Files in OHDSI/Cyclops
Cyclic Coordinate Descent for Logistic, Poisson and Survival Analysis
.Rbuildignore
.covrignore
.gitattributes
.github/workflows/R_CMD_check_Hades.yaml
.github/workflows/R_CMD_check_main_weekly.yaml
.github/workflows/nightly_cleanup_Hades.yml
.gitignore
CMakeLists.txt
Cyclops.Rproj
DESCRIPTION
NAMESPACE
NEWS.md
NEWS.old
R/CrossValidationControl.R
R/Cyclops-package.R
R/DataManagement.R
R/ExampleData.R
R/GetFrineGrayWeights.R
R/ModelFit.R
R/Multitype.R
R/NewDataConversion.R
R/PackageMaintenance.R
R/ParameterizedPrior.R
R/Predict.R
R/RcppExports.R
R/Simulation.R
R/SpecialPriors.R
R/Survfit.R
R/TimeEffects.R
R/WeightBasedSearchControl.R
R/cyclops.R
README.md
_pkgdown.yml
cleanup
compare_versions
configure
configure.win
cran-comments.md
data-raw/oxford.R
data/oxford.rda
deploy.sh
deprecated/LegacyDataConversion.R
docker/r-devel-san-clang/Dockerfile
docker/r-devel-san/Dockerfile
docs/404.html
docs/authors.html
docs/bootstrap-toc.css
docs/bootstrap-toc.js
docs/docsearch.css
docs/docsearch.js
docs/index.html
docs/link.svg
docs/news/index.html
docs/pkgdown.css
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/Cyclops-package.html
docs/reference/Multitype.html
docs/reference/Rplot001.png
docs/reference/aconfint.html
docs/reference/appendSqlCyclopsData.html
docs/reference/coef.cyclopsFit.html
docs/reference/confint.cyclopsFit.html
docs/reference/convertToCyclopsData.html
docs/reference/convertToCyclopsVariance.html
docs/reference/convertToGlmnetLambda.html
docs/reference/convertToTimeVaryingCoef.html
docs/reference/coverage.html
docs/reference/createAutoGridCrossValidationControl.html
docs/reference/createControl.html
docs/reference/createCyclopsData.html
docs/reference/createNonSeparablePrior.html
docs/reference/createParameterizedPrior.html
docs/reference/createPrior.html
docs/reference/createWeightBasedSearchControl.html
docs/reference/cyclops.html
docs/reference/finalizeSqlCyclopsData.html
docs/reference/fitCyclopsModel.html
docs/reference/fitCyclopsSimulation.html
docs/reference/getCovariateIds.html
docs/reference/getCovariateTypes.html
docs/reference/getCrossValidationInfo.html
docs/reference/getCyclopsPredictiveLogLikelihood.html
docs/reference/getCyclopsProfileLogLikelihood.html
docs/reference/getFineGrayWeights.html
docs/reference/getFloatingPointSize.html
docs/reference/getHyperParameter.html
docs/reference/getNumberOfCovariates.html
docs/reference/getNumberOfRows.html
docs/reference/getNumberOfStrata.html
docs/reference/getNumberOfTypes.html
docs/reference/getSEs.html
docs/reference/getUnivariableCorrelation.html
docs/reference/getUnivariableSeparability.html
docs/reference/index.html
docs/reference/isInitialized.html
docs/reference/isSorted.html
docs/reference/logLik.cyclopsFit.html
docs/reference/meanLinearPredictor.html
docs/reference/mse.html
docs/reference/oxford.html
docs/reference/plotCyclopsSimulationFit.html
docs/reference/predict.cyclopsFit.html
docs/reference/print.cyclopsData.html
docs/reference/print.cyclopsFit.html
docs/reference/printCyclopsRowIds.html
docs/reference/printMatrixMarket.html
docs/reference/readCyclopsData.html
docs/reference/reduce.html
docs/reference/simulateCyclopsData.html
docs/reference/splitTime.html
docs/reference/summary.cyclopsData.html
docs/reference/survfit.cyclopsFit.html
docs/reference/vcov.cyclopsFit.html
docs/sitemap.xml
extras/Cyclops.pdf
extras/PackageMaintenance.R
inst/CITATION
inst/extdata/CCD_LOGISTIC_TEST_17var.txt
inst/extdata/cpr_test.RData
inst/extdata/infert_ccd.txt
inst/extdata/test1-clr.txt
logo/Cyclops.png
man-roxygen/cyclopsData.R
