update docs

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)
 #'

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()

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
 #'

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
 #'

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`)

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,

src/RcppGpuInterface.cpp

@@ -15,6 +15,11 @@
  #include <cuda.h>
 #endif // HAVE_CUDA
 
+//' @title List available GPU devices
+//'
+//' @description
+//' \code{listOpenCLDevices} list available GPU devices
+//'
 //' @export
 // [[Rcpp::export("listOpenCLDevices")]]
 Rcpp::CharacterVector listOpenCLDevices() {