% -*- TeX -*- -*- Soft -*-
\documentclass[article,shortnames,nojss]{jss}

%\VignetteIndexEntry{An Object-Oriented Framework for Robust Multivariate Analysis}
%\VignetteKeywords{robustness, multivariate analysis, MCD, R, statistical design patterns}
%\VignettePackage{rrcov}

\usepackage{amsmath}                %% need for subequations
\usepackage{amssymb}
\usepackage{amsfonts}
\usepackage[english]{babel}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% declarations for jss.cls %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\newcommand{\vv}[1]{\mbox{\boldmath$#1$}}
\newcommand{\xv}{\mbox{\boldmath$x$}}
\newcommand{\yv}{\mbox{\boldmath$y$}}
\newcommand{\zv}{\mbox{\boldmath$z$}}
\newcommand{\mv}{\mbox{\boldmath$m$}}
\newcommand{\tv}{\mbox{\boldmath$t$}}
\newcommand{\xbarv}{\mbox{\boldmath$\bar x$}}
\newcommand{\uv}{\mbox{\boldmath$u$}}
\newcommand{\muv}{\mbox{\boldmath$\mu$}}
\newcommand{\nuv}{\mbox{\boldmath$\nu$}}
\newcommand{\deltav}{\mbox{\boldmath$\delta$}}
\newcommand{\chiv}{\mbox{\boldmath$\chi$}}
\newcommand{\ov}{\mbox{\boldmath$0$}}

\newcommand\MCD{\mathit{MCD}}
\newcommand\MVE{\mathit{MVE}}
\newcommand\OGK{\mathit{OGK}}
\newcommand\diag{\mathrm{diag}}
%\newcommand\det{\mathrm{det}}

\newcommand{\class}[1]{``\code{#1}''}
\newcommand{\fct}[1]{\code{#1()}}

%% almost as usual
\author{Valentin Todorov\\UNIDO \And
        Peter Filzmoser\\Vienna University of Technology}
\title{An Object Oriented Framework for Robust Multivariate Analysis}

%% for pretty printing and a nice hypersummary also set:
\Plainauthor{Valentin Todorov, Peter Filzmoser} %% comma-separated
\Plaintitle{Object Oriented Framework for Robust Multivariate Analysis} %% without formatting
\Shorttitle{OOF for Robust Multivariate Analysis} %% a short title (if necessary)

%% an abstract and keywords
\Abstract{
\noindent This introduction to the \proglang{R} package \pkg{rrcov} is a (slightly) modified version of \cite{todorov-oof}, published in the \emph{Journal of Statistical Software}.

\noindent Taking advantage of the \proglang{S}4 class system of the programming environment
  \proglang{R}, which facilitates the creation and maintenance of reusable
  and modular components, an object oriented framework for robust multivariate analysis was developed. The framework resides in the packages \pkg{robustbase} and \pkg{rrcov} and includes an almost complete set of algorithms for computing robust multivariate location and scatter, various robust methods for principal component analysis as well as robust linear and quadratic discriminant analysis.
  The design of these methods follows common patterns which we call statistical
  design patterns in analogy to the design patterns widely used in software engineering.
  The application of the framework to data analysis as well as possible extensions by the
  development of new methods is demonstrated on examples which themselves
  are part of the package \pkg{rrcov}.
} \Keywords{robustness, multivariate analysis, MCD, \proglang{R},
statistical design patterns}
\Plainkeywords{robustness, multivariate analysis, MCD, R, statistical design patterns} %% without formatting
%% at least one keyword must be supplied

%% publication information
%% NOTE: Typically, this can be left commented and will be filled out by the technical editor
%% \Volume{13}
%% \Issue{9}
%% \Month{September}
%% \Year{2004}
%% \Submitdate{2004-09-29}
%% \Acceptdate{2004-09-29}

%% The address of (at least) one author should be given
%% in the following format:
\Address{
  Valentin Todorov\\
  Research and Statistics Branch\\
  United Nations Industrial Development Organization (UNIDO)\\
  Vienna International Centre\\
  P.O.Box 300, 1400, Vienna, Austria\\
  E-mail: \email{valentin.todorov@chello.at}\\
%  URL: \url{http://statmath.wu-wien.ac.at/~zeileis/}
}
%% It is also possible to add a telephone and fax number
%% before the e-mail in the following format:
%% Telephone: +43/1/31336-5053
%% Fax: +43/1/31336-734

%% for those who use Sweave please include the following line (with % symbols):
%% need no \usepackage{Sweave.sty}

%% end of declarations %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

\newcommand{\bi}{\begin{itemize}}
\newcommand{\ei}{\end{itemize}}
\newcommand{\be}{\begin{enumerate}}
\newcommand{\ee}{\end{enumerate}}
\renewcommand{\v}[1]{\mathbf{#1}}
%% Sweave options for the complete document
%%\SweaveOpts{keep.source=TRUE}
%%\SweaveOpts{prefix.string=images/oofgen/oof}
\SweaveOpts{prefix.string=ooframework}

\begin{document}

%% include your article here, just as usual
%% Note that you should use the \pkg{}, \proglang{} and \code{} commands.

%\section[About Java]{About \proglang{Java}}
\section[Introduction]{Introduction}
%% Note: If there is markup in \(sub)section, then it has to be escape as above.
Outliers are present in virtually every data set in any application domain,
and the identification of outliers has a hundred years long history. Many
researchers in science, industry and economics work with huge amounts of
data and this even increases the possibility of anomalous data and
makes their (visual) detection more difficult. Taking into account the multivariate aspect of
the data, the outlyingness of the observations can be measured by the Mahalanobis
distance which is based on location and scatter estimates of the data set. In order
to avoid the masking effect, robust estimates of these parameters are called for,
even more, they must possess a positive breakdown point. The estimates of
the multivariate location vector
$\muv$ and the scatter matrix $\v{\Sigma}$ are also a cornerstone in the analysis of
multidimensional data, since they form the input to many classical
multivariate methods. The most common estimators of multivariate
location and scatter are the sample mean $\xbarv$
and the sample covariance matrix $\v{S}$, i.e., the
corresponding MLE estimates. These estimates are optimal if the data
come from a multivariate normal distribution but are extremely
sensitive to the presence of even a few outliers (atypical values,
anomalous observations, gross errors) in the data. If outliers are
present in the input data they will influence the estimates
$\xbarv$ and $\v{S}$ and subsequently
worsen the performance of the classical multivariate procedure based
on these estimates. Therefore it is important to consider robust
alternatives to these estimators and actually in the last two
decades much effort was devoted to the development of affine
equivariant estimators possessing a high breakdown point.
The most widely used estimators of this type are the minimum
covariance determinant (MCD) estimator of \citet{rousseeuw:85} for
which also a fast computing algorithm was constructed---\citet{rousseeuw-vandriessen}, the S~estimators
\citep{davies:87} and the Stahel-Donoho
estimator introduced by \citet{stahel:81, stahel-phd:81} and \citet{donoho:82}
and studied by \citet{maronna:95}. If we
give up the requirement for affine equivariance, estimators
like the one of \citet{maronna:2002} are available and the
reward is an extreme gain in speed. Substituting the classical
location and scatter estimates by their robust analogues is the most
straightforward method for robustifying many multivariate procedures
like principal components, discriminant and cluster analysis,
canonical correlation, etc. The reliable identification of multivariate outliers
which is an important task in itself, is another
approach to robustifying many classical multivariate methods.


Some of these estimates and procedures became available in the popular statistical
packages like \proglang{S-PLUS}, \proglang{SAS}, \proglang{MATLAB}
as well as in \proglang{R} but nevertheless it is recognized that the
robust methods have not yet replaced the ordinary least square techniques as it could be expected \citep{morgenthaler:2007, stromberg:2004}.
One reason is the lack of easily accessible and easy
to use software, that is software which presents the robust procedures
as extensions to the classical ones---similar input and output,
reasonable defaults for most of the estimation options and
visualization tools. As far as the easiness of access  is concerned,
the robust statistical methods should be implemented in the freely available statistical
software package \proglang{R}, \citep{RLanguage}, which provides a powerful platform
for the development of statistical software. These requirements have been
defined in the project ``Robust Statistics and \proglang{R}'', see
\url{http://www.statistik.tuwien.ac.at/rsr/}, and a first step in
this direction was the initial development of the collaborative
package \pkg{robustbase}, \citep{robustbase}, with the intention that it becomes the
\textit{essential robust statistics} \proglang{R} package
covering the methods described in the recent book \citet{maronna:2006}.


During the last decades the object oriented programming
paradigm has revolutionized the style of software system design and
development. A further step in the software reuse are the object
oriented frameworks \citep[see][]{gamma} which provide
technology for reusing both the architecture and the functionality
of software components. Taking advantage of the new \proglang{S}4 class system \citep{chambers:98}
of \proglang{R} which facilitate the creation of reusable and modular components
 an object oriented framework for robust multivariate
analysis was implemented. The goal of the framework is manyfold:
\be
\item{to provide the end-user with a flexible and easy access to newly
developed robust methods for multivariate data analysis;}
\item{to allow the programming statisticians an extension by developing,
implementing and testing new methods with minimum effort, and }
\item{to guarantee the original developers and
maintainer of the packages a high level of maintainability.}
\ee
The framework includes an almost complete set of algorithms for
computing robust multivariate location and scatter, such as minimum
covariance determinant, different S~estimators (SURREAL,
FAST-S, Bisquare, Rocke-type), orthogonalized
Gnanadesikan--Kettenring (OGK) estimator of \citet{maronna:2002}.
The next large group of classes are the methods for robust principal
component analysis (PCA) including ROBPCA of
\citet{hubert-ROBPCA:2005}, spherical principal components (SPC) of
\citet{locantore:1999}, the projection pursuit algorithms of
\citet{croux-Ruiz-Gazen:2005} and
\citet{croux-filzmoser-oliveira-pppca}.
Further applications
implemented in the framework are linear and quadratic discriminant
analysis \citep[see][for a review]{todorov-roblda},
multivariate tests
\citep{rousseeuw-willems:2002, todorov-manova} and
outlier detection tools.


The application of the framework to data analysis as well as
the development of new methods is illustrated on examples, which
themselves are part of the package. Some issues of the object
oriented paradigm as applied to the \proglang{R} object model
(naming conventions, access methods, coexistence of \proglang{S}3 and
\proglang{S}4 classes, usage of UML, etc.) are discussed.
The framework is implemented in the \proglang{R} packages \pkg{robustbase} and \pkg{rrcov}, \citep{todorov-rrcov},
which are available from Comprehensive \proglang{R} Archive Network (CRAN) at \url{http://CRAN.R-project.org} under the GNU General Public License.


The rest of the paper is organized as follows. In the
next Section~\ref{oof-sec:objmodel} the design principles
and the structure of the framework is presented as well as some related object oriented concepts are discussed. As a main tool for modeling of the robust estimation methods a statistical design pattern is proposed. Section~\ref{oof-sec:ex-intro} facilitates the quick start by an example session giving a brief overview of the framework. Section~\ref{oof-sec:multi} describes the robust multivariate methods, their computation and implementation. The Sections~\ref{oof-sec:cov}, \ref{oof-sec:pca} and \ref{oof-sec:lda} are dedicated to the estimation of multivariate location and scatter, principal component analysis and discriminant analysis, respectively. For each domain the object model, the available visualization tools, an example, and other relevant information are presented. We conclude in Section~\ref{oof-sec:conclusions} with discussion and outline of the future work.
\section{Design approach and structure of the framework}
\label{oof-sec:objmodel}
In classical multivariate statistics we rely on
parametric models based on assumptions about the  structural
and the stochastic parts of the model for which optimal procedures
are derived, like the least squares estimators and the maximum
likelihood estimators. The corresponding robust methods can be
seen as extensions to the classical ones which can cope with
deviations from the stochastic assumptions thus mitigating the
dangers for classical estimators. The developed statistical
procedures will  remain reliable and reasonably efficient even
when such deviations are present. For example in the case of
location and covariance estimation the classical
theory yields the sample mean $\xbarv$ and the sample
covariance matrix $\v{S}$, i.e.,
the corresponding MLE estimates as an optimal solution.
One (out of many) robust alternatives is the minimum
covariance determinant estimator. When we consider
this situation from an object oriented design point of view
we can think of an abstract base class representing the estimation problem,
a concrete realization of this object---the classical estimates, and
a second concrete derivative of the base class representing
the MCD estimates. Since there exist many other robust
estimators of multivariate location and covariance
which share common characteristics we would prefer to add one
more level of abstraction by defining an abstract ``robust'' object
from which all other robust estimators are derived. We encounter
a similar pattern in most of the other multivariate statistical
methods like principal component analysis, linear and quadratic
discriminant analysis, etc. and we will call it a
\textit{statistical design pattern}.
A schematic representation as an \textit{UML diagram} is shown
in Figure~\ref{oof-fig:objmodel}.
\begin{figure}[h!]
\begin{center}
\includegraphics[width=1.0\textwidth]{AModel}
\label{oof-fig:objmodel}
\caption{Class diagram of the statistical design pattern for robust estimation methods.}
\end{center}
\end{figure}
The following simple example demonstrates the functionality. We
start with a generic object model of a robust and the corresponding
classical multivariate method with all the necessary interfaces and
functionalities and then concretize it to represent the desired
class hierarchy. The basic idea is to define an abstract \proglang{S}4
class which has as slots the common data elements of the result of
the classical method and its robust counterparts (e.g., \code{Pca}).
For this abstract class we can implement the standard in \proglang{R}
generic functions like \code{print()}, \code{summary()}, \code{plot()} and maybe
also \code{predict()}. Now we can derive and implement a concrete
class which will represent the classical method, say
\code{PcaClassic}. Further we derive another abstract class which
represents a potential robust method we are going to implement, e.g.,
\code{PcaRobust}---it is abstract because we want to have a
``placeholder'' for the robust methods we are going to develop next.
The generic functions that we implemented for the class \code{Pca}
are still valid for \code{PcaRobust} but whenever necessary we can
override them with new functionality. Now we have the necessary
platform and of course we have had diligently documented everything
we have implemented so far---this is our investment in the future
development of robust methods from this family. The framework at
its current expansion stage provides such
platform for several important families of multivariate methods. It
is time to dedicate our effort to the development and implementation
of our new robust method/class, say \code{PcaHubert} and only to
this---here comes the first obvious benefit from the framework---we
do not need to care for the implementation of \code{print()},
\code{summary()}, \code{plot()} and \code{predict()} neither for their documentation or testing.


