[R] more attribute handling functionality
This commit is contained in:
Vadim Khotilovich
parent
ea9285dd4f
commit
8664217a5a
@ -10,6 +10,8 @@ S3method(predict,xgb.Booster.handle)
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S3method(setinfo,xgb.DMatrix)
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S3method(slice,xgb.DMatrix)
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export("xgb.attr<-")
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export("xgb.attributes<-")
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export("xgb.parameters<-")
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export(getinfo)
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export(print.xgb.DMatrix)
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export(setinfo)
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@ -17,6 +19,7 @@ export(slice)
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export(xgb.DMatrix)
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export(xgb.DMatrix.save)
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export(xgb.attr)
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export(xgb.attributes)
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export(xgb.create.features)
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export(xgb.cv)
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export(xgb.dump)
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@ -2,31 +2,28 @@
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# internal utility function
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xgb.Booster <- function(params = list(), cachelist = list(), modelfile = NULL) {
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if (typeof(cachelist) != "list") {
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stop("xgb.Booster: only accepts list of DMatrix as cachelist")
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stop("xgb.Booster only accepts list of DMatrix as cachelist")
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}
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for (dm in cachelist) {
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if (class(dm) != "xgb.DMatrix") {
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stop("xgb.Booster: only accepts list of DMatrix as cachelist")
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stop("xgb.Booster only accepts list of DMatrix as cachelist")
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}
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}
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handle <- .Call("XGBoosterCreate_R", cachelist, PACKAGE = "xgboost")
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if (length(params) != 0) {
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for (i in 1:length(params)) {
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p <- params[i]
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.Call("XGBoosterSetParam_R", handle, gsub("\\.", "_", names(p)), as.character(p),
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PACKAGE = "xgboost")
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}
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}
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if (!is.null(modelfile)) {
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if (typeof(modelfile) == "character") {
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.Call("XGBoosterLoadModel_R", handle, modelfile, PACKAGE = "xgboost")
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} else if (typeof(modelfile) == "raw") {
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.Call("XGBoosterLoadModelFromRaw_R", handle, modelfile, PACKAGE = "xgboost")
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} else {
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stop("xgb.Booster: modelfile must be character or raw vector")
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stop("modelfile must be character or raw vector")
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}
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}
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return(structure(handle, class = "xgb.Booster.handle"))
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class(handle) <- "xgb.Booster.handle"
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if (length(params) > 0) {
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xgb.parameters(handle) <- params
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}
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return(handle)
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}
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# Convert xgb.Booster.handle to xgb.Booster
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@ -38,6 +35,20 @@ xgb.handleToBooster <- function(handle, raw = NULL)
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return(bst)
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}
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# Return a verified to be valid handle out of either xgb.Booster.handle or xgb.Booster
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# internal utility function
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xgb.get.handle <- function(object) {
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handle <- switch(class(object)[1],
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xgb.Booster = object$handle,
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xgb.Booster.handle = object,
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stop("argument must be of either xgb.Booster or xgb.Booster.handle class")
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)
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if (is.null(handle) | .Call("XGCheckNullPtr_R", handle, PACKAGE="xgboost")) {
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stop("invalid xgb.Booster.handle")
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}
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handle
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}
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# Check whether an xgb.Booster object is complete
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# internal utility function
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xgb.Booster.check <- function(bst, saveraw = TRUE)
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@ -146,28 +157,43 @@ predict.xgb.Booster.handle <- function(object, ...) {
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#' Accessors for serializable attributes of a model.
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#'
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#' These methods allow to manipulate key-value attribute strings of an xgboost model.
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#' These methods allow to manipulate the key-value attribute strings of an xgboost model.
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#'
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#' @param object Object of class \code{xgb.Booster} or \code{xgb.Booster.handle}.
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#' @param which a non-empty character string specifying which attribute is to be accessed.
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#' @param value a value of an attribute. Non-character values are converted to character.
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#' When length of a \code{value} vector is more than one, only the first element is used.
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#' @param object Object of class \code{xgb.Booster} or \code{xgb.Booster.handle}.
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#' @param name a non-empty character string specifying which attribute is to be accessed.
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#' @param value a value of an attribute for \code{xgb.attr<-}; for \code{xgb.attributes<-}
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#' it's a list (or an object coercible to a list) with the names of attributes to set
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#' and the elements corresponding to attribute values.
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#' Non-character values are converted to character.
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#' When attribute value is not a scalar, only the first index is used.
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#' Use \code{NULL} to remove an attribute.
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#'
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#' @details
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#' Note that the xgboost model attributes are a separate concept from the attributes in R.
