R/RcppExports.R

Defines functions .cyclopsModelData .cyclopsReadData .cyclopsGetInterceptLabel .appendSqlCyclopsData .loadCyclopsDataX .loadCyclopsDataMultipleX .loadCyclopsDataY .cyclopsFinalizeData getTimeVector getYVector .cyclopsGetMeanOffset .cyclopsGetHasOffset .cyclopsGetHasIntercept .cyclopsSetHasIntercept .cyclopsNormalizeCovariates .cyclopsQuantile .cyclopsMedian .cyclopsNewSqlData .cyclopsSum .cyclopsSumByStratum .cyclopsSumByGroup .cyclopsUnivariableSeparability .cyclopsUnivariableCorrelation getNumberOfTypes getNumberOfRows printMatrixMarket getNumberOfCovariates getFloatingPointSize .getCovariateTypes getCovariateIds getNumberOfStrata .isRcppPtrNull .isSortedVectorList .isSorted .cyclopsInitializeModel .cyclopsLogModel .cyclopsFitModel .cyclopsRunCrossValidation .cyclopsSetControl .cyclopsPredictModel .cyclopsProfileModel .cyclopsGetProfileLikelihood .cyclopsSetParameterizedPrior .cyclopsTestParameterizedPrior .cyclopsSetPrior .cyclopsGetFisherInformation .cyclopsLogResults .cyclopsGetLogLikelihood .cyclopsGetNewPredictiveLogLikelihood .cyclopsSetCensorWeights .cyclopsSetWeights .cyclopsGetIsRegularized .cyclopsSetFixedBeta .cyclopsSetBeta .cyclopsGetComputeDevice .cyclopsGetUseOffsetNames .cyclopsGetIsSurvivalNames .cyclopsGetRemoveInterceptNames .cyclopsGetModelTypeNames

Documented in getCovariateIds getFloatingPointSize getNumberOfCovariates getNumberOfRows getNumberOfStrata getNumberOfTypes printMatrixMarket

# Generated by using Rcpp::compileAttributes() -> do not edit by hand
# Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393

.cyclopsGetModelTypeNames <- function() {
    .Call(`_Cyclops_cyclopsGetModelTypeNames`)
}

.cyclopsGetRemoveInterceptNames <- function() {
    .Call(`_Cyclops_cyclopsGetRemoveInterceptNames`)
}

.cyclopsGetIsSurvivalNames <- function() {
    .Call(`_Cyclops_cyclopsGetIsSurvivalNames`)
}

.cyclopsGetUseOffsetNames <- function() {
    .Call(`_Cyclops_cyclopsGetUseOffsetNames`)
}

.cyclopsGetComputeDevice <- function(inRcppCcdInterface) {
    .Call(`_Cyclops_cyclopsGetComputeDevice`, inRcppCcdInterface)
}

.cyclopsSetBeta <- function(inRcppCcdInterface, beta) {
    invisible(.Call(`_Cyclops_cyclopsSetBeta`, inRcppCcdInterface, beta))
}

.cyclopsSetFixedBeta <- function(inRcppCcdInterface, beta, fixed) {
    invisible(.Call(`_Cyclops_cyclopsSetFixedBeta`, inRcppCcdInterface, beta, fixed))
}

.cyclopsGetIsRegularized <- function(inRcppCcdInterface, index) {
    .Call(`_Cyclops_cyclopsGetIsRegularized`, inRcppCcdInterface, index)
}

.cyclopsSetWeights <- function(inRcppCcdInterface, weights) {
    invisible(.Call(`_Cyclops_cyclopsSetWeights`, inRcppCcdInterface, weights))
}

.cyclopsSetCensorWeights <- function(inRcppCcdInterface, weights) {
    invisible(.Call(`_Cyclops_cyclopsSetCensorWeights`, inRcppCcdInterface, weights))
}

