Package: Cyclops 3.5.0

Marc A. Suchard

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. Please see: Suchard, Simpson, Zorych, Ryan and Madigan (2013) <doi:10.1145/2414416.2414791>.

Authors:Marc A. Suchard [aut, cre], Martijn J. Schuemie [aut], Trevor R. Shaddox [aut], Yuxi Tian [aut], Jianxiao Yang [aut], Eric Kawaguchi [aut], Sushil Mittal [ctb], Observational Health Data Sciences and Informatics [cph], Marcus Geelnard [cph, ctb], Rutgers University [cph, ctb], R Development Core Team [cph, ctb]

Cyclops_3.5.0.tar.gz
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Cyclops.pdf |Cyclops.html✨
Cyclops/json (API)
NEWS

# Install 'Cyclops' in R:
install.packages('Cyclops', repos = c('https://ohdsi.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/ohdsi/cyclops/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:
  • oxford - Oxford self-controlled case series data

On CRAN:

hades

8.97 score 38 stars 3 packages 73 scripts 1.4k downloads 26 mentions 35 exports 40 dependencies

Last updated 21 days agofrom:997098c1a4. Checks:OK: 9. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 01 2024
R-4.5-win-x86_64OKNov 01 2024
R-4.5-linux-x86_64OKNov 01 2024
R-4.4-win-x86_64OKNov 01 2024
R-4.4-mac-x86_64OKNov 01 2024
R-4.4-mac-aarch64OKNov 01 2024
R-4.3-win-x86_64OKNov 01 2024
R-4.3-mac-x86_64OKNov 01 2024
R-4.3-mac-aarch64OKNov 01 2024

Exports:aconfintconvertToCyclopsDataconvertToTimeVaryingCoefcoveragecreateAutoGridCrossValidationControlcreateControlcreateCyclopsDatacreateNonSeparablePriorcreateParameterizedPriorcreatePriorcreateWeightBasedSearchControlfinalizeSqlCyclopsDatafitCyclopsModelfitCyclopsSimulationgetCovariateIdsgetCovariateTypesgetCyclopsProfileLogLikelihoodgetFineGrayWeightsgetFloatingPointSizegetHyperParametergetNumberOfCovariatesgetNumberOfRowsgetNumberOfStratagetUnivariableCorrelationgetUnivariableSeparabilityisInitializedlistGPUDevicesmeanLinearPredictormseMultitypereadCyclopsDatarunBootstrapsetOpenCLDevicesimulateCyclopsDatasplitTime

Dependencies:Andromedabitbit64blobcachemclicpp11DBIdbplyrdplyrfansifastmapgenericsgluehmslatticelifecyclemagrittrMatrixmemoisepillarpkgconfigplogrpurrrR6RcppRcppEigenRcppParallelrlangRSQLitestringistringrsurvivaltibbletidyrtidyselectutf8vctrswithrzip

Readme and manuals

Help Manual

Help pageTopics
Extract model coefficientscoef.cyclopsFit
Confidence intervals for Cyclops model parametersconfint.cyclopsFit
Convert data from two data frames or ffdf objects into a CyclopsData objectconvertToCyclopsData convertToCyclopsData.data.frame convertToCyclopsData.tbl_dbi
Convert short sparse covariate table to long sparse covariate table for time-varying coefficients.convertToTimeVaryingCoef
Coveragecoverage
Create a Cyclops control object that supports multiple hyperparameterscreateAutoGridCrossValidationControl
Create a Cyclops control objectcreateControl
Create a Cyclops data objectcreateCyclopsData
Create a Cyclops prior object that returns the MLE of non-separable coefficientscreateNonSeparablePrior
Create a Cyclops parameterized prior objectcreateParameterizedPrior
Create a Cyclops prior objectcreatePrior
Create a Cyclops control object that supports in- / out-of-sample hyperparameter search using weightscreateWeightBasedSearchControl
Cyclops: Cyclic coordinate descent for logistic, Poisson and survival analysiscyclops
Fit a Cyclops modelfitCyclopsModel
Fit simulated datafitCyclopsSimulation
Get covariate identifiersgetCovariateIds
Get covariate typesgetCovariateTypes
Profile likelihood for Cyclops model parametersgetCyclopsProfileLogLikelihood
Creates a 'Surv' object that forces in competing risks and the IPCW needed for Fine-Gray estimation.getFineGrayWeights
Get floating point sizegetFloatingPointSize
Get hyperparametergetHyperParameter
Get total number of covariatesgetNumberOfCovariates
Get total number of rowsgetNumberOfRows
Get number of stratagetNumberOfStrata
Get univariable correlationgetUnivariableCorrelation
Get univariable linear separabilitygetUnivariableSeparability
Check if a Cyclops data object is initializedisInitialized
List available GPU deviceslistGPUDevices
Extract log-likelihoodlogLik.cyclopsFit
Calculates xbar*betameanLinearPredictor
Mean squared errormse
Create a multitype outcome objectMultitype
Oxford self-controlled case series dataoxford
Model predictionspredict.cyclopsFit
Print a Cyclops data objectprint.cyclopsData
Print a Cyclops model fit objectprint.cyclopsFit
Read Cyclops data from filereadCyclopsData
Run Bootstrap for Cyclops model parameterrunBootstrap
Set GPU devicesetOpenCLDevice
Simulation Cyclops datasetsimulateCyclopsData
Split the analysis time into several intervals for time-varying coefficients.splitTime
Cyclops data object summarysummary.cyclopsData
Calculate baseline hazard functionsurvfit.cyclopsFit
Calculate variance-covariance matrix for a fitted Cyclops model objectvcov.cyclopsFit