Nothing
R/fanplot.R
In fsdaR: Robust Data Analysis Through Monitoring and Dynamic Visualization
Defines functions
fanplot
######
## VT::26.11.2021
##
##
## roxygen2::roxygenise("C:/users/valen/onedrive/myrepo/R/fsdaR", load_code=roxygen2:::load_installed)
##
#' Plots the fan plot for transformation in linear regression
#'
#' @description Plots the fan plot for transformation in linear regression
#'
#' @param out An object of S3 class \code{\link{fsrfan.object}} returned by
#' \code{\link{fsrfan}} - a list containing the following elements:
#' \enumerate{
#' \item \code{Score}: matrix of size \code{(n-init) x length(la)+1}:
#' itemize{
#' \item 1st col = fwd search index;
#' \item 2nd col = value of the score test in each step of the fwd search for \code{la[1]}.
#' \item ...
#' \item last col = value of the score test in each step of the fwd search for \code{la[length(la)]}.
#' }
#' \item \code{la}: vector containing the values of lambda for which fan plot is constructed.
#' \item \code{bs}: matrix of size \code{p x length(la)} containing the units forming the initial subset for each value of lambda.
#' \item \code{Un}: a three-dimensional array containing \code{length(la)} matrices of
#' size \code{retnUn=(n-init) X retpUn=11}. Each matrix contains
#' the unit(s) included in the subset at each step in the search associated
#' with the corresponding element of \code{la}.
#'%% \item \code{Un}: list of size \code{length(la)}. \code{Un[[i]]} is a \code{(n-init) x 11}
#'%% matrix which contains the unit(s) included in the subset at each step of the fwd
#'%% search (necessary only if option datatooltip or databrush are set).
#' \item \code{y}: a vector containing the response (necessary only if option \code{databrush} is set).
#' \item \code{X}: a matrix containing the explanatory variables (necessary only if option \code{databrush} is set).
#' }
#' @param ylim Controls the \code{y} scale in the plot. \code{ylim} is a vector with two elements controlling
#' minimum and maximum on the \code{y}-axis. Default is to use automatic scale.
#'
#' @param xlim Controls the \code{x} scale in the plot. \code{xlim} is a vector with two elements controlling
#' minimum and maximum on the \code{x}-axis. Default is to use automatic scale.
#'
#' @param xlab A title for the x axis
#' @param ylab A title for the y axis
#' @param main An overall title for the plot
#' @param lwd The line width, a positive number, default is \code{lwd=1}
#' @param lty The line type. Line types can either be specified as an integer (1=solid (default), 2=dashed,
#' 3=dotted, 4=dotdash, 5=longdash, 6=twodash) or as one of the character strings "solid",
#' "dashed", "dotted", "dotdash", "longdash", or "twodash".
#' The latter two are not supported by Matlab.
#' @param col Colors to be used for the highlighted units
#' @param cex.lab The magnification to be used for x and y labels relative to the current setting of cex
#' @param cex.axis The magnification to be used for axis annotation relative to the current setting of cex
#' @param subsize Numeric vector containing the subset size with length equal to the number of columns of
#' matrix of mahalanobis distances. The default value of subsize is \code{(nrow(MAL) - ncol(MAL) + 1):nrow(MAL)}
#'
#' @param fg.thresh (alternative to fg.unit) numeric vector of length 1 or 2 which specifies
#' the highlighted trajectories.
#' If \code{length(fg.thresh) == 1} the highlighted trajectories are those of units that throughtout
#' the search had at leat once a mahalanobis distance greater than \code{fg.thresh}.
#' The default value is \code{fg.thresh=2.5}. If \code{length(fg.thresh) == 2} the highlighted
#' trajectories are those of units that throughtout the search had a mahalanobis distance at
#' least once bigger than \code{fg.thresh[2]} or smaller than \code{fg.thresh[1]}.
#'
#' @param fg.unit (alternative to fg.thresh), vector containing the list of the units to be highlighted.
#' If \code{fg.unit} is supplied, \code{fg.thresh} is ignored.
#'
#' @param fg.labstep numeric vector which specifies the steps of the search where to put labels for
#' the highlighted trajectories (units). The default is to put the labels at the
#' initial and final steps of the search. \code{fg.labstep=''} means no label.
