Naive Bayes Classifier

Description

Computes the conditional a-posterior probabilities of a categorical class variable given independent predictor variables using the Bayes rule.

Usage

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## S3 method for class 'formula'
naiveBayes(formula, data, laplace = 0, ..., subset, na.action = na.pass)
## Default S3 method:
naiveBayes(x, y, laplace = 0, ...)


## S3 method for class 'naiveBayes'
predict(object, newdata,
  type = c("class", "raw"), threshold = 0.001, eps = 0, ...)

Arguments

x

A numeric matrix, or a data frame of categorical and/or numeric variables.

y

Class vector.

formula

A formula of the form class ~ x1 + x2 + .... Interactions are not allowed.

data

Either a data frame of predictors (categorical and/or numeric) or a contingency table.

laplace

positive double controlling Laplace smoothing. The default (0) disables Laplace smoothing.

...

Currently not used.

subset

For data given in a data frame, an index vector specifying the cases to be used in the training sample. (NOTE: If given, this argument must be named.)

na.action

A function to specify the action to be taken if NAs are found. The default action is not to count them for the computation of the probability factors. An alternative is na.omit, which leads to rejection of cases with missing values on any required variable. (NOTE: If given, this argument must be named.)

object

An object of class "naiveBayes".

newdata

A dataframe with new predictors (with possibly fewer columns than the training data). Note that the column names of newdata are matched against the training data ones.

type

If "raw", the conditional a-posterior probabilities for each class are returned, and the class with maximal probability else.

threshold

Value replacing cells with probabilities within eps range.

eps

double for specifying an epsilon-range to apply laplace smoothing (to replace zero or close-zero probabilities by theshold.)

Details

The standard naive Bayes classifier (at least this implementation) assumes independence of the predictor variables, and Gaussian distribution (given the target class) of metric predictors. For attributes with missing values, the corresponding table entries are omitted for prediction.

Value

An object of class "naiveBayes" including components:

apriori

Class distribution for the dependent variable.

tables

A list of tables, one for each predictor variable. For each categorical variable a table giving, for each attribute level, the conditional probabilities given the target class. For each numeric variable, a table giving, for each target class, mean and standard deviation of the (sub-)variable.

Author(s)

David Meyer David.Meyer@R-project.org. Laplace smoothing enhancement by Jinghao Xue.

Examples

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## Categorical data only:
data(HouseVotes84, package = "mlbench")
model <- naiveBayes(Class ~ ., data = HouseVotes84)
predict(model, HouseVotes84[1:10,])
predict(model, HouseVotes84[1:10,], type = "raw")

pred <- predict(model, HouseVotes84)
table(pred, HouseVotes84$Class)

## using laplace smoothing:
model <- naiveBayes(Class ~ ., data = HouseVotes84, laplace = 3)
pred <- predict(model, HouseVotes84[,-1])
table(pred, HouseVotes84$Class)


## Example of using a contingency table:
data(Titanic)
m <- naiveBayes(Survived ~ ., data = Titanic)
m
predict(m, as.data.frame(Titanic))

## Example with metric predictors:
data(iris)
m <- naiveBayes(Species ~ ., data = iris)
## alternatively:
m <- naiveBayes(iris[,-5], iris[,5])
m
table(predict(m, iris), iris[,5])

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