In contrast to the \proglang{S}3 class system the \proglang{S}4 system requires
the creation of objects to be done by the \code{new()} function which will
perform the necessary validity checks. We go one step
further and require that the \code{new()} function is not
used directly but only through special functions known in
\proglang{R} as \textit{generating functions} or as
\textit{constructors} in the conventional object
oriented programming languages. A constructor function
has the same name as the corresponding class, takes
the estimation options as parameters, organizes
the necessary computations and returns an object of
the class containing the results of the computation.
It can take as a parameter also a \textit{control object}
which itself is an \proglang{S}4 object and contains
the estimation options. More details on the generating
functions and their application for structuring
the user interface can be found in \citet{todorov-constructors}.


The main part of the framework is implemented in
the package \pkg{rrcov} but it relies on code in the
packages \pkg{robustbase} and \pkg{pcaPP} \citep{filzmoser-pcaPP}. The structure
of the framework and its relation to other \proglang{R}
packages is shown in Figure~\ref{oof-fig:structure}.
\begin{figure}[h!]
\begin{center}
\includegraphics[width=0.8\textwidth]{Structure}
\label{oof-fig:structure}
\caption{Class diagram: structure of the framework and relation to other \proglang{R} packages.}
\end{center}
\end{figure}
The framework can be used by other packages, like for example by \pkg{robust}
\citep[see][]{konis-robust} or can be further extended.
In Figure~\ref{oof-fig:structure} a hypothetical
package \pkg{rrcovNA} is shown, which could extend the available
robust multivariate methods with options for dealing
with missing values.


In the rest of this section some object-oriented programming (OOP) concepts will be discussed which
are essential for understanding the framework.
\newpage
\subsection{UML diagrams}
\label{oof-sec:UML}
Throughout this paper we exploit UML class diagrams to give a clear picture
of the framework and its components. UML stands for \textit{Unified Modeling Language}---an object-oriented system of notation which has evolved from previous works of Grady Booch, James Rumbaugh and Ivar Jacobson
to become a tool accepted by the Object Management Group (OMG) as
the standard for modeling object oriented programs \citep[see][]{umlInfra, umlSuper}.
A class diagram models the
structure and contents of a system by depicting classes, packages, objects and the relations
among them with the aim to increase the ease of understanding the considered application.
A class is denoted by a box with three compartments which contain the name,
the attributes (slots) and operations (methods) of the class, respectively.
The class name in italics indicates that the class is abstract.
The bottom two compartments could be omitted or they can contain only the
key attributes and operations which are useful for understanding
the particular diagram. Each attribute is followed by its
type and each operation---by the type of its return value.
We use the \proglang{R} types like \code{numeric}, \code{logical}, \code{vector},
\code{matrix}, etc. but the type can be also a name of an \proglang{S}4 class.


Relationships between classes are denoted by lines or arrows
with different form. The inheritance relationship is depicted
by a large empty triangular arrowhead pointing to the base class.
Composition means that one class contains another one as
a slot (not to be mistaken with the keyword ``contains''
signalling inheritance in \proglang{R}).
This relation is represented by an arrow with a solid
diamond on the side of the composed class.
If a class ``uses'' another one or depends on it,
the classes are connected by a dashed arrow
(dependence relation).
Packages can also be present in a class diagram---in our case they correspond more or less to \proglang{R} packages---and are shown as tabbed boxes with the name of the package
written in the tab (see Figure~\ref{oof-fig:structure}).


All UML diagrams of the framework were created with
the open source UML tool \pkg{ArgoUML} \citep{argo:phd, argo:2000} which is available for download from \url{http://argouml.tigris.org/}.

\subsection{Design patterns}
\label{oof-sec:patterns}
Design patterns are usually defined as general solutions to recurring design
problems and refer to both the description of a solution and
an instance of that solution solving a particular problem. The current use of
the term design patterns originates in the writings of the architect
Christopher Alexander devoted to urban planning and building architecture
\citep{alexander} but it was brought to the software development
community by the seminal book of \citet{gamma}.


A design pattern can be seen as a template for how to solve
a problem which can be used in many different situations.
Object-Oriented design patterns are about classes and
the relationships between classes or objects at abstract level,
without defining the final classes or objects of the particular application.
In order to be usable, design patterns must be defined formally and the
documentation, including a preferably evocative name,
describes the context in which the pattern is used,
the pattern structure, the participants and collaboration, thus presenting the suggested solution.


Design patterns are not limited to architecture or software development
but can be applied in any domain where solutions are searched for. During the development of the here presented framework several design patterns were identified, which we prefer to call \textit{statistical design patterns}.
The first one was already described earlier in this section and captures
the relations among a classical and one or more alternative robust multivariate estimators.
Another candidate is the control object encapsulating the estimation parameters and a third one is the factory-like construct which suggests selection of a robust estimation method and creation of the corresponding objects
based on the data set characteristics (see Section~\ref{oof-sec:cov}).
The formal description of these design patterns is beyond the scope of this
work and we will limit the discussion to several examples.
\subsection{Accessor methods}
\label{oof-sec:accessors}
One of the major characteristics and advantages of object oriented programming is the
encapsulation. Unfortunately real encapsulation (information hiding)
is missing in \proglang{R}, but as far as the access to the member
variables is concerned this could be mitigated by defining accessor
methods (i.e., methods used to examine or modify the slots (member variables)
of a class) and ``advising'' the users to use them instead of directly
accessing the slots. The usual way of defining accessor
functions in \proglang{R} is to use the same name as the name of the
corresponding slot. For example for the slot \code{a} these are:
\begin{Scode}
R> cc <- a(obj)
R> a(obj) <- cc
\end{Scode}
In many cases this is not possible, because of conflicts with other
existing functions. For example it is not possible to define an
accessor function \code{cov()} for the slot \code{cov} of class
\code{Cov}, since the function \code{cov()} already exists in the
\code{base} \proglang{R}. Also it is not immediately seen if a slot
is ``read only'' or can be modified by the user (unfortunately, as
already mentioned, every slot in \proglang{R} can be modified by
simply using \code{obj@a <- cc}). In \pkg{rrcov} a notation was
adopted, which is usual in \proglang{Java}: the accessors are defined as
\code{getXxx()} and \code{setXxx()} (if a \code{setXxx()} method is
missing, we are ``not allowed'' to change the slot). The use of
accessor methods allows to perform computations on demand
(\code{getMah(mcd)} computes the Mahalanobis distances,  stores them
into the object and returns them) or even have ``virtual'' slots
which are not at all stored in the object (e.g., \code{getCorr(mcd)}
computes each time and returns the correlation matrix without
storing it).
\subsection{Naming conventions}
\label{oof-sec:naming}
%%
%From Sun: "Class names should be nouns, in mixed case with the first letter of each
%internal word capitalized. Methods should be verbs, in mixed case with the first
%letter lowercase, with the first letter of each internal word capitalized."
%%
%No coding rules in R: the R Internals manual that is shipped with R
%also has a section on coding standards:
%http://cran.r-project.org/doc/manuals/R-ints.html#R-coding-standards
%though this is quite short and does not go much beyond the basic indentation
%%
There is no agreed naming convention (coding rules)
in \proglang{R} but to facilitate the  framework usage
several simple rules are in order, following the
recommended Sun's \proglang{Java} coding style (see \url{http://java.sun.com/docs/codeconv/}):
\bi
\item{Class, function, method and variable names are alphanumeric, do not contain ``-'' or ``.'' but rather use interchanging lower and upper case.}
\item{Class names start with an uppercase letter.}
\item{Methods, functions, and variables start with a lowercase letter.}
\item{Exceptions are functions returning an object of a given class (i.e., generating functions or constructors)---they have the same name as the class.}
\item{Variables and methods which are not intended to be seen by the user---i.e., private members---start with ``.''.}
\item{Violate these rules whenever necessary to maintain compatibility.}
\ei
\section{Example session}
\label{oof-sec:ex-intro}
In this section we will introduce the base functionalities of the
framework by an example session. First of all we have to load the
package \pkg{rrcov} which will cause all necessary packages to be
loaded too. The framework includes many example data sets but here we will
load only those which will be used throughout the following
examples. For the rest of the paper it will be assumed that the
package has been loaded already.
<<echo=FALSE, results=hide>>=
## set the prompt to "R> " and the continuation to "+ "
options(prompt="R> ", continue="+ ")
@

<<label=intro>>=
##
## Load the 'rrcov' package and the first two data sets to be
## used throughout the examples
##
library("rrcov")
data("delivery")
delivery.x <- delivery[,1:2]    # take only the X part
data("hbk")
hbk.x <- hbk[,1:3]              # take only the X part
@
Most of the multivariate statistical methods are based on estimates of
multivariate location and covariance, therefore these estimates play a
central role in the framework. We will start with computing
the robust \textit{minimum covariance determinant} estimate for the data set
\code{delivery} from the package \pkg{robustbase}.
The data set \citep[see][Table~23, p.~155]{rousseeuw-leroy} contains delivery time data in
25 observations with 3 variables.
The aim is to explain the time required to service
a vending  machine \code{(Y)} by means of the number of products stocked \code{(X1)}
and the  distance walked by the route driver \code{(X2)}. For this example
we will consider only the $\v{X}$ part of the data set. After computing
its robust location and covariance matrix using the MCD method implemented
in the function \code{CovMcd()} we can print the results by calling the default
\code{show()} method on the returned object \code{mcd} as well as summary
information by the \code{summary()} method. The standard output contains
the robust estimates of location and covariance.
The summary output contains additionally the eigenvalues of
the covariance matrix and the robust distances of the data
items (Mahalanobis type distances computed with the robust
location and covariance instead of the sample ones).
<<label=intro-mcd>>=
##
## Compute MCD estimates for the delivery data set
## - show() and summary() examples
##
mcd <- CovMcd(delivery.x)
mcd
summary(mcd)
@
<<label=intro-plot, fig=TRUE, include=FALSE>>=
##
## Example plot of the robust against classical
##  distances for the delivery data set
##
plot(mcd, which="dd")
@
\begin{center}
\begin{figure}[h!]
\setkeys{Gin}{width=0.8\textwidth}
\includegraphics{ooframework-intro-plot}
\caption{Example plot of the robust against classical distances for the \code{delivery} data set.}
\label{oof-fig:intro}
\end{figure}
\end{center}
Now we will show one of the available plots by calling the \code{plot()}
method---in Figure~\ref{oof-fig:intro} the Distance-Distance plot introduced by
\citet{Rousseeuw-van-Zomeren} is presented, which plots the robust distances
versus the classical Mahalanobis distances and allows to classify
the observations and identify the potential outliers. The description of
this plot as well as examples of more graphical displays based on the covariance structure
will be shown in Section~\ref{oof-sec:cov}.


