[R] maintenance Apr 2017 (#2237)
* [R] make sure things work for a single split model; fixes #2191 * [R] add option use_int_id to xgb.model.dt.tree * [R] add example of exporting tree plot to a file * [R] set save_period = NULL as default in xgboost() to be the same as in xgb.train; fixes #2182 * [R] it's a good practice after CRAN releases to bump up package version in dev * [R] allow xgb.DMatrix construction from integer dense matrices * [R] xgb.DMatrix: silent parameter; improve documentation * [R] xgb.model.dt.tree code style changes * [R] update NEWS with parameter changes * [R] code safety & style; handle non-strict matrix and inherited classes of input and model; fixes #2242 * [R] change to x.y.z.p R-package versioning scheme and set version to 0.6.4.3 * [R] add an R package versioning section to the contributors guide * [R] R-package/README.md: clean up the redundant old installation instructions, link the contributors guide
This commit is contained in:
Vadim Khotilovich
committed by
Tong He
Tong He
parent
d769b6bcb5
commit
a375ad2822
@@ -1,14 +1,17 @@
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#' Construct xgb.DMatrix object
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#'
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#' Contruct xgb.DMatrix object from dense matrix, sparse matrix
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#' or local file (that was created previously by saving an \code{xgb.DMatrix}).
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#' Construct xgb.DMatrix object from either a dense matrix, a sparse matrix, or a local file.
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#' Supported input file formats are either a libsvm text file or a binary file that was created previously by
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#' \code{\link{xgb.DMatrix.save}}).
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#'
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#' @param data a \code{matrix} object, a \code{dgCMatrix} object or a character representing a filename
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#' @param info a list of information of the xgb.DMatrix object
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#' @param missing Missing is only used when input is dense matrix, pick a float
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#' value that represents missing value. Sometime a data use 0 or other extreme value to represents missing values.
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#
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#' @param ... other information to pass to \code{info}.
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#' @param data a \code{matrix} object (either numeric or integer), a \code{dgCMatrix} object, or a character
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#' string representing a filename.
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#' @param info a named list of additional information to store in the \code{xgb.DMatrix} object.
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#' See \code{\link{setinfo}} for the specific allowed kinds of
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#' @param missing a float value to represents missing values in data (used only when input is a dense matrix).
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#' It is useful when a 0 or some other extreme value represents missing values in data.
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#' @param silent whether to suppress printing an informational message after loading from a file.
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#' @param ... the \code{info} data could be passed directly as parameters, without creating an \code{info} list.
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#'
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#' @examples
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#' data(agaricus.train, package='xgboost')
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@@ -17,19 +20,19 @@
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#' xgb.DMatrix.save(dtrain, 'xgb.DMatrix.data')
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#' dtrain <- xgb.DMatrix('xgb.DMatrix.data')
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#' @export
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xgb.DMatrix <- function(data, info = list(), missing = NA, ...) {
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xgb.DMatrix <- function(data, info = list(), missing = NA, silent = FALSE, ...) {
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cnames <- NULL
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if (typeof(data) == "character") {
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if (length(data) > 1)
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stop("'data' has class 'character' and length ", length(data),
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".\n 'data' accepts either a numeric matrix or a single filename.")
