Cyclic Coordinate Descent for Logistic, Poisson and Survival Analysis

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Documentation for package ‘Cyclops’ version 3.5.2

• DESCRIPTION file.
• Package NEWS.

Help Pages

Cyclops-package	Cyclops: Cyclic coordinate descent for logistic, Poisson and survival analysis
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 CyclopsData object
convertToCyclopsData.data.frame	Convert data from two data frames or ffdf objects into a CyclopsData object
convertToCyclopsData.tbl_dbi	Convert data from two data frames or ffdf objects into a CyclopsData object
convertToTimeVaryingCoef	Convert short sparse covariate table to long sparse covariate table for time-varying coefficients.
coverage	Coverage
createAutoGridCrossValidationControl	Create a Cyclops control object that supports multiple hyperparameters
createControl	Create a Cyclops control object
createCyclopsData	Create a Cyclops data object
createNonSeparablePrior	Create a Cyclops prior object that returns the MLE of non-separable coefficients
createParameterizedPrior	Create a Cyclops parameterized prior object
createPrior	Create a Cyclops prior object
createWeightBasedSearchControl	Create a Cyclops control object that supports in- / out-of-sample hyperparameter search using weights
Cyclops	Cyclops: Cyclic coordinate descent for logistic, Poisson and survival analysis
cyclops	Cyclops: Cyclic coordinate descent for logistic, Poisson and survival analysis
fitCyclopsModel	Fit a Cyclops model
fitCyclopsSimulation	Fit simulated data
getCovariateIds	Get covariate identifiers
getCovariateTypes	Get covariate types
getCyclopsProfileLogLikelihood	Profile likelihood for Cyclops model parameters
getFineGrayWeights	Creates a 'Surv' object that forces in competing risks and the IPCW needed for Fine-Gray estimation.
getFloatingPointSize	Get floating point size
getHyperParameter	Get hyperparameter
getNumberOfCovariates	Get total number of covariates
getNumberOfRows	Get total number of rows
getNumberOfStrata	Get number of strata
getUnivariableCorrelation	Get univariable correlation
getUnivariableSeparability	Get univariable linear separability
isInitialized	Check if a Cyclops data object is initialized
listGPUDevices	List available GPU devices
logLik.cyclopsFit	Extract log-likelihood
meanLinearPredictor	Calculates xbar*beta
mse	Mean squared error
Multitype	Create a multitype outcome object
oxford	Oxford self-controlled case series data
predict.cyclopsFit	Model predictions
print.cyclopsData	Print a Cyclops data object
print.cyclopsFit	Print a Cyclops model fit object
readCyclopsData	Read Cyclops data from file
residuals.cyclopsFit	Model residuals
runBootstrap	Run Bootstrap for Cyclops model parameter
setOpenCLDevice	Set GPU device
simulateCyclopsData	Simulation Cyclops dataset
splitTime	Split the analysis time into several intervals for time-varying coefficients.
summary.cyclopsData	Cyclops data object summary
survfit.cyclopsFit	Calculate baseline hazard function
testProportionality	Test hazard ratio proportionality assumption
vcov.cyclopsFit	Calculate variance-covariance matrix for a fitted Cyclops model object