R/xgb.Booster.R

Defines functions print.xgb.Booster xgb.ntree `xgb.parameters<-` `xgb.config<-` xgb.config `xgb.attributes<-` xgb.attributes `xgb.attr<-` xgb.attr predict.xgb.Booster.handle predict.xgb.Booster xgb.Booster.complete xgb.get.handle is.null.handle xgb.handleToBooster xgb.Booster.handle

Documented in predict.xgb.Booster predict.xgb.Booster.handle print.xgb.Booster xgb.attr xgb.attributes xgb.Booster.complete xgb.config

# Construct an internal xgboost Booster and return a handle to it.
# internal utility function
xgb.Booster.handle <- function(params = list(), cachelist = list(),
                               modelfile = NULL, handle = NULL) {
  if (typeof(cachelist) != "list" ||
      !all(vapply(cachelist, inherits, logical(1), what = 'xgb.DMatrix'))) {
    stop("cachelist must be a list of xgb.DMatrix objects")
  }
  ## Load existing model, dispatch for on disk model file and in memory buffer
  if (!is.null(modelfile)) {
    if (typeof(modelfile) == "character") {
      ## A filename
      handle <- .Call(XGBoosterCreate_R, cachelist)
      modelfile <- path.expand(modelfile)
      .Call(XGBoosterLoadModel_R, handle, modelfile[1])
      class(handle) <- "xgb.Booster.handle"
      if (length(params) > 0) {
        xgb.parameters(handle) <- params
      }
      return(handle)
    } else if (typeof(modelfile) == "raw") {
      ## A memory buffer
      bst <- xgb.unserialize(modelfile, handle)
      xgb.parameters(bst) <- params
      return (bst)
    } else if (inherits(modelfile, "xgb.Booster")) {
      ## A booster object
      bst <- xgb.Booster.complete(modelfile, saveraw = TRUE)
      bst <- xgb.unserialize(bst$raw)
      xgb.parameters(bst) <- params
      return (bst)
    } else {
      stop("modelfile must be either character filename, or raw booster dump, or xgb.Booster object")
    }
  }
  ## Create new model
  handle <- .Call(XGBoosterCreate_R, cachelist)
  class(handle) <- "xgb.Booster.handle"
  if (length(params) > 0) {
    xgb.parameters(handle) <- params
  }
  return(handle)
}

# Convert xgb.Booster.handle to xgb.Booster
# internal utility function
xgb.handleToBooster <- function(handle, raw = NULL) {
  bst <- list(handle = handle, raw = raw)
  class(bst) <- "xgb.Booster"
  return(bst)
}

# Check whether xgb.Booster.handle is null
# internal utility function
is.null.handle <- function(handle) {
  if (is.null(handle)) return(TRUE)

  if (!identical(class(handle), "xgb.Booster.handle"))
    stop("argument type must be xgb.Booster.handle")

  if (.Call(XGCheckNullPtr_R, handle))
    return(TRUE)

  return(FALSE)
}

# Return a verified to be valid handle out of either xgb.Booster.handle or
# xgb.Booster internal utility function
xgb.get.handle <- function(object) {
  if (inherits(object, "xgb.Booster")) {
    handle <- object$handle
  } else if (inherits(object, "xgb.Booster.handle")) {
    handle <- object
  } else {
    stop("argument must be of either xgb.Booster or xgb.Booster.handle class")
  }
  if (is.null.handle(handle)) {
    stop("invalid xgb.Booster.handle")
  }
  handle
}

