Cyclops: Cyclic Coordinate Descent for Logistic, Poisson and Survival Analysis

This model fitting tool incorporates cyclic coordinate descent and majorization-minimization approaches to fit a variety of regression models found in large-scale observational healthcare data. Implementations focus on computational optimization and fine-scale parallelization to yield efficient inference in massive datasets.

Author
Marc A. Suchard [aut, cre], Martijn J. Schuemie [aut], Trevor R. Shaddox [aut]
Date of publication
2016-10-06 19:15:26
Maintainer
Marc A. Suchard <msuchard@ucla.edu>
License
Apache License 2.0
Version
1.2.2
URLs

View on CRAN

Man pages

aconfint
Asymptotic confidence intervals for a fitted Cyclops model...
appendSqlCyclopsData
appendSqlCyclopsData
coef.cyclopsFit
Extract model coefficients
confint.cyclopsFit
Confidence intervals for Cyclops model parameters
convertToCyclopsData
Convert data from two data frames or ffdf objects into a...
convertToCyclopsVariance
Convert to Cyclops Prior Variance
convertToGlmnetLambda
Convert to glmnet regularization parameter
coverage
Coverage
createAbridgePrior
Create an ABRIDGE Cyclops prior object
createControl
Create a Cyclops control object
createCyclopsData
Create a Cyclops data object
createPrior
Create a Cyclops prior object
cyclops
Cyclops: Cyclic coordinate descent for logistic, Poisson and...
finalizeSqlCyclopsData
finalizeSqlCyclopsData
fitCyclopsModel
Fit a Cyclops model
fitCyclopsSimulation
Fit simulated data
getCovariateIds
Get covariate identifiers
getCovariateTypes
Get covariate types
getCyclopsPredictiveLogLikelihood
Compute predictive log-likelihood from a Cyclops model fit
getHyperParameter
Get hyperparameter
getNumberOfCovariates
Get total number of covariates
getNumberOfRows
Get total number of rows
getNumberOfStrata
Get number of strata
getNumberOfTypes
Get total number of outcome types
getSEs
Extract standard errors
getUnivariableCorrelation
Get univariable correlation
isInitialized
Check if a Cyclops data object is initialized
isSorted
Check if data are sorted by one or more columns
logLik.cyclopsFit
Extract log-likelihood
mse
Mean squared error
Multitype
Create a multitype outcome object
oxford
Oxford self-controlled case series data
plotCyclopsSimulationFit
Plot Cyclops simulation model fit
predict.cyclopsFit
Model predictions
print.cyclopsData
Print a Cyclops data object
print.cyclopsFit
Print a Cyclops model fit object
printCyclopsRowIds
Print row identifiers
readCyclopsData
Read Cyclops data from file
reduce
Apply simple data reductions
simulateCyclopsData
Simulation Cyclops dataset
summary.cyclopsData
Cyclops data object summary
vcov.cyclopsFit
Calculate variance-covariance matrix for a fitted Cyclops...

