diff --git a/R/GetFrineGrayWeights.R b/R/GetFrineGrayWeights.R index 71f06a77..8e4c5d21 100644 --- a/R/GetFrineGrayWeights.R +++ b/R/GetFrineGrayWeights.R @@ -22,6 +22,7 @@ #' #' @param ftime Numeric: Observed event (failure) times #' @param fstatus Numeric: Observed event (failure) types +#' @param cvweights Numeric: Vector of 0/1 (cross-validation) weights for each data row #' @param cencode Numeric: Code to denote censored observations (Default is 0) #' @param failcode Numeric: Code to denote event of interest (Default is 1) #' diff --git a/R/Gpu.R b/R/Gpu.R index 031523b1..32818853 100644 --- a/R/Gpu.R +++ b/R/Gpu.R @@ -1,6 +1,10 @@ -# -# - +#' @title Set GPU device +#' +#' @description +#' \code{setOpenCLDevice} set GPU device +#' +#' @param name String: Name of GPU device +#' #' @export setOpenCLDevice <- function(name) { devices <- listOpenCLDevices() diff --git a/R/ModelFit.R b/R/ModelFit.R index c61c3916..f4c37a82 100644 --- a/R/ModelFit.R +++ b/R/ModelFit.R @@ -532,6 +532,8 @@ print.cyclopsFit <- function(x, show.call=TRUE ,...) { #' @param initialBound Numeric: Starting trust-region size #' @param maxBoundCount Numeric: Maximum number of tries to decrease initial trust-region size #' @param algorithm String: name of fitting algorithm to employ; default is `ccd` +#' @param doItAll Currently unused +#' @param syncCV Currently unused #' #' Todo: Describe convegence types #' diff --git a/R/NewDataConversion.R b/R/NewDataConversion.R index 1f131c8d..905c1528 100644 --- a/R/NewDataConversion.R +++ b/R/NewDataConversion.R @@ -34,6 +34,7 @@ isSorted <- function(data, columnNames, ascending = rep(TRUE, length(columnNames #' @param normalize String: Name of normalization for all non-indicator covariates (possible values: stdev, max, median) #' @param quiet If true, (warning) messages are suppressed. #' @param floatingPoint Specified floating-point representation size (32 or 64) +#' @param timeEffectMap A data frame or ffdf object containing the convariates that have time-varying effects on the outcome #' #' @details #' These columns are expected in the outcome object: @@ -55,6 +56,11 @@ isSorted <- function(data, columnNames, ascending = rep(TRUE, length(columnNames #' \verb{covariateValue} \tab(real) \tab The value of the specified covariate \cr #' } #' +#' These columns are expected in the timeEffectMap object: +#' \tabular{lll}{ +#' \verb{covariateId} \tab(integer) \tab A numeric identifier of the covariates that have time-varying effects on the outcome \cr +#' } +#' #' @return #' An object of type cyclopsData #' diff --git a/R/RcppExports.R b/R/RcppExports.R index bfa4d2f8..65ac4ea5 100644 --- a/R/RcppExports.R +++ b/R/RcppExports.R @@ -117,6 +117,11 @@ .Call(`_Cyclops_cyclopsInitializeModel`, inModelData, modelType, computeDevice, computeMLE) } +#' @title List available GPU devices +#' +#' @description +#' \code{listOpenCLDevices} list available GPU devices +#' #' @export listOpenCLDevices <- function() { .Call(`_Cyclops_listOpenCLDevices`) diff --git a/R/Simulation.R b/R/Simulation.R index b25ecbc5..977d5dd6 100644 --- a/R/Simulation.R +++ b/R/Simulation.R @@ -250,6 +250,7 @@ simulateCyclopsData <- function(nstrata = 200, #' @param model String: Fitted regression model type #' @param coverage Logical: report coverage statistics #' @param includePenalty Logical: include regularized regression penalty in computing profile likelihood based confidence intervals +#' @param computeDevice String: Name of compute device to employ; defaults to \code{"native"} C++ on CPU #' #' @export fitCyclopsSimulation <- function(sim, diff --git a/man/convertToCyclopsData.Rd b/man/convertToCyclopsData.Rd index fa318407..34450f13 100644 --- a/man/convertToCyclopsData.Rd +++ b/man/convertToCyclopsData.Rd @@ -52,6 +52,8 @@ convertToCyclopsData( \item{modelType}{Cyclops model type. Current supported types are "pr", "cpr", lr", "clr", or "cox"} +\item{timeEffectMap}{A data frame or ffdf object containing the convariates that have time-varying effects on the outcome} + \item{addIntercept}{Add an intercept to the model?