#' Restore missing parts of an incomplete xgb.Booster object.
#'
#' It attempts to complete an \code{xgb.Booster} object by restoring either its missing
#' raw model memory dump (when it has no \code{raw} data but its \code{xgb.Booster.handle} is valid)
#' or its missing internal handle (when its \code{xgb.Booster.handle} is not valid
#' but it has a raw Booster memory dump).
#'
#' @param object object of class \code{xgb.Booster}
#' @param saveraw a flag indicating whether to append \code{raw} Booster memory dump data
#'                when it doesn't already exist.
#'
#' @details
#'
#' While this method is primarily for internal use, it might be useful in some practical situations.
#'
#' E.g., when an \code{xgb.Booster} model is saved as an R object and then is loaded as an R object,
#' its handle (pointer) to an internal xgboost model would be invalid. The majority of xgboost methods
#' should still work for such a model object since those methods would be using
#' \code{xgb.Booster.complete} internally. However, one might find it to be more efficient to call the
#' \code{xgb.Booster.complete} function explicitly once after loading a model as an R-object.
#' That would prevent further repeated implicit reconstruction of an internal booster model.
#'
#' @return
#' An object of \code{xgb.Booster} class.
#'
#' @examples
#'
#' data(agaricus.train, package='xgboost')
#' bst <- xgboost(data = agaricus.train$data, label = agaricus.train$label, max_depth = 2,
#'                eta = 1, nthread = 2, nrounds = 2, objective = "binary:logistic")
#' saveRDS(bst, "xgb.model.rds")
#'
#' # Warning: The resulting RDS file is only compatible with the current XGBoost version.
#' # Refer to the section titled "a-compatibility-note-for-saveRDS-save".
#' bst1 <- readRDS("xgb.model.rds")
#' if (file.exists("xgb.model.rds")) file.remove("xgb.model.rds")
#' # the handle is invalid:
#' print(bst1$handle)
#'
#' bst1 <- xgb.Booster.complete(bst1)
#' # now the handle points to a valid internal booster model:
#' print(bst1$handle)
#'
#' @export
xgb.Booster.complete <- function(object, saveraw = TRUE) {
  if (!inherits(object, "xgb.Booster"))
    stop("argument type must be xgb.Booster")

  if (is.null.handle(object$handle)) {
    object$handle <- xgb.Booster.handle(modelfile = object$raw, handle = object$handle)
  } else {
    if (is.null(object$raw) && saveraw) {
      object$raw <- xgb.serialize(object$handle)
    }
  }

  attrs <- xgb.attributes(object)
  if (!is.null(attrs$best_ntreelimit)) {
    object$best_ntreelimit <- as.integer(attrs$best_ntreelimit)
  }
  if (!is.null(attrs$best_iteration)) {
    ## Convert from 0 based back to 1 based.
    object$best_iteration <- as.integer(attrs$best_iteration) + 1
  }
  if (!is.null(attrs$best_score)) {
    object$best_score <- as.numeric(attrs$best_score)
  }
  if (!is.null(attrs$best_msg)) {
    object$best_msg <- attrs$best_msg
  }
  if (!is.null(attrs$niter)) {
    object$niter <- as.integer(attrs$niter)
  }

