R/ML_MDAModel.R

In brian-j-smith/MachineShop: Machine Learning Models and Tools

#' Mixture Discriminant Analysis Model
#'
#' Performs mixture discriminant analysis.
#'
#' @param subclasses numeric value or vector of subclasses per class.
#' @param sub.df effective degrees of freedom of the centroids per class if
#'   subclass centroid shrinkage is performed.
#' @param tot.df specification of the total degrees of freedom as an alternative
#'   to \code{sub.df}.
#' @param dimension dimension of the discriminant subspace to use for
#'   prediction.
#' @param eps numeric threshold for automatically truncating the dimension.
#' @param iter limit on the total number of iterations.
#' @param method regression function used in optimal scaling.  The default of
#'   linear regression is provided by \code{\link[mda]{polyreg}} from the
#'   \pkg{mda} package.  For penalized mixture discriminant models,
#'   \code{\link[mda]{gen.ridge}} is appropriate.  Other possibilities are
#'   \code{\link[mda]{mars}} for multivariate adaptive regression splines and
#'   \code{\link[mda]{bruto}} for adaptive backfitting of additive splines.  Use
#'   the \code{\link[=quote]{.}} operator to quote specified functions.
#' @param trace logical indicating whether iteration information is printed.
#' @param ... additional arguments to \code{mda.start} and \code{method}.
#'
#' @details
#' \describe{
#'   \item{Response types:}{\code{factor}}
#'   \item{\link[=TunedModel]{Automatic tuning} of grid parameter:}{
#'     \code{subclasses}
#'   }
#' }
#'
#' The \code{\link{predict}} function for this model additionally accepts the
#' following argument.
#' \describe{
#'   \item{\code{prior}}{prior class membership probabilities for prediction data
#'     if different from the training set.}
#' }
#'
#' Default argument values and further model details can be found in the source
#' See Also links below.
#'
#' @return \code{MLModel} class object.
#'
#' @seealso \code{\link[mda]{mda}}, \code{\link[mda]{predict.mda}},
#' \code{\link{fit}}, \code{\link{resample}}
#'
#' @examples
#' \donttest{
#' ## Requires prior installation of suggested package mda to run
#'
#' fit(Species ~ ., data = iris, model = MDAModel)
#' }
#'
MDAModel <- function(
  subclasses = 3, sub.df = numeric(), tot.df = numeric(),
  dimension = sum(subclasses) - 1, eps = .Machine$double.eps, iter = 5,
  method = .(mda::polyreg), trace = FALSE, ...
) {

  MLModel(

    name = "MDAModel",
    label = "Mixture Discriminant Analysis",
    packages = "mda",
    response_types = "factor",
    predictor_encoding = "model.matrix",
    na.rm = TRUE,
    params = new_params(environment(), ...),

    gridinfo = new_gridinfo(
      param = "subclasses",
      get_values = c(
        function(n, ...) seq_int(2, length = min(n, 10))
      )
    ),

    fit = function(formula, data, weights, ...) {
      mda::mda(formula, data = as.data.frame(formula, data = data), ...)
    },

    predict = function(object, newdata, prior = object$prior, ...) {
      newdata <- as.data.frame(newdata)
      predict(object, newdata = newdata, type = "posterior", prior = prior)
    }

  )

}

MLModelFunction(MDAModel) <- NULL