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...

Functions

aconfint Man page
appendSqlCyclopsData Man page
coef.cyclopsFit Man page
confint.cyclopsFit Man page
convertToCyclopsData Man page
convertToCyclopsData.data.frame Man page
convertToCyclopsData.ffdf Man page
convertToCyclopsVariance Man page
convertToGlmnetLambda Man page
coverage Man page
createAbridgePrior Man page
createControl Man page
createCyclopsData Man page
createPrior Man page
cyclops Man page
cyclops-package Man page
finalizeSqlCyclopsData Man page
fitCyclopsModel Man page
fitCyclopsSimulation Man page
getCovariateIds Man page
getCovariateTypes Man page
getCyclopsPredictiveLogLikelihood Man page
getHyperParameter Man page
getNumberOfCovariates Man page
getNumberOfRows Man page
getNumberOfStrata Man page
getNumberOfTypes Man page
getSEs Man page
getUnivariableCorrelation Man page
isInitialized Man page
isSorted Man page
isSorted.data.frame Man page
isSorted.ffdf Man page
logLik.cyclopsFit Man page
mse Man page
Multitype Man page
oxford Man page
plotCyclopsSimulationFit Man page
predict.cyclopsFit Man page
print.cyclopsData Man page
print.cyclopsFit Man page
printCyclopsRowIds Man page
readCyclopsData Man page
reduce Man page
simulateCyclopsData Man page
summary.cyclopsData Man page
vcov.cyclopsFit Man page

Files

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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