#' One parameter transformations for linear models
#'
#' The function transforms the dependent variable of a linear model using the
#' one parameter transformations. The transformation parameter can either be
#' estimated using different estimation methods or given.
#'
#' @param object an object of type lm.
#' @param trafo character that determines the selected transformation.
#' @param lambda either a character named "estim" if the optimal transformation
#' parameter should be estimated or a numeric value determining a given
#' transformation parameter. Defaults to "estim".
#' @param method a character string. Different estimation methods can be used
#' for the estimation of the optimal transformation parameter:
#' (i) Maximum likelihood approach ("ml"), (ii) Skewness minimization ("skew"),
#' (iii) Kurtosis optimization ("kurt"), (iv) Divergence minimization by
#' Kolmogorov-Smirnov ("div.ks"), by Cramer-von-Mises ("div.cvm") or by
#' Kullback-Leibler ("div.kl"). Defaults to "ml".
#' @param lambdarange a numeric vector with two elements defining an interval
#' that is used for the estimation of the optimal transformation parameter.
#' Defaults to \code{c(-2, 2)}.
#' @param plotit logical. If \code{TRUE}, a plot that illustrates the optimal
#' transformation parameter or the given transformation parameter is returned.
#' @param custom_trafo a list that determines a one parameter transformation and
#' the standardized one parameter transformation.
#' @param ... other parameters that can be passed to the function.
#' @return an object of class \code{trafo}.
#' @keywords internal
oneparam.lm <- function(object, trafo, lambda = "estim", method = "ml",
lambdarange, plotit = TRUE, custom_trafo = NULL, ...) {
if (is.null(lambdarange) && trafo %in% c("boxcox", "boxcoxshift", "manly",
"modulus", "yeojohnson", "gpower")) {
lambdarange <- c(-2,2)
} else if (is.null(lambdarange) && trafo == "bickeldoksum") {
lambdarange <- c(1e-11, 2)
} else if (is.null(lambdarange) && trafo == "dual") {
lambdarange <- c(0,2)
} else if (is.null(lambdarange) && trafo %in% c("logshiftopt", "sqrtshift")) {
span <- range(object$model[, paste0(formula(object)[2])])
if ((span[1] + 1) <= 1) {
lower = abs(span[1]) + 1
} else {
lower <- -span[1] + 1
}
upper <- diff(span)
lambdarange <- c(lower,upper)
}
check_oneparam(trafo = trafo, lambda = lambda, method = method,
lambdarange = lambdarange, plotit = plotit,
custom_trafo = custom_trafo)
# Get model variables: dependent variable y and explanatory variables x
model_frame <- object$model
# Check if arguments are as expected (for model variables)
if (is.null(y <- model.response(model_frame)))
stop("Dependent variable y must not be empty")
if (is.null(x <- model.matrix(attr(model_frame, "terms"), data = model_frame)))
stop("Matrix of covariates X must not be empty")
if (trafo == "custom") {
custom_func <- custom_trafo[[1]]
custom_func_std <- custom_trafo[[2]]
custom_family <- names(custom_trafo)[[1]]
}
# For saving returns
ans <- list()
# Get the optimal transformation parameter
if (lambda == "estim") {
optim <- est_lm(y = y, x = x, trafo = trafo, method = method,
lambdarange = lambdarange,
custom_func = custom_func,
custom_func_std = custom_func_std)
lambdaoptim <- optim$lambdaoptim
measoptim <- optim$measoptim
} else if (is.numeric(lambda)) {
lambdaoptim <- lambda
measoptim <- estim_lm(lambda = lambdaoptim, y = y, x = x,
trafo = trafo, method = method)
}
# Plot the curve of the measure with line at the optimal transformation
# parameter
if (plotit == TRUE) {
plot_meas <- plot_trafolm(lambdarange = lambdarange, lambdaoptim = lambdaoptim,
measoptim = measoptim, y = y, x = x,
trafo = trafo, method = method,
custom_func = custom_func,
custom_func_std = custom_func_std)
# Get plot measures
ans$lambdavector <- plot_meas$lambdavector
ans$measvector <- plot_meas$measvector
} else if (plotit == FALSE) {
ans$lambdavector <- NULL
ans$measvector <- NULL
}
# Get vector of transformed and standardized transformed variable
#ans$yt <- Yeo_john(y = y, lambda = lambdaoptim)
#ans$zt <- Yeo_john_std(y = y, lambda = lambdaoptim)
# Save transformation family and method
#ans$family <- "Yeo-Johnson"
ans <- get_transformed(trafo = trafo, ans = ans, y = y, lambda = lambdaoptim,
custom_func = custom_func,
custom_func_std = custom_func_std,
custom_family = custom_family)
ans$method <- method
ans$lambdahat <- lambdaoptim
ans$measoptim <- measoptim
# Get transformed model
#ans$modelt <- get_modelt(object = object, trans_mod = ans, std = FALSE)
ans$object <- object
# New class trafo
class(ans) <- c("trafo", "oneparam")
ans
}
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