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#' Specifically, they refer to key-value strings that can be attached to an xgboost model
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#' and stored within the model's binary representation.
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#' The primary purpose of xgboost model attributes is to store some meta-data about the model.
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#' Note that they are a separate concept from the object attributes in R.
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#' Specifically, they refer to key-value strings that can be attached to an xgboost model,
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#' stored together with the model's binary representation, and accessed later
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#' (from R or any other interface).
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#' In contrast, any R-attribute assigned to an R-object of \code{xgb.Booster} class
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#' would not be saved by \code{xgb.save}, since xgboost model is an external memory object
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#' would not be saved by \code{xgb.save} because an xgboost model is an external memory object
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#' and its serialization is handled extrnally.
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#' Also, setting an attribute that has the same name as one of xgboost's parameters wouldn't
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#' change the value of that parameter for a model.
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#' Use \code{\link{`xgb.parameters<-`}} to set or change model parameters.
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#'
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#' Also note that the attribute setter would usually work more efficiently for \code{xgb.Booster.handle}
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#' than for \code{xgb.Booster}, since only just a handle would need to be copied.
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#' The attribute setters would usually work more efficiently for \code{xgb.Booster.handle}
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#' than for \code{xgb.Booster}, since only just a handle (pointer) would need to be copied.
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#'
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#' The \code{xgb.attributes<-} setter either updates the existing or adds one or several attributes,
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#' but doesn't delete the existing attributes which don't have their names in \code{names(attributes)}.
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#'
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#' @return
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#' \code{xgb.attr} returns either a string value of an attribute
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#' or \code{NULL} if an attribute wasn't stored in a model.
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#'
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#' \code{xgb.attributes} returns a list of all attribute stored in a model
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#' or \code{NULL} if a model has no stored attributes.
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#'
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#' @examples
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#' data(agaricus.train, package='xgboost')
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#' train <- agaricus.train
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@ -177,42 +203,117 @@ predict.xgb.Booster.handle <- function(object, ...) {
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#'
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#' xgb.attr(bst, "my_attribute") <- "my attribute value"
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#' print(xgb.attr(bst, "my_attribute"))
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#' xgb.attributes(bst) <- list(a = 123, b = "abc")
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#'
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#' xgb.save(bst, 'xgb.model')
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#' bst1 <- xgb.load('xgb.model')
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#' print(xgb.attr(bst1, "my_attribute"))
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#'
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#' print(xgb.attributes(bst1))
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#'
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#' # deletion:
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#' xgb.attr(bst1, "my_attribute") <- NULL
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#' print(xgb.attributes(bst1))
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#' xgb.attributes(bst1) <- list(a = NULL, b = NULL)
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#' print(xgb.attributes(bst1))
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#'
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#' @rdname xgb.attr
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#' @export
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xgb.attr <- function(object, which) {
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if (is.null(which) | nchar(as.character(which)[1]) == 0) stop("invalid attribute name")
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handle = xgb.get.handle(object, "xgb.attr")
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.Call("XGBoosterGetAttr_R", handle, as.character(which)[1], PACKAGE="xgboost")
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xgb.attr <- function(object, name) {
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if (is.null(name) || nchar(as.character(name[1])) == 0) stop("invalid attribute name")
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handle <- xgb.get.handle(object)
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.Call("XGBoosterGetAttr_R", handle, as.character(name[1]), PACKAGE="xgboost")
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}
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#' @rdname xgb.attr
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#' @export
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`xgb.attr<-` <- function(object, which, value) {
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if (is.null(which) | nchar(as.character(which)[1]) == 0) stop("invalid attribute name")
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handle = xgb.get.handle(object, "xgb.attr")
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# TODO: setting NULL value to remove an attribute
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.Call("XGBoosterSetAttr_R", handle, as.character(which)[1], as.character(value)[1], PACKAGE="xgboost")
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`xgb.attr<-` <- function(object, name, value) {
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if (is.null(name) || nchar(as.character(name[1])) == 0) stop("invalid attribute name")
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handle <- xgb.get.handle(object)
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if (!is.null(value)) {
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# Coerce the elements to be scalar strings.
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# Q: should we warn user about non-scalar elements?