  return(object)
}

#' Predict method for eXtreme Gradient Boosting model
#'
#' Predicted values based on either xgboost model or model handle object.
#'
#' @param object Object of class \code{xgb.Booster} or \code{xgb.Booster.handle}
#' @param newdata takes \code{matrix}, \code{dgCMatrix}, \code{dgRMatrix}, \code{dsparseVector},
#'        local data file or \code{xgb.DMatrix}.
#'
#'        For single-row predictions on sparse data, it's recommended to use CSR format. If passing
#'        a sparse vector, it will take it as a row vector.
#' @param missing Missing is only used when input is dense matrix. Pick a float value that represents
#'        missing values in data (e.g., sometimes 0 or some other extreme value is used).
#' @param outputmargin whether the prediction should be returned in the for of original untransformed
#'        sum of predictions from boosting iterations' results. E.g., setting \code{outputmargin=TRUE} for
#'        logistic regression would result in predictions for log-odds instead of probabilities.
#' @param ntreelimit Deprecated, use \code{iterationrange} instead.
#' @param predleaf whether predict leaf index.
#' @param predcontrib whether to return feature contributions to individual predictions (see Details).
#' @param approxcontrib whether to use a fast approximation for feature contributions (see Details).
#' @param predinteraction whether to return contributions of feature interactions to individual predictions (see Details).
#' @param reshape whether to reshape the vector of predictions to a matrix form when there are several
#'        prediction outputs per case. This option has no effect when either of predleaf, predcontrib,
#'        or predinteraction flags is TRUE.
#' @param training whether is the prediction result used for training.  For dart booster,
#'        training predicting will perform dropout.
#' @param iterationrange Specifies which layer of trees are used in prediction.  For
#'        example, if a random forest is trained with 100 rounds.  Specifying
#'        `iterationrange=(1, 21)`, then only the forests built during [1, 21) (half open set)
#'        rounds are used in this prediction.  It's 1-based index just like R vector.  When set
#'        to \code{c(1, 1)} XGBoost will use all trees.
#' @param strict_shape  Default is \code{FALSE}. When it's set to \code{TRUE}, output
#'        type and shape of prediction are invariant to model type.
#'
#' @param ... Parameters passed to \code{predict.xgb.Booster}
#'
#' @details
#'
#' Note that \code{iterationrange} would currently do nothing for predictions from gblinear,
#' since gblinear doesn't keep its boosting history.
#'
#' One possible practical applications of the \code{predleaf} option is to use the model
#' as a generator of new features which capture non-linearity and interactions,
#' e.g., as implemented in \code{\link{xgb.create.features}}.
#'
#' Setting \code{predcontrib = TRUE} allows to calculate contributions of each feature to
#' individual predictions. For "gblinear" booster, feature contributions are simply linear terms
#' (feature_beta * feature_value). For "gbtree" booster, feature contributions are SHAP
#' values (Lundberg 2017) that sum to the difference between the expected output
#' of the model and the current prediction (where the hessian weights are used to compute the expectations).
#' Setting \code{approxcontrib = TRUE} approximates these values following the idea explained
#' in \url{http://blog.datadive.net/interpreting-random-forests/}.
#'
#' With \code{predinteraction = TRUE}, SHAP values of contributions of interaction of each pair of features
#' are computed. Note that this operation might be rather expensive in terms of compute and memory.
#' Since it quadratically depends on the number of features, it is recommended to perform selection
#' of the most important features first. See below about the format of the returned results.
#'
#' @return
#' The return type is different depending whether \code{strict_shape} is set to \code{TRUE}.  By default,
#' for regression or binary classification, it returns a vector of length \code{nrows(newdata)}.
#' For multiclass classification, either a \code{num_class * nrows(newdata)} vector or
#' a \code{(nrows(newdata), num_class)} dimension matrix is returned, depending on
#' the \code{reshape} value.
#'
#' When \code{predleaf = TRUE}, the output is a matrix object with the
#' number of columns corresponding to the number of trees.
#'
#' When \code{predcontrib = TRUE} and it is not a multiclass setting, the output is a matrix object with
#' \code{num_features + 1} columns. The last "+ 1" column in a matrix corresponds to bias.
#' For a multiclass case, a list of \code{num_class} elements is returned, where each element is
#' such a matrix. The contribution values are on the scale of untransformed margin
#' (e.g., for binary classification would mean that the contributions are log-odds deviations from bias).
