consolidated DMatrix&Booster stuff into xgb.DMatrix.R & xgb.Booster.R

R-package/R/getinfo.xgb.DMatrix.R

@@ -1,55 +0,0 @@
-setClass('xgb.DMatrix')
-
-#' Get information of an xgb.DMatrix object
-#' 
-#' Get information of an xgb.DMatrix object
-#' 
-#' The information can be one of the following:
-#' 
-#' \itemize{
-#'     \item \code{label}: label Xgboost learn from ;
-#'     \item \code{weight}: to do a weight rescale ;
-#'     \item \code{base_margin}: base margin is the base prediction Xgboost will boost from ;
-#'     \item \code{nrow}: number of rows of the \code{xgb.DMatrix}.
-#' }
-#' 
-#' @examples
-#' data(agaricus.train, package='xgboost')
-#' train <- agaricus.train
-#' dtrain <- xgb.DMatrix(train$data, label=train$label)
-#' labels <- getinfo(dtrain, 'label')
-#' setinfo(dtrain, 'label', 1-labels)
-#' labels2 <- getinfo(dtrain, 'label')
-#' stopifnot(all(labels2 == 1-labels))
-#' @rdname getinfo
-#' @export
-getinfo <- function(object, ...){
-    UseMethod("getinfo")
-}
-
-
-
-#' @param object Object of class \code{xgb.DMatrix}
-#' @param name the name of the field to get
-#' @param ... other parameters
-#' @rdname getinfo
-#' @method getinfo xgb.DMatrix
-setMethod("getinfo", signature = "xgb.DMatrix",
-          definition = function(object, name) {
-              if (typeof(name) != "character") {
-                  stop("xgb.getinfo: name must be character")
-              }
-              if (class(object) != "xgb.DMatrix") {
-                  stop("xgb.setinfo: first argument dtrain must be xgb.DMatrix")
-              }
-              if (name != "label" && name != "weight" &&
-                      name != "base_margin" && name != "nrow") {
-                  stop(paste("xgb.getinfo: unknown info name", name))
-              }
-              if (name != "nrow"){
-                  ret <- .Call("XGDMatrixGetInfo_R", object, name, PACKAGE = "xgboost")
-              } else {
-                  ret <- xgb.numrow(object)
-              }
-              return(ret)
-          })

R-package/R/nrow.xgb.DMatrix.R

@@ -1,19 +0,0 @@
-setGeneric("nrow")
-
-#' @title Number of xgb.DMatrix rows
-#' @description \code{nrow} return the number of rows present in the \code{xgb.DMatrix}.
-#' @param x Object of class \code{xgb.DMatrix}
-#' 
-#' @examples
-#' data(agaricus.train, package='xgboost')
-#' train <- agaricus.train
-#' dtrain <- xgb.DMatrix(train$data, label=train$label)
-#' stopifnot(nrow(dtrain) == nrow(train$data))
-#' 
-#' @export
-setMethod("nrow",
-          signature = "xgb.DMatrix",
-          definition = function(x) {
-            xgb.numrow(x)
-          }
-)

R-package/R/predict.xgb.Booster.R

@@ -1,80 +0,0 @@
-setClass("xgb.Booster.handle")
-setClass("xgb.Booster",
-         slots = c(handle = "xgb.Booster.handle",
-                   raw = "raw"))
-
-#' Predict method for eXtreme Gradient Boosting model
-#' 
-#' Predicted values based on xgboost model object.
-#' 
-#' @param object Object of class "xgb.Boost"
-#' @param newdata takes \code{matrix}, \code{dgCMatrix}, local data file or 
-#'   \code{xgb.DMatrix}. 
-#' @param missing Missing is only used when input is dense matrix, pick a float 
-#'     value that represents missing value. Sometime a data use 0 or other extreme value to represents missing values.
-#' @param outputmargin whether the prediction should be shown in the original
-#'   value of sum of functions, when outputmargin=TRUE, the prediction is 
-#'   untransformed margin value. In logistic regression, outputmargin=T will
-#'   output value before logistic transformation.
-#' @param ntreelimit limit number of trees used in prediction, this parameter is
-#'  only valid for gbtree, but not for gblinear. set it to be value bigger 
-#'  than 0. It will use all trees by default.
-#' @param predleaf whether predict leaf index instead. If set to TRUE, the output will be a matrix object.
-#' 
-#' @details  
-#' The option \code{ntreelimit} purpose is to let the user train a model with lots 
-#' of trees but use only the first trees for prediction to avoid overfitting 
-#' (without having to train a new model with less trees).
-#' 
-#' The option \code{predleaf} purpose is inspired from §3.1 of the paper 
-#' \code{Practical Lessons from Predicting Clicks on Ads at Facebook}.
-#' The idea is to use the model as a generator of new features which capture non linear link 
-#' from original features.
-#' 
-#' @examples
-#' data(agaricus.train, package='xgboost')
-#' data(agaricus.test, package='xgboost')
-#' train <- agaricus.train
-#' test <- agaricus.test
-#' bst <- xgboost(data = train$data, label = train$label, max.depth = 2, 
-#'                eta = 1, nthread = 2, nround = 2,objective = "binary:logistic")
-#' pred <- predict(bst, test$data)
-#' @export
-setMethod("predict", signature = "xgb.Booster",
-          definition = function(object, newdata, missing = NA,
-                                outputmargin = FALSE, ntreelimit = NULL, predleaf = FALSE) {
-  if (class(object) != "xgb.Booster"){
-    stop("predict: model in prediction must be of class xgb.Booster")
-  } else {
-    object <- xgb.Booster.check(object, saveraw = FALSE)
-  }
-  if (class(newdata) != "xgb.DMatrix") {
-    newdata <- xgb.DMatrix(newdata, missing = missing)
-  }
-  if (is.null(ntreelimit)) {
-    ntreelimit <- 0
-  } else {
-    if (ntreelimit < 1){
-      stop("predict: ntreelimit must be equal to or greater than 1")
-    }
-  }
-  option <- 0
-  if (outputmargin) {
-    option <- option + 1
-  }
-  if (predleaf) {
-    option <- option + 2
-  }
-  ret <- .Call("XGBoosterPredict_R", object$handle, newdata, as.integer(option),
-               as.integer(ntreelimit), PACKAGE = "xgboost")
-  if (predleaf){
-      len <- getinfo(newdata, "nrow")
-      if (length(ret) == len){
-          ret <- matrix(ret,ncol = 1)
-      } else {
-          ret <- matrix(ret, ncol = len)
-          ret <- t(ret)
-      }
-  }
-  return(ret)
-})