Apart from the demonstrated MCD method the framework provides many other
robust estimators of multivariate location and covariance,
actually almost all of the well established estimates in the contemporary
robustness literature. The most fascinating feature of the framework is that
one will get the output and the graphs in the same format, whatever estimation
method was used. For example the following code lines will compute the S~estimates
for the same data set and provide the standard and extended output (not shown here).
<<label=intro-S, results=hide>>=
##
## Compute the S-estimates for the delivery data set
##  and provide the standard and extended output
##
est <- CovSest(delivery.x, method="bisquare")
est
summary(est)
@
Nevertheless, this variety of methods could pose a serious
hurdle for the novice and could be quite tedious even for
the experienced user. Therefore a shortcut is provided too---the function
\code{CovRobust()} can be called with a parameter
set specifying any of the available estimation methods,
but if this parameter set is omitted the function will
decide on the basis of the data size which method to use.
As we see in the example below, in this case it selects
the Stahel-Donoho estimates. For details and further examples
see Section~\ref{oof-sec:cov}.
<<label=intro-CovRobust>>=
##
## Automatically select the appropriate estimator according
##  to the problem size - in this example the Stahel-Donoho estimates
##  will be selected.
##
est <- CovRobust(delivery.x)
est
@
\section{Robust multivariate methods}
\label{oof-sec:multi}
\subsection{Multivariate location and scatter}
\label{oof-sec:cov} The framework provides an almost complete set of
estimators for multivariate location and scatter with high breakdown
point. The first such estimator was proposed
by \citet{stahel:81, stahel-phd:81} and \citet{donoho:82} and it is recommended for
small data sets, but the most widely
used high breakdown estimator is the minimum covariance determinant estimate \citep{rousseeuw:85}. Several algorithms for computing the
S~estimators \citep{davies:87} are provided
\citep{ruppert:1992, rocke:94, rocke:96a, salibian:2005}. The
minimum volume ellipsoid (MVE) estimator \citep{rousseeuw:85} is
also included since it has some desirable properties when used as
initial estimator for computing the S~estimates \citep[see][p.
198]{maronna:2006}. In the rest of this section the definitions of
the different estimators of location and scatter will be briefly
reviewed and the algorithms for their computation will be discussed.
Further details can be found in the relevant references.
The object model is presented and examples of its usage, as well as further examples of the graphical
displays are given.
\subsubsection{The Minimum covariance determinant estimator and its computation}
\label{oof-sec:cov-mcd} The MCD estimator for a data set
$\{\xv_1, \ldots, \xv_n\}$ in $\Re^p$
is defined by that subset $\{\xv_{i_1}, \ldots, \xv_{i_h}\}$ of
$h$ observations whose covariance matrix has the smallest
determinant among all possible subsets of size $h$. The MCD location
and scatter estimate $\v{T}_{\MCD}$ and $\v{C}_{\MCD}$ are then given
as the arithmetic mean and a multiple of the sample covariance
matrix of that subset
\begin{eqnarray}
\label{oof-eq:mcd} \v{T}_{\MCD} &=& \frac{1}{h}\sum^{h}_{j=1} \xv_{i_j}
\nonumber\\
\v{C}_{MCD} &=& c_{ccf}c_{sscf}\frac{1}{h-1}\sum^{h}_{j=1}
(\xv_{i_j}-\v{T}_{\MCD})(\xv_{i_j}-\v{T}_{\MCD})^{\top}.
\end{eqnarray}
The multiplication factors $c_{ccf}$ (consistency correction factor)
and $c_{sscf}$ (small sample correction factor) are selected so that
$\v{C}$ is consistent at the multivariate normal model and unbiased
at small samples \citep[see][]{butler:1993, croux-haesbroeck:99,
pison:2002, todorov-cf}. A recommendable choice for $h$ is
$\lfloor(n+p+1)/2\rfloor$ because then the BP of the MCD is
maximized, but any integer $h$ within the interval $[(n + p +
1)/2,n]$ can be chosen, see \citet{rousseeuw-leroy}. Here $\lfloor
z\rfloor$ denotes the integer part of $z$ which is not less than
$z$. If $h = n$ then the MCD location  and scatter estimate
$\v{T}_{\MCD}$ and $\v{C}_{\MCD}$ reduce to the  sample mean and
covariance matrix of the full data set.


The computation of the MCD estimator is far from being trivial. The
naive algorithm would proceed by exhaustively investigating all
subsets of size $h$ out of $n$ to find the subset with the smallest
determinant of its covariance matrix, but this will be feasible only
for very small data sets. Initially MCD was neglected in favor of MVE
because the simple resampling
algorithm was more efficient for MVE.
Meanwhile several heuristic search algorithms
\citep[see][]{todorov:92, rocke:94, hawkins:94}
and exact algorithms \citep[][]{agullo:96} were
proposed but now a very fast algorithm due to
\citet{rousseeuw-vandriessen} exists and this
algorithm is usually used in practice.
The algorithm is based on the C-step which moves from one approximation
$(\v{T}_1, \v{C}_1)$ of the MCD estimate of a data set $\v{X}=\{\xv_1, \ldots, \xv_n\}$
to the next one $(\v{T}_2, \v{C}_2)$ with possibly lower determinant
$\det(\v{C}_2) \le \det(\v{C}_1)$ by computing the distances $d_1, \ldots, d_n$ relative to
$(\v{T}_1, \v{C}_1)$, i.e.,
\begin{equation}
\label{oof-eq:mah}
d_i=\sqrt{(\xv_i-\v{T}_1)^{\top}\v{C}_1^{-1}(\xv_i-\v{T}_1)}
\end{equation}
and then computing $(\v{T}_2, \v{C}_2)$ for those $h$
observations which have smallest distances.
``C'' in C-step stands for ``concentration'' since we are looking
for a more ``concentrated'' covariance matrix with lower determinant.
\citet{rousseeuw-vandriessen} have proven a theorem stating that
the iteration process given by the C-step converges in a finite
number of steps to a (local) minimum. Since there is no guarantee
that the global minimum of the MCD objective function will be reached,
the iteration must be started many times from different initial subsets,
to obtain an approximate solution. The procedure is very fast for small
data sets but to make it really ``fast'' also for large data sets several
computational improvements are used.
\bi
\item{\textit{initial subsets}: It is possible to restart the
    iterations from randomly generated subsets of size $h$, but in order to increase
    the probability of drawing subsets without outliers, $p+1$ points are
    selected randomly. These $p+1$ points are used to compute ($\v{T}_0,\v{C}_0)$.
    Then the distances $d_1,\ldots, d_n$ are computed and sorted in increasing order.
    Finally the first $h$ are selected to form the initial $h-$subset $H_0$.}
\item{\textit{reduced number of C-steps}: The C-step involving the computation
    of the covariance matrix, its determinant and the relative distances, is the most
    computationally intensive part of the algorithm. Therefore instead of iterating
    to convergence for each initial subset only two C-steps are performed and the
    10 subsets with lowest determinant are kept. Only these subsets are iterated to
    convergence. }
\item{\textit{partitioning}: For large $n$ the computation time of the algorithm increases
    mainly because all $n$ distances given by Equation~(\ref{oof-eq:mah})
    have to be computed at each iteration. An improvement is to partition
    the data set into a maximum of say five subsets of approximately equal
    size (but not larger than say 300) and iterate in each subset separately.
    The ten best solutions for each data set are kept and finally
    only those are iterated on the complete data set. }
\item{\textit{nesting}: Further decrease of the computational time can be achieved
    for data sets with $n$ larger than say 1500 by drawing 1500 observations without
    replacement and performing the computations (including the partitioning)
    on this subset. Only the final iterations are carried out on the complete
    data set. The number of these iterations depends on the actual size of
    the data set at hand.}
\ei

The MCD estimator is not very efficient at normal models, especially
if $h$ is selected so that maximal BP is achieved. To overcome the
low efficiency of the MCD estimator, a reweighed version can be
used. For this purpose a weight $w_i$ is assigned to each observation $\xv_i$,
defined as $w_i=1$ if
$(\xv_i-\v{T}_{\MCD})^{\top}\v{C}_{\MCD}^{-1}(\xv_i-\v{T}_{\MCD}) \le \chi^2_{p,0.975}$
and $w_i=0$ otherwise, relative to the raw MCD estimates
$(\v{T}_{\MCD}, \v{C}_{\MCD})$. Then the reweighted estimates are
computed as
\begin{eqnarray}
\label{oof-eq:mcd-rew}
\v{T}_R &=& \frac{1}{\nu}\sum^{n}_{i=1}{w_i\xv_i},\nonumber\\
\v{C}_R &=&
c_{r.ccf}c_{r.sscf}\frac{1}{\nu-1}\sum^n_{i=1}{w_i(\xv_i-\v{T}_R)(\xv_i-\v{T}_R)^{\top}},
\end{eqnarray}
where $\nu$ is the sum of the weights, $\nu =\sum^n_{i=1}{w_i}$.
Again, the multiplication factors $c_{r.ccf}$  and $c_{r.sscf}$
 are selected so that $\v{C}_R$ is
consistent at the multivariate normal model and unbiased at small
samples \citep[see][and the references therein]{pison:2002,
todorov-cf}. These reweighted estimates $(\v{T}_R,\v{C}_R)$ which
have the same breakdown point as the initial (raw) estimates but
better statistical efficiency are computed and used by default.
\subsubsection{The Minimum volume ellipsoid estimates}
\label{oof-sec:cov-mve} The minimum volume ellipsoid estimator
searches for the ellipsoid of minimal volume containing at least
half of the points in the data set $\v{X}$. Then the location
estimate is defined as the center of this ellipsoid and the
covariance estimate is provided by its shape. Formally the estimate
is defined as these $\v{T}_{\MVE},\v{C}_{\MVE}$ that minimize
$\det(\v{C})$ subject to
\begin{equation}
\label{oof-eq:mve}
\#\{i:(\xv_i - \v{T})^{\top}\v{C}^{-1}(\xv_i - \v{T}) \le c^2\} \ge
\left \lfloor \frac{n+p+1}{2} \right \rfloor,
\end{equation}
where \# denotes the cardinality. The constant $c$ is chosen as
$\chi^2_{p,0.5}$.


The search for the approximate solution is made over ellipsoids
determined by the covariance matrix of $p+1$ of the data points and by
applying a simple but effective improvement of the sub-sampling
procedure as described in \citet{maronna:2006}, p. 198. Although
there exists no formal proof of this improvement (as for MCD and
LTS), simulations show that it can be recommended as an
approximation of the MVE. The MVE was the first popular high breakdown point
estimator of location and scatter but later it was
replaced by the MCD, mainly because of the availability of an efficient algorithm for its computation \citep{rousseeuw-vandriessen}. Recently
the MVE gained importance as initial estimator for S~estimation because
of its small maximum bias \citep[see][Table~6.2, p.~196]{maronna:2006}.
\subsubsection{The Stahel-Donoho estimator}
\label{oof-sec:cov-sde}
The first multivariate equivariant estimator of location
and scatter with high breakdown point was proposed
by \citet{stahel:81, stahel-phd:81} and \citet{donoho:82} but became better
known after the analysis of \citet{maronna:95}. For a data set
$\v{X}=\{\xv_1,\ldots,\xv_n\}$ in  $\Re^p$ it is defined as a weighted mean
and covariance matrix of the form given by Equation~(\ref{oof-eq:mcd-rew})
where the weight $w_i$ of each observation is inverse proportional to
the ``outlyingness'' of the observation.
Let the univariate outlyingness of a point $\xv_i$ with respect to
the data set $\v{X}$ along a vector $\v{a} \in \Re^p, ||\v{a}|| \ne \v{0}$ be given by
\begin{equation}
\label{oof-eq:sde1}
r(\xv_i,\v{a}) = \frac{|\xv^{\top}\v{a}-m(\v{a}^{\top}\v{X})|}{s(\v{a}^{\top}\v{X})}~~~i=1,\ldots,n
\end{equation}
where $(\v{a}^{\top}\v{X})$ is the projection of the data set $\v{X}$ on $\v{a}$
and the functions $m()$ and $s()$ are robust univariate location and scale
statistics, for example the median and MAD, respectively.
Then the multivariate outlyingness of $\xv_i$ is defined by
\begin{equation}
\label{oof-eq:sde2}
r_i=r(\xv_i) = \max_{\v{a}} r(\xv_i,\v{a}).
\end{equation}
The weights are computed by $w_i=w(r_i)$ where $w(r)$ is a nonincreasing
function of $r$ and $w(r)$ and $w(r)r^2$ are bounded. \citet{maronna:95} use the weights
\begin{equation}
\label{oof-eq:sde-weight}
w(r)=\min \left ( 1,\left (\frac{c}{t} \right )^2 \right )
\end{equation}
with $c=\sqrt{\chi^2_{p,\beta}}$ and $\beta=0.95$, that are known in the literature as ``Huber weights''.


