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.

AuthorMarc A. Suchard [aut, cre], Martijn J. Schuemie [aut], Trevor R. Shaddox [aut]
Date of publication2016-10-06 19:15:26
MaintainerMarc A. Suchard <msuchard@ucla.edu>
LicenseApache License 2.0
Version1.2.2
https://github.com/ohdsi/cyclops

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

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