │ │ ├── cov2kronSumLR.py │ │ ├── cov3kronSumLR.py │ │ ├── cov_reml.py │ │ ├── covar_base.py │ │ ├── diagonal.py │ │ ├── dirIndirCov.py │ │ ├── fixed.py │ │ ├── freeform.py │ │ ├── kronecker.py │ │ ├── lowrank.py │ │ ├── sqexp.py │ │ ├── test │ │ │ ├── __init__.py │ │ │ ├── test_ZKZ.py │ │ │ ├── test_categorical.py │ │ │ ├── test_combinators.py │ │ │ ├── test_cov2kronSum.py │ │ │ ├── test_cov2kronSumLR.py │ │ │ ├── test_cov3kronSumLR.py │ │ │ ├── test_dirIndirCov.py │ │ │ ├── test_fixed.py │ │ │ ├── test_freeform.py │ │ │ ├── test_kronecker.py │ │ │ ├── test_lowrank.py │ │ │ └── test_sqexp.py │ │ ├── util │ │ │ └── __init__.py │ │ └── zkz.py │ ├── gp │ │ ├── __init__.py │ │ ├── gp2kronSum.py │ │ ├── gp2kronSumLR.py │ │ ├── gp3kronSumLR.py │ │ ├── gp_base.py │ │ └── relay.py │ ├── likelihood │ │ ├── __init__.py │ │ └── likelihood_base.py │ ├── linalg │ │ ├── __init__.py │ │ ├── dist.py │ │ └── linalg_matrix.py │ ├── mean │ │ ├── __init__.py │ │ ├── base.py │ │ ├── linear.py │ │ ├── mean.py │ │ ├── meanKronSum.py │ │ ├── mean_base.py │ │ ├── mean_efficient.py │ │ └── tests │ │ │ └── test_mean.py │ ├── old │ │ ├── __init__.py │ │ ├── cobj.py │ │ ├── covar │ │ │ └── covariance.py │ │ ├── gp │ │ │ └── gp_base.py │ │ └── test │ │ │ ├── dev_assoc_D.py │ │ │ ├── test_association_D.py │ │ │ ├── test_gp.py │ │ │ ├── test_gp3kronSumApprox_D.py │ │ │ ├── test_gp3kronSumApprox_old_D.py │ │ │ ├── test_gp_D.py │ │ │ └── test_mean_D.py │ ├── optimize │ │ ├── __init__.py │ │ └── optimize_bfgs.py │ ├── test │ │ ├── __init__.py │ │ ├── test_gp2kronSum.py │ │ ├── test_gp2kronSumLR.py │ │ ├── test_gp3kronSumLR.py │ │ ├── test_gp_base.py │ │ └── test_gp_more.py │ ├── type │ │ ├── __init__.py │ │ ├── exception.py │ │ └── observed.py │ └── utils │ │ └── __init__.py ├── deprecated │ ├── .gitignore │ ├── __init__.py │ ├── archive │ │ ├── FastVDMM.py │ │ ├── data_deprecated.py │ │ ├── qtl_old.py │ │ ├── util.py │ │ └── varianceDecompositionOld.py │ ├── core.py │ ├── io │ │ ├── __init__.py │ │ ├── conversion.py │ │ ├── data.py │ │ ├── data_util.py │ │ ├── genotype_reader.py │ │ ├── output_writer.py │ │ ├── phenotype_reader.py │ │ └── plink.py │ ├── modules │ │ ├── BLUP.py │ │ ├── __init__.py │ │ ├── grm.py │ │ ├── lmm_fast.py │ │ ├── lmm_forest.py │ │ ├── lmmlasso.py │ │ ├── mixedForestUtils.py │ │ ├── multiPanama.py │ │ ├── panama.py │ │ ├── parMixedForest.py │ │ ├── pySplittingCore.py │ │ ├── qtl.py │ │ ├── sim │ │ │ ├── __init__.py │ │ │ └── sampler.py │ │ ├── varDecompSet.py │ │ └── varianceDecomposition.py │ ├── stats │ │ ├── __init__.py │ │ ├── fdr.py │ │ ├── geno_summary.py │ │ ├── pca.py │ │ └── power.py │ └── utils │ │ ├── __init__.py │ │ ├── fastlmm.py │ │ ├── plot.py │ │ └── preprocess.py ├── ensemble │ ├── .gitignore │ ├── __init__.py │ ├── blup.py │ ├── lmm_fast.py │ ├── lmm_forest.py │ ├── lmm_forest_utils.py │ ├── par_lmm_forest.py │ └── py_splitting_core.py ├── hcache │ ├── __init__.py │ └── _hcache.py ├── iSet │ ├── __init__.py │ ├── iset.py │ ├── linalg_utils.py │ ├── mvSet.py │ ├── mvSetFull.py │ └── mvSetInc.py ├── io │ ├── __init__.py │ ├── conversion.py │ ├── data.py │ ├── data_util.py │ ├── genotype_reader.py │ ├── output_writer.py │ ├── phenotype_reader.py │ └── plink.py ├── modules │ ├── BLUP.py │ ├── __init__.py │ ├── dirIndirVD_commented_forDistrib.py │ ├── grm.py │ ├── lmm_fast.py │ ├── lmm_forest.py │ ├── lmmlasso.py │ ├── mixedForestUtils.py │ ├── multiPanama.py │ ├── panama.py │ ├── parMixedForest.py │ ├── pySplittingCore.py │ ├── qtl.py │ ├── sim │ │ ├── __init__.py │ │ └── sampler.py │ ├── social_data_HSmice_paper.py │ ├── varDecompSet.py │ └── varianceDecomposition.py ├── mtSet │ ├── __init__.py │ ├── core │ │ ├── __init__.py │ │ ├── analyzeCore.py │ │ ├── iset_utils.py │ │ ├── plink_reader.py │ │ ├── postprocessCore.py │ │ ├── preprocessCore.py │ │ ├── read_utils.py │ │ ├── simPhenoCore.py │ │ ├── simulator.py │ │ ├── splitter.py │ │ └── splitter_bed.py │ ├── iset.py │ └── mtset.py ├── scripts │ ├── __init__.py │ ├── iSet_analyze.py │ ├── iSet_postprocess.py │ ├── limix_converter.py │ ├── limix_runner.py │ ├── mtSet_analyze.py │ ├── mtSet_postprocess.py │ ├── mtSet_preprocess.py │ └── mtSet_simPheno.py ├── stats │ ├── __init__.py │ ├── chi2mixture.py │ ├── fdr.py │ ├── geno_summary.py │ ├── pca.py │ └── power.py ├── test │ ├── __init__.py │ ├── covar │ │ ├── __init__.py │ │ ├── covar.py │ │ ├── test_combinators.py │ │ ├── test_freeform.py │ │ ├── test_lik.py │ │ ├── test_linear.py │ │ └── test_se.py │ ├── data.py │ ├── data │ │ └── plinkdata │ │ │ ├── toydata.bed │ │ │ ├── toydata.bim │ │ │ ├── toydata.fam │ │ │ ├── toydata.phe │ │ │ └── toydata.phe6 │ ├── gdb_python_debug.sh │ ├── gp │ │ ├── __init__.py │ │ ├── test_gp.py │ │ └── test_gplvm.py │ ├── lmm │ │ ├── lmm_data1 │ │ │ ├── Beta.txt │ │ │ ├── BetaSte.txt │ │ │ ├── Cov.txt │ │ │ ├── K.txt │ │ │ ├── X.txt │ │ │ ├── Y.txt │ │ │ └── pv.txt │ │ ├── test_CInteractLMM.py │ │ ├── test_CKroneckerLMM.py │ │ ├── test_CLMM.py │ │ └── test_CLMM_large.py │ ├── lmm_forest │ │ ├── test_data │ │ │ └── lmm_forest_toy_data.h5 │ │ └── test_lmm_forest.py │ ├── lmm_lasso │ │ ├── lmmlasso │ │ │ ├── K.txt │ │ │ ├── X.txt │ │ │ ├── causal_idx.txt │ │ │ ├── params_true.txt │ │ │ ├── y.txt │ │ │ └── yhat.txt │ │ └── test_lmmlasso.py │ ├── mtSet │ │ ├── data │ │ │ ├── XX.txt │ │ │ ├── Xr.txt │ │ │ ├── Y.txt │ │ │ ├── check.py │ │ │ ├── gendata.py │ │ │ ├── res_mtSetNull_Cg.txt │ │ │ ├── res_mtSetNull_Cn.txt │ │ │ ├── res_mtSetNull_fixed_Cg.txt │ │ │ ├── res_mtSetNull_fixed_Cn.txt │ │ │ ├── res_mtSetNull_fixed_weights.txt │ │ │ ├── res_mtSetPC_base_Cg.txt │ │ │ ├── res_mtSetPC_base_Cn.txt │ │ │ ├── res_mtSetPC_base_Cr.txt │ │ │ ├── res_mtSetPC_fixed_Cn.txt │ │ │ ├── res_mtSetPC_fixed_Cr.txt │ │ │ ├── res_mtSetPCnull_Cn.txt │ │ │ ├── res_mtSetPCnull_fixed_Cg.txt │ │ │ ├── res_mtSetPCnull_fixed_Cn.txt │ │ │ ├── res_mtSetPCnull_fixed_weights.txt │ │ │ ├── res_mtSet_base_Cg.txt │ │ │ ├── res_mtSet_base_Cn.txt │ │ │ ├── res_mtSet_base_Cr.txt │ │ │ ├── res_mtSet_fixed_Cg.txt │ │ │ ├── res_mtSet_fixed_Cn.txt │ │ │ └── res_mtSet_fixed_Cr.txt │ │ └── test_mtset.py │ ├── python_debug.py │ ├── run_all.py │ ├── test_modules.py │ └── varDecomp │ │ ├── test_varDecomp.py │ │ └── varDecomp │ │ ├── X.txt │ │ ├── Y.txt │ │ └── params_true.txt ├── utils │ ├── __init__.py │ ├── check_grad.py │ ├── eigen.py │ ├── linalg.py │ ├── plot.py │ ├── preprocess.py │ ├── psd_solve.py │ ├── svd_utils.py │ └── util_functions.py └── varDecomp │ ├── __init__.py │ └── varianceDecomposition.py ├── setup.cfg ├── setup.py ├── src ├── archive │ ├── LMM │ │ ├── CGPLMM.cpp │ │ ├── CGPLMM.h │ │ ├── kronecker_lmm_old.cpp │ │ ├── kronecker_lmm_old.h │ │ ├── lmm_old.cpp │ │ └── lmm_old.h │ ├── lasso │ │ ├── lasso.cpp │ │ └── lasso.h │ ├── modules │ │ ├── CVqtl.cpp │ │ └── CVqtl.h │ └── utils │ │ ├── matrix_like.cpp │ │ └── matrix_like.h ├── interfaces │ ├── R │ │ ├── CMakeLists.txt │ │ └── gpmix.i │ ├── README │ ├── covar.i │ ├── doxy2swig.py │ ├── gp.i │ ├── io.i │ ├── java │ │ ├── CMakeLists.txt │ │ └── limix.i │ ├── lik.i │ ├── lmm.i │ ├── mean.i │ ├── modules.i │ ├── python │ │ ├── CMakeLists.txt │ │ ├── SConscript │ │ ├── eigen.i │ │ ├── eigen_old.i │ │ ├── limix.i │ │ ├── limix_wrap.cpp │ │ ├── numpy.i │ │ └── numpy_old.i │ └── types.i ├── limix │ ├── LMM │ │ ├── kronecker_lmm.cpp │ │ ├── kronecker_lmm.h │ │ ├── kronecker_lmm.i │ │ ├── lmm.cpp │ │ ├── lmm.h │ │ └── lmm.i │ ├── LMM_forest │ │ ├── SplittingCore.h │ │ ├── lmm_forest.cpp │ │ ├── lmm_forest.h │ │ └── lmm_forest.i │ ├── SConscript │ ├── covar │ │ ├── combinators.cpp │ │ ├── combinators.h │ │ ├── combinators.i │ │ ├── covariance.cpp │ │ ├── covariance.h │ │ ├── covariance.i │ │ ├── dist.cpp │ │ ├── dist.h │ │ ├── freeform.cpp │ │ ├── freeform.h │ │ ├── freeform.i │ │ ├── linear.cpp │ │ ├── linear.h │ │ ├── linear.i │ │ ├── se.cpp │ │ ├── se.h │ │ └── se.i │ ├── gp │ │ ├── gp_Sum.cpp │ │ ├── gp_Sum.h │ │ ├── gp_Sum.i │ │ ├── gp_base.cpp │ │ ├── gp_base.h │ │ ├── gp_base.i │ │ ├── gp_kronSum.cpp │ │ ├── gp_kronSum.h │ │ ├── gp_kronSum.i │ │ ├── gp_kronecker.cpp │ │ ├── gp_kronecker.h │ │ ├── gp_kronecker.i │ │ ├── gp_opt.cpp │ │ ├── gp_opt.h │ │ └── gp_opt.i │ ├── io │ │ ├── dataframe.cpp │ │ ├── dataframe.h │ │ ├── dataframe.i │ │ ├── genotype.cpp │ │ ├── genotype.h │ │ ├── genotype.i │ │ ├── split.cpp │ │ └── split.h │ ├── likelihood │ │ ├── likelihood.cpp │ │ ├── likelihood.h │ │ └── likelihood.i │ ├── mean │ │ ├── ADataTerm.cpp │ │ ├── ADataTerm.h │ │ ├── ADataTerm.i │ │ ├── CData.cpp │ │ ├── CData.h │ │ ├── CData.i │ │ ├── CKroneckerMean.cpp │ │ ├── CKroneckerMean.h │ │ ├── CKroneckerMean.i │ │ ├── CLinearMean.cpp │ │ ├── CLinearMean.h │ │ ├── CLinearMean.i │ │ ├── CSumLinear.cpp │ │ ├── CSumLinear.h │ │ └── CSumLinear.i │ ├── modules │ │ ├── CVarianceDecomposition.cpp │ │ ├── CVarianceDecomposition.h │ │ └── 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