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value <- as.character(value[1])
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}
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.Call("XGBoosterSetAttr_R", handle, as.character(name[1]), value, PACKAGE="xgboost")
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if (is(object, 'xgb.Booster') && !is.null(object$raw)) {
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object$raw <- xgb.save.raw(object$handle)
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object$raw <- xgb.save.raw(object$handle)
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}
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object
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}
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# Return a valid handle out of either xgb.Booster.handle or xgb.Booster
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# internal utility function
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xgb.get.handle <- function(object, caller="") {
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handle = switch(class(object),
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xgb.Booster = object$handle,
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xgb.Booster.handle = object,
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stop(caller, ": argument must be either xgb.Booster or xgb.Booster.handle")
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)
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if (is.null(handle) | .Call("XGCheckNullPtr_R", handle, PACKAGE="xgboost")) {
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stop(caller, ": invalid xgb.Booster.handle")
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}
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handle
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#' @rdname xgb.attr
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#' @export
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xgb.attributes <- function(object) {
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handle <- xgb.get.handle(object)
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attr_names <- .Call("XGBoosterGetAttrNames_R", handle, PACKAGE="xgboost")
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if (is.null(attr_names)) return(NULL)
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res <- lapply(attr_names, function(x) {
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.Call("XGBoosterGetAttr_R", handle, x, PACKAGE="xgboost")
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})
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names(res) <- attr_names
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res
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}
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#' @rdname xgb.attr
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#' @export
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`xgb.attributes<-` <- function(object, value) {
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a <- as.list(value)
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if (is.null(names(a)) || any(nchar(names(a)) == 0)) {
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stop("attribute names cannot be empty strings")
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}
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# Coerce the elements to be scalar strings.
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# Q: should we warn a user about non-scalar elements?
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a <- lapply(a, function(x) {
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if (is.null(x)) return(NULL)
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as.character(x[1])
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})
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handle <- xgb.get.handle(object)
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for (i in seq_along(a)) {
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.Call("XGBoosterSetAttr_R", handle, names(a[i]), a[[i]], PACKAGE="xgboost")
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}
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if (is(object, 'xgb.Booster') && !is.null(object$raw)) {
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object$raw <- xgb.save.raw(object$handle)
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}
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object
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}
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#' Accessors for model parameters.
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#'
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#' Only the setter for xgboost parameters is currently implemented.
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#'
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#' @param object Object of class \code{xgb.Booster} or \code{xgb.Booster.handle}.
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#' @param value a list (or an object coercible to a list) with the names of parameters to set
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#' and the elements corresponding to parameter values.
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#'
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#' @details
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#' Note that the setter would usually work more efficiently for \code{xgb.Booster.handle}
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#' than for \code{xgb.Booster}, since only just a handle would need to be copied.
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#'
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#' @examples
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#' data(agaricus.train, package='xgboost')
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#' train <- agaricus.train
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#'
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#' bst <- xgboost(data = train$data, label = train$label, max.depth = 2,
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#' eta = 1, nthread = 2, nround = 2, objective = "binary:logistic")
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#'
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#' xgb.parameters(bst) <- list(eta = 0.1)
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#'
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#' @rdname xgb.parameters
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#' @export
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`xgb.parameters<-` <- function(object, value) {
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if (length(value) == 0) return(object)
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p <- as.list(value)
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if (is.null(names(p)) || any(nchar(names(p)) == 0)) {
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stop("parameter names cannot be empty strings")
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}
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names(p) <- gsub("\\.", "_", names(p))
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p <- lapply(p, function(x) as.character(x)[1])
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handle <- xgb.get.handle(object)
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for (i in seq_along(p)) {
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.Call("XGBoosterSetParam_R", handle, names(p[i]), p[[i]], PACKAGE = "xgboost")
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}
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if (is(object, 'xgb.Booster') && !is.null(object$raw)) {
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object$raw <- xgb.save.raw(object$handle)
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}
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object
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}
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@ -3,37 +3,58 @@
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\name{xgb.attr}
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\alias{xgb.attr}
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\alias{xgb.attr<-}
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\alias{xgb.attributes}
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\alias{xgb.attributes<-}
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\title{Accessors for serializable attributes of a model.}
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\usage{
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xgb.attr(object, which)
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xgb.attr(object, name)
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xgb.attr(object, which) <- value
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xgb.attr(object, name) <- value
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xgb.attributes(object)
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xgb.attributes(object) <- value
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}
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\arguments{
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\item{object}{Object of class \code{xgb.Booster} or \code{xgb.Booster.handle}.}
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\item{object}{Object of class \code{xgb.Booster} or \code{xgb.Booster.handle}.}
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\item{which}{a non-empty character string specifying which attribute is to be accessed.}
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\item{name}{a non-empty character string specifying which attribute is to be accessed.}
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\item{value}{a value of an attribute. Non-character values are converted to character.