man-roxygen/elaborateExample.R
man-roxygen/prior.R
man-roxygen/types.R
man/Cyclops-package.Rd
man/Multitype.Rd
man/aconfint.Rd
man/appendSqlCyclopsData.Rd
man/coef.cyclopsFit.Rd
man/confint.cyclopsFit.Rd
man/convertToCyclopsData.Rd
man/convertToCyclopsVariance.Rd
man/convertToGlmnetLambda.Rd
man/convertToTimeVaryingCoef.Rd
man/coverage.Rd
man/createAutoGridCrossValidationControl.Rd
man/createControl.Rd
man/createCyclopsData.Rd
man/createNonSeparablePrior.Rd
man/createParameterizedPrior.Rd
man/createPrior.Rd
man/createWeightBasedSearchControl.Rd
man/cyclops.Rd
man/finalizeSqlCyclopsData.Rd
man/fitCyclopsModel.Rd
man/fitCyclopsSimulation.Rd
man/getCovariateIds.Rd
man/getCovariateTypes.Rd
man/getCrossValidationInfo.Rd
man/getCyclopsPredictiveLogLikelihood.Rd
man/getCyclopsProfileLogLikelihood.Rd
man/getFineGrayWeights.Rd
man/getFloatingPointSize.Rd
man/getHyperParameter.Rd
man/getNumberOfCovariates.Rd
man/getNumberOfRows.Rd
man/getNumberOfStrata.Rd
man/getNumberOfTypes.Rd
man/getSEs.Rd
man/getUnivariableCorrelation.Rd
man/getUnivariableSeparability.Rd
man/isInitialized.Rd
man/logLik.cyclopsFit.Rd
man/meanLinearPredictor.Rd
man/mse.Rd
man/oxford.Rd
man/plotCyclopsSimulationFit.Rd
man/predict.cyclopsFit.Rd
man/print.cyclopsData.Rd
man/print.cyclopsFit.Rd
man/printMatrixMarket.Rd
man/readCyclopsData.Rd
man/reduce.Rd
man/simulateCyclopsData.Rd
man/splitTime.Rd
man/summary.cyclopsData.Rd
man/survfit.cyclopsFit.Rd
man/vcov.cyclopsFit.Rd
notes/TODO_efron.txt
notes/parallel_transform.h
src/IsSorted.cpp
src/IsSorted.h
src/Makevars.in
src/Makevars.win.in
src/RcppCyclopsInterface.cpp
src/RcppCyclopsInterface.h
src/RcppExports.cpp
src/RcppIsSorted.cpp
src/RcppModelData.cpp
src/RcppModelData.h
src/RcppOutputHelper.h
src/RcppProgressLogger.h
src/cyclops/CcdInterface.cpp
src/cyclops/CcdInterface.h
src/cyclops/CompressedDataMatrix.cpp
src/cyclops/CompressedDataMatrix.h
src/cyclops/CyclicCoordinateDescent.cpp
src/cyclops/CyclicCoordinateDescent.h
src/cyclops/Iterators.h
src/cyclops/ModelData.cpp
src/cyclops/ModelData.h
src/cyclops/Thread.h
src/cyclops/Timer.cpp
src/cyclops/Timer.h
src/cyclops/Timing.h
src/cyclops/Types.h
src/cyclops/drivers/AbstractCrossValidationDriver.cpp
src/cyclops/drivers/AbstractCrossValidationDriver.h
src/cyclops/drivers/AbstractDriver.cpp
src/cyclops/drivers/AbstractDriver.h
src/cyclops/drivers/AbstractSelector.cpp
src/cyclops/drivers/AbstractSelector.h
src/cyclops/drivers/AutoSearchCrossValidationDriver.cpp
src/cyclops/drivers/AutoSearchCrossValidationDriver.h
src/cyclops/drivers/BootstrapDriver.cpp
src/cyclops/drivers/BootstrapDriver.h
src/cyclops/drivers/BootstrapSelector.cpp
src/cyclops/drivers/BootstrapSelector.h
src/cyclops/drivers/CrossValidationSelector.cpp
src/cyclops/drivers/CrossValidationSelector.h
src/cyclops/drivers/GridSearchCrossValidationDriver.cpp
src/cyclops/drivers/GridSearchCrossValidationDriver.h
src/cyclops/drivers/HierarchyAutoSearchCrossValidationDriver.cpp
src/cyclops/drivers/HierarchyAutoSearchCrossValidationDriver.h
src/cyclops/drivers/HierarchyGridSearchCrossValidationDriver.cpp
src/cyclops/drivers/HierarchyGridSearchCrossValidationDriver.h
src/cyclops/drivers/ProportionSelector.cpp
src/cyclops/drivers/ProportionSelector.h
src/cyclops/drivers/WeightBasedSelector.cpp
src/cyclops/drivers/WeightBasedSelector.h
src/cyclops/engine/AbstractModelSpecifics.cpp
src/cyclops/engine/AbstractModelSpecifics.h
src/cyclops/engine/ModelSpecifics.h
src/cyclops/engine/ModelSpecifics.hpp
src/cyclops/engine/ParallelLoops.h
src/cyclops/engine/Ranges.h
src/cyclops/engine/Recursions.hpp
src/cyclops/engine/ThreadPool.h
