caret: classDist – R documentation

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classDist

Compute and predict the distances to class centroids

Description

This function computes the class centroids and covariance matrix for a training set for determining Mahalanobis distances of samples to each class centroid.

Usage

classDist(x, ...)

## Default S3 method:
classDist(x, y, groups = 5, pca = FALSE, keep = NULL, ...)

## S3 method for class 'classDist'
predict(object, newdata, trans = log, ...)

Arguments

`x`	a matrix or data frame of predictor variables
`...`	optional arguments to pass (not currently used)
`y`	a numeric or factor vector of class labels
`groups`	an integer for the number of bins for splitting a numeric outcome
`pca`	a logical: should principal components analysis be applied to the dataset prior to splitting the data by class?
`keep`	an integer for the number of PCA components that should by used to predict new samples (`NULL` uses all within a tolerance of `sqrt(.Machine$double.eps)`)
`object`	an object of class `classDist`
`newdata`	a matrix or data frame. If `vars` was previously specified, these columns should be in `newdata`
`trans`	an optional function that can be applied to each class distance. `trans = NULL` will not apply a function

Details

For factor outcomes, the data are split into groups for each class and the mean and covariance matrix are calculated. These are then used to compute Mahalanobis distances to the class centers (using predict.classDist The function will check for non-singular matrices.

For numeric outcomes, the data are split into roughly equal sized bins based on groups. Percentiles are used to split the data.

Value

for classDist, an object of class classDist with elements:

`values`	a list with elements for each class. Each element contains a mean vector for the class centroid and the inverse of the class covariance matrix
`classes`	a character vector of class labels
`pca`	the results of `prcomp` when `pca = TRUE`
`call`	the function call
`p`	the number of variables
`n`	a vector of samples sizes per class

For predict.classDist, a matrix with columns for each class. The columns names are the names of the class with the prefix dist.. In the case of numeric y, the class labels are the percentiles. For example, of groups = 9, the variable names would be dist.11.11, dist.22.22, etc.

Author(s)

Max Kuhn

References

Forina et al. CAIMAN brothers: A family of powerful classification and class modeling techniques. Chemometrics and Intelligent Laboratory Systems (2009) vol. 96 (2) pp. 239-245

Examples

trainSet <- sample(1:150, 100)

distData <- classDist(iris[trainSet, 1:4],
                      iris$Species[trainSet])

newDist <- predict(distData,
                   iris[-trainSet, 1:4])

splom(newDist, groups = iris$Species[-trainSet])

caret

Classification and Regression Training

v6.0-86

GPL (>= 2)

Authors

Max Kuhn [aut, cre], Jed Wing [ctb], Steve Weston [ctb], Andre Williams [ctb], Chris Keefer [ctb], Allan Engelhardt [ctb], Tony Cooper [ctb], Zachary Mayer [ctb], Brenton Kenkel [ctb], R Core Team [ctb], Michael Benesty [ctb], Reynald Lescarbeau [ctb], Andrew Ziem [ctb], Luca Scrucca [ctb], Yuan Tang [ctb], Can Candan [ctb], Tyler Hunt [ctb]

Initial release