Exact computation of the estimator is not possible and an approximate solution is
found by subsampling a large number of directions $\v{a}$ and computing the
outlyingness measures $r_i, i=1,\ldots,n$ for them. For each subsample
of $p$ points the vector $\v{a}$ is taken as the norm 1 vector orthogonal
to the hyperplane spanned by these points. It has been shown by simulations
\citep{maronna:2006} that one step reweighting does not improve the estimator.
\subsubsection{Orthogonalized Gnanadesikan/Kettenring}
\label{oof-sec:cov-ogk} The MCD estimator and all other known affine
equivariant high-breakdown point estimates are solutions to a highly
non-convex optimization problem and as such pose a serious
computational challenge. Much faster estimates with high breakdown
point can be computed if one gives up the requirements of affine
equivariance of the covariance matrix. Such an algorithm was
proposed by \citet{maronna:2002} which is based on the very simple
robust bivariate covariance estimator $s_{jk}$ proposed by
\citet{Gnanadesikan-Kettenring:1972} and studied by
\citet{devlin:81}. For a pair of random variables $Y_j$ and $Y_k$
and a standard deviation function $\sigma()$, $s_{jk}$ is defined as
\begin{equation}
\label{oof-eq:GK}
s_{jk}=\frac{1}{4}\left(\sigma \left(\frac{Y_j}{\sigma(Y_j)}+\frac{Y_k}{\sigma(Y_k)}\right)^2 -
\sigma \left(\frac{Y_j}{\sigma(Y_j)}-\frac{Y_k}{\sigma(Y_k)}\right)^2\right).
\end{equation}
If a robust function is chosen for $\sigma()$ then $s_{jk}$ is also
robust and an estimate of the covariance matrix can be obtained by
computing each of its elements $s_{jk}$ for each $j=1,\ldots,p$ and
$k=1,\ldots,p$ using Equation~(\ref{oof-eq:GK}). This estimator does
not necessarily produce a positive definite matrix (although
symmetric) and it is not affine equivariant.
\citet{maronna:2002} overcome the lack of positive definiteness by
the following steps:
\bi
\item{Define $\yv_i=\vv{D}^{-1}\xv_i, i=1,\ldots,n$ with
    $\v{D}=\diag(\sigma(X_1),\ldots,\sigma(X_p))$ where $X_l,
    l=1,\ldots,p$ are the columns of the data matrix $\vv{X}=\{\xv_1, \ldots, \xv_n\}$.
    Thus a normalized data matrix $\vv{Y}=\{\yv_1, \ldots, \yv_n\}$ is computed.}
\item{Compute the matrix $\vv{U}=(u_{jk})$ as
    $u_{jk}= s_{jk}=s(Y_j, Y_k)$ if $j \ne k$ or $u_{jk}= 1$ otherwise.
    Here $Y_l, l=1,\ldots,p$ are the columns of the transformed data
    matrix $\vv{Y}$ and $s(.,.)$ is a robust estimate of the covariance of two random variables like the one in Equation~(\ref{oof-eq:GK}).}
\item{Obtain the ``principal component decomposition'' of $\vv{Y}$ by decomposing $\vv{U}=\vv{E}\vv{\Lambda}\vv{E}^{\top}$
    where $\vv{\Lambda}$ is a diagonal matrix $\vv{\Lambda}=\diag(\lambda_1,\ldots,\lambda_p)$ with the eigenvalues $\lambda_j$ of $\vv{U}$ and $\vv{E}$ is a matrix with columns the eigenvalues $\vv{e}_j$ of $\vv{U}$.}
\item{Define $\zv_i=\vv{E}^{\top}\yv_i=\vv{E}^{\top}\vv{D}^{-1}\xv_i$ and $\vv{A}=\vv{D}\vv{E}$.
    Then the estimator of $\vv{\Sigma}$ is
    $\vv{C}_{\OGK}=\vv{A}\vv{\Gamma}\vv{A}^{\top}$ where
    $\vv{\Gamma}=\diag(\sigma(Z_j)^2), j=1,\ldots,p$} and the location
    estimator is $\vv{T}_{\OGK}=\vv{A}\mv$ where
    $\mv=m(\zv_i) = (m(Z_1),\ldots,m(Z_p))$ is a robust mean function.
\ei
This can be iterated by computing $\vv{C}_{\OGK}$ and $\vv{T}_{\OGK}$ for $\vv{Z}=\{\zv_1, \ldots, \zv_n\}$ obtained in the last step of the procedure and then transforming back to the original coordinate system. Simulations \citep{maronna:2002} show that iterations beyond the second did not lead to improvement.


Similarly as for the MCD estimator a one-step reweighting can be performed using
Equations~(\ref{oof-eq:mcd-rew}) but the weights $w_i$ are based on
the 0.9 quantile of the $\chi^2_p$ distribution (instead of 0.975)
and the correction factors $c_r.ccf$ and $c_r.sscf$ are not used.


In order to complete the algorithm we need a robust and efficient
location function $m()$ and scale function $\sigma()$, and one
proposal is given in \citet{maronna:2002}. Further, the robust
estimate of covariance between two random vectors $s()$ given by
Equation~(\ref{oof-eq:GK}) can be replaced by another one. In the
framework two such functions are predefined but the user can
provide as a parameter an own function.
\subsubsection{S estimates}
\label{oof-sec:cov-s} S~estimators of $\muv$ and $\v{\Sigma}$ were
introduced by \citet{davies:87} and further studied by \citet{lopuhaa:1989} \citep[see also][p. 263]{rousseeuw-leroy}.
For a data set of
$p$-variate observations $\{\xv_1, \ldots, \xv_n\}$
an S~estimate $(\v{T},\v{C})$ is defined as the solution of
$\sigma(d_1,\ldots,d_n)= \min$ where
$d_i=(\xv-\v{T})^{\top}\v{C}^{-1}(\xv-\v{T})$ and $\det(\v{C})=1$. Here
$\sigma=\sigma(\zv)$ is the M-scale estimate of a data set
$\zv=\{z_1,\ldots,z_n\}$ defined as the solution of
$\frac{1}{n}\Sigma\rho(z/\sigma)=\delta$ where $\rho$ is
nondecreasing, $\rho(0)=0$ and $\rho(\infty)=1$ and $\delta
\in(0,1)$. An equivalent definition is to find the vector $\v{T}$
and a positive definite symmetric matrix $\v{C}$ that minimize
$\det(\v{C})$ subject to
\begin{equation}
\label{oof-eq:s-def}
 \frac{1}{n}\sum_{i=1}^{n}\rho(d_i)=b_0
\end{equation}
with the above $d_i$ and $\rho$.


As shown by \citet{lopuhaa:1989} S~estimators have a close
connection to the M~estimators and the solution $(\v{T},\v{C})$ is
also a solution to an equation defining an M~estimator as well as a
weighted sample mean and covariance matrix:
\begin{eqnarray}
\label{oof-eq:s-iter}
d_i^{j}&=&[(\xv_i-\v{T}^{(j-1)})^{\top}\v{(C}^{(j-1)})^{-1}(\xv-\v{T}^{(j-1)})]^{1/2}
\nonumber\\
\v{T}^{(j)} &=& \frac{\Sigma w(d_i^{(j)})\xv_i}{\Sigma w(d_i^{(j)})}
\nonumber\\
\v{C}^{(j)} &=& \frac{\Sigma
w(d_i^{(j)})(\xv_i-\v{T}^{(j)})(\xv_i-\v{T}^{(j)})^{\top}}{\Sigma
w(d_i^{(j)})}
\end{eqnarray}
The framework implements the S~estimates in the class
\code{CovSest} and provides four different algorithms for their computation.
\be
\item{\emph{SURREAL}: This algorithm was proposed by
    \citet{ruppert:1992} as an analog to the algorithm
    proposed by the same author for computing S~estimators of regression.}
\item{\emph{Bisquare S~estimation with HBDP start}: S~estimates with the biweight
    $\rho$ function can be obtained using the
    Equations~(\ref{oof-eq:s-iter}) by a reweighted sample covariance and reweighted sample mean algorithm as described in \citet{maronna:2006}. The preferred
    approach is to start the iteration from a bias-robust but possibly
    inefficient estimate which is computed by some form of sub-sampling.
    Since \citet{maronna:2006} have shown that the MVE has smallest
    maximum bias (Table~6.2, p.~196) it is recommended to use it as initial estimate.}
\item{\emph{Rocke type S~estimates}: In \citet{rocke:96a} it is shown
    that S~estimators in high dimensions can be sensitive to outliers
    even if the breakdown point is set to 50\%. Therefore they propose
    a modified $\rho$ function called translated biweight (or t-biweight)
    and replace the standardization step given in Equation~(\ref{oof-eq:s-def})
    with a standardization step consisting of equating the median
    of $\rho(d_i)$ with the median under normality. The estimator
    is shown to be more outlier resistant in high dimensions than
    the typical S~estimators. The specifics of the iteration are given
    in \citet{rocke:96}, see also \citet{maronna:2006}. As starting values for the iteration any of
    the available methods in the framework can be used. The recommended
    (and consequently the default) one is the MVE estimator computed
    by \code{CovMve()}.}
\item{\emph{Fast~S~estimates}: \citet{salibian:2005} proposed
    a fast algorithm for regression S~estimates similar to the
    FAST-LTS algorithm of \citet{rousseeuw-vandriessen:LTS} and
    borrowing ideas from the SURREAL algorithm of \citet{ruppert:1992}.
    Similarly, the FAST-S algorithm for multivariate location
    and scatter is based on modifying each candidate to improve
    the S-optimality criterion thus reducing the number of
    the necessary sub-samples required to achieve desired high breakdown
    point with high probability.}
\ee
\subsubsection{Object model for robust location and scatter estimation}
\label{oof-sec:cov-objmodel}
The object model for the \proglang{S}4
classes and methods implementing the different multivariate location
and scatter estimators follows the proposed class hierarchy given in
Section~\ref{oof-sec:objmodel} and is presented in
Figure~\ref{fig:uml-cov}.
\begin{figure}[h!]
\begin{center}
\includegraphics[width=\textwidth]{CovModel}
\caption{Object model for robust location and scatter estimation.}
\label{fig:uml-cov}
\end{center}
\end{figure}

The abstract class \code{Cov} serves as a base class for deriving all classes
representing classical and robust location and scatter estimation methods. It
defines the common slots and the corresponding accessor methods, provides
implementation for the general methods like \code{show()}, \code{plot()}
and \code{summary()}. The slots of \code{Cov} hold some input or
default parameters as well as the
results of the computations: the location, the covariance matrix and the distances.
The \code{show()} method presents brief results of the
computations and the \code{summary()} method returns an object of class
\code{SummaryCov} which has its own \code{show()} method. As in the other
sections of the framework these slots and methods are defined and documented
only once in this base class and can be used by all derived classes. Whenever
new data (slots) or functionality (methods) are necessary, they can be defined
or redefined in the particular class.


The classical location and scatter estimates are represented by the
class \code{CovClassic} which inherits directly from \code{Cov} (and
uses all slots and methods defined there). The function
\code{CovClassic()} serves as a constructor (generating function) of
the class. It can be called by providing a data frame or
matrix.
As already demonstrated in Section~\ref{oof-sec:ex-intro} the methods
\code{show()} and \code{summary()} present the results of the computations.
The \code{plot()} method draws different diagnostic plots which
are shown in one of the next sections.
The accessor functions like \code{getCenter()}, \code{getCov()}, etc.
are used to access the corresponding slots.


Another abstract class, \code{CovRobust} is
derived from \code{Cov}, which serves as a base class for all robust
location and scatter estimators.


The classes representing robust estimators like
\code{CovMcd}, \code{CovMve}, etc. are  derived
from \code{CovRobust} and provide implementation
for the corresponding methods. Each of the constructor
functions \code{CovMcd()},
\code{CovMve()},\code{CovOgk()}, \code{CovMest()} and
\code{CovSest()} performs the necessary computations and returns an
object of the class containing the results. Similarly
as the \code{CovClassic()} function, these functions can be
called either with a data frame or a numeric matrix.
\subsubsection{Controlling the estimation options}
\label{oof-sec:cov-control}
Although the different robust estimators of multivariate location
and scatter have some controlling options in common, like the
tracing flag \code{trace} or the numeric tolerance \code{tolSolve}
to be used for inversion (\code{solve}) of the covariance matrix in
\code{mahalanobis()}, each of them has more specific options. For
example, the MCD and MVE estimators (\code{CovMcd()} and
\code{CovMve()}) can specify \code{alpha} which controls the size of
the subsets over which the determinant (the volume of the ellipsoid)
is minimized. The allowed values are between 0.5 and 1 and the
default is 0.5. Similarly, these estimators have parameters
\code{nsamp} for the number of subsets used for initial estimates
and \code{seed} for the initial seed for \proglang{R}'s random number generator
while the M and S~estimators (\code{CovMest} and \code{CovSest})
have to specify the required breakdown point (allowed values between
$(n - p)/(2*n)$ and 1 with default 0.5) as well as the asymptotic
rejection point, i.e., the fraction of points receiving zero weight
\citep{rocke:96}.


These parameters can be passed directly to the corresponding constructor
function but additionally there exists the possibility to use a control object
serving as a container for the parameters. The object model for the control
objects shown in Figure~\ref{oof-fig:cov-control} follows the proposed class
hierarchy---there is a base class \code{CovControl} which holds the common
parameters and from this class all control classes holding the specific parameters of their
estimators are derived. These classes have only a
constructor function for creating new objects and a method \code{restimate()}
which takes a data frame or a matrix, calls the corresponding estimator to
perform the calculations and returns the created class
with the results.


\begin{figure}[h!]
\begin{center}
\includegraphics[width=\textwidth]{CovControl}
\caption{Object model of the control classes for robust location and scatter estimation.}
\label{oof-fig:cov-control}
\end{center}
\end{figure}
Apart from providing a structured container for the estimation parameters this
class hierarchy has the following additional benefits:
\bi
\item{the parameters can be passed easily to another
    multivariate method, for example the principal components analysis
    based on a covariance matrix \code{PcaCov()} (see Section~\ref{oof-sec:pca})
    can take a control object which will be used to estimate
    the desired covariance (or correlation) matrix.
    In the following example a control object holding
    the parameters for S~estimation will be created and
    then \code{PcaCov()} will be called with this object.}
<<echo=FALSE, results=hide>>=
set.seed(1234)
@
<<label=CovControl>>=
##
## Controlling the estimation options with a control object
##
control <- CovControlSest(method="biweight")
PcaCov(hbk.x, cov.control=control)

@
\item{the class hierarchy of the control objects allows to
    handle different estimator objects using a uniform interface
    thus leveraging one of the most important features of
    the object oriented programming, the polymorphism.
    In the following example we create a list containing different
    control objects and then via \code{sapply} we call the generic
    function \code{restimate()} on each of the objects in the list.
    The outcome will be a list containing the objects resulting from
    these calls (all are derived from \code{CovRobust}). This
    looping over the different estimation methods is very useful
    for implementing simulation studies.}