R-package/R/predict.xgb.Booster.handle.R

@@ -1,18 +0,0 @@
-#' Predict method for eXtreme Gradient Boosting model handle
-#' 
-#' Predicted values based on xgb.Booster.handle object.
-#' 
-#' @param object Object of class "xgb.Boost.handle"
-#' @param ... Parameters pass to \code{predict.xgb.Booster}
-#' 
-setMethod("predict", signature = "xgb.Booster.handle",
-          definition = function(object, ...) {
-  if (class(object) != "xgb.Booster.handle"){
-    stop("predict: model in prediction must be of class xgb.Booster.handle")
-  }
-
-  bst <- xgb.handleToBooster(object)
-
-  ret <- predict(bst, ...)
-  return(ret)
-})

R-package/R/setinfo.xgb.DMatrix.R

@@ -1,37 +0,0 @@
-#' Set information of an xgb.DMatrix object
-#' 
-#' Set information of an xgb.DMatrix object
-#' 
-#' It can be one of the following:
-#' 
-#' \itemize{
-#'     \item \code{label}: label Xgboost learn from ;
-#'     \item \code{weight}: to do a weight rescale ;
-#'     \item \code{base_margin}: base margin is the base prediction Xgboost will boost from ;
-#'     \item \code{group}.
-#' }
-#' 
-#' @examples
-#' data(agaricus.train, package='xgboost')
-#' train <- agaricus.train
-#' dtrain <- xgb.DMatrix(train$data, label=train$label)
-#' labels <- getinfo(dtrain, 'label')
-#' setinfo(dtrain, 'label', 1-labels)
-#' labels2 <- getinfo(dtrain, 'label')
-#' stopifnot(all(labels2 == 1-labels))
-#' @rdname setinfo
-#' @export
-setinfo <- function(object, ...){
-  UseMethod("setinfo")
-}
-
-#' @param object Object of class "xgb.DMatrix"
-#' @param name the name of the field to get
-#' @param info the specific field of information to set
-#' @param ... other parameters
-#' @rdname setinfo
-#' @method setinfo xgb.DMatrix
-setMethod("setinfo", signature = "xgb.DMatrix",
-          definition = function(object, name, info) {
-            xgb.setinfo(object, name, info)
-          })

R-package/R/slice.xgb.DMatrix.R

@@ -1,44 +0,0 @@
-setClass('xgb.DMatrix')
-
-#' Get a new DMatrix containing the specified rows of
-#' orginal xgb.DMatrix object
-#'
-#' Get a new DMatrix containing the specified rows of
-#' orginal xgb.DMatrix object
-#' 
-#' @examples
-#' data(agaricus.train, package='xgboost')
-#' train <- agaricus.train
-#' dtrain <- xgb.DMatrix(train$data, label=train$label)
-#' dsub <- slice(dtrain, 1:3)
-#' @rdname slice
-#' @export
-slice <- function(object, ...){
-    UseMethod("slice")
-}
-
-#' @param object Object of class "xgb.DMatrix"
-#' @param idxset a integer vector of indices of rows needed
-#' @param ... other parameters
-#' @rdname slice
-#' @method slice xgb.DMatrix
-setMethod("slice", signature = "xgb.DMatrix",
-          definition = function(object, idxset, ...) {
-              if (class(object) != "xgb.DMatrix") {
-                  stop("slice: first argument dtrain must be xgb.DMatrix")
-              }
-              ret <- .Call("XGDMatrixSliceDMatrix_R", object, idxset,
-                           PACKAGE = "xgboost")
-
-              attr_list <- attributes(object)
-              nr <- xgb.numrow(object)
-              len <- sapply(attr_list,length)
-              ind <- which(len == nr)
-              if (length(ind) > 0) {
-                  nms <- names(attr_list)[ind]
-                  for (i in 1:length(ind)) {
-                    attr(ret,nms[i]) <- attr(object,nms[i])[idxset]
-                  }
-              }
-              return(structure(ret, class = "xgb.DMatrix"))
-          })