#'
#' @param fg.lwd The line width for the highlighted trajectories (units). Default is 1.
#' @param fg.lty The line type for the highlighted trajectories (units). Line types can
#' either be specified as an integer (1=solid (default), 2=dashed,
#' 3=dotted, 4=dotdash, 5=longdash, 6=twodash) or as one of the character strings "solid",
#' "dashed", "dotted", "dotdash", "longdash", or "twodash".
#' The latter two are not supported by Matlab.
#' @param fg.col colors to be used for the highlighted units.
#'
#' @param fg.mark Controlls whether to plot highlighted trajectories as symbols.
#' if \code{fg.mark==TRUE} each line is plotted using a different
#' symbol else no marker is used (default).
#'
#' @param fg.cex Controls the font size of the labels of the trajectories in foreground. If
#' \code{fg.cex=0} no labels will be shown - equivalent to \code{fg.labstop=""}.
#'
#' @param bg.thresh Numeric vector of length 1 or 2 which specifies how to define the \emph{unimmportant trajectories}.
#' Unimmportant trajectories will be plotted using a colormap, in greysh or will be hidden.
#' If \code{length(bg.thresh) == 1} the irrelevant units are those which always
#' had a mahalanobis distance smaller than \code{bg.thresh}.
#' If \code{length(bg.thresh) == 2} the irrelevant units are those which always
#' had a mahalanobis distance greater than \code{bg.thresh[1]} and smaller than \code{bg.thresh[2]}.
#' The default is \code{bg.thresh=2.5} if \code{n > 100} and \code{bg.thresh=-Inf} if \code{n <= 100}
#' i.e. to treat all trajectories as important if \code{n <= 100} and, if \code{n > 100},
#' to reduce emphasis only to trajectories having in all steps of the search a value
#' of mahalanobis distance smaller than 2.5.
#'
#' @param bg.style Specifies how to plot the unimportant trajectories as defined in option bg.thresh.
#' \enumerate{
#' \item \code{bg.style="faint"}: unimportant trajectories are plotted using a colormap.
#' \item \code{bg.style="hide"}: unimportant trajectories are hidden.
#' \item \code{bg.style="greyish"}: unimportant trajectories are displayed in a faint grey.
#' }
#' When \code{n > 100} the default option is \code{bg.style='faint'}. When \code{n <= 100}
#' and \code{bg.thresh == -Inf} option bg.style is ignored.
#' Remark: bground='' is equivalent to -Inf that is all trajectories are considered relevant.
#'
#' @param tag Plot handle. String which identifies the handle of the plot which is about to be created.
#' The default is to use tag 'pl_resfwd'. Notice that if the program finds a plot which has
#' a tag equal to the one specified by the user, then the output of the new plot overwrites
#' the existing one in the same window else a new window is created.
#'
#' @param datatooltip Interactive clicking. It is inactive if this parameter is set to FALSE.
#' The default is \code{datatooltip=TRUE}, the user can select with the mouse an individual
#' mahalanobis distance trajectory in order to have information about the corresponding unit, the associated
#' label and the step of the search in which the unit enters the subset.
#' If datatooltip is a list it may contain the following fields:
#' \enumerate{
#' \item DisplayStyle determines how the data cursor displays. Possible values are
#' \code{'datatip'} and \code{'window'} (default). \code{'datatip'} displays
#' data cursor information in a small yellow text box attached to a black
#' square marker at a data point you interactively select. \code{'window'}
#' displays data cursor information for the data point you interactively
#' select in a floating window within the figure.
#' \item SnapToDataVertex: specifies whether the data cursor snaps to the nearest data value or
#' is located at the actual pointer position.
#' Possible values are \code{SnapToDataVertex='on'} (default) and \code{SnapToDataVertex='off'}.
#' \item LineColor: controls the color of the trajectory selected with the mouse. It can be an RGB triplet
#' of values between 0 and 1, or character vector indicating a color name. Note that a RGB vector
#' can be conveniently chosen with our MATLAB class FSColor, see documentation.