<<label=CovControl-loop>>=
##
## Controlling the estimation options: example
##  of looping through several estimators
##
cc <- list(CovControlMcd(), CovControlMest(), CovControlOgk(), CovControlSest(), CovControlSest(method="rocke"))
clist <- sapply(cc, restimate, x=delivery.x)

sapply(clist, data.class)
sapply(clist, getMeth)
@
\ei
\subsubsection[A generalized function for robust location and
covariance estimation: CovRobust()]{A generalized function
for robust location and covariance estimation: \code{CovRobust()}}
\label{oof-sec:cov-covrobust}
The provided variety of estimation methods, each of them with different
parameters as well as the object models described in
the previous sections can be overwhelming for the user,
especially for the novice who does not care much about the technical
implementation of the framework. Therefore a function is provided which
gives a quick access to the robust estimates of location and covariance matrix.
This function is loosely modeled around the
\textit{abstract factory design pattern} \citep[see][page 87]{gamma} in
the sense that it creates concrete objects of derived classes and returns
the result over a base class interface.
The class \code{CovRobust} is abstract (defined as \textit{VIRTUAL}) and no
objects of it can be created but any of the classes derived from \code{CovRobust},
such as \code{CovMcd} or \code{CovOgk}, can act as an object of class \code{CovRobust}.
The function \code{CovRobust()} which is technically not a constructor function can
return an object of any of the classes derived from \code{CovRobust} according
to the user request. This request can be specified in one of three forms:
\bi
\item{If only a data frame or matrix is provided and the control parameter
    is omitted, the function decides which estimate to apply according
    to the size of the problem at hand. If there are less than 1000
    observations and less than 10 variables or less than 5000 observations
    and less than 5 variables, Stahel-Donoho estimator will be used. Otherwise,
    if there are less than 50000 observations, either bisquare S~estimates
    (in case of less than 10 variables) or Rocke type S~estimates (for 10 to 20 variables)
    will be used. In both cases the S iteration starts at the initial MVE estimate.
    And finally, if there are more than 50000 observations and/or more than 20 variables
    the Orthogonalized Quadrant Correlation estimator (\code{CovOgk} with the
    corresponding parameters) is used. This is illustrated by the following example.}
<<label=CovRobust>>=
##
## Automatically select the appropriate estimator according
##  to the problem size.
##
getMeth(CovRobust(matrix(rnorm(40), ncol=2)))       # 20x2      - SDE
getMeth(CovRobust(matrix(rnorm(16000), ncol=8)))    # 2000x8    - bisquare S
getMeth(CovRobust(matrix(rnorm(20000), ncol=10)))   # 2000x10   - Rocke S
getMeth(CovRobust(matrix(rnorm(200000), ncol=2)))   # 100000x2  - OGK
@
\item{The simplest way to choose an estimator is to provide a character string with
    the name of the estimator---one of \code{"mcd"}, \code{"ogk"}, \code{"m"}, \code{"s-fast"}, \code{"s-rocke"}, etc.}
<<label=CovControl-S>>=
##
## Rocke-type S-estimates
##
    getMeth(CovRobust(matrix(rnorm(40), ncol=2), control="rocke"))
@
\item{If it is necessary to specify also some estimation parameters,
    the user can create a control object (derived from \code{CovControl})
    and pass it to the function together with the data. For example to compute
    the OGK estimator using the median absolute deviation (MAD) as a
    scale estimate and the quadrant correlation (QC) as a pairwise
    correlation estimate we create a control object \code{ctrl}
    passing the parameters \code{s_mad} and \code{s_qc} to the
    constructor function and then call \code{CovRobust} with this
    object. The last command line illustrates the accessor method
    for getting the correlation matrix of the estimate as well as
    a nice formatting method for covariance matrices.}
<<label=CovControl-CovRobust>>=
##
## Specify some estimation parameters through a control object.
##  The last command line illustrates the accessor method
##  for getting the correlation matrix of the estimate
##  as well as a nice formatting method for covariance
##  matrices.
##
    data("toxicity")
    ctrl <- CovControlOgk(smrob = "s_mad", svrob = "qc")
    est <- CovRobust(toxicity, ctrl)
    round(getCenter(est),2)
    as.dist(round(getCorr(est), 2))
@
\ei
\subsubsection{Visualization of the results}
\label{oof-sec:cov-vis}
The default plot accessed through the method \code{plot()} of class
\code{CovRobust} is the Distance-Distance plot introduced by
\citet{Rousseeuw-van-Zomeren}. An example of this graph, which plots
the robust distances versus the classical Mahalanobis distances is
shown in Figure~\ref{oof-fig:intro}. The dashed line represents the
points for which the robust and classical distances are equal.
The horizontal and vertical lines are drawn at values $x=y=\sqrt{\chi_{p,0.975}^2}$.
Points beyond these lines can be considered as outliers and
are identified by their labels.


The other available plots are accessible either interactively or
through the \code{which} parameter of the \code{plot()} method.
The left panel of Figure~\ref{oof-fig:cov-lattice} shows
an example of the distance plot in which robust and classical
Mahalanobis distances are shown in parallel panels.
The outliers have large robust distances and are identified by their labels.
The right panel of Figure~\ref{oof-fig:cov-lattice} shows a Quantile-Quantile
comparison plot of the robust and the classical Mahalanobis distances versus
the square root of the quantiles of the chi-squared distribution.
<<label=ex-cov-plot-lattice, echo=FALSE, fig=TRUE, results=hide, include=FALSE, width=12, height=6>>=
##
## Distance plot and Chi-square Q-Q plot of the robust and classical distances
##  Lattice plots (currently not available in rrcov)
##
    library("lattice")
    library("grid")
    library("rrcov")

    data("delivery")
    X <- delivery[,1:2]

    myPanel.dd <- function(x, y, subscripts, cutoff, ...) {
        panel.xyplot(x, y, ...)
        panel.abline(h=cutoff,lty="dashed")

        n <- length(y)
        id.n <- length(which(y>cutoff))
        if(id.n > 0){
            ind <- sort(y, index.return=TRUE)$ix
            ind <- ind[(n-id.n+1):n]

            xrange<-range(y)
            adj <- (xrange[2]-xrange[1])/20
            ltext(x[ind] + adj, y[ind] + adj, ind, cex=1.0)
        }
    }

    myPanel.qchi <- function(x, y, subscripts, cutoff, ...) {
        y <- sort(y, index.return=TRUE)
        iy <- y$ix
        y <- y$x
        panel.xyplot(x, y, ...)
        panel.abline(0,1,lty="dashed")

        n <- length(y)
        id.n <- length(which(y>cutoff))
        if(id.n > 0){
            ind <- (n-id.n+1):n

            xrange<-range(y)
            adj <- (xrange[2]-xrange[1])/50
            ltext(x[ind] + adj, y[ind] + adj, iy[ind], cex=1.0)
        }
    }


    n<-nrow(X)
    p <- ncol(X)
    cutoff <- sqrt(qchisq(0.975, p))

    mm <- covMcd(X)
    dd1 <- sqrt(mm$mah)                             # robust distances

    vv<-cov.wt(X)
    dd2 <- sqrt(mahalanobis(X,vv$center,vv$cov))    # classical distances

    dd<-c(dd1,dd2)                                  # both robust and classical distances

    gr  <- as.factor(c(rep(1,n), rep(2,n)))
    levels(gr)[1] <- "Robust"
    levels(gr)[2] <- "Classical"

    qq  <- sqrt(qchisq(((1:n)-1/3)/(n+1/3), p))

    ind.dd <- c(1:n, 1:n)
    ind.qchi <- c(qq, qq)

    dplot <- xyplot(dd~ind.dd|gr,
                cutoff=cutoff,
                panel = myPanel.dd,
                xlab="Index",
                ylab="Mahalanobis distance",
                main="Distance Plot",
                col = "darkred",
                scales=list(cex=1.0))

    qplot <- xyplot(dd~ind.qchi|gr,
                cutoff=cutoff,
                panel = myPanel.qchi,
                xlab="Quantiles of the chi-squared distribution",
                ylab="Mahalanobis distance",
                main="Chi-Square QQ-Plot",
                col = "darkred",
                scales=list(cex=1.0))

    plot(dplot, split = c(1, 1, 2, 1), more = TRUE)
    plot(qplot, split = c(2, 1, 2, 1), more = FALSE)
@
\begin{center}
\begin{figure}[h!]
\setkeys{Gin}{width=1.0\textwidth}
\includegraphics{ooframework-ex-cov-plot-lattice}
\caption{Distance plot and Chi-square Q-Q plot of the robust and classical distances.}
\label{oof-fig:cov-lattice}
\end{figure}
\end{center}
The next plot shown in Figure~\ref{oof-fig:cov-ellipse}
presents a scatter plot of the data on which the 97.5\%
robust and classical confidence ellipses are superimposed.
Currently this plot is available only for bivariate data.
The observations with distances larger than
$\sqrt{\chi_{p,0.975}^2}$ are identified by their subscript.
In the right panel of Figure~\ref{oof-fig:cov-ellipse} a \code{screeplot} of the \code{milk}
data set is shown, presenting the robust and classical eigenvalues.
<<label=ex-cov-plot-ellipse, echo=TRUE, fig=TRUE, results=hide, include=FALSE, width=12, height=6>>=
##
## a) scatter plot of the data with robust and classical confidence ellipses.
## b) screeplot presenting the robust and classical eigenvalues
##
data("milk")
usr<-par(mfrow=c(1,2))
plot(CovMcd(delivery[,1:2]), which="tolEllipsePlot", classic=TRUE)
plot(CovMcd(milk), which="screeplot", classic=TRUE)
par(usr)
@
\begin{center}
\begin{figure}[h!]
\setkeys{Gin}{width=1.0\textwidth}
\includegraphics{ooframework-ex-cov-plot-ellipse}
\caption{Robust and classical tolerance ellipse for the \code{delivery}
data and robust and classical screeplot for the \code{milk} data.}
\label{oof-fig:cov-ellipse}
\end{figure}
\end{center}
\subsection{Principal component analysis}
\label{oof-sec:pca} Principal component analysis is a widely
used technique for dimension reduction achieved by finding a smaller
number $q$ of linear combinations of the originally observed $p$
variables and retaining most of the variability of the data. Thus
PCA is usually aiming at a graphical representation of the data in a
lower dimensional space. The classical approach to PCA measures the
variability through the empirical variance and is essentially based on
computation of eigenvalues and eigenvectors of the sample covariance
or correlation matrix. Therefore the results may be extremely
sensitive to the presence of even a few atypical observations in the
data. These discrepancies will carry over to any subsequent analysis
and to any graphical display related to the principal components
such as the biplot.


%%% Example - hbk data
The following example in Figure~\ref{oof-fig:pca-hbk} illustrates the effect of
outliers on the classical PCA. The data set \code{hbk} from the package
\pkg{robustbase} consists of 75
observations in 4 dimensions (one response and three explanatory
variables) and was constructed by Hawkins, Bradu and Kass in 1984
for illustrating some of the merits of a robust technique
\citep[see][]{rousseeuw-leroy}. The first 10 observations are bad
leverage points, and the next four points are good leverage points
(i.e., their $\xv$ are outlying, but the corresponding $y$ fit the model
quite well). We will consider only the X-part of the data.
The left panel shows the plot of the scores on the first
two classical principal components
(the first two components account for more than
98\% of the total variation). The outliers are identified as separate groups,
but the regular points are far from the origin
(where the mean of the scores should be located).
Furthermore, the ten bad leverage points 1--10 lie within
the 97.5\% tolerance ellipse and influence the classical
estimates of location and scatter. The right panel
shows the same plot based on robust estimates. We see
that the estimate of the center is not shifted by the outliers
and these outliers are clearly separated by the 97.5\% tolerance ellipse.
\begin{center}
\begin{figure}[h!]
\setkeys{Gin}{width=1.0\textwidth}
<<pca-ex-hbk, echo=FALSE, fig=TRUE, height=6, width=12>>=
##
## Principal Component Analysis example:
##  Plot of the first two principal components of the
##  Hawkins, Bradu and Kass data set: classical and robust
##
par(mfrow=c(1,2))
pca <- PcaClassic(hbk.x, k=2)
cpca <- list(center=c(0,0), cov=diag(pca@eigenvalues), n.obs=pca@n.obs)
rrcov:::.myellipse(pca@scores, xcov=cpca, main="Classical",  xlab="PC1", ylab="PC2", ylim=c(-30,30), id.n=0)
abline(v=0)
abline(h=0)
text(-29,6,labels="1-10", cex=0.8)
text(-37,-13,labels="14", cex=0.8)
text(-31,-5,labels="11-13", cex=0.8)
hub <- PcaHubert(hbk.x, k=2, mcd=TRUE)
chub <- list(center=c(0,0), cov=diag(hub@eigenvalues), n.obs=hub@n.obs)
rrcov:::.myellipse(hub@scores, xcov=chub, main="Robust (MCD)", xlab="PC1", ylab="PC2", xlim=c(-10,45), ylim=c(-25,15), id.n=0)
abline(v=0)
abline(h=0)
text(30,-9,labels="1-10", cex=0.8)
text(36,-11,labels="11", cex=0.8)
text(42,-4,labels="12", cex=0.8)
text(41,-11,labels="13", cex=0.8)
text(44,-15,labels="14", cex=0.8)
@
\caption{Plot of the first two principal components of the Hawkins, Bradu and Kass data set: classical and robust.}
\label{oof-fig:pca-hbk}
\end{figure}
\end{center}

PCA was probably the first multivariate technique subjected to
robustification, either by simply computing the eigenvalues and
eigenvectors of a robust estimate of the covariance matrix or
directly by estimating each principal component in a robust manner.
Different approaches to robust PCA are briefly presented in the next
subsections with the emphasis on those methods which are available
in the framework. Details about the methods and algorithms can be
found in the corresponding references. The object model is described and examples are given.
\subsubsection{PCA based on robust covariance matrix (MCD, OGK, MVE, etc.)}
The most straightforward and intuitive method to obtain robust PCA
is to replace the classical estimates of location and covariance
by their robust analogues. In the earlier works M~estimators
of location and scatter were used for this purpose
\citep[see][]{devlin:81, campbell:80} but these estimators have
the disadvantage of low breakdown point in high dimensions. To cope
with this problem \citet{naga:1990} used the MVE estimator and
\citet{todorov-compstat:94} used the MCD estimator.
\citet{croux-Haesbroeck:2000} investigated the properties of the MCD
estimator and computed its influence function and
efficiency.