src/cyclops/io/BaseInputReader.h
src/cyclops/io/InputReader.cpp
src/cyclops/io/InputReader.h
src/cyclops/io/NewGenericInputReader.h
src/cyclops/io/OutputWriter.h
src/cyclops/io/ProgressLogger.h
src/cyclops/io/SparseIndexer.h
src/cyclops/priors/CovariatePrior.cpp
src/cyclops/priors/CovariatePrior.h
src/cyclops/priors/JointPrior.h
src/cyclops/priors/NewCovariatePrior.h
src/cyclops/priors/PriorFunction.h
src/tinythread/fast_mutex.h
src/tinythread/tinythread.cpp
src/tinythread/tinythread.h
src/utils/HParSearch.cpp
src/utils/HParSearch.h
src/utils/RZeroIn.h
standalone/CMake/FindCUDA.cmake
standalone/CMake/FindCUDA/make2cmake.cmake
standalone/CMake/FindCUDA/parse_cubin.cmake
standalone/CMake/FindCUDA/run_nvcc.cmake
standalone/Compile-using-RTools.txt
standalone/build/Makefile.dogfish
standalone/build/suppress_cuda.valgrind
standalone/codebase/CCD-DP/CMakeLists.txt
standalone/codebase/CCD/CMakeLists.txt
standalone/codebase/CCD/CmdLineCcdInterface.cpp
standalone/codebase/CCD/CmdLineCcdInterface.h
standalone/codebase/CCD/GPUCyclicCoordinateDescent.cpp
standalone/codebase/CCD/GPUCyclicCoordinateDescent.h
standalone/codebase/CCD/ccd.cpp
standalone/codebase/CCD/imputation/ImputationPolicy.cpp
standalone/codebase/CCD/imputation/ImputationPolicy.h
standalone/codebase/CCD/imputation/ImputeVariables.cpp
standalone/codebase/CCD/imputation/ImputeVariables.h
standalone/codebase/CCD/imputation/ccdimpute.cpp
standalone/codebase/CCD/imputation/ccdimpute.h
standalone/codebase/CCD/io/BBRInputReader.h
standalone/codebase/CCD/io/BBROutputWriter.h
standalone/codebase/CCD/io/CCTestInputReader.cpp
standalone/codebase/CCD/io/CCTestInputReader.h
standalone/codebase/CCD/io/CLRInputReader.cpp
standalone/codebase/CCD/io/CLRInputReader.h
standalone/codebase/CCD/io/CSVInputReader.h
standalone/codebase/CCD/io/CmdLineProgressLogger.h
standalone/codebase/CCD/io/CoxInputReader.cpp
standalone/codebase/CCD/io/CoxInputReader.h
standalone/codebase/CCD/io/HierarchyReader.cpp
standalone/codebase/CCD/io/HierarchyReader.h
standalone/codebase/CCD/io/NewCLRInputReader.h
standalone/codebase/CCD/io/NewCoxInputReader.h
standalone/codebase/CCD/io/NewSCCSInputReader.h
standalone/codebase/CCD/io/RTestInputReader.cpp
standalone/codebase/CCD/io/RTestInputReader.h
standalone/codebase/CCD/io/SCCSInputReader.cpp
standalone/codebase/CCD/io/SCCSInputReader.h
standalone/codebase/Eigen/Array
standalone/codebase/Eigen/CMakeLists.txt
standalone/codebase/Eigen/Cholesky
standalone/codebase/Eigen/CholmodSupport
standalone/codebase/Eigen/Core
standalone/codebase/Eigen/Dense
standalone/codebase/Eigen/Eigen
standalone/codebase/Eigen/Eigen2Support
standalone/codebase/Eigen/Eigenvalues
standalone/codebase/Eigen/Geometry
standalone/codebase/Eigen/Householder
standalone/codebase/Eigen/IterativeLinearSolvers
standalone/codebase/Eigen/Jacobi
standalone/codebase/Eigen/LU
standalone/codebase/Eigen/LeastSquares
standalone/codebase/Eigen/OrderingMethods
standalone/codebase/Eigen/PaStiXSupport
standalone/codebase/Eigen/PardisoSupport
standalone/codebase/Eigen/QR
standalone/codebase/Eigen/QtAlignedMalloc
standalone/codebase/Eigen/SVD
standalone/codebase/Eigen/Sparse
standalone/codebase/Eigen/SparseCholesky
standalone/codebase/Eigen/SparseCore
standalone/codebase/Eigen/StdDeque
standalone/codebase/Eigen/StdList
standalone/codebase/Eigen/StdVector
standalone/codebase/Eigen/SuperLUSupport
standalone/codebase/Eigen/UmfPackSupport
standalone/codebase/Eigen/src/CMakeLists.txt
standalone/codebase/Eigen/src/Cholesky/CMakeLists.txt
standalone/codebase/Eigen/src/Cholesky/LDLT.h
standalone/codebase/Eigen/src/Cholesky/LLT.h