#' \item SubsetLinesColor: enables to control the color of the trajectories of the units that are
#' in the subset at a given step of the search (if \code{resfwdplot()} is applied to an
#' object of class \code{\link{fsreda.object}}) or have a weight greater than 0.9 (if
#' \code{resfwdplot()} is applied to an object of class \code{\link{sregeda.object}}
#' or \code{\link{mmregeda.object}}). This can be done (repeatedly) with a left mouse
#' click in proximity of the step of interest. A right mouse click will terminate the
#' selection by marking with a up-arrow the step corresponding to the highlighted
#' lines. The highlighted lines by default are in red, but a different color can be
#' specified as RGB triplet or character of color name. Note that a RGB vector can
#' be conveniently chosen with our MATLAB class FSColor, see documentation.
#' By default \code{SubsetLinesColor=""}, i.e. the modality is not active.
#' Any initialization for \code{SubsetLinesColor} which cannot be interpreted as
#' RGB vector will be converted to blue, i.e. \code{SubsetLinesColor} will be forced to be [0 0 1].
#' If \code{SubsetLinesColor} is not empty the previous option \code{LineColor} is ignored.
#' }
#'
#' @param label Character vector containing the labels of the units (optional argument used when
#' \code{datatooltip=TRUE}. If this field is not present labels
#' row1, ..., rown will be automatically created and included
#' in the pop up datatooltip window).
#' @param nameX Add variable labels in plot. A vector of strings of length \code{p}
#' containing the labels of the variables in the dataset.
#' If it is empty (default) the sequence \code{X1, ..., Xp} will be created automatically
#'
#' @param standard MATLAB-style arguments - appearance of the plot in terms of xlim, ylim, axes labels
#' and their font size style, color of the lines, etc.
#' @param fground MATLAB-style arguments - for the trajectories in foregroud.
#' @param bground MATLAB-style arguments - for the trajectories in backgroud.
#'
#' @param databrush Interactive mouse brushing. If databrush is missing or empty (default), no brushing is done.
#' The activation of this option (databrush is \code{TRUE} or a list) enables the user to select
#' a set of trajectories in the current plot and to see them highlighted in the scatterplot matrix.
#' If the scatterplot matrix does not exist it is automatically created.
#' In addition, brushed units can be highlighted in the monitoring mahalanobis distance plot.
#' Note that the window style of the other figures is set equal to that which contains the monitoring mahalanobis distance plot.
#' In other words, if the monitoring mahalanobis distance plot is docked all the other figures will be docked too.
#'
#' If \code{databrush=TRUE} the default selection tool is a rectangular brush and it is
#' possible to brush only once (that is persist='').
#'
#' If \code{databrush=list(...)}, it is possible to use all optional arguments of
#' the MATLAB function \code{selectdataFS()} and the following optional arguments:
#' \itemize{
#' \item persist. Persist is an empty value or a character containing 'on' or 'off'.
#' The default value is \code{persist=""}, that is brushing is allowed only once.
#' If \code{persist="on"} or \code{persis="off"} brushing can be done as many time as
#' the user requires. If \code{persist='on'} then the unit(s) currently brushed are
#' added to those previously brushed. It is possible, every time a new brushing is
#' done, to use a different color for the brushed units. If \code{persist='off'}
#' every time a new brush is performed units previously brushed are removed.
#' \item \code{label}: add labels of brushed units in the monitoring plot.
#' \item \code{labeladd}: add labels of brushed units in the scatterplot matrix.
#' If this option is '1', we label the units of the last selected group with
#' the unit row index in the matrix X. The default value is labeladd='',
#' i.e. no label is added.
#' }
#'
#' @param conflev confidence interval for the horizontal bands. It can be a vector of
#' different confidence level values, e.g. c(0.95, 0.99, 0.999).
#' The confidence interval is based on the $chi^2$ distribution.
#'
#' @param trace Whether to print intermediate results. Default is \code{trace=FALSE}.
#'
#' @param ... potential further arguments passed to lower level functions.
#' @return none
#' @references
#' Atkinson, A.C. and Riani, M. (2000), \emph{Robust Diagnostic Regression Analysis} Springer Verlag, New York.
#'
#' Atkinson, A.C. and Riani, M. (2002), Tests in the fan plot for robust, diagnostic transformations in regression,
#' \emph{Chemometrics and Intelligent Laboratory Systems}, \bold{60}, pp. 87--100.