The package \pkg{stats} in base \proglang{R} contains the function
\code{princomp()} which performs a principal components analysis on
a given numeric data matrix and returns the results as an object of
\proglang{S}3 class \code{princomp}. This function has a parameter
\code{covmat} which can take a covariance matrix, or a covariance
list as returned by \code{cov.wt}, and if supplied, it is used rather
than the covariance matrix of the input data. This allows to obtain
robust principal components by supplying the covariance matrix
computed by \code{cov.mve} or \code{cov.mcd} from the package
\pkg{MASS}. One could ask why is it then necessary to include such
type of function in the framework (since it already exists in the base package).
The essential value added of the
framework, apart from implementing many new robust multivariate
methods is the unification of the interfaces by leveraging the
object orientation provided by the \proglang{S}4 classes and
methods. The function \code{PcaCov()} computes robust PCA by
replacing the classical covariance matrix with one of the robust
covariance estimators available in the framework---MCD, OGK, MVE,
M, S or Stahel-Donoho, i.e., the parameter \code{cov.control} can be any object of a class
derived from the base class \code{CovControl}. This control class will be used to compute a robust estimate of the covariance matrix. If this parameter is omitted, MCD will be used by default.
Of course any newly developed
estimator following the concepts of the framework can be used as
input to the function \code{PcaCov()}.
\subsubsection{Projection pursuit methods}
The second approach to robust PCA uses \textit{projection pursuit}
(PP) and calculates directly the robust estimates of the eigenvalues
and eigenvectors. Directions are seeked for, which maximize the
variance (classical PCA) of the data projected onto them. Replacing
the variance with a robust measure of spread yields robust PCA. Such
a method was first introduced by \citet{li:1985} using an
M~estimator of scale $S_n$ as a \textit{projection index (PI)}. They
showed that the PCA estimates inherit the robustness properties of
the scale estimator $S_n$. Unfortunately, in spite of the good
statistical properties of the method, the algorithm they proposed
was too complicated to be used in practice. A more tractable
algorithm in these lines was first proposed by
\citet{croux-Ruiz-Gazen:1996} and later improved by
\citet{croux-Ruiz-Gazen:2005}. To improve the performance of the
algorithm for high dimensional data a new improved version was
proposed by \citet{croux-filzmoser-oliveira-pppca}. The latter two
algorithms are available in the package \pkg{pcaPP}
\citep[see][]{filzmoser-pcaPP} as functions \code{PCAproj()} and
\code{PCAgrid()}.


In the framework these methods are represented by the classes
\code{PcaProj} and \code{PcaGrid}. Their generating functions
provide simple wrappers around the original functions from
\pkg{pcaPP} and return objects of the corresponding
class, derived from \code{PcaRobust}.


A major advantage of the PP-approach is that it searches for the
eigenvectors consecutively and in case of high dimensional data when
we are interested in only the first one or two principal components
this results in reduced computational time. Even more, the
PP-estimates cope with the main drawback of the covariance-based
estimates---they can be computed for data matrices with more
variables than observations.
\subsubsection{Hubert method (ROBPCA)}
The PCA method proposed by \citet{hubert-ROBPCA:2005} tries to
combine the advantages of both approaches---the PCA based on a
robust covariance matrix and PCA based on projection pursuit. A
brief description of the algorithm follows, for details see the
relevant references \citep{hubert:2008}.


Let $n$ denote the number of observations, and $p$ the number of
original variables in the input data matrix $\v{X}$. The ROBPCA
algorithm finds a robust center $\mv$ of the data and a loading matrix
$\v{P}$ of dimension $p \times k$. Its columns are orthogonal and
define a new coordinate system. The scores $\v{T}$, an $n \times k$
matrix, are the coordinates of the centered observations with
respect to the loadings:
\begin{equation}
\label{oof-eq:pca-scores}
\v{T}=(\v{X}-\v{1}\mv^{\top})\v{P}
\end{equation}
where $\v{1}$ is a column vector with all $n$ components equal to 1.
The ROBPCA algorithm yields also a robust covariance matrix (often
singular) which can be computed as
\begin{equation}
\label{oof-eq:pca-S}
\v{S}=\v{PLP}^{\top}
\end{equation}
where $\v{L}$ is the diagonal matrix with the eigenvalues $l_1,
\dots, l_k$. This is done in the following three main steps:
\paragraph{Step 1:} The data are preprocessed by reducing their
data space to the subspace spanned by the $n$ observations. This is
done by singular value decomposition of the input data matrix. As a
result the data are represented in a space whose dimension is $rank(\v{X})$,
being at most $n-1$ without loss of information.

\paragraph{Step 2:} In this step a measure of outlyingness is computed
for each data point. For this purpose the data points are projected on
the $n(n-1)/2$ univariate directions through each two points. If $n$
is too large,  \code{maxdir} directions are chosen at random (\code{maxdir}
defaults to 250 but can be changed by the user). On every direction
the univariate MCD estimator of location and scale is computed and
the standardized distance to the center is measured. The largest
of these distances (over all considered directions) is the outlyingness
measure of the data point. The $h$ data points with smallest
outlyingness measure are used to compute the covariance matrix
$\v{\Sigma}_h$ and to select the number $k$ of principal components
to retain. This is done by finding $k$ such that $l_k/l_1
\ge 10^{-3}$ and $\Sigma_{j=1}^k l_j/\Sigma_{j=1}^r l_j \ge 0.8$.
Alternatively the number of principal components $k$ can be
specified by the user after inspecting the scree plot.
\paragraph{Step 3:} The data points are projected on the
$k$-dimensional subspace spanned by the $k$ eigenvectors
corresponding to the largest $k$ eigenvalues of the matrix
$\v{\Sigma}_h$. The location and scatter of the projected data are
computed using the reweighted MCD estimator, and the eigenvectors of
this scatter matrix yield the robust principal components.
\subsubsection{Spherical principal components (SPC)}
The spherical principal components procedure was first proposed by
\cite{locantore:1999} as a method for functional data analysis. The idea
is to perform classical PCA on the data, projected onto a unit
sphere. The estimates of the eigenvectors are consistent if the data
are elliptically distributed \cite[see][]{boente-fraiman:1999} and
the procedure is extremely fast. Although not much is known about
the efficiency of this method, the simulations of
\cite{maronna:2005} show that it has very good performance. If each
coordinate of the data is normalized using some kind of robust
scale, like for example the MAD, and then SPC is applied, we obtain
``elliptical PCA'', but unfortunately this procedure is not
consistent.
\subsubsection{Object model for robust PCA and examples}
\label{oof-sec:pca-objmodel}
The object model for the \proglang{S}4
classes and methods implementing the principal component analysis
methods follows the proposed class hierarchy given in
Section~\ref{oof-sec:objmodel} and is presented in
Figure~\ref{fig:uml-pca}.
\begin{figure}[h!]
\begin{center}
\includegraphics[width=\textwidth]{PcaModel}
\caption{Object model for robust Principal Component Analysis.}
\label{fig:uml-pca}
\end{center}
\end{figure}
The abstract class \code{Pca} serves as a base class for deriving all classes
representing classical and robust principal components analysis methods. It
defines the common slots and the corresponding accessor methods, provides
implementation for the general methods like \code{show()}, \code{plot()},
\code{summary()} and \code{predict()}. The slots of \code{Pca} hold some input or
default parameters like the requested number of components as well as the
results of the computations: the eigenvalues, the loadings
and the scores. The \code{show()} method presents brief results of the
computations, and the \code{predict()} method projects the
original or new data to the space spanned by the principal components.
It can be used either with new observations or with the scores (if no new data are
provided). The \code{summary()} method returns an object of class
\code{SummaryPca} which has its own \code{show()} method. As in the other
sections of the framework these slots and methods are defined and documented
only once in this base class and can be used by all derived classes. Whenever
new information (slots) or functionality (methods) are necessary, they can be defined
or redefined in the particular class.


Classical principal component analysis is represented by the
class \code{PcaClassic} which inherits directly from \code{Pca} (and
uses all slots and methods defined there). The function
\code{PcaClassic()} serves as a constructor (generating function) of
the class. It can be called either by providing a data frame or
matrix or a formula with no response variable, referring only to
numeric variables. Let us consider the following simple example with
the data set \code{hbk} from the package \pkg{robustbase}. The code line
\begin{Scode}
R> PcaClassic(hbk.x)
\end{Scode}
can be rewritten as (and is equivalent to) the following code line using the
formula interface
\begin{Scode}
R> PcaClassic(~ ., data = hbk.x)
\end{Scode}
The function \code{PcaClassic()} performs the standard principal
components analysis and returns an object of the class
\code{PcaClassic}.

<<label=pca-classic, echo=TRUE, fig=FALSE, >>=
##
## Classical PCA
##
pca <- PcaClassic(~., data=hbk.x)
pca
summary(pca)
plot(pca)
getLoadings(pca)
@
The \code{show()} method displays the standard deviations of
the resulting principal components, the loadings and the original call.
The \code{summary()} method presents the importance of
the calculated components.
The \code{plot()} draws a PCA diagnostic plot which is shown and described later.
The accessor functions like \code{getLoadings()}, \code{getEigenvalues()}, etc.
are used to access the corresponding slots, and \code{predict()} is used to rotate
the original or new data to the space of the principle components.


Another abstract class, \code{PcaRobust} is
derived from \code{Pca}, which serves as a base class for all robust
principal components methods.


The classes representing robust PCA methods like
\code{PcaHubert}, \code{PcaLocantore}, etc. are  derived from
\code{PcaRobust} and provide implementation for the corresponding
methods. Each of the constructor functions \code{PcaCov()},
\code{PcaHubert()}, \code{PcaLocantore()}, \code{PcaGrid()} and
\code{PcaProj()} performs the necessary computations and returns an
object of the class containing the results. In the following
example the same data are analyzed using the projection pursuit
method \code{PcaGrid()}.
<<label=pca-robust, echo=TRUE, fig=FALSE, >>=
##
## Robust PCA
##
rpca <- PcaGrid(~., data=hbk.x)
rpca
summary(rpca)
@
Similar to the function \code{PcaClassic()},
these functions can be called either with a data frame or matrix or
by a formula interface.
\subsubsection{Visualization of PCA results}
\label{oof-sec:pca-vis}
One of the most important applications of PCA, besides
dimensionality reduction is data visualization. In the framework
several plots for visualizing the results of the
analysis are available. The \code{plot()} methods are implemented in the base
class \code{Pca} and thus they are available for all objects derived from the class \code{Pca}
no matter if classical and robust. The most straightforward plot is the
\textit{screeplot} which plots the variances against the number of
principal components (similar to the screeplot for the standard
\code{prcomp()} and \code{princomp()} functions). It is a useful tool
for determining the number of relevant principal components. An example
of the classical and robust screeplot for the \code{milk} data from
\pkg{robustbase} is shown in Figure~\ref{oof-fig:pca-screeplot}.