.cyclopsGetNewPredictiveLogLikelihood <- function(inRcppCcdInterface, weights) {
    .Call(`_Cyclops_cyclopsGetNewPredictiveLogLikelihood`, inRcppCcdInterface, weights)
}

.cyclopsGetLogLikelihood <- function(inRcppCcdInterface) {
    .Call(`_Cyclops_cyclopsGetLogLikelihood`, inRcppCcdInterface)
}

.cyclopsLogResults <- function(inRcppCcdInterface, fileName, withASE) {
    invisible(.Call(`_Cyclops_cyclopsLogResult`, inRcppCcdInterface, fileName, withASE))
}

.cyclopsGetFisherInformation <- function(inRcppCcdInterface, sexpBitCovariates) {
    .Call(`_Cyclops_cyclopsGetFisherInformation`, inRcppCcdInterface, sexpBitCovariates)
}

.cyclopsSetPrior <- function(inRcppCcdInterface, priorTypeName, variance, excludeNumeric, sexpGraph, sexpNeighborhood) {
    invisible(.Call(`_Cyclops_cyclopsSetPrior`, inRcppCcdInterface, priorTypeName, variance, excludeNumeric, sexpGraph, sexpNeighborhood))
}

.cyclopsTestParameterizedPrior <- function(priorFunction, startingParameters, indices, values) {
    .Call(`_Cyclops_cyclopsTestParameterizedPrior`, priorFunction, startingParameters, indices, values)
}

.cyclopsSetParameterizedPrior <- function(inRcppCcdInterface, priorTypeName, priorFunction, startingParameters, excludeNumeric) {
    invisible(.Call(`_Cyclops_cyclopsSetParameterizedPrior`, inRcppCcdInterface, priorTypeName, priorFunction, startingParameters, excludeNumeric))
}

.cyclopsGetProfileLikelihood <- function(inRcppCcdInterface, inCovariate, points, threads, includePenalty) {
    .Call(`_Cyclops_cyclopsGetProfileLikelihood`, inRcppCcdInterface, inCovariate, points, threads, includePenalty)
}

.cyclopsProfileModel <- function(inRcppCcdInterface, sexpCovariates, threads, threshold, override, includePenalty) {
    .Call(`_Cyclops_cyclopsProfileModel`, inRcppCcdInterface, sexpCovariates, threads, threshold, override, includePenalty)
}

.cyclopsPredictModel <- function(inRcppCcdInterface) {
    .Call(`_Cyclops_cyclopsPredictModel`, inRcppCcdInterface)
}

.cyclopsSetControl <- function(inRcppCcdInterface, maxIterations, tolerance, convergenceType, useAutoSearch, fold, foldToCompute, lowerLimit, upperLimit, gridSteps, noiseLevel, threads, seed, resetCoefficients, startingVariance, useKKTSwindle, swindleMultipler, selectorType, initialBound, maxBoundCount, algorithm) {
    invisible(.Call(`_Cyclops_cyclopsSetControl`, inRcppCcdInterface, maxIterations, tolerance, convergenceType, useAutoSearch, fold, foldToCompute, lowerLimit, upperLimit, gridSteps, noiseLevel, threads, seed, resetCoefficients, startingVariance, useKKTSwindle, swindleMultipler, selectorType, initialBound, maxBoundCount, algorithm))
}

.cyclopsRunCrossValidation <- function(inRcppCcdInterface) {
    .Call(`_Cyclops_cyclopsRunCrossValidationl`, inRcppCcdInterface)
}

.cyclopsFitModel <- function(inRcppCcdInterface) {
    .Call(`_Cyclops_cyclopsFitModel`, inRcppCcdInterface)
}

.cyclopsLogModel <- function(inRcppCcdInterface) {
    .Call(`_Cyclops_cyclopsLogModel`, inRcppCcdInterface)
}

.cyclopsInitializeModel <- function(inModelData, modelType, computeDevice, computeMLE = FALSE) {
    .Call(`_Cyclops_cyclopsInitializeModel`, inModelData, modelType, computeDevice, computeMLE)
}