#'
#' Atkinson, A.C. Riani, M. and Corbellini A. (2019), The analysis of transformations for profit-and-loss data,
#' \emph{Journal of the Royal Statistical Society, Series C, "Applied Statistics"}, \bold{69}, pp. 251--275.
#' \doi{10.1111/rssc.12389}
#'
#' Atkinson, A.C. Riani, M. and Corbellini A. (2021), The Box-Cox Transformation: Review and Extensions,
#' \emph{Statistical Science}, \bold{36}(2), pp. 239--255. \doi{10.1214/20-STS778}.
#'
#' @examples
#'
#' \dontrun{
#' }
#'
#' @export
#' @author FSDA team, \email{valentin.todorov@@chello.at}
fanplot <- function(out,
xlab="Subset of size m", ylab="Score test statistic", main="Fan plot",
xlim, ylim, cex.lab, cex.axis, lwd=2, lwd.env=1,
## lty, col,
## subsize,
## fg.thresh, fg.unit, fg.labstep, fg.lwd, fg.lty, fg.col, fg.mark, fg.cex,
## bg.thresh, bg.style,
## standard, fground, bground,
tag, datatooltip, label, nameX, databrush, conflev,
trace=FALSE, ...)
{
## Perform check on the structure of 'out'
if(missing(out) | !inherits(out, "fsrfan"))
stop("Function defined only for monitoring type output.")
## The needed elements are MAL and Y=X, and Un (FS) or bdp (S) or eff (MM).
## The R class name is mapped to a Matlab class name
## outStr <- list(MAL=out$MAL, Loc=out$Loc, Y=out$X, class=getMatlabClass(class(out)))
outStr <- out
control <- list(...)
## Graphical parameters
if(!missing(xlab))
control$labx <- xlab
if(!missing(ylab))
control$laby <- ylab
if(!missing(main))
control$titl <- main
if(!missing(xlim))
control$xlimx <- xlim
if(!missing(ylim))
control$ylimy <- ylim
if(!missing(cex.lab))
{
control$FontSize <- 12 ## the default
control$FontSize <- cex.lab * control$FontSize
}
if(!missing(cex.axis))
{
control$SizeAxesNum <- 12 ## the default
control$SizeAxesNum <- cex.axis * control$SizeAxesNum
}
control$lwd <- lwd
control$lwdenv <- lwd.env
if(!missing(tag))
control$tag <- as.character(tag)
if(!missing(datatooltip))
{
if(is.logical(datatooltip))
control$datatooltip <- ifelse(datatooltip, 1, "")
else if(is.list(datatooltip))
control$datatooltip <- datatooltip
else
stop(paste("Wrong argument 'datatooltip':", datatooltip))
}
if(!missing(label))
control$label <- label
if(!missing(nameX))
control$nameX <- nameX
if(!missing(databrush))
{
if(is.logical(databrush))
{
if(databrush)
control$databrush <- 1
}else if(is.list(databrush))
control$databrush <- databrush
else
stop(paste("Wrong argument 'databrush':", databrush))
}
if(!missing(conflev)) {
control$conflev <- conflev
} else {
control$conflev <- 0.975
}
if(trace)
{
cat("\nOptional parameters to fanplot(): \n")
print(control)