<<label=ex-pca-plot-screeplot, echo=TRUE, fig=TRUE, results=hide, include=FALSE, height=6, width=12, keep.source=TRUE>>=
##
## Screeplot for classical and robust PCA of the milk data set.
##
usr <- par(mfrow=c(1,2))
screeplot(PcaClassic(milk), type="lines",
main="Screeplot: classical PCA", sub="milk data")
screeplot(PcaHubert(milk), type="lines", main="Screeplot: robust PCA",
sub="milk data")
par(usr)
@
\begin{center}
\begin{figure}[h!]
\setkeys{Gin}{width=1.0\textwidth}
\includegraphics{ooframework-ex-pca-plot-screeplot}
\caption{Screeplot for classical and robust PCA of the \code{milk} data set.}
\label{oof-fig:pca-screeplot}
\end{figure}
\end{center}
Another plot borrowed from standard \proglang{R} is the \textit{biplot}.
The biplot \citep{gabriel} represents both the observations and variables in the plane of
(the first) two principal components allowing the visualization of
the magnitude and sign of each variable's contribution to
these principal components. Each observation
(row of scores) is represented as a point in the biplot and each
variable is represented as an arrow. The arrows graphically
indicate the proportion of the original variance explained by
the (first) two principal components and their direction indicates
the relative loadings on these components.
Figure~\ref{oof-fig:pca-biplot} shows an example of the
robust biplot of the \code{un86} data set which contains seven socioeconomic
variables observed for 73 countries. The data set is from
World Statistics in Brief, Number 10, a 1986 UN publication.
It was used in \citet{Daigle:1992} to illustrate a robust biplot method.
<<label=ex-pca-plot-biplot, fig=TRUE, include=FALSE, keep.source=TRUE, height=6, width=12>>=
##
## Robust biplot for the UN86 data
##
data("un86")
set.seed(9)

usr<-par(mfrow=c(1,2))
biplot(PcaCov(un86, corr=TRUE, cov.control=NULL),
main="Classical biplot", col=c("gray55", "red"))
biplot(PcaCov(un86, corr=TRUE), main="Robust biplot",
col=c("gray55", "red"))
par(usr)
@
\begin{center}
\begin{figure}[h!]
\setkeys{Gin}{width=1.0\textwidth}
\includegraphics{ooframework-ex-pca-plot-biplot}
\caption{Classical (left panel) and robust (right panel) biplot for the \code{UN86} data.}
\label{oof-fig:pca-biplot}
\end{figure}
\end{center}
%% diagnostic plot (outlier map)
In the context of PCA \citet{hubert-ROBPCA:2005} defined a \textit{diagnostic
plot} or \textit{outlier map} which helps to distinguish between the regular
observations and the different types of outliers. This plot is based on the
\textit{score distances} and \textit{orthogonal distances} computed for each
observation. The score distances are given by
\begin{equation}
\label{oof-eq:pca-SD} SD_i=\sqrt{\sum_{j=1}^k{\frac{t_{ij}^2}{l_j}}},~~~~
i=1,\ldots,n
\end{equation}
where $t_{ij}$ are the elements of the scores from (\ref{oof-eq:pca-scores}) and
$l_j$ are the eignevalues (the diagonal elements of the matrix
$\v{L}$ in (\ref{oof-eq:pca-S})). The orthogonal distances $OD_i$ of
each observation to the subspace spanned by the first $k$ ($1\le k
\le r$, $r$ is the rank of the data) principal components are
defined by
\begin{equation}
\label{oof-eq:pca-OD} OD_i=||\xv_i - \hat{\muv} - \v{P}^{(k)}\tv_i^{(k)}||,~~~~
i=1,\ldots,n
\end{equation}
where $\xv_i$ denotes the $i$th observation, $\hat{\muv}$ is the
estimated center of the data, $\tv_i^{(k)}$ is the $i$th score
vector in the space of the first $k$ principal components and the
matrix $\v{P}^{(k)}$ contains the first $k$ estimated eigenvectors in its columns.
The diagnostic plot is constructed by plotting the score distances
on the horizontal axis, the orthogonal distances on the vertical
axis and drawing two cutoff lines which will help to classify the
observations. The cutoff value on the horizontal axis (for the score
distances) is taken as the 97.5\% quantile of $\chi_k^2$
distribution, i.e., $c_h=\sqrt{\chi^2_{k,0.975}}$. For the cutoff
value on the vertical axis (for the orthogonal distances)
the Wilson-Hilferty transformation for a $\chi^2$ distribution
is used (which assumes that the $OD_i$ to the power of 2/3 are approximately
normally distributed). The parameters $\mu$ and $\sigma$ of the
normal distribution can be estimated by the median and MAD of the
values $OD_i^{2/3}$, and the critical value can be taken as
$c_v=(\hat{\mu} + \hat{\sigma}z_{0.975})^{3/2}$ where $z_{0.975}$ is
the the 97.5\% quantile of the standard normal distribution.


An example of the classical and robust diagnostic plot for the
\code{hbk} data set from \pkg{robustbase}
is shown in Figure~\ref{oof-fig:pca-diagplot}.

<<label=ex-pca-plot-diagplot, echo=TRUE, fig=TRUE, results=hide, include=FALSE, height=6, width=12>>=
##
## An example of the classical and robust diagnostic
##  plot for the hbk data set
##
usr<-par(mfrow=c(1,2))
plot(PcaClassic(hbk.x, k=2), sub="data set: hbk, k=2")
plot(PcaHubert(hbk.x, k=2), sub="data set: hbk, k=2")
par(usr)
@
\begin{center}
\begin{figure}[h!]
\setkeys{Gin}{width=1.0\textwidth}
\includegraphics{ooframework-ex-pca-plot-diagplot}
\caption{Classical and robust diagnostic plot for the \code{hbk} data with $k=2$.}
\label{oof-fig:pca-diagplot}
\end{figure}
\end{center}
If $k=p$ the orthogonal distances are not meaningful and the diagnostic
plot shows a simple distance plot of the score distances (distances vs index). An
example is shown in Figure~\ref{oof-fig:pca-distplot}.
<<label=ex-pca-plot-distplot, echo=TRUE, fig=TRUE, results=hide, include=FALSE, height=6, width=12>>=
##
## If k=p the orthogonal distances are not meaningful and
##  simple distance plot of the score distances will be shown
##
usr<-par(mfrow=c(1,2))
plot(PcaClassic(hbk.x, k=3), sub="data set: hbk.x, k=3")
plot(PcaHubert(hbk.x, k=3), sub="data set: hbk.x, k=3")
par(usr)
@
\begin{center}
\begin{figure}[h!]
\setkeys{Gin}{width=1.0\textwidth}
\includegraphics{ooframework-ex-pca-plot-distplot}
\caption{Classical and robust diagnostic plot for the x-part of the \code{hbk} data set with $k=3=p$.}
\label{oof-fig:pca-distplot}
\end{figure}
\end{center}
\subsection{Linear and quadratic discriminant analysis}
\label{oof-sec:lda}
The problem of discriminant analysis arises when
one wants to assign an individual to one of $g$ populations at the
basis of a $p$-dimensional feature vector $\xv$. Let the
$p$-dimensional random variable $\xv_k$ come from a population
$\pi_k$ with underlying density $\v{f}_k$. Further let the prior
probability of group $k$, i.e., the probability that an individual
comes from population $\pi_k$ be $\alpha_k$, $\Sigma_{k=1}^g
\alpha_k = 1$. The prior probabilities $\alpha_k$ are usually
estimated by the empirical frequencies $n_k$ in the $k$-th group of the training set, i.e.,
$\hat{\alpha}_k=n_k/\Sigma_{j=1}^gn_j$. Then the Bayesian
discriminant rule assigns an observation $\xv$ to that population
$\pi_k$ for which the expression $\ln(\alpha_k \v{f}_k(\xv))$ is
maximal over all groups $k=1,\ldots,g$. Usually it is assumed that
the $k$ populations $\pi_k$ are $p$-dimensional normally distributed,
\begin{equation}
\label{oof-eq:discrim-distr}
\pi_k \sim N({\muv}_k,\v{\Sigma}_k)~~~~~k=1,\ldots,g.
\end{equation}
With this assumption the discriminant
rule is equivalent to maximizing the discriminant scores
$D_k(\xv)$ given by
\begin{equation}
\label{oof-eq:QDA}
D_k(\xv) = -\frac{1}{2}\ln|\v{\Sigma}_k| -
\frac{1}{2}(\xv-\muv_k)^{\top}\v{\Sigma}_k^{-1}(\xv-\muv_k) +
\ln(\alpha_k)~~~~~(k=1,\ldots,g),
\end{equation}
and individual $\xv$ is assigned to $\pi_k$ if
\begin{equation}
\label{oof-eq:QDA-rule}
D_k(\xv)=\arg\max_j D_j(\xv).
\end{equation}
The application of the discrimination rule given by
Equations~(\ref{oof-eq:QDA}) and (\ref{oof-eq:QDA-rule}) is referred
to as quadratic discriminant analysis (QDA), since the groups are
separated by quadratic boundaries.


If it is further assumed that all group covariance matrices are equal
$(\v{\Sigma}_{1}= \ldots= \v{\Sigma}_g=\v{\Sigma})$, then the overall
probability of misclassification is minimized by assigning a new
observation $\xv$ to population $\pi_k$ which maximizes
\begin{equation}
\label{oof-eq:LDA}
%%%%%%%%d_k(\xv)=\frac{1}{2}(\xv-\muv_k)^{\top}\v{\Sigma}^{-1}(\xv-\muv_k) + \ln(\alpha_k)~~~~~(k=1,\ldots,g).
d_k(\xv)=\xv^{\top}\v{\Sigma}^{-1}\muv_k -
\frac{1}{2}\muv_k^{\top}\v{\Sigma}^{-1}\muv_k +
\ln(\alpha_k)~~~~~(k=1,\ldots,g).
\end{equation}
The application of the discriminant rule given by
Equation~(\ref{oof-eq:LDA}) is referred to as linear discriminant
analysis (LDA), since the scores $d_k(\xv)$ are linear in $\xv$.


If the means $\muv_k, k=1,\ldots,g$, and the common covariance
matrix $\v{\Sigma}$ are unknown, which is usually the case, a
training set consisting of samples drawn from each of the
populations is required. In classical QDA and LDA the sample group
means and sample covariance matrices are used to estimate $\muv_k$,
$\v{\Sigma}_k$ and $\v{\Sigma}$. The prior probabilities can    be
estimated by the relative frequencies of observations in each
particular group. Both QDA and LDA using the classical estimates in
(\ref{oof-eq:QDA}) and (\ref{oof-eq:LDA}) are vulnerable to the
presence of outliers. The problem of the non-robustness of the
classical estimates in the setting of the quadratic and linear
discriminant analysis has been addressed by many authors:
\citet*{todorov:90, todorov:94} replaced the classical estimates by
MCD estimates; \citet*{chork} used MVE instead; \citet*{hawkins:97}
defined the minimum within-group covariance determinant estimator (MWCD)
especially for the case of linear discriminant analysis;
\citet*{he:2000} and \citet*{croux-dehon:01} used S~estimates;
\citet*{hubert:04} applied the MCD estimates computed by the FAST-MCD
algorithm. For a recent review and comparison of these methods
see \citet{todorov-roblda}.


A robust version of quadratic
discriminant analysis can be obtained by substituting the parameters
$\muv_k$, $\v{\Sigma}_k$ by their robust estimates. For this purpose
the reweighted MCD estimates, S~estimates or OGK can be used. In the
case of linear discriminant analysis a robust version of the common
covariance matrix $\v{\Sigma}$ is necessary. There are several
methods for estimating the common covariance matrix based on a high
breakdown point estimator which are considered in one of the next
subsections.
\subsubsection{Object model for robust LDA and QDA}
The object model for the \proglang{S}4 classes and methods implementing the
linear and quadratic discriminant analysis methods follows the proposed class
hierarchy given in Section~\ref{oof-sec:objmodel} and is presented in
Figure~\ref{fig:uml-lda-qda}.


\begin{figure}[h!]
\begin{center}
\includegraphics[width=\textwidth]{DAModel}
\caption{Object models for robust linear discriminant analysis
and quadratic discriminant analysis.} \label{fig:uml-lda-qda}
\end{center}
\end{figure}
The abstract classes \code{Lda} and \code{Qda} serve as base classes
for deriving all classes representing classical and robust methods
for linear and quadratic discriminant analysis methods. They define
the common slots and the corresponding accessor methods, provide
implementation for the general methods like \code{show()},
\code{plot()}, \code{summary()} and \code{predict()}. This base
classes also host several utility functions which are not directly
exported but are documented and can be used by quoting the
namespace. The slots of \code{Lda} hold some input or default
parameters like the prior probabilities, the original data matrix
and the grouping variable as well as the results of the
computations: the group means and the common covariance matrix, the
linear discriminant functions and the corresponding constants. The
\code{show()} method presents brief results of the computations, and
\code{predict()} can be used either for classifying new observations
or for the evaluation of the discriminant rules on the basis of the
training sample. The method \code{predict()} returns an object of
class \code{PredictLda} which has its own \code{show()} method to
print the results of the classification or evaluation. The
\code{summary()} method returns an object of class \code{SummaryLda}
which has its own \code{show()} method. As in the other sections of
the framework these slots and methods are defined and documented
only once in this base class and can be used by all derived classes.
Whenever new data (slots) or functionality (methods) are necessary,
they can be defined or redefined in the
particular class.


Classical linear discriminant analysis is represented by the
class \code{LdaClassic} which inherits directly from \code{Lda} (and
uses all slots and methods defined there). The function
\code{LdaClassic()} serves as a constructor (generating function) of
the class. It can  be called either by providing a data frame or
matrix and a grouping variable (factor) or a formula specifying the
model to be used. Let us consider the following simple example with
the data set \code{diabetes}: the grouping
variable is \code{group} and the
explanatory variables are \code{insulin}, \code{glucose} and \code{sspg}. The code
\begin{Scode}
R> x <- diabetes[, c("insulin", "glucose", "sspg")]
R> grpvar <- diabetes$group
R> LdaClassic(x, grpvar)
\end{Scode}
can be rewritten as (and is equivalent to) the following code using
the formula interface:
\begin{Scode}
R> LdaClassic(group~insulin+glucose+sspg, data = diabetes)
\end{Scode}

The function \code{LdaClassic()} performs standard linear
discriminant analysis and returns an object of class
\code{LdaClassic}. Another abstract class, \code{LdaRobust} is
derived from \code{Lda}, which serves as a base class for all robust
linear discriminant analysis methods. The only slot added in this
class is
a character variable specifying the robust method to be used.