standalone/codebase/Eigen/src/Cholesky/LLT_MKL.h
standalone/codebase/Eigen/src/CholmodSupport/CMakeLists.txt
standalone/codebase/Eigen/src/CholmodSupport/CholmodSupport.h
standalone/codebase/Eigen/src/Core/Array.h
standalone/codebase/Eigen/src/Core/ArrayBase.h
standalone/codebase/Eigen/src/Core/ArrayWrapper.h
standalone/codebase/Eigen/src/Core/Assign.h
standalone/codebase/Eigen/src/Core/Assign_MKL.h
standalone/codebase/Eigen/src/Core/BandMatrix.h
standalone/codebase/Eigen/src/Core/Block.h
standalone/codebase/Eigen/src/Core/BooleanRedux.h
standalone/codebase/Eigen/src/Core/CMakeLists.txt
standalone/codebase/Eigen/src/Core/CommaInitializer.h
standalone/codebase/Eigen/src/Core/CwiseBinaryOp.h
standalone/codebase/Eigen/src/Core/CwiseNullaryOp.h
standalone/codebase/Eigen/src/Core/CwiseUnaryOp.h
standalone/codebase/Eigen/src/Core/CwiseUnaryView.h
standalone/codebase/Eigen/src/Core/DenseBase.h
standalone/codebase/Eigen/src/Core/DenseCoeffsBase.h
standalone/codebase/Eigen/src/Core/DenseStorage.h
standalone/codebase/Eigen/src/Core/Diagonal.h
standalone/codebase/Eigen/src/Core/DiagonalMatrix.h
standalone/codebase/Eigen/src/Core/DiagonalProduct.h
standalone/codebase/Eigen/src/Core/Dot.h
standalone/codebase/Eigen/src/Core/EigenBase.h
standalone/codebase/Eigen/src/Core/Flagged.h
standalone/codebase/Eigen/src/Core/ForceAlignedAccess.h
standalone/codebase/Eigen/src/Core/Functors.h
standalone/codebase/Eigen/src/Core/Fuzzy.h
standalone/codebase/Eigen/src/Core/GeneralProduct.h
standalone/codebase/Eigen/src/Core/GenericPacketMath.h
standalone/codebase/Eigen/src/Core/GlobalFunctions.h
standalone/codebase/Eigen/src/Core/IO.h
standalone/codebase/Eigen/src/Core/Map.h
standalone/codebase/Eigen/src/Core/MapBase.h
standalone/codebase/Eigen/src/Core/MathFunctions.h
standalone/codebase/Eigen/src/Core/Matrix.h
standalone/codebase/Eigen/src/Core/MatrixBase.h
standalone/codebase/Eigen/src/Core/NestByValue.h
standalone/codebase/Eigen/src/Core/NoAlias.h
standalone/codebase/Eigen/src/Core/NumTraits.h
standalone/codebase/Eigen/src/Core/PermutationMatrix.h
standalone/codebase/Eigen/src/Core/PlainObjectBase.h
standalone/codebase/Eigen/src/Core/Product.h
standalone/codebase/Eigen/src/Core/ProductBase.h
standalone/codebase/Eigen/src/Core/Random.h
standalone/codebase/Eigen/src/Core/Redux.h
standalone/codebase/Eigen/src/Core/Replicate.h
standalone/codebase/Eigen/src/Core/ReturnByValue.h
standalone/codebase/Eigen/src/Core/Reverse.h
standalone/codebase/Eigen/src/Core/Select.h
standalone/codebase/Eigen/src/Core/SelfAdjointView.h
standalone/codebase/Eigen/src/Core/SelfCwiseBinaryOp.h
standalone/codebase/Eigen/src/Core/SolveTriangular.h
standalone/codebase/Eigen/src/Core/StableNorm.h
standalone/codebase/Eigen/src/Core/Stride.h
standalone/codebase/Eigen/src/Core/Swap.h
standalone/codebase/Eigen/src/Core/Transpose.h
standalone/codebase/Eigen/src/Core/Transpositions.h
standalone/codebase/Eigen/src/Core/TriangularMatrix.h
standalone/codebase/Eigen/src/Core/VectorBlock.h
standalone/codebase/Eigen/src/Core/VectorwiseOp.h
standalone/codebase/Eigen/src/Core/Visitor.h
standalone/codebase/Eigen/src/Core/arch/AltiVec/CMakeLists.txt
standalone/codebase/Eigen/src/Core/arch/AltiVec/Complex.h
standalone/codebase/Eigen/src/Core/arch/AltiVec/PacketMath.h
standalone/codebase/Eigen/src/Core/arch/CMakeLists.txt
standalone/codebase/Eigen/src/Core/arch/Default/CMakeLists.txt
standalone/codebase/Eigen/src/Core/arch/Default/Settings.h
standalone/codebase/Eigen/src/Core/arch/NEON/CMakeLists.txt
standalone/codebase/Eigen/src/Core/arch/NEON/Complex.h
standalone/codebase/Eigen/src/Core/arch/NEON/PacketMath.h