}
# Initialize parlist to the input values. All parameters from the control structure
# must be added to the R list *before* converting it into a MATLAB struct
## VT::16.10.2017: the mandatory input parameters are all contained
## in an S3 class (a list), which is the output of one of the XXXeda() fucntions.
## Convert the S3 class to a Matlab structure and initialize with it the parameter list.
## NOTE: this is identical to the initialization of the parameter list in fsreg()
## with the mandatory X and y.
##
parlist <- list(list2MatlabStruct(outStr))
paramNames = names(control)
if (length(paramNames) > 0) {
for (i in 1:length(paramNames)) {
paramName = paramNames[i];
paramValue = control[[i]];
##matlabValue = rType2MatlabType(paramName, paramValue, forceStringsToCellArray = TRUE)
matlabValue = rType2MatlabType(paramName, paramValue, forceStringsToCellArray = FALSE)
parlist = c(parlist, .jnew("java/lang/String", paramName), matlabValue)
}
}
callFsdaFunctionNoArgout("fanplot", "[Ljava/lang/Object;", parlist)
return(invisible(NULL))
}
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Defines functions fanplot
######
## VT::26.11.2021
##
##
## roxygen2::roxygenise("C:/users/valen/onedrive/myrepo/R/fsdaR", load_code=roxygen2:::load_installed)
##
#' Plots the fan plot for transformation in linear regression
#'
#' @description Plots the fan plot for transformation in linear regression
#'
#' @param out An object of S3 class \code{\link{fsrfan.object}} returned by
#' \code{\link{fsrfan}} - a list containing the following elements:
#' \enumerate{
#' \item \code{Score}: matrix of size \code{(n-init) x length(la)+1}:
#' itemize{
#' \item 1st col = fwd search index;
#' \item 2nd col = value of the score test in each step of the fwd search for \code{la[1]}.
#' \item ...
#' \item last col = value of the score test in each step of the fwd search for \code{la[length(la)]}.
#' }
#' \item \code{la}: vector containing the values of lambda for which fan plot is constructed.
#' \item \code{bs}: matrix of size \code{p x length(la)} containing the units forming the initial subset for each value of lambda.
#' \item \code{Un}: a three-dimensional array containing \code{length(la)} matrices of
#' size \code{retnUn=(n-init) X retpUn=11}. Each matrix contains
#' the unit(s) included in the subset at each step in the search associated
#' with the corresponding element of \code{la}.
#'%% \item \code{Un}: list of size \code{length(la)}. \code{Un[[i]]} is a \code{(n-init) x 11}
#'%% matrix which contains the unit(s) included in the subset at each step of the fwd
#'%% search (necessary only if option datatooltip or databrush are set).
#' \item \code{y}: a vector containing the response (necessary only if option \code{databrush} is set).
#' \item \code{X}: a matrix containing the explanatory variables (necessary only if option \code{databrush} is set).
#' }
#' @param ylim Controls the \code{y} scale in the plot. \code{ylim} is a vector with two elements controlling
#' minimum and maximum on the \code{y}-axis. Default is to use automatic scale.
#'
#' @param xlim Controls the \code{x} scale in the plot. \code{xlim} is a vector with two elements controlling
#' minimum and maximum on the \code{x}-axis. Default is to use automatic scale.
#'
#' @param xlab A title for the x axis
#' @param ylab A title for the y axis
#' @param main An overall title for the plot
#' @param lwd The line width, a positive number, default is \code{lwd=1}
#' @param lty The line type. Line types can either be specified as an integer (1=solid (default), 2=dashed,
#' 3=dotted, 4=dotdash, 5=longdash, 6=twodash) or as one of the character strings "solid",
#' "dashed", "dotted", "dotdash", "longdash", or "twodash".
#' The latter two are not supported by Matlab.
#' @param col Colors to be used for the highlighted units
#' @param cex.lab The magnification to be used for x and y labels relative to the current setting of cex
#' @param cex.axis The magnification to be used for axis annotation relative to the current setting of cex
#' @param subsize Numeric vector containing the subset size with length equal to the number of columns of
#' matrix of mahalanobis distances. The default value of subsize is \code{(nrow(MAL) - ncol(MAL) + 1):nrow(MAL)}
#'
#' @param fg.thresh (alternative to fg.unit) numeric vector of length 1 or 2 which specifies
#' the highlighted trajectories.
#' If \code{length(fg.thresh) == 1} the highlighted trajectories are those of units that throughtout
#' the search had at leat once a mahalanobis distance greater than \code{fg.thresh}.
#' The default value is \code{fg.thresh=2.5}. If \code{length(fg.thresh) == 2} the highlighted
#' trajectories are those of units that throughtout the search had a mahalanobis distance at
#' least once bigger than \code{fg.thresh[2]} or smaller than \code{fg.thresh[1]}.
#'
#' @param fg.unit (alternative to fg.thresh), vector containing the list of the units to be highlighted.
#' If \code{fg.unit} is supplied, \code{fg.thresh} is ignored.
#'
#' @param fg.labstep numeric vector which specifies the steps of the search where to put labels for
#' the highlighted trajectories (units). The default is to put the labels at the
#' initial and final steps of the search. \code{fg.labstep=''} means no label.
