Nothing
######
## VT::3.12.2019
##
##
## roxygen2::roxygenise("C:/users/valen/onedrive/myrepo/R/fsdaR", load_code=roxygen2:::load_installed)
##
#' Computes MLE of transformation parameters
#'
#' @description Computes MLE of transformation parameters. It uses the multivariate
#' version of the parametric family of power transformations.
#'
#' @param x Input data matrix of size \code{n x p} (n observations and p variables).
#' Rows of \code{x} represent observations, and columns represent variables.
#'
#' Missing values (NA's) and infinite values (Inf's) are allowed,
#' since observations (rows) with missing or infinite values will
#' automatically be excluded from the computations.
#'
#' @param plot If \code{plot=FALSE} (default) or \code{plot=0} no plot is produced.
#' If \code{plot=TRUE} a fan plot is shown.
#'
#' @param plotslrt MATLAB-style arguments - appearance of the plot of the likelihood
#' ratio tests in terms of xlim, ylim, axes labels and their font size style, color of the lines, etc.
#'
#' @param plotsmle MATLAB-style arguments - appearance of the plot of maximum
#' likelihood estimates of the transformation parameters in terms of xlim, ylim, axes labels
#' and their font size style, color of the lines, etc.
#'
#' @param msg Controls whether to display or not messages on the screen If \code{msg==TRUE} (default)
#' messages are displayed on the screen. If \code{msg=2}, detailed messages are displayed,
#' for example the information at iteration level.
#'
#' @param trace Whether to print intermediate results. Default is \code{trace=FALSE}.
#'
#' @param ... potential further arguments passed to lower level functions.
#'
#' @return An S3 object of class \code{\link{fsmtra.object}}
#'
#' @references
#' Atkinson, A.C., Riani, M. and Cerioli, A. (2004), '\emph{Exploring multivariate data with the forward search}, Springer Verlag, New York.
#'
#' @examples
#' \dontrun{
#' }
#' @export
#' @author FSDA team, \email{valentin.todorov@chello.at}
fsmtra <- function(x, plot=c("none", "LRT", "MLE", "ALL"), plotslrt, plotsmle,
plotslrt.xlim, plotslrt.ylim, plotslrt.lwd, plotslrt.lwd2, plotslrt.conflev, plotslrt.tag,
plotsmle.xlim, plotsmle.ylim, plotsmle.lwd, plotsmle.lwd2, plotsmle.lty, plotsmle.cex, plotsmle.tag,
msg=TRUE,
trace=FALSE, ...)
{
plot <- match.arg(plot)
if(is.data.frame(x))
x <- data.matrix(x)
else if(!is.matrix(x))
x <- matrix(x, length(x), 1,
dimnames = list(names(x), deparse(substitute(x))))
if(!is.numeric(x)) stop("x is not a numeric")
dx <- dim(x)
xn <- (dnx <- dimnames(x))[[2]]
xn <- if (!is.null(xn))
xn
else if (dx[2] > 1)
paste("X", 1:dx[2], sep = "")
else if(dx[2])
"X"
dimnames(x) <- list(dnx[[1]], xn)
n <- nrow(x)
p <- ncol(x)
control <- list(...)
if(missing(plotslrt))
plotslrt <- list()
if(!missing(plotslrt.xlim))
plotslrt$xlim <- plotslrt.xlim
if(!missing(plotslrt.ylim))
plotslrt$ylim <- plotslrt.ylim
if(!missing(plotslrt.lwd))
plotslrt$LineWidth <- plotslrt.lwd
if(!missing(plotslrt.lwd2))
plotslrt$LineWidthEnv <- plotslrt.lwd2
if(!missing(plotslrt.conflev))
plotslrt$conflev <- plotslrt.conflev
if(!missing(plotslrt.tag))
plotslrt$Tag <- plotslrt.tag
if(length(plotslrt) > 0)
control$plotslrt <- plotslrt
else if(plot == "LRT" || plot == "ALL")
control$plotslrt <- 1
if(missing(plotsmle))
plotsmle <- list()
if(!missing(plotsmle.xlim))
plotsmle$xlim <- plotsmle.xlim
if(!missing(plotsmle.ylim))
plotsmle$ylim <- plotsmle.ylim
if(!missing(plotsmle.lwd))
plotsmle$LineWidth <- plotsmle.lwd
if(!missing(plotsmle.lwd2))
plotsmle$LineWidthEnv <- plotsmle.lwd2
if(!missing(plotsmle.lty))
plotsmle$LineStyle <- plotsmle.lty
if(!missing(plotsmle.tag))
plotsmle$Tag <- plotsmle.tag
if(!missing(plotsmle.cex))
{
plotsmle$FontSize <- 12 ## the default
plotsmle$FontSize <- plotsmle.cex * plotsmle$FontSize
}
if(length(plotsmle) > 0)
control$plotsmle <- plotsmle
else if(plot == "MLE" || plot == "ALL")
control$plotsmle <- 1
xmsg <- 0
if(is.logical(msg))
xmsg <- ifelse(msg, 1, 0)
else if(is.numeric(msg) && msg >= 0 && msg <= 2)
xmsg <- msg
else
stop("Invalid parameter 'msg'. Should be TRUE/FALSE or 0, 1, 2.")
control$msg <- xmsg
outclass <- "fsmtra"
## ES 27.06.2018: parameters that are mandatory to the MATLAB function
## cannot be put into the MATLAB function because they have to be supplied
## to the function individually and not in (name, value) pairs
parlist = c(.jarray(x, dispatch=TRUE))
paramNames = names(control)
if(trace)
print(control)
if(length(paramNames) > 0)
{
for (i in 1:length(paramNames)) {
paramName = paramNames[i]
paramValue = control[[i]]
matlabValue = rType2MatlabType(paramName, paramValue)
parlist = c(parlist, .jnew("java/lang/String", paramName), matlabValue)
}
}
out <- callFsdaFunction("FSMtra", "[Ljava/lang/Object;", 1, parlist)
if(is.null(out))
return(NULL)
arr1 = .jcast(out[[1]], "com/mathworks/toolbox/javabuilder/MWStructArray")
arr = .jnew("org/jrc/ipsc/globesec/sitaf/fsda/FsdaMWStructArray", arr1)
## The 'arr' variable is a MATLAB struct containing all the info returned
## by the resfwdplot() MATLAB function. Now 'arr' must be converted into an R list
## ('ans') containing all the return info from the resfwdplot() R function
if(trace)
{
cat("\nReturning from MATLAB FSMfan(). Fields returned by MATLAB: \n")
print(arr$fieldNames())
}
MLEtra <- as.matrix(.jevalArray(arr$get("MLEtra", as.integer(1))))
LIKrat <- as.matrix(.jevalArray(arr$get("LIKrat", as.integer(1))))
Exflag <- as.matrix(.jevalArray(arr$get("Exflag", as.integer(1))))
Un <- as.matrix(.jevalArray(arr$get("Un", as.integer(1))))
ans <- list(call=match.call(), MLEtra=MLEtra, LIKrat=LIKrat, Exflag=Exflag, Un=Un)
freeMatlabResources(out)
class(ans) <- outclass
return (ans)
}
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