standalone/codebase/Eigen/src/Core/arch/SSE/CMakeLists.txt
standalone/codebase/Eigen/src/Core/arch/SSE/Complex.h
standalone/codebase/Eigen/src/Core/arch/SSE/MathFunctions.h
standalone/codebase/Eigen/src/Core/arch/SSE/PacketMath.h
standalone/codebase/Eigen/src/Core/products/CMakeLists.txt
standalone/codebase/Eigen/src/Core/products/CoeffBasedProduct.h
standalone/codebase/Eigen/src/Core/products/GeneralBlockPanelKernel.h
standalone/codebase/Eigen/src/Core/products/GeneralMatrixMatrix.h
standalone/codebase/Eigen/src/Core/products/GeneralMatrixMatrixTriangular.h
standalone/codebase/Eigen/src/Core/products/GeneralMatrixMatrixTriangular_MKL.h
standalone/codebase/Eigen/src/Core/products/GeneralMatrixMatrix_MKL.h
standalone/codebase/Eigen/src/Core/products/GeneralMatrixVector.h
standalone/codebase/Eigen/src/Core/products/GeneralMatrixVector_MKL.h
standalone/codebase/Eigen/src/Core/products/Parallelizer.h
standalone/codebase/Eigen/src/Core/products/SelfadjointMatrixMatrix.h
standalone/codebase/Eigen/src/Core/products/SelfadjointMatrixMatrix_MKL.h
standalone/codebase/Eigen/src/Core/products/SelfadjointMatrixVector.h
standalone/codebase/Eigen/src/Core/products/SelfadjointMatrixVector_MKL.h
standalone/codebase/Eigen/src/Core/products/SelfadjointProduct.h
standalone/codebase/Eigen/src/Core/products/SelfadjointRank2Update.h
standalone/codebase/Eigen/src/Core/products/TriangularMatrixMatrix.h
standalone/codebase/Eigen/src/Core/products/TriangularMatrixMatrix_MKL.h
standalone/codebase/Eigen/src/Core/products/TriangularMatrixVector.h
standalone/codebase/Eigen/src/Core/products/TriangularMatrixVector_MKL.h
standalone/codebase/Eigen/src/Core/products/TriangularSolverMatrix.h
standalone/codebase/Eigen/src/Core/products/TriangularSolverMatrix_MKL.h
standalone/codebase/Eigen/src/Core/products/TriangularSolverVector.h
standalone/codebase/Eigen/src/Core/util/BlasUtil.h
standalone/codebase/Eigen/src/Core/util/CMakeLists.txt
standalone/codebase/Eigen/src/Core/util/Constants.h
standalone/codebase/Eigen/src/Core/util/DisableStupidWarnings.h
standalone/codebase/Eigen/src/Core/util/ForwardDeclarations.h
standalone/codebase/Eigen/src/Core/util/MKL_support.h
standalone/codebase/Eigen/src/Core/util/Macros.h
standalone/codebase/Eigen/src/Core/util/Memory.h
standalone/codebase/Eigen/src/Core/util/Meta.h
standalone/codebase/Eigen/src/Core/util/NonMPL2.h
standalone/codebase/Eigen/src/Core/util/ReenableStupidWarnings.h
standalone/codebase/Eigen/src/Core/util/StaticAssert.h
standalone/codebase/Eigen/src/Core/util/XprHelper.h
standalone/codebase/Eigen/src/Eigen2Support/Block.h
standalone/codebase/Eigen/src/Eigen2Support/CMakeLists.txt
standalone/codebase/Eigen/src/Eigen2Support/Cwise.h
standalone/codebase/Eigen/src/Eigen2Support/CwiseOperators.h
standalone/codebase/Eigen/src/Eigen2Support/Geometry/AlignedBox.h
standalone/codebase/Eigen/src/Eigen2Support/Geometry/All.h
standalone/codebase/Eigen/src/Eigen2Support/Geometry/AngleAxis.h
standalone/codebase/Eigen/src/Eigen2Support/Geometry/CMakeLists.txt
standalone/codebase/Eigen/src/Eigen2Support/Geometry/Hyperplane.h
standalone/codebase/Eigen/src/Eigen2Support/Geometry/ParametrizedLine.h
standalone/codebase/Eigen/src/Eigen2Support/Geometry/Quaternion.h
standalone/codebase/Eigen/src/Eigen2Support/Geometry/Rotation2D.h
standalone/codebase/Eigen/src/Eigen2Support/Geometry/RotationBase.h
standalone/codebase/Eigen/src/Eigen2Support/Geometry/Scaling.h
standalone/codebase/Eigen/src/Eigen2Support/Geometry/Transform.h
standalone/codebase/Eigen/src/Eigen2Support/Geometry/Translation.h
standalone/codebase/Eigen/src/Eigen2Support/LU.h