#'
#' @param fg.lwd The line width for the highlighted trajectories (units). Default is 1.
#' @param fg.lty The line type for the highlighted trajectories (units). Line types can
#' either be specified as an integer (1=solid (default), 2=dashed,
#' 3=dotted, 4=dotdash, 5=longdash, 6=twodash) or as one of the character strings "solid",
#' "dashed", "dotted", "dotdash", "longdash", or "twodash".
#' The latter two are not supported by Matlab.
#' @param fg.col colors to be used for the highlighted units.
#'
#' @param fg.mark Controlls whether to plot highlighted trajectories as symbols.
#' if \code{fg.mark==TRUE} each line is plotted using a different
#' symbol else no marker is used (default).
#'
#' @param fg.cex Controls the font size of the labels of the trajectories in foreground. If
#' \code{fg.cex=0} no labels will be shown - equivalent to \code{fg.labstop=""}.
#'
#' @param bg.thresh Numeric vector of length 1 or 2 which specifies how to define the \emph{unimmportant trajectories}.
#' Unimmportant trajectories will be plotted using a colormap, in greysh or will be hidden.
#' If \code{length(bg.thresh) == 1} the irrelevant units are those which always
#' had a mahalanobis distance smaller than \code{bg.thresh}.
#' If \code{length(bg.thresh) == 2} the irrelevant units are those which always
#' had a mahalanobis distance greater than \code{bg.thresh[1]} and smaller than \code{bg.thresh[2]}.
#' The default is \code{bg.thresh=2.5} if \code{n > 100} and \code{bg.thresh=-Inf} if \code{n <= 100}
#' i.e. to treat all trajectories as important if \code{n <= 100} and, if \code{n > 100},
#' to reduce emphasis only to trajectories having in all steps of the search a value
#' of mahalanobis distance smaller than 2.5.
#'
#' @param bg.style Specifies how to plot the unimportant trajectories as defined in option bg.thresh.
#' \enumerate{
#' \item \code{bg.style="faint"}: unimportant trajectories are plotted using a colormap.
#' \item \code{bg.style="hide"}: unimportant trajectories are hidden.
#' \item \code{bg.style="greyish"}: unimportant trajectories are displayed in a faint grey.
#' }
#' When \code{n > 100} the default option is \code{bg.style='faint'}. When \code{n <= 100}
#' and \code{bg.thresh == -Inf} option bg.style is ignored.
#' Remark: bground='' is equivalent to -Inf that is all trajectories are considered relevant.
#'
#' @param tag Plot handle. String which identifies the handle of the plot which is about to be created.
#' The default is to use tag 'pl_resfwd'. Notice that if the program finds a plot which has
#' a tag equal to the one specified by the user, then the output of the new plot overwrites
#' the existing one in the same window else a new window is created.
#'
#' @param datatooltip Interactive clicking. It is inactive if this parameter is set to FALSE.
#' The default is \code{datatooltip=TRUE}, the user can select with the mouse an individual
#' mahalanobis distance trajectory in order to have information about the corresponding unit, the associated
#' label and the step of the search in which the unit enters the subset.
#' If datatooltip is a list it may contain the following fields:
#' \enumerate{
#' \item DisplayStyle determines how the data cursor displays. Possible values are
#' \code{'datatip'} and \code{'window'} (default). \code{'datatip'} displays
#' data cursor information in a small yellow text box attached to a black
#' square marker at a data point you interactively select. \code{'window'}
#' displays data cursor information for the data point you interactively
#' select in a floating window within the figure.
#' \item SnapToDataVertex: specifies whether the data cursor snaps to the nearest data value or
#' is located at the actual pointer position.
#' Possible values are \code{SnapToDataVertex='on'} (default) and \code{SnapToDataVertex='off'}.
#' \item LineColor: controls the color of the trajectory selected with the mouse. It can be an RGB triplet
#' of values between 0 and 1, or character vector indicating a color name. Note that a RGB vector
#' can be conveniently chosen with our MATLAB class FSColor, see documentation.