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handle <- .Call("XGDMatrixCreateFromFile_R", data, as.integer(FALSE),
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handle <- .Call("XGDMatrixCreateFromFile_R", data, as.integer(silent),
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PACKAGE = "xgboost")
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} else if (is.matrix(data)) {
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handle <- .Call("XGDMatrixCreateFromMat_R", data, missing,
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PACKAGE = "xgboost")
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cnames <- colnames(data)
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} else if (class(data) == "dgCMatrix") {
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} else if (inherits(data, "dgCMatrix")) {
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handle <- .Call("XGDMatrixCreateFromCSC_R", data@p, data@i, data@x, nrow(data),
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PACKAGE = "xgboost")
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cnames <- colnames(data)
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@@ -51,10 +54,9 @@ xgb.DMatrix <- function(data, info = list(), missing = NA, ...) {
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# get dmatrix from data, label
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# internal helper method
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xgb.get.DMatrix <- function(data, label = NULL, missing = NA, weight = NULL) {
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inClass <- class(data)
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if ("dgCMatrix" %in% inClass || "matrix" %in% inClass ) {
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if (inherits(data, "dgCMatrix") || is.matrix(data)) {
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if (is.null(label)) {
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stop("xgboost: need label when data is a matrix")
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stop("label must be provided when data is a matrix")
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}
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dtrain <- xgb.DMatrix(data, label = label, missing = missing)
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if (!is.null(weight)){
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@@ -64,11 +66,11 @@ xgb.get.DMatrix <- function(data, label = NULL, missing = NA, weight = NULL) {
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if (!is.null(label)) {
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warning("xgboost: label will be ignored.")
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}
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if (inClass == "character") {
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dtrain <- xgb.DMatrix(data)
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} else if (inClass == "xgb.DMatrix") {
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if (is.character(data)) {
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dtrain <- xgb.DMatrix(data[1])
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} else if (inherits(data, "xgb.DMatrix")) {
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dtrain <- data
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} else if ("data.frame" %in% inClass) {
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} else if (inherits(data, "data.frame")) {
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stop("xgboost doesn't support data.frame as input. Convert it to matrix first.")
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} else {
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stop("xgboost: invalid input data")
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@@ -98,8 +100,8 @@ xgb.get.DMatrix <- function(data, label = NULL, missing = NA, weight = NULL) {
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#'
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#' @export
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dim.xgb.DMatrix <- function(x) {
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c(.Call("XGDMatrixNumRow_R", x, PACKAGE="xgboost"),
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.Call("XGDMatrixNumCol_R", x, PACKAGE="xgboost"))
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c(.Call("XGDMatrixNumRow_R", x, PACKAGE = "xgboost"),
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.Call("XGDMatrixNumCol_R", x, PACKAGE = "xgboost"))
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}
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@@ -297,8 +299,8 @@ slice <- function(object, ...) UseMethod("slice")
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#' @rdname slice.xgb.DMatrix
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#' @export
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slice.xgb.DMatrix <- function(object, idxset, ...) {
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if (class(object) != "xgb.DMatrix") {
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stop("slice: first argument dtrain must be xgb.DMatrix")
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if (!inherits(object, "xgb.DMatrix")) {
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stop("object must be xgb.DMatrix")
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}
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ret <- .Call("XGDMatrixSliceDMatrix_R", object, idxset, PACKAGE = "xgboost")
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@@ -317,7 +319,7 @@ slice.xgb.DMatrix <- function(object, idxset, ...) {
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#' @rdname slice.xgb.DMatrix
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#' @export
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`[.xgb.DMatrix` <- function(object, idxset, colset=NULL) {
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`[.xgb.DMatrix` <- function(object, idxset, colset = NULL) {
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slice(object, idxset)
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}
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@@ -341,7 +343,7 @@ slice.xgb.DMatrix <- function(object, idxset, ...) {
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#'
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#' @method print xgb.DMatrix
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#' @export
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print.xgb.DMatrix <- function(x, verbose=FALSE, ...) {
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print.xgb.DMatrix <- function(x, verbose = FALSE, ...) {
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cat('xgb.DMatrix dim:', nrow(x), 'x', ncol(x), ' info: ')
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infos <- c()
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if(length(getinfo(x, 'label')) > 0) infos <- 'label'
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@@ -353,7 +355,7 @@ print.xgb.DMatrix <- function(x, verbose=FALSE, ...) {
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cat(' colnames:')
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if (verbose & !is.null(cnames)) {
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cat("\n'")
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cat(cnames, sep="','")
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cat(cnames, sep = "','")
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cat("'")
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} else {
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if (is.null(cnames)) cat(' no')
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