standalone/codebase/Eigen/src/Eigen2Support/Lazy.h
standalone/codebase/Eigen/src/Eigen2Support/LeastSquares.h
standalone/codebase/Eigen/src/Eigen2Support/Macros.h
standalone/codebase/Eigen/src/Eigen2Support/MathFunctions.h
standalone/codebase/Eigen/src/Eigen2Support/Memory.h
standalone/codebase/Eigen/src/Eigen2Support/Meta.h
standalone/codebase/Eigen/src/Eigen2Support/Minor.h
standalone/codebase/Eigen/src/Eigen2Support/QR.h
standalone/codebase/Eigen/src/Eigen2Support/SVD.h
standalone/codebase/Eigen/src/Eigen2Support/TriangularSolver.h
standalone/codebase/Eigen/src/Eigen2Support/VectorBlock.h
standalone/codebase/Eigen/src/Eigenvalues/CMakeLists.txt
standalone/codebase/Eigen/src/Eigenvalues/ComplexEigenSolver.h
standalone/codebase/Eigen/src/Eigenvalues/ComplexSchur.h
standalone/codebase/Eigen/src/Eigenvalues/ComplexSchur_MKL.h
standalone/codebase/Eigen/src/Eigenvalues/EigenSolver.h
standalone/codebase/Eigen/src/Eigenvalues/GeneralizedSelfAdjointEigenSolver.h
standalone/codebase/Eigen/src/Eigenvalues/HessenbergDecomposition.h
standalone/codebase/Eigen/src/Eigenvalues/MatrixBaseEigenvalues.h
standalone/codebase/Eigen/src/Eigenvalues/RealSchur.h
standalone/codebase/Eigen/src/Eigenvalues/RealSchur_MKL.h
standalone/codebase/Eigen/src/Eigenvalues/SelfAdjointEigenSolver.h
standalone/codebase/Eigen/src/Eigenvalues/SelfAdjointEigenSolver_MKL.h
standalone/codebase/Eigen/src/Eigenvalues/Tridiagonalization.h
standalone/codebase/Eigen/src/Geometry/AlignedBox.h
standalone/codebase/Eigen/src/Geometry/AngleAxis.h
standalone/codebase/Eigen/src/Geometry/CMakeLists.txt
standalone/codebase/Eigen/src/Geometry/EulerAngles.h
standalone/codebase/Eigen/src/Geometry/Homogeneous.h
standalone/codebase/Eigen/src/Geometry/Hyperplane.h
standalone/codebase/Eigen/src/Geometry/OrthoMethods.h
standalone/codebase/Eigen/src/Geometry/ParametrizedLine.h
standalone/codebase/Eigen/src/Geometry/Quaternion.h
standalone/codebase/Eigen/src/Geometry/Rotation2D.h
standalone/codebase/Eigen/src/Geometry/RotationBase.h
standalone/codebase/Eigen/src/Geometry/Scaling.h
standalone/codebase/Eigen/src/Geometry/Transform.h
standalone/codebase/Eigen/src/Geometry/Translation.h
standalone/codebase/Eigen/src/Geometry/Umeyama.h
standalone/codebase/Eigen/src/Geometry/arch/CMakeLists.txt
standalone/codebase/Eigen/src/Geometry/arch/Geometry_SSE.h
standalone/codebase/Eigen/src/Householder/BlockHouseholder.h
standalone/codebase/Eigen/src/Householder/CMakeLists.txt
standalone/codebase/Eigen/src/Householder/Householder.h
standalone/codebase/Eigen/src/Householder/HouseholderSequence.h
standalone/codebase/Eigen/src/IterativeLinearSolvers/BasicPreconditioners.h
standalone/codebase/Eigen/src/IterativeLinearSolvers/BiCGSTAB.h
standalone/codebase/Eigen/src/IterativeLinearSolvers/CMakeLists.txt
standalone/codebase/Eigen/src/IterativeLinearSolvers/ConjugateGradient.h
standalone/codebase/Eigen/src/IterativeLinearSolvers/IncompleteLUT.h
standalone/codebase/Eigen/src/IterativeLinearSolvers/IterativeSolverBase.h
standalone/codebase/Eigen/src/Jacobi/CMakeLists.txt
standalone/codebase/Eigen/src/Jacobi/Jacobi.h
standalone/codebase/Eigen/src/LU/CMakeLists.txt
standalone/codebase/Eigen/src/LU/Determinant.h
standalone/codebase/Eigen/src/LU/FullPivLU.h
standalone/codebase/Eigen/src/LU/Inverse.h
standalone/codebase/Eigen/src/LU/PartialPivLU.h
standalone/codebase/Eigen/src/LU/PartialPivLU_MKL.h
standalone/codebase/Eigen/src/LU/arch/CMakeLists.txt
standalone/codebase/Eigen/src/LU/arch/Inverse_SSE.h
standalone/codebase/Eigen/src/OrderingMethods/Amd.h
standalone/codebase/Eigen/src/OrderingMethods/CMakeLists.txt