#' \item SubsetLinesColor: enables to control the color of the trajectories of the units that are
#' in the subset at a given step of the search (if \code{resfwdplot()} is applied to an
#' object of class \code{\link{fsreda.object}}) or have a weight greater than 0.9 (if
#' \code{resfwdplot()} is applied to an object of class \code{\link{sregeda.object}}
#' or \code{\link{mmregeda.object}}). This can be done (repeatedly) with a left mouse
#' click in proximity of the step of interest. A right mouse click will terminate the
#' selection by marking with a up-arrow the step corresponding to the highlighted
#' lines. The highlighted lines by default are in red, but a different color can be
#' specified as RGB triplet or character of color name. Note that a RGB vector can
#' be conveniently chosen with our MATLAB class FSColor, see documentation.
#' By default \code{SubsetLinesColor=""}, i.e. the modality is not active.
#' Any initialization for \code{SubsetLinesColor} which cannot be interpreted as
#' RGB vector will be converted to blue, i.e. \code{SubsetLinesColor} will be forced to be [0 0 1].
#' If \code{SubsetLinesColor} is not empty the previous option \code{LineColor} is ignored.
#' }
#'
#' @param label Character vector containing the labels of the units (optional argument used when
#' \code{datatooltip=TRUE}. If this field is not present labels
#' row1, ..., rown will be automatically created and included
#' in the pop up datatooltip window).
#' @param nameX Add variable labels in plot. A vector of strings of length \code{p}
#' containing the labels of the variables in the dataset.
#' If it is empty (default) the sequence \code{X1, ..., Xp} will be created automatically
#'
#' @param standard MATLAB-style arguments - appearance of the plot in terms of xlim, ylim, axes labels
#' and their font size style, color of the lines, etc.
#' @param fground MATLAB-style arguments - for the trajectories in foregroud.
#' @param bground MATLAB-style arguments - for the trajectories in backgroud.
#'
#' @param databrush Interactive mouse brushing. If databrush is missing or empty (default), no brushing is done.
#' The activation of this option (databrush is \code{TRUE} or a list) enables the user to select
#' a set of trajectories in the current plot and to see them highlighted in the scatterplot matrix.
#' If the scatterplot matrix does not exist it is automatically created.
#' In addition, brushed units can be highlighted in the monitoring mahalanobis distance plot.
#' Note that the window style of the other figures is set equal to that which contains the monitoring mahalanobis distance plot.
#' In other words, if the monitoring mahalanobis distance plot is docked all the other figures will be docked too.
#'
#' If \code{databrush=TRUE} the default selection tool is a rectangular brush and it is
#' possible to brush only once (that is persist='').
#'
#' If \code{databrush=list(...)}, it is possible to use all optional arguments of
#' the MATLAB function \code{selectdataFS()} and the following optional arguments:
#' \itemize{
#' \item persist. Persist is an empty value or a character containing 'on' or 'off'.
#' The default value is \code{persist=""}, that is brushing is allowed only once.
#' If \code{persist="on"} or \code{persis="off"} brushing can be done as many time as
#' the user requires. If \code{persist='on'} then the unit(s) currently brushed are
#' added to those previously brushed. It is possible, every time a new brushing is
#' done, to use a different color for the brushed units. If \code{persist='off'}
#' every time a new brush is performed units previously brushed are removed.
#' \item \code{label}: add labels of brushed units in the monitoring plot.
#' \item \code{labeladd}: add labels of brushed units in the scatterplot matrix.
#' If this option is '1', we label the units of the last selected group with
#' the unit row index in the matrix X. The default value is labeladd='',
#' i.e. no label is added.
#' }
#'
#' @param conflev confidence interval for the horizontal bands. It can be a vector of
#' different confidence level values, e.g. c(0.95, 0.99, 0.999).
#' The confidence interval is based on the $chi^2$ distribution.
#'
#' @param trace Whether to print intermediate results. Default is \code{trace=FALSE}.
#'
#' @param ... potential further arguments passed to lower level functions.
#' @return none
#' @references
#' Atkinson, A.C. and Riani, M. (2000), \emph{Robust Diagnostic Regression Analysis} Springer Verlag, New York.
#'
#' Atkinson, A.C. and Riani, M. (2002), Tests in the fan plot for robust, diagnostic transformations in regression,
#' \emph{Chemometrics and Intelligent Laboratory Systems}, \bold{60}, pp. 87--100.