.isSorted <- function(dataFrame, indexes, ascending) {
    .Call(`_Cyclops_isSorted`, dataFrame, indexes, ascending)
}

.isSortedVectorList <- function(vectorList, ascending) {
    .Call(`_Cyclops_isSortedVectorList`, vectorList, ascending)
}

.isRcppPtrNull <- function(x) {
    .Call(`_Cyclops_isRcppPtrNull`, x)
}

#' @title Get number of strata
#'
#' @description
#' \code{getNumberOfStrata} return the number of unique strata in a Cyclops data object
#'
#' @param object    A Cyclops data object
#'
#' @export
getNumberOfStrata <- function(object) {
    .Call(`_Cyclops_cyclopsGetNumberOfStrata`, object)
}

#' @title Get covariate identifiers
#'
#' @description
#' \code{getCovariateIds} returns a vector of integer64 covariate identifiers in a Cyclops data object
#'
#' @param object    A Cyclops data object
#'
#' @export
getCovariateIds <- function(object) {
    .Call(`_Cyclops_cyclopsGetCovariateIds`, object)
}

.getCovariateTypes <- function(object, bitCovariateLabel) {
    .Call(`_Cyclops_cyclopsGetCovariateType`, object, bitCovariateLabel)
}

#' @title Get floating point size
#'
#' @description
#' \code{getFloatingPointSize} returns the floating-point representation size in a Cyclops data object
#'
#' @param object   A Cyclops data object
#'
#' @export
getFloatingPointSize <- function(object) {
    .Call(`_Cyclops_cyclopsGetFloatingPointSize`, object)
}

#' @title Get total number of covariates
#'
#' @description
#' \code{getNumberOfCovariates} returns the total number of covariates in a Cyclops data object
#'
#' @param object    A Cyclops data object
#'
#' @export
getNumberOfCovariates <- function(object) {
    .Call(`_Cyclops_cyclopsGetNumberOfColumns`, object)
}

#' @title Print Cyclops data matrix to file
#'
#' @description
#' \code{printMatrixMarket} prints the data matrix to a file
#'
#' @param object      A Cyclops data object
#' @param file        Filename
#'
#' @keywords internal
printMatrixMarket <- function(object, file) {
    invisible(.Call(`_Cyclops_cyclopsPrintMatrixMarket`, object, file))
}

#' @title Get total number of rows
#'
#' @description
#' \code{getNumberOfRows} returns the total number of outcome rows in a Cyclops data object
#'
#' @param object    A Cyclops data object
#'
#' @export
getNumberOfRows <- function(object) {
    .Call(`_Cyclops_cyclopsGetNumberOfRows`, object)
}

#' @title Get total number of outcome types
#'
#' @description
#' \code{getNumberOfTypes} returns the total number of outcome types in a Cyclops data object
#'
#' @param object    A Cyclops data object
#'
#' @keywords internal
getNumberOfTypes <- function(object) {
    .Call(`_Cyclops_cyclopsGetNumberOfTypes`, object)
}

.cyclopsUnivariableCorrelation <- function(x, bitCovariateLabel) {
    .Call(`_Cyclops_cyclopsUnivariableCorrelation`, x, bitCovariateLabel)
}

.cyclopsUnivariableSeparability <- function(x, bitCovariateLabel) {
    .Call(`_Cyclops_cyclopsUnivariableSeparability`, x, bitCovariateLabel)
}

.cyclopsSumByGroup <- function(x, bitCovariateLabel, bitGroupByLabel, power) {
    .Call(`_Cyclops_cyclopsSumByGroup`, x, bitCovariateLabel, bitGroupByLabel, power)
}

.cyclopsSumByStratum <- function(x, bitCovariateLabel, power) {
    .Call(`_Cyclops_cyclopsSumByStratum`, x, bitCovariateLabel, power)
}