#'
#' When \code{predinteraction = TRUE} and it is not a multiclass setting, the output is a 3d array with
#' dimensions \code{c(nrow, num_features + 1, num_features + 1)}. The off-diagonal (in the last two dimensions)
#' elements represent different features interaction contributions. The array is symmetric WRT the last
#' two dimensions. The "+ 1" columns corresponds to bias. Summing this array along the last dimension should
#' produce practically the same result as predict with \code{predcontrib = TRUE}.
#' For a multiclass case, a list of \code{num_class} elements is returned, where each element is
#' such an array.
#'
#' When \code{strict_shape} is set to \code{TRUE}, the output is always an array.  For
#' normal prediction, the output is a 2-dimension array \code{(num_class, nrow(newdata))}.
#'
#' For \code{predcontrib = TRUE}, output is \code{(ncol(newdata) + 1, num_class, nrow(newdata))}
#' For \code{predinteraction = TRUE}, output is \code{(ncol(newdata) + 1, ncol(newdata) + 1, num_class, nrow(newdata))}
#' For \code{predleaf = TRUE}, output is \code{(n_trees_in_forest, num_class, n_iterations, nrow(newdata))}
#'
#' @seealso
#' \code{\link{xgb.train}}.
#'
#' @references
#'
#' Scott M. Lundberg, Su-In Lee, "A Unified Approach to Interpreting Model Predictions", NIPS Proceedings 2017, \url{https://arxiv.org/abs/1705.07874}
#'
#' Scott M. Lundberg, Su-In Lee, "Consistent feature attribution for tree ensembles", \url{https://arxiv.org/abs/1706.06060}
#'
#' @examples
#' ## binary classification:
#'
#' 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 = 0.5, nthread = 2, nrounds = 5, objective = "binary:logistic")
#' # use all trees by default
#' pred <- predict(bst, test$data)
#' # use only the 1st tree
#' pred1 <- predict(bst, test$data, iterationrange = c(1, 2))
#'
#' # Predicting tree leafs:
#' # the result is an nsamples X ntrees matrix
#' pred_leaf <- predict(bst, test$data, predleaf = TRUE)
#' str(pred_leaf)
#'
#' # Predicting feature contributions to predictions:
#' # the result is an nsamples X (nfeatures + 1) matrix
#' pred_contr <- predict(bst, test$data, predcontrib = TRUE)
#' str(pred_contr)
#' # verify that contributions' sums are equal to log-odds of predictions (up to float precision):
#' summary(rowSums(pred_contr) - qlogis(pred))
#' # for the 1st record, let's inspect its features that had non-zero contribution to prediction:
#' contr1 <- pred_contr[1,]
#' contr1 <- contr1[-length(contr1)]    # drop BIAS
#' contr1 <- contr1[contr1 != 0]        # drop non-contributing features
#' contr1 <- contr1[order(abs(contr1))] # order by contribution magnitude
#' old_mar <- par("mar")
#' par(mar = old_mar + c(0,7,0,0))
#' barplot(contr1, horiz = TRUE, las = 2, xlab = "contribution to prediction in log-odds")
#' par(mar = old_mar)
#'
#'
#' ## multiclass classification in iris dataset:
#'
#' lb <- as.numeric(iris$Species) - 1
#' num_class <- 3
#' set.seed(11)
#' bst <- xgboost(data = as.matrix(iris[, -5]), label = lb,
#'                max_depth = 4, eta = 0.5, nthread = 2, nrounds = 10, subsample = 0.5,
#'                objective = "multi:softprob", num_class = num_class)
#' # predict for softmax returns num_class probability numbers per case:
#' pred <- predict(bst, as.matrix(iris[, -5]))
#' str(pred)
#' # reshape it to a num_class-columns matrix
#' pred <- matrix(pred, ncol=num_class, byrow=TRUE)
#' # convert the probabilities to softmax labels
#' pred_labels <- max.col(pred) - 1
#' # the following should result in the same error as seen in the last iteration
#' sum(pred_labels != lb)/length(lb)
#'
#' # compare that to the predictions from softmax:
#' set.seed(11)
#' bst <- xgboost(data = as.matrix(iris[, -5]), label = lb,
#'                max_depth = 4, eta = 0.5, nthread = 2, nrounds = 10, subsample = 0.5,
#'                objective = "multi:softmax", num_class = num_class)
#' pred <- predict(bst, as.matrix(iris[, -5]))
#' str(pred)
#' all.equal(pred, pred_labels)
#' # prediction from using only 5 iterations should result
#' # in the same error as seen in iteration 5:
#' pred5 <- predict(bst, as.matrix(iris[, -5]), iterationrange=c(1, 6))
#' sum(pred5 != lb)/length(lb)
#'
#' @rdname predict.xgb.Booster
#' @export
predict.xgb.Booster <- function(object, newdata, missing = NA, outputmargin = FALSE, ntreelimit = NULL,
                                predleaf = FALSE, predcontrib = FALSE, approxcontrib = FALSE, predinteraction = FALSE,
                                reshape = FALSE, training = FALSE, iterationrange = NULL, strict_shape = FALSE, ...) {
  object <- xgb.Booster.complete(object, saveraw = FALSE)
  if (!inherits(newdata, "xgb.DMatrix"))
    newdata <- xgb.DMatrix(newdata, missing = missing)
  if (!is.null(object[["feature_names"]]) &&
      !is.null(colnames(newdata)) &&
      !identical(object[["feature_names"]], colnames(newdata)))
    stop("Feature names stored in `object` and `newdata` are different!")