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When length of a \code{value} vector is more than one, only the first element is used.}
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\item{value}{a value of an attribute for \code{xgb.attr<-}; for \code{xgb.attributes<-}
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it's a list (or an object coercible to a list) with the names of attributes to set
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and the elements corresponding to attribute values.
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Non-character values are converted to character.
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When attribute value is not a scalar, only the first index is used.
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Use \code{NULL} to remove an attribute.}
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}
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\value{
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\code{xgb.attr} returns either a string value of an attribute
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or \code{NULL} if an attribute wasn't stored in a model.
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\code{xgb.attributes} returns a list of all attribute stored in a model
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or \code{NULL} if a model has no stored attributes.
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}
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\description{
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These methods allow to manipulate key-value attribute strings of an xgboost model.
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These methods allow to manipulate the key-value attribute strings of an xgboost model.
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}
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\details{
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Note that the xgboost model attributes are a separate concept from the attributes in R.
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Specifically, they refer to key-value strings that can be attached to an xgboost model
|
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and stored within the model's binary representation.
|
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The primary purpose of xgboost model attributes is to store some meta-data about the model.
|
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Note that they are a separate concept from the object attributes in R.
|
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Specifically, they refer to key-value strings that can be attached to an xgboost model,
|
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stored together with the model's binary representation, and accessed later
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(from R or any other interface).
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In contrast, any R-attribute assigned to an R-object of \code{xgb.Booster} class
|
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would not be saved by \code{xgb.save}, since xgboost model is an external memory object
|
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would not be saved by \code{xgb.save} because an xgboost model is an external memory object
|
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and its serialization is handled extrnally.
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Also, setting an attribute that has the same name as one of xgboost's parameters wouldn't
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change the value of that parameter for a model.
|
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Use \code{\link{`xgb.parameters<-`}} to set or change model parameters.
|
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|
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Also note that the attribute setter would usually work more efficiently for \code{xgb.Booster.handle}
|
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than for \code{xgb.Booster}, since only just a handle would need to be copied.
|
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The attribute setters would usually work more efficiently for \code{xgb.Booster.handle}
|
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than for \code{xgb.Booster}, since only just a handle (pointer) would need to be copied.
|
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The \code{xgb.attributes<-} setter either updates the existing or adds one or several attributes,
|
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but doesn't delete the existing attributes which don't have their names in \code{names(attributes)}.
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}
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\examples{
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data(agaricus.train, package='xgboost')
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@ -44,10 +65,18 @@ bst <- xgboost(data = train$data, label = train$label, max.depth = 2,
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xgb.attr(bst, "my_attribute") <- "my attribute value"
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print(xgb.attr(bst, "my_attribute"))
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xgb.attributes(bst) <- list(a = 123, b = "abc")
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xgb.save(bst, 'xgb.model')
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bst1 <- xgb.load('xgb.model')
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print(xgb.attr(bst1, "my_attribute"))
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print(xgb.attributes(bst1))
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# deletion:
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xgb.attr(bst1, "my_attribute") <- NULL
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print(xgb.attributes(bst1))
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xgb.attributes(bst1) <- list(a = NULL, b = NULL)
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print(xgb.attributes(bst1))
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}
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32
R-package/man/xgb.parameters.Rd
Normal file
32
R-package/man/xgb.parameters.Rd
Normal file
@ -0,0 +1,32 @@
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% Generated by roxygen2: do not edit by hand
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% Please edit documentation in R/xgb.Booster.R
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\name{xgb.parameters<-}
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\alias{xgb.parameters<-}
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\title{Accessors for model parameters.}
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\usage{
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xgb.parameters(object) <- value
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}
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\arguments{
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\item{object}{Object of class \code{xgb.Booster} or \code{xgb.Booster.handle}.}
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\item{value}{a list (or an object coercible to a list) with the names of parameters to set
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and the elements corresponding to parameter values.}
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}
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\description{
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Only the setter for xgboost parameters is currently implemented.
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}
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\details{
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Note that the setter would usually work more efficiently for \code{xgb.Booster.handle}
|
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than for \code{xgb.Booster}, since only just a handle would need to be copied.
