mlNaiveBayes {mlearning}

Supervised classification using naive Bayes

Description

Unified (formula-based) interface version of the naive Bayes algorithm provided by e1071::naiveBayes().

Usage

mlNaiveBayes(train, ...)

ml_naive_bayes(train, ...)

## S3 method for class 'formula'
mlNaiveBayes(formula, data, laplace = 0, ..., subset, na.action)

## Default S3 method:
mlNaiveBayes(train, response, laplace = 0, ...)

## S3 method for class 'mlNaiveBayes'
predict(
  object,
  newdata,
  type = c("class", "membership", "both"),
  method = c("direct", "cv"),
  na.action = na.exclude,
  threshold = 0.001,
  eps = 0,
  ...
)

Arguments

train

a matrix or data frame with predictors.

...

further arguments passed to the classification method or its predict() method (not used here for now).

formula

a formula with left term being the factor variable to predict and the right term with the list of independent, predictive variables, separated with a plus sign. If the data frame provided contains only the dependent and independent variables, one can use the class ~ . short version (that one is strongly encouraged). Variables with minus sign are eliminated. Calculations on variables are possible according to usual formula convention (possibly protected by using I()).

data

a data.frame to use as a training set.

laplace

positive number controlling Laplace smoothing for the naive Bayes classifier. The default (0) disables Laplace smoothing.

subset

index vector with the cases to define the training set in use (this argument must be named, if provided).

na.action

function to specify the action to be taken if NAs are found. For ml_naive_bayes() na.fail is used by default. The calculation is stopped if there is any NA in the data. Another option is na.omit, where cases with missing values on any required variable are dropped (this argument must be named, if provided). For the predict() method, the default, and most suitable option, is na.exclude. In that case, rows with NAs in ⁠newdata=⁠ are excluded from prediction, but reinjected in the final results so that the number of items is still the same (and in the same order as ⁠newdata=⁠).

response

a vector of factor with the classes.

object

an mlNaiveBayes object

newdata

a new dataset with same conformation as the training set (same variables, except may by the class for classification or dependent variable for regression). Usually a test set, or a new dataset to be predicted.

type

the type of prediction to return. "class" by default, the predicted classes. Other options are "membership", the posterior probability or "both" to return classes and memberships,

method

"direct" (default) or "cv". "direct" predicts new cases in ⁠newdata=⁠ if this argument is provided, or the cases in the training set if not. Take care that not providing ⁠newdata=⁠ means that you just calculate the self-consistency of the classifier but cannot use the metrics derived from these results for the assessment of its performances. Either use a different dataset in ⁠newdata=⁠ or use the alternate cross-validation ("cv") technique. If you specify method = "cv" then cvpredict() is used and you cannot provide ⁠newdata=⁠ in that case.

threshold

value replacing cells with probabilities within 'eps' range.

eps

number for specifying an epsilon-range to apply Laplace smoothing (to replace zero or close-zero probabilities by 'threshold').

Value

ml_naive_bayes()/mlNaiveBayes() creates an mlNaiveBayes, mlearning object containing the classifier and a lot of additional metadata used by the functions and methods you can apply to it like predict() or cvpredict(). In case you want to program new functions or extract specific components, inspect the "unclassed" object using unclass().

See Also

mlearning(), cvpredict(), confusion(), also e1071::naiveBayes() that actually does the classification.

Examples

# Prepare data: split into training set (2/3) and test set (1/3)
data("iris", package = "datasets")
train <- c(1:34, 51:83, 101:133)
iris_train <- iris[train, ]
iris_test <- iris[-train, ]
# One case with missing data in train set, and another case in test set
iris_train[1, 1] <- NA
iris_test[25, 2] <- NA

iris_nb <- ml_naive_bayes(data = iris_train, Species ~ .)
summary(iris_nb)
predict(iris_nb) # Default type is class
predict(iris_nb, type = "membership")
predict(iris_nb, type = "both")
# Self-consistency, do not use for assessing classifier performances!
confusion(iris_nb)
# Use an independent test set instead
confusion(predict(iris_nb, newdata = iris_test), iris_test$Species)

# Another dataset
data("HouseVotes84", package = "mlbench")
house_nb <- ml_naive_bayes(data = HouseVotes84, Class ~ .,
  na.action = na.omit)
summary(house_nb)
confusion(house_nb) # Self-consistency
confusion(cvpredict(house_nb), na.omit(HouseVotes84)$Class)