  if (NVL(object$params[['booster']], '') == 'gblinear' || is.null(ntreelimit))
    ntreelimit <- 0

  if (ntreelimit != 0 && is.null(iterationrange)) {
    ## only ntreelimit, initialize iteration range
    iterationrange <- c(0, 0)
  } else if (ntreelimit == 0 && !is.null(iterationrange)) {
    ## only iteration range, handle 1-based indexing
    iterationrange <- c(iterationrange[1] - 1, iterationrange[2] - 1)
  } else if (ntreelimit != 0 && !is.null(iterationrange)) {
    ## both are specified, let libgxgboost throw an error
  } else {
    ## no limit is supplied, use best
    if (is.null(object$best_iteration)) {
      iterationrange <- c(0, 0)
    } else {
      ## We don't need to + 1 as R is 1-based index.
      iterationrange <- c(0, as.integer(object$best_iteration))
    }
  }
  ## Handle the 0 length values.
  box <- function(val) {
    if (length(val) == 0) {
      cval <- vector(, 1)
      cval[0] <- val
      return(cval)
    }
    return (val)
  }

  ## We set strict_shape to TRUE then drop the dimensions conditionally
  args <- list(
    training = box(training),
    strict_shape = box(TRUE),
    iteration_begin = box(as.integer(iterationrange[1])),
    iteration_end = box(as.integer(iterationrange[2])),
    ntree_limit = box(as.integer(ntreelimit)),
    type = box(as.integer(0))
  )

  set_type <- function(type) {
    if (args$type != 0) {
      stop("One type of prediction at a time.")
    }
    return(box(as.integer(type)))
  }
  if (outputmargin) {
    args$type <- set_type(1)
  }
  if (predcontrib) {
    args$type <- set_type(if (approxcontrib) 3 else 2)
  }
  if (predinteraction) {
    args$type <- set_type(if (approxcontrib) 5 else 4)
  }
  if (predleaf) {
    args$type <- set_type(6)
  }

  predts <- .Call(
    XGBoosterPredictFromDMatrix_R, object$handle, newdata, jsonlite::toJSON(args, auto_unbox = TRUE)
  )
  names(predts) <- c("shape", "results")
  shape <- predts$shape
  ret <- predts$results

  n_ret <- length(ret)
  n_row <- nrow(newdata)
  if (n_row != shape[1]) {
    stop("Incorrect predict shape.")
  }

  arr <- array(data = ret, dim = rev(shape))

  cnames <- if (!is.null(colnames(newdata))) c(colnames(newdata), "BIAS") else NULL
  n_groups <- shape[2]

  ## Needed regardless of whether strict shape is being used.
  if (predcontrib) {
    dimnames(arr) <- list(cnames, NULL, NULL)
  } else if (predinteraction) {
    dimnames(arr) <- list(cnames, cnames, NULL, NULL)
  }
  if (strict_shape) {
    return(arr) # strict shape is calculated by libxgboost uniformly.
  }

  if (predleaf) {
    ## Predict leaf
    arr <- if (n_ret == n_row) {
      matrix(arr, ncol = 1)
    } else {
      matrix(arr, nrow = n_row, byrow = TRUE)
    }
  } else if (predcontrib) {
    ## Predict contribution
    arr <- aperm(a = arr, perm = c(2, 3, 1)) # [group, row, col]
    arr <- if (n_ret == n_row) {
      matrix(arr, ncol =  1, dimnames = list(NULL, cnames))
    } else if (n_groups != 1) {
      ## turns array into list of matrices
      lapply(seq_len(n_groups), function(g) arr[g, , ])
    } else {
      ## remove the first axis (group)
      dn <- dimnames(arr)
      matrix(arr[1, , ], nrow = dim(arr)[2], ncol = dim(arr)[3], dimnames = c(dn[2], dn[3]))
    }
  } else if (predinteraction) {
    ## Predict interaction
    arr <- aperm(a = arr, perm = c(3, 4, 1, 2)) # [group, row, col, col]
    arr <- if (n_ret == n_row) {
      matrix(arr, ncol = 1, dimnames = list(NULL, cnames))
    } else if (n_groups != 1) {
      ## turns array into list of matrices
      lapply(seq_len(n_groups), function(g) arr[g, , , ])
    } else {
      ## remove the first axis (group)
      arr <- arr[1, , , , drop = FALSE]
      array(arr, dim = dim(arr)[2:4], dimnames(arr)[2:4])
    }
  } else {
    ## Normal prediction
    arr <- if (reshape && n_groups != 1) {
      matrix(arr, ncol = n_groups, byrow = TRUE)
    } else {
      as.vector(ret)
    }
  }
  return(arr)
}

