Cyclic Coordinate Descent for Logistic, Poisson and Survival Analysis

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Documentation for package ‘Cyclops’ version 3.4.1

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 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
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
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
vcov.cyclopsFit Calculate variance-covariance matrix for a fitted Cyclops model object