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}
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\examples{
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data(agaricus.train, package='xgboost')
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train <- agaricus.train
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bst <- xgboost(data = train$data, label = train$label, max.depth = 2,
|
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eta = 1, nthread = 2, nround = 2, objective = "binary:logistic")
|
||||
|
||||
xgb.parameters(bst) <- list(eta = 0.1)
|
||||
|
||||
}
|
||||
|
||||
@ -390,9 +390,30 @@ SEXP XGBoosterGetAttr_R(SEXP handle, SEXP name) {
|
||||
|
||||
SEXP XGBoosterSetAttr_R(SEXP handle, SEXP name, SEXP val) {
|
||||
R_API_BEGIN();
|
||||
const char *v = isNull(val) ? nullptr : CHAR(asChar(val));
|
||||
CHECK_CALL(XGBoosterSetAttr(R_ExternalPtrAddr(handle),
|
||||
CHAR(asChar(name)),
|
||||
CHAR(asChar(val))));
|
||||
CHAR(asChar(name)), v));
|
||||
R_API_END();
|
||||
return R_NilValue;
|
||||
}
|
||||
|
||||
SEXP XGBoosterGetAttrNames_R(SEXP handle) {
|
||||
SEXP out;
|
||||
R_API_BEGIN();
|
||||
bst_ulong len;
|
||||
const char **res;
|
||||
CHECK_CALL(XGBoosterGetAttrNames(R_ExternalPtrAddr(handle),
|
||||
&len, &res));
|
||||
if (len > 0) {
|
||||
out = PROTECT(allocVector(STRSXP, len));
|
||||
for (size_t i = 0; i < len; ++i) {
|
||||
SET_STRING_ELT(out, i, mkChar(res[i]));
|
||||
}
|
||||
} else {
|
||||
out = PROTECT(R_NilValue);
|
||||
}
|
||||
UNPROTECT(1);
|
||||
R_API_END();
|
||||
return out;
|
||||
}
|
||||
|
||||
|
||||
@ -198,9 +198,15 @@ XGB_DLL SEXP XGBoosterGetAttr_R(SEXP handle, SEXP name);
|
||||
* \brief set learner attribute value
|
||||
* \param handle handle
|
||||
* \param name attribute name
|
||||
* \param val attribute value
|
||||
* \param val attribute value; NULL value would delete an attribute
|
||||
* \return R_NilValue
|
||||
*/
|
||||
XGB_DLL SEXP XGBoosterSetAttr_R(SEXP handle, SEXP name, SEXP val);
|
||||
|
||||
/*!
|
||||
* \brief get the names of learner attributes
|
||||
* \return string vector containing attribute names
|
||||
*/
|
||||
XGB_DLL SEXP XGBoosterGetAttrNames_R(SEXP handle);
|
||||
|
||||
#endif // XGBOOST_WRAPPER_R_H_ // NOLINT(*)
|
||||
|
||||
@ -28,15 +28,32 @@ test_that("xgb.dump works", {
|
||||
expect_true(xgb.dump(bst.Tree, 'xgb.model.dump', with.stats = T))
|
||||
})
|
||||
|
||||
test_that("xgb.attr", {
|
||||
test_that("xgb-attribute functionality", {
|
||||
val <- "my attribute value"
|
||||
list.val <- list(my_attr=val, a=123, b='ok')
|
||||
list.ch <- list.val[order(names(list.val))]
|
||||
list.ch <- lapply(list.ch, as.character)
|
||||
# proper input:
|
||||
expect_error(xgb.attr(bst.Tree, NULL))
|
||||
expect_error(xgb.attr(val, val))
|
||||
# set & get:
|
||||
expect_null(xgb.attr(bst.Tree, "asdf"))
|
||||
expect_null(xgb.attributes(bst.Tree)) # initially, expect no attributes
|
||||
xgb.attr(bst.Tree, "my_attr") <- val
|
||||
expect_equal(xgb.attr(bst.Tree, "my_attr"), val)
|
||||
xgb.attributes(bst.Tree) <- list.val
|
||||
expect_equal(xgb.attributes(bst.Tree), list.ch)
|
||||
# serializing:
|
||||
xgb.save(bst.Tree, 'xgb.model')
|
||||
bst1 <- xgb.load('xgb.model')
|
||||
expect_equal(xgb.attr(bst1, "my_attr"), val)
|
||||
bst <- xgb.load('xgb.model')
|
||||
expect_equal(xgb.attr(bst, "my_attr"), val)
|
||||
expect_equal(xgb.attributes(bst), list.ch)
|
||||
# deletion:
|
||||
xgb.attr(bst, "my_attr") <- NULL
|
||||
expect_null(xgb.attr(bst, "my_attr"))
|
||||
expect_equal(xgb.attributes(bst), list.ch[c("a", "b")])
|
||||
xgb.attributes(bst) <- list(a=NULL, b=NULL)
|
||||
expect_null(xgb.attributes(bst))
|
||||
})
|
||||
|
||||
test_that("xgb.model.dt.tree works with and without feature names", {
|
||||
|
||||
Loading…
x
Reference in New Issue
Block a user