#' @rdname predict.xgb.Booster
#' @export
predict.xgb.Booster.handle <- function(object, ...) {

  bst <- xgb.handleToBooster(object)

  ret <- predict(bst, ...)
  return(ret)
}


#' Accessors for serializable attributes of a model.
#'
#' These methods allow to manipulate the key-value attribute strings of an xgboost model.
#'
#' @param object Object of class \code{xgb.Booster} or \code{xgb.Booster.handle}.
#' @param name a non-empty character string specifying which attribute is to be accessed.
#' @param value a value of an attribute for \code{xgb.attr<-}; for \code{xgb.attributes<-}
#'        it's a list (or an object coercible to a list) with the names of attributes to set
#'        and the elements corresponding to attribute values.
#'        Non-character values are converted to character.
#'        When attribute value is not a scalar, only the first index is used.
#'        Use \code{NULL} to remove an attribute.
#'
#' @details
#' The primary purpose of xgboost model attributes is to store some meta-data about the model.
#' Note that they are a separate concept from the object attributes in R.
#' Specifically, they refer to key-value strings that can be attached to an xgboost model,
#' stored together with the model's binary representation, and accessed later
#' (from R or any other interface).
#' In contrast, any R-attribute assigned to an R-object of \code{xgb.Booster} class
#' would not be saved by \code{xgb.save} because an xgboost model is an external memory object
#' and its serialization is handled externally.
#' Also, setting an attribute that has the same name as one of xgboost's parameters wouldn't
#' change the value of that parameter for a model.
#' Use \code{\link{xgb.parameters<-}} to set or change model parameters.
#'
#' The attribute setters would usually work more efficiently for \code{xgb.Booster.handle}
#' than for \code{xgb.Booster}, since only just a handle (pointer) would need to be copied.
#' That would only matter if attributes need to be set many times.
#' Note, however, that when feeding a handle of an \code{xgb.Booster} object to the attribute setters,
#' the raw model cache of an \code{xgb.Booster} object would not be automatically updated,
#' and it would be user's responsibility to call \code{xgb.serialize} to update it.
#'
#' The \code{xgb.attributes<-} setter either updates the existing or adds one or several attributes,
#' but it doesn't delete the other existing attributes.
#'
#' @return
#' \code{xgb.attr} returns either a string value of an attribute
#' or \code{NULL} if an attribute wasn't stored in a model.
#'
#' \code{xgb.attributes} returns a list of all attribute stored in a model
#' or \code{NULL} if a model has no stored attributes.
#'
#' @examples
#' data(agaricus.train, package='xgboost')
#' train <- agaricus.train
#'
#' bst <- xgboost(data = train$data, label = train$label, max_depth = 2,
#'                eta = 1, nthread = 2, nrounds = 2, objective = "binary:logistic")
#'
#' xgb.attr(bst, "my_attribute") <- "my attribute value"
#' print(xgb.attr(bst, "my_attribute"))
#' xgb.attributes(bst) <- list(a = 123, b = "abc")
#'
#' xgb.save(bst, 'xgb.model')
#' bst1 <- xgb.load('xgb.model')
#' if (file.exists('xgb.model')) file.remove('xgb.model')
#' print(xgb.attr(bst1, "my_attribute"))
#' print(xgb.attributes(bst1))
#'
#' # deletion:
#' xgb.attr(bst1, "my_attribute") <- NULL
#' print(xgb.attributes(bst1))
#' xgb.attributes(bst1) <- list(a = NULL, b = NULL)
#' print(xgb.attributes(bst1))
#'
#' @rdname xgb.attr
#' @export
xgb.attr <- function(object, name) {
  if (is.null(name) || nchar(as.character(name[1])) == 0) stop("invalid attribute name")
  handle <- xgb.get.handle(object)
  .Call(XGBoosterGetAttr_R, handle, as.character(name[1]))
}