#'
#' Atkinson, A.C. Riani, M. and Corbellini A. (2019), The analysis of transformations for profit-and-loss data,
#' \emph{Journal of the Royal Statistical Society, Series C, "Applied Statistics"}, \bold{69}, pp. 251--275.
#' \doi{10.1111/rssc.12389}
#'
#' Atkinson, A.C. Riani, M. and Corbellini A. (2021), The Box-Cox Transformation: Review and Extensions,
#' \emph{Statistical Science}, \bold{36}(2), pp. 239--255. \doi{10.1214/20-STS778}.
#'
#' @examples
#'
#' \dontrun{
#' }
#'
#' @export
#' @author FSDA team, \email{valentin.todorov@@chello.at}
fanplot <- function(out,
xlab="Subset of size m", ylab="Score test statistic", main="Fan plot",
xlim, ylim, cex.lab, cex.axis, lwd=2, lwd.env=1,
## lty, col,
## subsize,
## fg.thresh, fg.unit, fg.labstep, fg.lwd, fg.lty, fg.col, fg.mark, fg.cex,
## bg.thresh, bg.style,
## standard, fground, bground,
tag, datatooltip, label, nameX, databrush, conflev,
trace=FALSE, ...)
{
## Perform check on the structure of 'out'
if(missing(out) | !inherits(out, "fsrfan"))
stop("Function defined only for monitoring type output.")
## The needed elements are MAL and Y=X, and Un (FS) or bdp (S) or eff (MM).
## The R class name is mapped to a Matlab class name
## outStr <- list(MAL=out$MAL, Loc=out$Loc, Y=out$X, class=getMatlabClass(class(out)))
outStr <- out
control <- list(...)
## Graphical parameters
if(!missing(xlab))
control$labx <- xlab
if(!missing(ylab))
control$laby <- ylab
if(!missing(main))
control$titl <- main
if(!missing(xlim))
control$xlimx <- xlim
if(!missing(ylim))
control$ylimy <- ylim
if(!missing(cex.lab))
{
control$FontSize <- 12 ## the default
control$FontSize <- cex.lab * control$FontSize
}
if(!missing(cex.axis))
{
control$SizeAxesNum <- 12 ## the default
control$SizeAxesNum <- cex.axis * control$SizeAxesNum
}
control$lwd <- lwd
control$lwdenv <- lwd.env
if(!missing(tag))
control$tag <- as.character(tag)
if(!missing(datatooltip))
{
if(is.logical(datatooltip))
control$datatooltip <- ifelse(datatooltip, 1, "")
else if(is.list(datatooltip))
control$datatooltip <- datatooltip
else
stop(paste("Wrong argument 'datatooltip':", datatooltip))
}
if(!missing(label))
control$label <- label
if(!missing(nameX))
control$nameX <- nameX
if(!missing(databrush))
{
if(is.logical(databrush))
{
if(databrush)
control$databrush <- 1
}else if(is.list(databrush))
control$databrush <- databrush
else
stop(paste("Wrong argument 'databrush':", databrush))
}
if(!missing(conflev)) {
control$conflev <- conflev
} else {
control$conflev <- 0.975
}
if(trace)
{
cat("\nOptional parameters to fanplot(): \n")
print(control)
}
# Initialize parlist to the input values. All parameters from the control structure
# must be added to the R list *before* converting it into a MATLAB struct
## VT::16.10.2017: the mandatory input parameters are all contained
## in an S3 class (a list), which is the output of one of the XXXeda() fucntions.
## Convert the S3 class to a Matlab structure and initialize with it the parameter list.
## NOTE: this is identical to the initialization of the parameter list in fsreg()
## with the mandatory X and y.
##
parlist <- list(list2MatlabStruct(outStr))
paramNames = names(control)
if (length(paramNames) > 0) {
for (i in 1:length(paramNames)) {
paramName = paramNames[i];
paramValue = control[[i]];
##matlabValue = rType2MatlabType(paramName, paramValue, forceStringsToCellArray = TRUE)
matlabValue = rType2MatlabType(paramName, paramValue, forceStringsToCellArray = FALSE)
parlist = c(parlist, .jnew("java/lang/String", paramName), matlabValue)
}
}
callFsdaFunctionNoArgout("fanplot", "[Ljava/lang/Object;", parlist)
return(invisible(NULL))
}
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