The class \code{Linda} is derived from \code{LdaRobust} and provides
implementation for all methods for robust LDA currently available
in the framework. If we wanted to be precisely object oriented, we
should define a separate class for each robust method---for example
\code{LdaRobustMcd}, \code{LdaRobustFsa}, etc. but this would lead
to explosion of the necessary code and documentation. The
constructor function \code{Linda()} takes a character parameter
\code{method} specifying which robust location and scatter
estimator to use and how to compute the common covariance matrix
and returns an object of class \code{Linda}. Similarly as the function \code{LdaClassic()},
\code{Linda()} can be called either with a data matrix and grouping
variable or by a formula interface.
\subsubsection{Computing the common covariance matrix}
\label{oof-sec:common-cov} The easiest way to estimate the common
covariance matrix $\v{\Sigma}$ is to obtain the estimates of the
group means $\muv_k$ and group covariance matrices $\v{\Sigma}_k$
from the individual groups as $(\mv_k,\v{C}_k), k=1,\ldots,g$,
and then pool the estimates $\v{C}_k,
k=1,\ldots,g$ to yield the common covariance matrix
\begin{equation}
\v{C} = {\sum_{k=1}^g{n_k\v{C}_k} \over \sum_{k=1}^g{n_k-g}}.
\end{equation}
This method, using MVE and MCD estimates, was proposed by
\citet{todorov:90, todorov:94} and was also used, based on the MVE
estimator by \citet*{chork}. \newline \citet*{croux-dehon:01} applied this
procedure for robustifying linear discriminant analysis based on S~estimates.
A drawback of this method is that the same trimming
proportions are applied to all groups which could lead to a loss of
efficiency if some groups are outlier free. We will denote this
method as ``$A$'' and the corresponding estimator as XXX-A. For example,
in the case of the MCD estimator this will be MCD-A.


Another method was proposed by \citet*{he:2000} for the S~estimates
and was later adapted by \citet*{hubert:04} for the MCD estimates.
Instead of pooling the group covariance matrices, the observations
are centered and pooled to obtain a single sample for which the
covariance matrix is estimated. It starts by obtaining the
individual group location estimates $\tv_k, k=1,\ldots,g$, as the
reweighted MCD location estimates of each group. These group means
are swept from the original observations $\xv_{ik}~(i=1,\ldots,n_k;~k=1,\ldots,g)$
to obtain the centered observations
\begin{eqnarray}
\v{Z} = \{\zv_{ik}\}, ~~~~~\zv_{ik} = \xv_{ik} - \tv_k.
\end{eqnarray}
The common covariance matrix $\v{C}$ is estimated as the reweighted
MCD covariance matrix of the centered observations $\v{Z}$. The
location estimate $\deltav$ of $\v{Z}$ is used to adjust the group
means $\mv_k$ and thus the final group means are
\begin{equation}
\mv_k = {\tv_k + \deltav}.
\end{equation}
This process could be iterated until convergence, but since the
improvements from such iterations are negligible \citep[see][]{
he:2000, hubert:04} we are not going to use it. This method will be
denoted by ``$B$'' and as already mentioned, the corresponding estimator
as XXX-B, for example MCD-B.


The third approach is to modify the algorithm for high breakdown
point estimation itself in order to accommodate the pooled sample.
\citet*{he:2000} modified Ruperts's SURREAL algorithm for S~estimation in case of two groups. \citet*{hawkins:97} defined the
minimum within-group covariance determinant estimator which
does not apply the same trimming proportion to each group but
minimizes directly the determinant of the common within groups
covariance matrix by pairwise swaps of observations. Unfortunately
their estimator is based on the Feasible Solution Algorithm
\citep[see][and the references therein]{hawkins:97}, which is
extremely time consuming as compared to the FAST-MCD algorithm.
\citet*{hubert:04} proposed a modification of this algorithm taking
advantage of the FAST-MCD, but it is still necessary to compute the
MCD for each individual group. This method will be denoted by
MCD-C.


Using the estimates $\mv^0_k$ and $\v{C}_0$ obtained by one of the
methods, we can calculate the initial robust distances
\citep{Rousseeuw-van-Zomeren}
\begin{equation}
RD^0_{ik}=
\sqrt{(\xv_{ik}-\mv^0_k)^{\top}\v{C}_0^{-1}(\xv_{ik}-\mv^0_k)}.
\end{equation}
With these initial robust distances we can define a weight for each
observation $\xv_{ik}, ~ i=1, \ldots , n_k$ and $k=1, \ldots, g$,
by setting the weight to $1$ if the corresponding robust distance is
less or equal to a suitable cut-off, usually
$\sqrt{\chi^2_{p,0.975}}$, and to 0 otherwise, i.e.,
\begin{equation}
\label{oof-eq:mdiv} w_{ik} =
\begin{cases}
1&RD^0_{ik} \leq \sqrt{\chi^2_{p,0.975}} \\
0&\text{otherwise}.\\
\end{cases}
\end{equation}
With these weights we can calculate the final reweighted estimates
of the group means, $\mv_k$, and the common within-groups
covariance matrix, $\v{C}$, which are necessary for constructing the
robust classification rules,
\begin{eqnarray}
\mv_k &=& (\sum^{n_k}_{i=1}{w_{ik}\xv_{ik}})/\nu_k, \nonumber\\
\v{C} &=&
\frac{1}{\nu-g}\sum^g_{k=1}\sum^{n_k}_{i=1}{w_{ik}(\xv_{ik}-\mv_k)(\xv_{ik}-\mv_k)^{\top}},
\end{eqnarray}
where $\nu_k$ are the sums of the weights within group $k$, for
$k=1,\ldots,g$, and $\nu$ is the total sum of weights,
\begin{equation}
\nu_k =\sum^{n_k}_{i=1}{w_{ik}}, ~~~~\nu = \sum^{g}_{k=1}{\nu_k}.
\nonumber
\end{equation}

\subsubsection{Evaluation of the discriminant rules}
In order to evaluate and compare different discriminant rules, their
discriminating power has to be determined in the classification of
future observations, i.e., we need an estimate of the overall
probability of misclassification. A number of methods to estimate
this probability exists in the literature---see for example
\citet{lachenbruch:1975}. The \textit{apparent error rate} (known
also as resubstitution error rate or reclassification error rate) is
the most straightforward estimator of the actual error rate
in discriminant analysis and is calculated by applying the
classification criterion to the same data set from which it was
derived. The number of misclassified observations for each group is
divided by the group sample size. An estimate of the apparent error
rate is calculated by the method \code{predict()} of the class
\code{Lda}. Examples are given in the next section.


It is well known that this method is too optimistic (the true error
is likely to be higher). If there are plenty of observations in each
class, the error rate can be estimated by splitting the data into
training and validation set. The first one is used to estimate the
discriminant rules and the second to estimate the misclassification
error. This method is fast and easy to apply but it is wasteful of
data. Another method is the
\textit{leave-one-out} \textit{cross-validation}
\citep{lachenbruch-michey:68} which proceeds by removing one
observation from the data set, estimating the discriminant rule,
using the remaining $n-1$ observations and then classifying this
observation with the estimated discriminant rule. For the classical
discriminant analysis there exist updating formulas which avoid the
re-computation of the discriminant rule at each step, but no such
formulas are available for the robust methods. Thus the estimation
of the error rate by this method can be very time consuming
depending on the size of the data set. Nevertheless, \pkg{rrcov}
provides an (internal, not exported) function \code{rrcov:::.CV()}
which calculates the leave-one-out cross-validation error rate by ``brute force'',
but the user should be aware that its usage is appropriate only for
moderate data sets. An improvement will be the implementation of a
cross-validation technique similar to the one proposed by
\citet{hubert:2007-CV}.

\subsubsection{Example: Diabetes data}
\label{oof:sec-diabetes} As an example for demonstrating the usage
of the robust discriminant analysis classes and methods we use the
\code{diabetes} data set, which was analyzed by \citet*{reaven-miller} in an
attempt to examine the relationship between chemical diabetes and
overt diabetes in 145 nonobese adult subjects. Their analysis was
focused on three primary variables and the 145 individuals were
classified initially on the basis of their plasma glucose levels
into three groups: normal subjects, chemical diabetes and overt
diabetes. This data set was also analyzed by \citet*{hawkins:97} in
the context of robust linear discriminant analysis.

We start with bringing the data set \code{diabetes} into the workspace by typing
<<lda-prelim>>=
data("diabetes")
@
Using the package \pkg{lattice} \citep{Sarkar:2008} we produce a three dimensional
cloud plot of the data (Figure~\ref{lda-cloud}).
<< lda-cloud, fig=FALSE>>=
library("lattice")    # load the graphical library

## set different plot symbols - important for black-and-white print
sup.sym <- trellis.par.get("superpose.symbol")
sup.sym$pch <- c(1,2,3,4,5)
trellis.par.set("superpose.symbol", sup.sym)
cloud.plt <- cloud(insulin ~ glucose + sspg, 
    groups = group, data = diabetes, auto.key=TRUE)
@
\begin{center}
\begin{figure}[h!]
<< lda-cloud-fig, fig=TRUE>>=
print(cloud.plt)
@
\caption{Three dimensional scatter plot of the \code{diabetes} data.}
\label{lda-cloud}
\end{figure}
\end{center}
We will first apply the classical linear discriminant analysis as implemented in \code{LdaClassic()}
by the formula interface of the function---the grouping variable is \code{class}
and all the remaining variables in \code{diabetes} are used as predictor variables.
The \code{show()} method will present the results of the computations:
the group means, the (common) within group covariance matrix,
the linear discriminant functions together with the corresponding constants.
The prior probabilities (either provided by the user or estimated as
a proportion of the groups) are also presented.
<< lda-classic>>=
lda <- LdaClassic(group~insulin+glucose+sspg, data=diabetes)
lda
@
Now the \code{predict()} method can be used on the \code{Lda} object
(\code{Lda} is the base class for both \code{LdaClassic} and \code{LdaRobust}) in order to classify
new observations. The method returns an object of class \code{PredictLda} which has its own \code{show()} method.
If no new data are supplied, the training sample will be reclassified and a classification table will be produced
to estimate the apparent error rate of the classification rules.
<< lda-classic-predict>>=
predict(lda)
@
Robust linear discriminant analysis can be performed in a similar way but using
the function \code{Linda} (which will create an object of class \code{Linda}). As before
the \code{predict()} method called without new data returns a classification
table of the training subsample. Using
the internal convenience function \code{rrcov:::.AER()}
we can calculate and print the apparent error rate
(which now is equal to 0.1103 and is lower than the obtained with the classical LDA 0.1310).
<< lda-robust>>=
rlda <- Linda(group~insulin+glucose+sspg, data=diabetes)
rlda

rlda.predict <- predict(rlda)
cat("\nApparent error rate: ", round(rrcov:::.AER(rlda.predict@ct),4))
@
In the above example we did not specify which method for computing the
common covariance matrix should be used (thus using the default
method ``MCD-B'' described above).
We could choose the method by providing the \code{method}
parameter to the function \code{Linda()}. For example the following call
\begin{Scode}
R> rlda <- Linda(group~insulin+glucose+sspg, data = diabetes, method = "fsa")
\end{Scode}
will use the \citet*{hawkins:97} \textit{feasible solution algorithm} method.


The variance-covariance structures of the three classes in the \code{diabetes}
data set differ substantially and we can expect improved results if quadratic
discriminant analysis is used. Robust quadratic discriminant analysis is
performed by the function \code{QdaCov()} which will return an object of class \code{QdaCov}.
<< qda-robust>>=
rqda <- QdaCov(group~insulin+glucose+sspg, data=diabetes)
rqda
rqda.predict <- predict(rqda)
cat("\nApparent error rate: ", round(rrcov:::.AER(rqda.predict@ct),4))
@
The accuracy of the prediction improves compared to the linear discriminant analysis.
\section{Conclusions}
\label{oof-sec:conclusions}
In this paper we presented an object oriented framework for
robust multivariate analysis developed in the \proglang{S}4 class
system of the programming environment \proglang{R}. The main
goal of the framework is to support the usage, experimentation,
development and testing of robust multivariate methods as well as
simplifying comparisons with related methods.
It minimizes the effort for performing any of the following tasks:
\bi
\item{application of the already existing robust multivariate methods for practical data analysis;}
\item{implementation of new robust multivariate methods or variants of the existing ones;}
\item{evaluation of existing and new methods by carrying out comparison studies.}
\ei
A major design goal was the openness to extensions by the development
of new robust methods in the package \pkg{rrcov} or in other
packages depending on \pkg{rrcov}.
Further classes implementing robust multivariate methods like
principal component regression and partial least squares will
follow but the user is encouraged to develop own methods using
the proposed reusable statistical design patterns.
\section*{Acknowledgements}
We wish to express our thanks to the organizers of and participants in the
``Robust Statistics and \proglang{R}'' workshops for the valuable comments and suggestions
which were a major input for the development of this framework.
We are also grateful to many people, notably Matias Salibian-Barrera, Victor Yohai,
Kjell Konis, and Christophe Croux  for the provided code. The careful review and
constructive comments of the editor and the anonymous reviewers helped us to
substantially improve the manuscript.


The views expressed herein are those of the authors and do not necessarily reflect the views of the United Nations Industrial Development Organization (UNIDO).

\bibliography{mybiblio}
\end{document}