#' @rdname xgb.attr
#' @export
`xgb.attr<-` <- function(object, name, value) {
  if (is.null(name) || nchar(as.character(name[1])) == 0) stop("invalid attribute name")
  handle <- xgb.get.handle(object)
  if (!is.null(value)) {
    # Coerce the elements to be scalar strings.
    # Q: should we warn user about non-scalar elements?
    if (is.numeric(value[1])) {
      value <- format(value[1], digits = 17)
    } else {
      value <- as.character(value[1])
    }
  }
  .Call(XGBoosterSetAttr_R, handle, as.character(name[1]), value)
  if (is(object, 'xgb.Booster') && !is.null(object$raw)) {
    object$raw <- xgb.serialize(object$handle)
  }
  object
}

#' @rdname xgb.attr
#' @export
xgb.attributes <- function(object) {
  handle <- xgb.get.handle(object)
  attr_names <- .Call(XGBoosterGetAttrNames_R, handle)
  if (is.null(attr_names)) return(NULL)
  res <- lapply(attr_names, function(x) {
    .Call(XGBoosterGetAttr_R, handle, x)
  })
  names(res) <- attr_names
  res
}

#' @rdname xgb.attr
#' @export
`xgb.attributes<-` <- function(object, value) {
  a <- as.list(value)
  if (is.null(names(a)) || any(nchar(names(a)) == 0)) {
    stop("attribute names cannot be empty strings")
  }
  # Coerce the elements to be scalar strings.
  # Q: should we warn a user about non-scalar elements?
  a <- lapply(a, function(x) {
    if (is.null(x)) return(NULL)
    if (is.numeric(x[1])) {
      format(x[1], digits = 17)
    } else {
      as.character(x[1])
    }
  })
  handle <- xgb.get.handle(object)
  for (i in seq_along(a)) {
    .Call(XGBoosterSetAttr_R, handle, names(a[i]), a[[i]])
  }
  if (is(object, 'xgb.Booster') && !is.null(object$raw)) {
    object$raw <- xgb.serialize(object$handle)
  }
  object
}

#' Accessors for model parameters as JSON string.
#'
#' @param object Object of class \code{xgb.Booster}
#' @param value A JSON string.
#'
#' @examples
#' data(agaricus.train, package='xgboost')
#' train <- agaricus.train
#'
#' bst <- xgboost(data = train$data, label = train$label, max_depth = 2,
#'                eta = 1, nthread = 2, nrounds = 2, objective = "binary:logistic")
#' config <- xgb.config(bst)
#'
#' @rdname xgb.config
#' @export
xgb.config <- function(object) {
  handle <- xgb.get.handle(object)
  .Call(XGBoosterSaveJsonConfig_R, handle);
}

#' @rdname xgb.config
#' @export
`xgb.config<-` <- function(object, value) {
  handle <- xgb.get.handle(object)
  .Call(XGBoosterLoadJsonConfig_R, handle, value)
  object$raw <- NULL  # force renew the raw buffer
  object <- xgb.Booster.complete(object)
  object
}

#' Accessors for model parameters.
#'
#' Only the setter for xgboost parameters is currently implemented.
#'
#' @param object Object of class \code{xgb.Booster} or \code{xgb.Booster.handle}.
#' @param value a list (or an object coercible to a list) with the names of parameters to set
#'        and the elements corresponding to parameter values.
#'
#' @details
#' Note that the setter would usually work more efficiently for \code{xgb.Booster.handle}
#' than for \code{xgb.Booster}, since only just a handle would need to be copied.
#'
#' @examples
#' data(agaricus.train, package='xgboost')
#' train <- agaricus.train
#'
#' bst <- xgboost(data = train$data, label = train$label, max_depth = 2,
#'                eta = 1, nthread = 2, nrounds = 2, objective = "binary:logistic")
#'
#' xgb.parameters(bst) <- list(eta = 0.1)
#'
#' @rdname xgb.parameters
#' @export
`xgb.parameters<-` <- function(object, value) {
  if (length(value) == 0) return(object)
  p <- as.list(value)
  if (is.null(names(p)) || any(nchar(names(p)) == 0)) {
    stop("parameter names cannot be empty strings")
  }
  names(p) <- gsub("\\.", "_", names(p))
  p <- lapply(p, function(x) as.character(x)[1])
  handle <- xgb.get.handle(object)
  for (i in seq_along(p)) {
    .Call(XGBoosterSetParam_R, handle, names(p[i]), p[[i]])
  }
  if (is(object, 'xgb.Booster') && !is.null(object$raw)) {
    object$raw <- xgb.serialize(object$handle)
  }
  object
}