.cyclopsSum <- function(x, bitCovariateLabel, power) {
    .Call(`_Cyclops_cyclopsSum`, x, bitCovariateLabel, power)
}

.cyclopsNewSqlData <- function(modelTypeName, noiseLevel, floatingPoint) {
    .Call(`_Cyclops_cyclopsNewSqlData`, modelTypeName, noiseLevel, floatingPoint)
}

.cyclopsMedian <- function(vector) {
    .Call(`_Cyclops_cyclopsMedian`, vector)
}

.cyclopsQuantile <- function(vector, q) {
    .Call(`_Cyclops_cyclopsQuantile`, vector, q)
}

.cyclopsNormalizeCovariates <- function(x, normalizationName) {
    .Call(`_Cyclops_cyclopsNormalizeCovariates`, x, normalizationName)
}

.cyclopsSetHasIntercept <- function(x, hasIntercept) {
    invisible(.Call(`_Cyclops_cyclopsSetHasIntercept`, x, hasIntercept))
}

.cyclopsGetHasIntercept <- function(x) {
    .Call(`_Cyclops_cyclopsGetHasIntercept`, x)
}

.cyclopsGetHasOffset <- function(x) {
    .Call(`_Cyclops_cyclopsGetHasOffset`, x)
}

.cyclopsGetMeanOffset <- function(x) {
    .Call(`_Cyclops_cyclopsGetMeanOffset`, x)
}

getYVector <- function(object) {
    .Call(`_Cyclops_cyclopsGetYVector`, object)
}

getTimeVector <- function(object) {
    .Call(`_Cyclops_cyclopsGetTimeVector`, object)
}

.cyclopsFinalizeData <- function(x, addIntercept, sexpOffsetCovariate, offsetAlreadyOnLogScale, sortCovariates, sexpCovariatesDense, magicFlag = FALSE) {
    invisible(.Call(`_Cyclops_cyclopsFinalizeData`, x, addIntercept, sexpOffsetCovariate, offsetAlreadyOnLogScale, sortCovariates, sexpCovariatesDense, magicFlag))
}

.loadCyclopsDataY <- function(x, stratumId, rowId, y, time) {
    invisible(.Call(`_Cyclops_cyclopsLoadDataY`, x, stratumId, rowId, y, time))
}

.loadCyclopsDataMultipleX <- function(x, covariateId, rowId, covariateValue, checkCovariateIds, checkCovariateBounds, append, forceSparse) {
    .Call(`_Cyclops_cyclopsLoadDataMultipleX`, x, covariateId, rowId, covariateValue, checkCovariateIds, checkCovariateBounds, append, forceSparse)
}

.loadCyclopsDataX <- function(x, bitCovariateId, rowId, covariateValue, replace, append, forceSparse) {
    .Call(`_Cyclops_cyclopsLoadDataX`, x, bitCovariateId, rowId, covariateValue, replace, append, forceSparse)
}

.appendSqlCyclopsData <- function(x, oStratumId, oRowId, oY, oTime, cRowId, cCovariateId, cCovariateValue) {
    .Call(`_Cyclops_cyclopsAppendSqlData`, x, oStratumId, oRowId, oY, oTime, cRowId, cCovariateId, cCovariateValue)
}

.cyclopsGetInterceptLabel <- function(x) {
    .Call(`_Cyclops_cyclopsGetInterceptLabel`, x)
}

.cyclopsReadData <- function(fileName, modelTypeName) {
    .Call(`_Cyclops_cyclopsReadFileData`, fileName, modelTypeName)
}

.cyclopsModelData <- function(pid, y, z, offs, dx, sx, ix, modelTypeName, useTimeAsOffset = FALSE, numTypes = 1L, floatingPoint = 64L) {
    .Call(`_Cyclops_cyclopsModelData`, pid, y, z, offs, dx, sx, ix, modelTypeName, useTimeAsOffset, numTypes, floatingPoint)
}

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Cyclops documentation built on Aug. 10, 2022, 5:08 p.m.