bag provides a framework for bagging classification or regression models. The user can provide their own functions for model building, prediction and aggregation of predictions (see Details below).
bag(x, ...)bagControl(
fit = NULL,
predict = NULL,
aggregate = NULL,
downSample = FALSE,
oob = TRUE,
allowParallel = TRUE
)
# S3 method for default
bag(x, y, B = 10, vars = ncol(x), bagControl = NULL, ...)
# S3 method for bag
predict(object, newdata = NULL, ...)
# S3 method for bag
print(x, ...)
# S3 method for bag
summary(object, ...)
# S3 method for summary.bag
print(x, digits = max(3, getOption("digits") - 3), ...)
ldaBag
plsBag
nbBag
ctreeBag
svmBag
nnetBag
bag produces an object of class bag with elements
a list with two sub-objects: the fit object has the actual model fit for that #' bagged samples and the vars object is either NULL or a vector of integers corresponding to which predictors were sampled for that model
a mirror of the arguments passed into bagControl
the call
the number of bagging iterations
the dimensions of the training set
An object of class list of length 3.
An object of class list of length 3.
An object of class list of length 3.
An object of class list of length 3.
An object of class list of length 3.
An object of class list of length 3.
a matrix or data frame of predictors
arguments to pass to the model function
a function that has arguments x, y and ... and produces a model object #' that can later be used for prediction. Example functions are found in ldaBag, plsBag, #' nbBag, svmBag and nnetBag.
a function that generates predictions for each sub-model. The function should have #' arguments object and x. The output of the function can be any type of object (see the #' example below where posterior probabilities are generated. Example functions are found in ldaBag#' , plsBag, nbBag, svmBag and nnetBag.)
a function with arguments x and type. The function that takes the output #' of the predict function and reduces the bagged predictions to a single prediction per sample. #' the type argument can be used to switch between predicting classes or class probabilities for #' classification models. Example functions are found in ldaBag, plsBag, nbBag, #' svmBag and nnetBag.
logical: for classification, should the data set be randomly sampled so that each #' class has the same number of samples as the smallest class?
logical: should out-of-bag statistics be computed and the predictions retained?
a parallel backend is loaded and available, should the function use it?
a vector of outcomes
the number of bootstrap samples to train over.
an integer. If this argument is not NULL, a random sample of size vars is taken of the predictors in each bagging iteration. If NULL, all predictors are used.
a list of options.
an object of class bag.
a matrix or data frame of samples for prediction. Note that this argument must have a non-null value
minimal number of significant digits.
Max Kuhn
The function is basically a framework where users can plug in any model in to assess
the effect of bagging. Examples functions can be found in ldaBag, plsBag
, nbBag, svmBag and nnetBag.
Each has elements fit, pred and aggregate.
One note: when vars is not NULL, the sub-setting occurs prior to the fit and #' predict functions are called. In this way, the user probably does not need to account for the #' change in predictors in their functions.
When using bag with train, classification models should use type = "prob" #' inside of the predict function so that predict.train(object, newdata, type = "prob") will #' work.
If a parallel backend is registered, the foreach package is used to train the models in parallel.
## A simple example of bagging conditional inference regression trees:
data(BloodBrain)
## treebag <- bag(bbbDescr, logBBB, B = 10,
## bagControl = bagControl(fit = ctreeBag$fit,
## predict = ctreeBag$pred,
## aggregate = ctreeBag$aggregate))
## An example of pooling posterior probabilities to generate class predictions
data(mdrr)
## remove some zero variance predictors and linear dependencies
mdrrDescr <- mdrrDescr[, -nearZeroVar(mdrrDescr)]
mdrrDescr <- mdrrDescr[, -findCorrelation(cor(mdrrDescr), .95)]
## basicLDA <- train(mdrrDescr, mdrrClass, "lda")
## bagLDA2 <- train(mdrrDescr, mdrrClass,
## "bag",
## B = 10,
## bagControl = bagControl(fit = ldaBag$fit,
## predict = ldaBag$pred,
## aggregate = ldaBag$aggregate),
## tuneGrid = data.frame(vars = c((1:10)*10 , ncol(mdrrDescr))))
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