# Extract the number of trees in a model.
# TODO: either add a getter to C-interface, or simply set an 'ntree' attribute after each iteration.
# internal utility function
xgb.ntree <- function(bst) {
  length(grep('^booster', xgb.dump(bst)))
}


#' Print xgb.Booster
#'
#' Print information about xgb.Booster.
#'
#' @param x an xgb.Booster object
#' @param verbose whether to print detailed data (e.g., attribute values)
#' @param ... not currently used
#'
#' @examples
#' data(agaricus.train, package='xgboost')
#' train <- agaricus.train
#' bst <- xgboost(data = train$data, label = train$label, max_depth = 2,
#'                eta = 1, nthread = 2, nrounds = 2, objective = "binary:logistic")
#' attr(bst, 'myattr') <- 'memo'
#'
#' print(bst)
#' print(bst, verbose=TRUE)
#'
#' @method print xgb.Booster
#' @export
print.xgb.Booster <- function(x, verbose = FALSE, ...) {
  cat('##### xgb.Booster\n')

  valid_handle <- !is.null.handle(x$handle)
  if (!valid_handle)
    cat("Handle is invalid! Suggest using xgb.Booster.complete\n")

  cat('raw: ')
  if (!is.null(x$raw)) {
    cat(format(object.size(x$raw), units = "auto"), '\n')
  } else {
    cat('NULL\n')
  }
  if (!is.null(x$call)) {
    cat('call:\n  ')
    print(x$call)
  }

  if (!is.null(x$params)) {
    cat('params (as set within xgb.train):\n')
    cat('  ',
         paste(names(x$params),
               paste0('"', unlist(x$params), '"'),
               sep = ' = ', collapse = ', '), '\n', sep = '')
  }
  # TODO: need an interface to access all the xgboosts parameters

  attrs <- character(0)
  if (valid_handle)
    attrs <- xgb.attributes(x)
  if (length(attrs) > 0) {
    cat('xgb.attributes:\n')
    if (verbose) {
        cat(paste(paste0('  ', names(attrs)),
                  paste0('"', unlist(attrs), '"'),
                  sep = ' = ', collapse = '\n'), '\n', sep = '')
    } else {
      cat('  ', paste(names(attrs), collapse = ', '), '\n', sep = '')
    }
  }

  if (!is.null(x$callbacks) && length(x$callbacks) > 0) {
    cat('callbacks:\n')
    lapply(callback.calls(x$callbacks), function(x) {
      cat('  ')
      print(x)
    })
  }

  if (!is.null(x$feature_names))
    cat('# of features:', length(x$feature_names), '\n')

  cat('niter: ', x$niter, '\n', sep = '')
  # TODO: uncomment when faster xgb.ntree is implemented
  #cat('ntree: ', xgb.ntree(x), '\n', sep='')

  for (n in setdiff(names(x), c('handle', 'raw', 'call', 'params', 'callbacks',
                                'evaluation_log', 'niter', 'feature_names'))) {
    if (is.atomic(x[[n]])) {
      cat(n, ':', x[[n]], '\n', sep = ' ')
    } else {
      cat(n, ':\n\t', sep = ' ')
      print(x[[n]])
    }
  }

  if (!is.null(x$evaluation_log)) {
    cat('evaluation_log:\n')
    print(x$evaluation_log, row.names = FALSE, topn = 2)
  }

  invisible(x)
}

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xgboost documentation built on April 16, 2022, 5:05 p.m.