# Cyclic Coordinate Descent for Logistic, Poisson and Survival Analysis

## Documentation for package ‘Cyclops’ version 2.0.3

- DESCRIPTION file.

## Help Pages

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.ffdf | Convert data from two data frames or ffdf objects into a CyclopsData object
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
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
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
isSorted | Check if data are sorted by one or more columns
isSorted.data.frame | Check if data are sorted by one or more columns
isSorted.ffdf | Check if data are sorted by one or more columns
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
simulateCyclopsData | Simulation Cyclops dataset
summary.cyclopsData | Cyclops data object summary
survfit.cyclopsFit | Calculate baseline hazard function
vcov.cyclopsFit | Calculate variance-covariance matrix for a fitted Cyclops model object