standalone/codebase/Eigen/src/PaStiXSupport/CMakeLists.txt
standalone/codebase/Eigen/src/PaStiXSupport/PaStiXSupport.h
standalone/codebase/Eigen/src/PardisoSupport/CMakeLists.txt
standalone/codebase/Eigen/src/PardisoSupport/PardisoSupport.h
standalone/codebase/Eigen/src/QR/CMakeLists.txt
standalone/codebase/Eigen/src/QR/ColPivHouseholderQR.h
standalone/codebase/Eigen/src/QR/ColPivHouseholderQR_MKL.h
standalone/codebase/Eigen/src/QR/FullPivHouseholderQR.h
standalone/codebase/Eigen/src/QR/HouseholderQR.h
standalone/codebase/Eigen/src/QR/HouseholderQR_MKL.h
standalone/codebase/Eigen/src/SVD/CMakeLists.txt
standalone/codebase/Eigen/src/SVD/JacobiSVD.h
standalone/codebase/Eigen/src/SVD/JacobiSVD_MKL.h
standalone/codebase/Eigen/src/SVD/UpperBidiagonalization.h
standalone/codebase/Eigen/src/SparseCholesky/CMakeLists.txt
standalone/codebase/Eigen/src/SparseCholesky/SimplicialCholesky.h
standalone/codebase/Eigen/src/SparseCore/AmbiVector.h
standalone/codebase/Eigen/src/SparseCore/CMakeLists.txt
standalone/codebase/Eigen/src/SparseCore/CompressedStorage.h
standalone/codebase/Eigen/src/SparseCore/ConservativeSparseSparseProduct.h
standalone/codebase/Eigen/src/SparseCore/CoreIterators.h
standalone/codebase/Eigen/src/SparseCore/MappedSparseMatrix.h
standalone/codebase/Eigen/src/SparseCore/SparseAssign.h
standalone/codebase/Eigen/src/SparseCore/SparseBlock.h
standalone/codebase/Eigen/src/SparseCore/SparseCwiseBinaryOp.h
standalone/codebase/Eigen/src/SparseCore/SparseCwiseUnaryOp.h
standalone/codebase/Eigen/src/SparseCore/SparseDenseProduct.h
standalone/codebase/Eigen/src/SparseCore/SparseDiagonalProduct.h
standalone/codebase/Eigen/src/SparseCore/SparseDot.h
standalone/codebase/Eigen/src/SparseCore/SparseFuzzy.h
standalone/codebase/Eigen/src/SparseCore/SparseMatrix.h
standalone/codebase/Eigen/src/SparseCore/SparseMatrixBase.h
standalone/codebase/Eigen/src/SparseCore/SparsePermutation.h
standalone/codebase/Eigen/src/SparseCore/SparseProduct.h
standalone/codebase/Eigen/src/SparseCore/SparseRedux.h
standalone/codebase/Eigen/src/SparseCore/SparseSelfAdjointView.h
standalone/codebase/Eigen/src/SparseCore/SparseSparseProductWithPruning.h
standalone/codebase/Eigen/src/SparseCore/SparseTranspose.h
standalone/codebase/Eigen/src/SparseCore/SparseTriangularView.h
standalone/codebase/Eigen/src/SparseCore/SparseUtil.h
standalone/codebase/Eigen/src/SparseCore/SparseVector.h
standalone/codebase/Eigen/src/SparseCore/SparseView.h
standalone/codebase/Eigen/src/SparseCore/TriangularSolver.h
standalone/codebase/Eigen/src/StlSupport/CMakeLists.txt
standalone/codebase/Eigen/src/StlSupport/StdDeque.h
standalone/codebase/Eigen/src/StlSupport/StdList.h
standalone/codebase/Eigen/src/StlSupport/StdVector.h
standalone/codebase/Eigen/src/StlSupport/details.h
standalone/codebase/Eigen/src/SuperLUSupport/CMakeLists.txt
standalone/codebase/Eigen/src/SuperLUSupport/SuperLUSupport.h
standalone/codebase/Eigen/src/UmfPackSupport/CMakeLists.txt
standalone/codebase/Eigen/src/UmfPackSupport/UmfPackSupport.h
standalone/codebase/Eigen/src/misc/CMakeLists.txt
standalone/codebase/Eigen/src/misc/Image.h
standalone/codebase/Eigen/src/misc/Kernel.h
standalone/codebase/Eigen/src/misc/Solve.h
standalone/codebase/Eigen/src/misc/SparseSolve.h
standalone/codebase/Eigen/src/misc/blas.h
standalone/codebase/Eigen/src/plugins/ArrayCwiseBinaryOps.h
standalone/codebase/Eigen/src/plugins/ArrayCwiseUnaryOps.h
standalone/codebase/Eigen/src/plugins/BlockMethods.h
standalone/codebase/Eigen/src/plugins/CMakeLists.txt
standalone/codebase/Eigen/src/plugins/CommonCwiseBinaryOps.h
standalone/codebase/Eigen/src/plugins/CommonCwiseUnaryOps.h