Files in this package

Cyclops
Cyclops/inst
Cyclops/inst/CITATION
Cyclops/inst/NEWS.Rd
Cyclops/inst/extdata
Cyclops/inst/extdata/infert_ccd.txt
Cyclops/inst/extdata/test1-clr.txt
Cyclops/inst/extdata/CCD_LOGISTIC_TEST_17var.txt
Cyclops/inst/extdata/cpr_test.RData
Cyclops/tests
Cyclops/tests/testthat.R
Cyclops/tests/testthat
Cyclops/tests/testthat/test-cv.R
Cyclops/tests/testthat/test-KKTSwindle.R
Cyclops/tests/testthat/test-dataConversionUnstratified.R
Cyclops/tests/testthat/test-largeBernoulli.R
Cyclops/tests/testthat/test-smallCLR.R
Cyclops/tests/testthat/test-dataManagement.R
Cyclops/tests/testthat/test-conditionalPoisson.R
Cyclops/tests/testthat/test-smallExactCLR.R
Cyclops/tests/testthat/test-reductions.R
Cyclops/tests/testthat/test-normalization.R
Cyclops/tests/testthat/test-cprViaSql.R
Cyclops/tests/testthat/test-offsetPoisson.R
Cyclops/tests/testthat/test-believedBroken.R
Cyclops/tests/testthat/test-multitypePoisson.R
Cyclops/tests/testthat/test-Abridge.R
Cyclops/tests/testthat/test-sqlConstructor.R
Cyclops/tests/testthat/test-dataConversionStratified.R
Cyclops/tests/testthat/test-xyConstructor.R
Cyclops/tests/testthat/test-smallPoisson.R
Cyclops/tests/testthat/test-smallCox.R
Cyclops/tests/testthat/test-smallBernoulli.R
Cyclops/tests/testthat/test-weighted_cv.R
Cyclops/tests/testthat/test-correlation.R
Cyclops/tests/testthat/test-covariateRegularization.R
Cyclops/tests/testthat/test-isSorted.R
Cyclops/tests/testthat/test-predict.R
Cyclops/src
Cyclops/src/RcppProgressLogger.h
Cyclops/src/tinythread
Cyclops/src/tinythread/tinythread.cpp
Cyclops/src/tinythread/tinythread.h
Cyclops/src/tinythread/fast_mutex.h
Cyclops/src/Makevars
Cyclops/src/BySum.cpp
Cyclops/src/RcppModelData.cpp
Cyclops/src/RcppBySum.cpp
Cyclops/src/IsSorted.h
Cyclops/src/cyclops
Cyclops/src/cyclops/Thread.h
Cyclops/src/cyclops/ModelData.cpp
Cyclops/src/cyclops/CyclicCoordinateDescent.cpp
Cyclops/src/cyclops/drivers
Cyclops/src/cyclops/drivers/ProportionSelector.h
Cyclops/src/cyclops/drivers/CrossValidationSelector.h
Cyclops/src/cyclops/drivers/BootstrapDriver.h
Cyclops/src/cyclops/drivers/CrossValidationSelector.cpp
Cyclops/src/cyclops/drivers/BootstrapSelector.cpp
Cyclops/src/cyclops/drivers/HierarchyAutoSearchCrossValidationDriver.cpp
Cyclops/src/cyclops/drivers/AbstractCrossValidationDriver.cpp
Cyclops/src/cyclops/drivers/ProportionSelector.cpp
Cyclops/src/cyclops/drivers/AbstractSelector.cpp
Cyclops/src/cyclops/drivers/BootstrapDriver.cpp
Cyclops/src/cyclops/drivers/GridSearchCrossValidationDriver.h
Cyclops/src/cyclops/drivers/AbstractDriver.cpp
Cyclops/src/cyclops/drivers/BootstrapSelector.h
Cyclops/src/cyclops/drivers/AutoSearchCrossValidationDriver.h
Cyclops/src/cyclops/drivers/HierarchyGridSearchCrossValidationDriver.cpp
Cyclops/src/cyclops/drivers/AbstractCrossValidationDriver.h
Cyclops/src/cyclops/drivers/AbstractDriver.h
Cyclops/src/cyclops/drivers/GridSearchCrossValidationDriver.cpp
Cyclops/src/cyclops/drivers/HierarchyAutoSearchCrossValidationDriver.h
Cyclops/src/cyclops/drivers/HierarchyGridSearchCrossValidationDriver.h
Cyclops/src/cyclops/drivers/AutoSearchCrossValidationDriver.cpp
Cyclops/src/cyclops/drivers/AbstractSelector.h
Cyclops/src/cyclops/engine
Cyclops/src/cyclops/engine/Recursions.hpp
Cyclops/src/cyclops/engine/Ranges.h
Cyclops/src/cyclops/engine/ParallelLoops.h
Cyclops/src/cyclops/engine/AbstractModelSpecifics.h
Cyclops/src/cyclops/engine/ModelSpecifics.h
Cyclops/src/cyclops/engine/AbstractModelSpecifics.cpp
Cyclops/src/cyclops/engine/ModelSpecifics.hpp
Cyclops/src/cyclops/engine/ThreadPool.h
Cyclops/src/cyclops/Timer.cpp
Cyclops/src/cyclops/priors
Cyclops/src/cyclops/priors/JointPrior.h
Cyclops/src/cyclops/priors/CovariatePrior.h
Cyclops/src/cyclops/priors/CovariatePrior.cpp
Cyclops/src/cyclops/io
Cyclops/src/cyclops/io/SparseIndexer.h
Cyclops/src/cyclops/io/InputReader.h
Cyclops/src/cyclops/io/BaseInputReader.h
Cyclops/src/cyclops/io/OutputWriter.h
Cyclops/src/cyclops/io/InputReader.cpp
Cyclops/src/cyclops/io/ProgressLogger.h
Cyclops/src/cyclops/io/NewGenericInputReader.h
Cyclops/src/cyclops/imputation