} \item{checkSorting}{(DEPRECATED) Check if the data are sorted appropriately, and if not, sort.} @@ -89,6 +91,11 @@ These columns are expected in the covariates object: \verb{covariateId} \tab(integer) \tab A numeric identifier of a covariate \cr \verb{covariateValue} \tab(real) \tab The value of the specified covariate \cr } + +These columns are expected in the timeEffectMap object: +\tabular{lll}{ + \verb{covariateId} \tab(integer) \tab A numeric identifier of the covariates that have time-varying effects on the outcome \cr +} } \section{Methods (by class)}{ \itemize{ diff --git a/man/createControl.Rd b/man/createControl.Rd index 4641897b..03bc7152 100644 --- a/man/createControl.Rd +++ b/man/createControl.Rd @@ -77,7 +77,11 @@ the average number of rows per stratum is smaller than the number of strata.} \item{maxBoundCount}{Numeric: Maximum number of tries to decrease initial trust-region size} -\item{algorithm}{String: name of fitting algorithm to employ; default is `ccd` +\item{algorithm}{String: name of fitting algorithm to employ; default is `ccd`} + +\item{doItAll}{Currently unused} + +\item{syncCV}{Currently unused Todo: Describe convegence types} } diff --git a/man/fitCyclopsSimulation.Rd b/man/fitCyclopsSimulation.Rd index 5bcb427e..454942bb 100644 --- a/man/fitCyclopsSimulation.Rd +++ b/man/fitCyclopsSimulation.Rd @@ -23,6 +23,8 @@ fitCyclopsSimulation( \item{coverage}{Logical: report coverage statistics} \item{includePenalty}{Logical: include regularized regression penalty in computing profile likelihood based confidence intervals} + +\item{computeDevice}{String: Name of compute device to employ; defaults to \code{"native"} C++ on CPU} } \description{ \code{fitCyclopsSimulation} fits simulated Cyclops data using Cyclops or a standard routine. diff --git a/man/getFineGrayWeights.Rd b/man/getFineGrayWeights.Rd index 0e92dce3..5f4336c1 100644 --- a/man/getFineGrayWeights.Rd +++ b/man/getFineGrayWeights.Rd @@ -11,6 +11,8 @@ getFineGrayWeights(ftime, fstatus, cvweights = NULL, cencode = 0, failcode = 1) \item{fstatus}{Numeric: Observed event (failure) types} +\item{cvweights}{Numeric: Vector of 0/1 (cross-validation) weights for each data row} + \item{cencode}{Numeric: Code to denote censored observations (Default is 0)} \item{failcode}{Numeric: Code to denote event of interest (Default is 1)} diff --git a/man/listOpenCLDevices.Rd b/man/listOpenCLDevices.Rd new file mode 100644 index 00000000..69ef9f1b --- /dev/null +++ b/man/listOpenCLDevices.Rd @@ -0,0 +1,11 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/RcppExports.R +\name{listOpenCLDevices} +\alias{listOpenCLDevices} +\title{List available GPU devices} +\usage{ +listOpenCLDevices() +} +\description{ +\code{listOpenCLDevices} list available GPU devices +} diff --git a/man/setOpenCLDevice.Rd b/man/setOpenCLDevice.Rd new file mode 100644 index 00000000..cb6c32e8 --- /dev/null +++ b/man/setOpenCLDevice.Rd @@ -0,0 +1,14 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/Gpu.R +\name{setOpenCLDevice} +\alias{setOpenCLDevice} +\title{Set GPU device} +\usage{ +setOpenCLDevice(name) +} +\arguments{ +\item{name}{String: Name of GPU device} +} +\description{ +\code{setOpenCLDevice} set GPU device +} diff --git a/src/RcppGpuInterface.cpp b/src/RcppGpuInterface.cpp index 763fdca2..976c5290 100644 --- a/src/RcppGpuInterface.cpp +++ b/src/RcppGpuInterface.cpp @@ -15,6 +15,11 @@ #include #endif // HAVE_CUDA +//' @title List available GPU devices +//' +//' @description +//' \code{listOpenCLDevices} list available GPU devices +//' //' @export // [[Rcpp::export("listOpenCLDevices")]] Rcpp::CharacterVector listOpenCLDevices() {