standalone/codebase/Eigen/src/plugins/MatrixCwiseBinaryOps.h
standalone/codebase/Eigen/src/plugins/MatrixCwiseUnaryOps.h
standalone/codebase/GPU-DP/CMakeLists.txt
standalone/codebase/GPU/CMakeLists.txt
standalone/codebase/GPU/GPUImplDefs.h
standalone/codebase/GPU/GPUImplHelper.cpp
standalone/codebase/GPU/GPUImplHelper.h
standalone/codebase/GPU/GPUInterface.h
standalone/codebase/GPU/GPUInterfaceCUDA.cpp
standalone/codebase/GPU/KernelLauncher.h
standalone/codebase/GPU/KernelLauncherCCD.cpp
standalone/codebase/GPU/KernelLauncherCCD.h
standalone/codebase/GPU/kernels/kernelAll.cu
standalone/codebase/GPU/kernels/kernelReductions.cu
standalone/codebase/GPU/kernels/kernelSpmvCoo.cu
standalone/codebase/GPU/kernels/kernelSpmvCsr.cu
standalone/codebase/MT/MersenneTwister.h
standalone/codebase/jni/CMakeLists.txt
standalone/codebase/jni/dr_inference_regression_RegressionJNIWrapper.cpp
standalone/codebase/jni/dr_inference_regression_RegressionJNIWrapper.h
standalone/codebase/tclap/Arg.h
standalone/codebase/tclap/ArgException.h
standalone/codebase/tclap/ArgTraits.h
standalone/codebase/tclap/CmdLine.h
standalone/codebase/tclap/CmdLineInterface.h
standalone/codebase/tclap/CmdLineOutput.h
standalone/codebase/tclap/Constraint.h
standalone/codebase/tclap/DocBookOutput.h
standalone/codebase/tclap/HelpVisitor.h
standalone/codebase/tclap/IgnoreRestVisitor.h
standalone/codebase/tclap/MultiArg.h
standalone/codebase/tclap/MultiSwitchArg.h
standalone/codebase/tclap/OptionalUnlabeledTracker.h
standalone/codebase/tclap/StandardTraits.h
standalone/codebase/tclap/StdOutput.h
standalone/codebase/tclap/SwitchArg.h
standalone/codebase/tclap/UnlabeledMultiArg.h
standalone/codebase/tclap/UnlabeledValueArg.h
standalone/codebase/tclap/ValueArg.h
standalone/codebase/tclap/ValuesConstraint.h
standalone/codebase/tclap/VersionVisitor.h
standalone/codebase/tclap/Visitor.h
standalone/codebase/tclap/XorHandler.h
standalone/codebase/tclap/ZshCompletionOutput.h
standalone/example/cox-tiny-test.txt
standalone/example/fg-tiny-sparse-test.txt
standalone/example/fg-tiny-test.txt
standalone/example/fg-tiny-tied-sparse-test.txt
standalone/example/fg-tiny-tied-test.txt
tests/testthat.R
tests/testthat/test-RcppDataModel.R
tests/testthat/test-believedBroken.R
tests/testthat/test-conditionalPoisson.R
tests/testthat/test-correlation.R
tests/testthat/test-covariateRegularization.R
tests/testthat/test-cprViaSql.R
tests/testthat/test-cv.R
tests/testthat/test-dataConversionStratified.R
tests/testthat/test-dataConversionUnstratified.R
tests/testthat/test-dataManagement.R
tests/testthat/test-fastBarUpdate.R
tests/testthat/test-finiteMLE.R
tests/testthat/test-floatingPoint.R
tests/testthat/test-int64.R
tests/testthat/test-largeBernoulli.R
tests/testthat/test-largeProfileLikelihood.R
tests/testthat/test-multitypePoisson.R
tests/testthat/test-normalization.R
tests/testthat/test-offsetPoisson.R
tests/testthat/test-outOfSample.R
tests/testthat/test-parameterizedPriors.R
tests/testthat/test-predict.R
tests/testthat/test-profileLikelihood.R
tests/testthat/test-reductions.R
tests/testthat/test-simulation.R
tests/testthat/test-smallBernoulli.R
tests/testthat/test-smallCLR.R
tests/testthat/test-smallCox.R
tests/testthat/test-smallExactCLR.R
tests/testthat/test-smallFineGray.R
tests/testthat/test-smallMM.R
tests/testthat/test-smallNormal.R
tests/testthat/test-smallPoisson.R
tests/testthat/test-sorting.R
tests/testthat/test-sqlConstructor.R
tests/testthat/test-survfit.R
tests/testthat/test-weighted_cv.R
tests/testthat/test-weighting.R
tests/testthat/test-xyConstructor.R
tools/configure.R
