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 getCovariateTypes getCovariateIds getNumberOfStrata sRcppPtrNull printCyclopsRowIds sSortedVectorList sSorted cyclopsInitializeModel cyclopsLogModel cyclopsFitModel cyclopsRunCrossValidation cyclopsSetControl cyclopsPredictModel cyclopsProfileModel cyclopsSetParameterizedPrior cyclopsTestParameterizedPrior cyclopsSetPrior cyclopsGetFisherInformation cyclopsGetLogLikelihood cyclopsGetPredictiveLogLikelihood cyclopsSetWeights cyclopsGetIsRegularized cyclopsSetFixedBeta cyclopsSetBeta cyclopsGetUseOffsetNames cyclopsGetIsSurvivalNames cyclopsGetRemoveInterceptNames cyclopsGetModelTypeNames bySum

Documented in appendSqlCyclopsData getCovariateIds getCovariateTypes getNumberOfCovariates getNumberOfRows getNumberOfStrata getNumberOfTypes printCyclopsRowIds printMatrixMarket

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

.bySum <- function(ffValues, ffBins) {
    .Call(`_Cyclops_bySum`, ffValues, ffBins)
}

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

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

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

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

.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))
}

.cyclopsGetPredictiveLogLikelihood <- function(inRcppCcdInterface, weights) {
    .Call(`_Cyclops_cyclopsGetPredictiveLogLikelihood`, inRcppCcdInterface, weights)
}

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

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

.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))
}

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

.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, computeMLE = FALSE) {
    .Call(`_Cyclops_cyclopsInitializeModel`, inModelData, modelType, computeMLE)
}

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

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

#' @title Print row identifiers
#'
#' @description
#' \code{printCcdRowIds} return the row identifiers in a Cyclops data object
#'
#' @param object    A Cyclops data object
#'
#' @keywords internal
printCyclopsRowIds <- function(object) {
    invisible(.Call(`_Cyclops_cyclopsPrintRowIds`, object))
}

.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 integer covariate identifiers in a Cyclops data object
#'
#' @param object    A Cyclops data object
#'
#' @export
getCovariateIds <- function(object) {
    .Call(`_Cyclops_cyclopsGetCovariateIds`, object)
}

#' @title Get covariate types
#'
#' @description
#' \code{getCovariateTypes} returns a vector covariate types in a Cyclops data object
#'
#' @param object    A Cyclops data object
#' @param covariateLabel Integer vector: covariate identifiers to return
#'
#' @export
getCovariateTypes <- function(object, covariateLabel) {
    .Call(`_Cyclops_cyclopsGetCovariateType`, object, covariateLabel)
}

#' @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
#'
#' @export
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, covariateLabel) {
    .Call(`_Cyclops_cyclopsUnivariableCorrelation`, x, covariateLabel)
}

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

.cyclopsSumByGroup <- function(x, covariateLabel, groupByLabel, power) {
    .Call(`_Cyclops_cyclopsSumByGroup`, x, covariateLabel, groupByLabel, power)
}

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

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

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

.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, covariateId, rowId, covariateValue, replace, append, forceSparse) {
    .Call(`_Cyclops_cyclopsLoadDataX`, x, covariateId, 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) {
    .Call(`_Cyclops_cyclopsModelData`, pid, y, z, offs, dx, sx, ix, modelTypeName, useTimeAsOffset, numTypes)
}

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Cyclops documentation built on June 16, 2018, 1:38 p.m.