R/lda-pseudo.r
lda_pseudo.Rd
Given a set of training data, this function builds the Linear Discriminant Analysis (LDA) classifier, where the distributions of each class are assumed to be multivariate normal and share a common covariance matrix. When the pooled sample covariance matrix is singular, the linear discriminant function is incalculable. A common method to overcome this issue is to replace the inverse of the pooled sample covariance matrix with the Moore-Penrose pseudo-inverse, which is unique and always exists. Note that when the pooled sample covariance matrix is nonsingular, it is equal to the pseudo-inverse.
The Linear Discriminant Analysis (LDA) classifier involves the assumption that the distributions of each class are assumed to be multivariate normal and share a common covariance matrix. When the pooled sample covariance matrix is singular, the linear discriminant function is incalculable. A common method to overcome this issue is to replace the inverse of the pooled sample covariance matrix with the Moore-Penrose pseudo-inverse, which is unique and always exists. Note that when the pooled sample covariance matrix is nonsingular, it is equal to the pseudo-inverse.
lda_pseudo(x, ...) # S3 method for default lda_pseudo(x, y, prior = NULL, tol = 1e-08, ...) # S3 method for formula lda_pseudo(formula, data, prior = NULL, tol = 1e-08, ...) # S3 method for lda_pseudo predict(object, newdata, type = c("class", "prob", "score"), ...)
x | Matrix or data frame containing the training data. The rows are the sample observations, and the columns are the features. Only complete data are retained. |
---|---|
... | additional arguments (not currently used). |
y | Vector of class labels for each training observation. Only complete data are retained. |
prior | Vector with prior probabilities for each class. If NULL (default), then equal probabilities are used. See details. |
tol | tolerance value below which eigenvalues are considered numerically equal to 0 |
formula | A formula of the form |
data | data frame from which variables specified in |
object | Fitted model object |
newdata | Matrix or data frame of observations to predict. Each row corresponds to a new observation. |
type | Prediction type: either `"class"`, `"prob"`, or `"score"`. |
lda_pseudo
object that contains the trained lda_pseudo
classifier
The matrix of training observations are given in x
. The rows of x
contain the sample observations, and the columns contain the features for each
training observation.
The vector of class labels given in y
are coerced to a factor
.
The length of y
should match the number of rows in x
.
An error is thrown if a given class has less than 2 observations because the variance for each feature within a class cannot be estimated with less than 2 observations.
The vector, prior
, contains the a priori class membership for
each class. If prior
is NULL (default), the class membership
probabilities are estimated as the sample proportion of observations belonging
to each class. Otherwise, prior
should be a vector with the same length
as the number of classes in y
. The prior
probabilities should be
nonnegative and sum to one.
library(modeldata) data(penguins) pred_rows <- seq(1, 344, by = 20) penguins <- penguins[, c("species", "body_mass_g", "flipper_length_mm")] lda_pseudo_out <- lda_pseudo(species ~ ., data = penguins[-pred_rows, ]) predicted <- predict(lda_pseudo_out, penguins[pred_rows, -1], type = "class") lda_pseudo_out2 <- lda_pseudo(x = penguins[-pred_rows, -1], y = penguins$species[-pred_rows]) predicted2 <- predict(lda_pseudo_out2, penguins[pred_rows, -1], type = "class") all.equal(predicted, predicted2)#> [1] TRUE