Cyclops/src/cyclops/imputation/ImputeVariables.cpp
Cyclops/src/cyclops/imputation/ImputationPolicy.cpp
Cyclops/src/cyclops/imputation/ImputeVariables.h
Cyclops/src/cyclops/imputation/ImputationPolicy.h
Cyclops/src/cyclops/CyclicCoordinateDescent.h
Cyclops/src/cyclops/CcdInterface.h
Cyclops/src/cyclops/Iterators.h
Cyclops/src/cyclops/CompressedDataMatrix.cpp
Cyclops/src/cyclops/CompressedDataMatrix.h
Cyclops/src/cyclops/CcdInterface.cpp
Cyclops/src/cyclops/Timer.h
Cyclops/src/cyclops/Timing.h
Cyclops/src/cyclops/ModelData.h
Cyclops/src/cyclops/Types.h
Cyclops/src/RcppModelData.h
Cyclops/src/BySum.h
Cyclops/src/RcppCyclopsInterface.h
Cyclops/src/IsSorted.cpp
Cyclops/src/RcppCyclopsInterface.cpp
Cyclops/src/boost
Cyclops/src/boost/iterator
Cyclops/src/boost/iterator/is_readable_iterator.hpp
Cyclops/src/boost/iterator/is_lvalue_iterator.hpp
Cyclops/src/boost/iterator/interoperable.hpp
Cyclops/src/boost/iterator/iterator_categories.hpp
Cyclops/src/boost/iterator/indirect_iterator.hpp
Cyclops/src/boost/iterator/new_iterator_tests.hpp
Cyclops/src/boost/iterator/function_input_iterator.hpp
Cyclops/src/boost/iterator/iterator_adaptor.hpp
Cyclops/src/boost/iterator/filter_iterator.hpp
Cyclops/src/boost/iterator/iterator_archetypes.hpp
Cyclops/src/boost/iterator/detail
Cyclops/src/boost/iterator/detail/any_conversion_eater.hpp
Cyclops/src/boost/iterator/detail/config_undef.hpp
Cyclops/src/boost/iterator/detail/minimum_category.hpp
Cyclops/src/boost/iterator/detail/facade_iterator_category.hpp
Cyclops/src/boost/iterator/detail/config_def.hpp
Cyclops/src/boost/iterator/detail/enable_if.hpp
Cyclops/src/boost/iterator/minimum_category.hpp
Cyclops/src/boost/iterator/reverse_iterator.hpp
Cyclops/src/boost/iterator/transform_iterator.hpp
Cyclops/src/boost/iterator/zip_iterator.hpp
Cyclops/src/boost/iterator/iterator_traits.hpp
Cyclops/src/boost/iterator/iterator_concepts.hpp
Cyclops/src/boost/iterator/counting_iterator.hpp
Cyclops/src/boost/iterator/permutation_iterator.hpp
Cyclops/src/boost/iterator/iterator_facade.hpp
Cyclops/src/boost/iterator.hpp
Cyclops/src/boost/iterator_adaptors.hpp
Cyclops/src/Makevars.win
Cyclops/src/RcppExports.cpp
Cyclops/src/RcppOutputHelper.h
Cyclops/src/RcppIsSorted.cpp
Cyclops/src/utils
Cyclops/src/utils/RZeroIn.h
Cyclops/src/utils/HParSearch.h
Cyclops/src/utils/HParSearch.cpp
Cyclops/NAMESPACE
Cyclops/NEWS
Cyclops/data
Cyclops/data/oxford.rda
Cyclops/R
Cyclops/R/ExampleData.R
Cyclops/R/LegacyDataConversion.R
Cyclops/R/Multitype.R
Cyclops/R/cyclops.R
Cyclops/R/DataManagement.R
Cyclops/R/NewDataConversion.R
Cyclops/R/Abridge.R
Cyclops/R/RcppExports.R
Cyclops/R/Predict.R
Cyclops/R/Simulation.R
Cyclops/R/ModelFit.R
Cyclops/R/PackageMaintenance.R
Cyclops/README.md
Cyclops/MD5
Cyclops/DESCRIPTION
Cyclops/man
Cyclops/man/print.cyclopsFit.Rd
Cyclops/man/getCyclopsPredictiveLogLikelihood.Rd
Cyclops/man/getNumberOfRows.Rd
Cyclops/man/plotCyclopsSimulationFit.Rd
Cyclops/man/convertToCyclopsVariance.Rd
Cyclops/man/readCyclopsData.Rd
Cyclops/man/summary.cyclopsData.Rd
Cyclops/man/coverage.Rd
Cyclops/man/coef.cyclopsFit.Rd
Cyclops/man/getNumberOfTypes.Rd
Cyclops/man/convertToGlmnetLambda.Rd
Cyclops/man/printCyclopsRowIds.Rd
Cyclops/man/fitCyclopsModel.Rd
Cyclops/man/simulateCyclopsData.Rd
Cyclops/man/appendSqlCyclopsData.Rd
Cyclops/man/createPrior.Rd
Cyclops/man/Multitype.Rd
Cyclops/man/finalizeSqlCyclopsData.Rd
Cyclops/man/cyclops.Rd
Cyclops/man/createAbridgePrior.Rd
Cyclops/man/getSEs.Rd
Cyclops/man/getNumberOfStrata.Rd
Cyclops/man/confint.cyclopsFit.Rd
Cyclops/man/getCovariateTypes.Rd
Cyclops/man/predict.cyclopsFit.Rd
Cyclops/man/print.cyclopsData.Rd
Cyclops/man/isInitialized.Rd
Cyclops/man/getNumberOfCovariates.Rd
Cyclops/man/oxford.Rd
Cyclops/man/aconfint.Rd
Cyclops/man/fitCyclopsSimulation.Rd
Cyclops/man/getHyperParameter.Rd
Cyclops/man/createCyclopsData.Rd
Cyclops/man/convertToCyclopsData.Rd
Cyclops/man/mse.Rd
Cyclops/man/createControl.Rd
Cyclops/man/reduce.Rd
Cyclops/man/isSorted.Rd
Cyclops/man/getCovariateIds.Rd
Cyclops/man/logLik.cyclopsFit.Rd
Cyclops/man/vcov.cyclopsFit.Rd
Cyclops/man/getUnivariableCorrelation.Rd