# Cyclic Coordinate Descent for Logistic, Poisson and Survival Analysis

## Documentation for package ‘Cyclops’ version 3.6.0

- DESCRIPTION file
- Package NEWS
- Package README

## Help Pages

Cyclops-package | Cyclops: Cyclic coordinate descent for logistic, Poisson and survival analysis
cacheCyclopsModelForJava | Place Cyclops model fit object in a persistent cache
clearCyclopsModelCache | Clear the Cyclops persistent cache
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
cyclopsLibraryFileName | Get full path to installed Cyclops library
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
gradient | Extract gradient
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 parameters
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