
\input{HSAUR_title}

\SweaveOpts{prefix.string=figures/HSAUR,eps=FALSE,keep.source=TRUE}

<<setup, echo = FALSE, results = hide>>=
source("setup.R")
@

\frame{
\begin{center}
\Large{Part 1: An Introduction to R}
\end{center}

teaches some \R{} philosophy, explains how to install \R{} 
and how to make the first steps in \R{}.

}


\section{What Is R?} %%\R{}?}

\frame{
    \frametitle{What Is R?}

The \R{} system for statistical computing is an environment for
data analysis and graphics.

The root of \R{} is the \S{} language, developed by John
Chambers and colleagues
at Bell Laboratories starting in the 1960s. 

The \S{} language was designed
and developed as a programming language for data analysis tasks but in fact
it is a full-featured programming language in its current implementations.

The development of the \R{} system for statistical computing is heavily
influenced by the open source idea: The base distribution of \R{}
\index{Base distribution}
and a large number of
user contributed extensions are available under the
terms of the Free Software Foundation's GNU General %%'
Public License in source code form.
\index{GNU General Public License}

}

\frame{

The base distribution of \R{} is maintained by a small group of statisticians,
the \R{} Development Core Team. 

A huge amount of additional functionality is implemented in add-on packages
\index{Add-on packages}
authored and maintained by a large group of
volunteers. 

The main source of information about the \R{} system is the world
wide web with the official home page of the \R{} project being
\curl{http://www.R-project.org} 

}
\section{Installing R} %%\R{}}

\index{Base system|(}

\frame{
    \frametitle{Installing the Base System}

The \R{} system for statistical computing consists of two major parts: the
base system and a collection of user contributed add-on packages. 

A package is a collection of functions, examples and documentation. 

Both the base system and packages are distributed via the Comprehensive \R{} Archive
Network (CRAN) accessible under \curl{http://CRAN.R-project.org} 
as precompiled binary distribution and in source form.

}

\subsection{The Base System and the First Steps \label{AItR:Base}}

\frame{
    \frametitle{First Steps in R}

\begin{columns}
  \begin{column}{3cm}
    \includegraphics[width = 2.5cm]{graphics/Rlogo}
  \end{column}
  \begin{column}{7cm}
Depending on the operating system, \R{} can be started either by typing
`\texttt{R}' on the shell (Unix systems) or by clicking on the %'
\R{} symbol (as shown left) created by the installer (Windows).
\end{column}
\end{columns}

}

\begin{frame}[fragile]
    \frametitle{R as Pocket Calculator}

<<AItR-firstex, echo = TRUE>>=
x <- sqrt(25) + 2
@

The assignment operator
\Roperator{<-} binds the value of its right hand side to a variable name on the
left hand side. The value of the object \Robject{x} can be inspected
simply by typing
<<AItR-firstex-print, echo = TRUE>>=
x
@
which, implicitly, calls the \Rcmd{print} method:
<<AItR-firstex-print, echo = TRUE>>=
print(x)
@

\end{frame}

\subsection{Packages}

\begin{frame}[fragile]
  \frametitle{Important Packages}

The base distribution already comes with some high-priority add-on packages, namely
\begin{center}
\texttt{
<<AItR-recommended, echo = FALSE, results=hide>>=
colwidth <- 4
ip <- installed.packages(priority = "high")
pkgs <- unique(ip[,"Package"])
pkgs <- paste("\\Rpackage{", pkgs, "}", sep = "")
nrows <- ceiling(length(pkgs) / colwidth)
cat(paste(c("\\begin{tabular}{", paste(rep("l", colwidth), collapse=""), "}"), collapse = ""),
    "\n", file = "tables/rec.tex", append = FALSE)
for (i in 1:nrows) {
    cat(paste(pkgs[(1:colwidth) + (i-1)*colwidth], collapse = " & "),
        file = "tables/rec.tex", append = TRUE)
    cat("\\\\ \n", file = "tables/rec.tex", append = TRUE)
}
cat("\\end{tabular}\n", file = "tables/rec.tex", append = TRUE)
rm(ip, nrows)
@
\input{tables/rec}
}
\end{center}
The packages listed here
%% #Z
%% are maintained by members of the \R{} core development team and
implement standard statistical functionality, for example linear models,
classical tests, a huge collection of high-level plotting functions or tools
for survival analysis.

\end{frame}

<<AItR-CRAN, echo = FALSE, results = hide>>=
cp <- available.packages(contriburl = "http://CRAN.r-project.org/src/contrib")
ncp <- sum(!rownames(cp) %in% pkgs)
rm(cp, pkgs)
@

\begin{frame}[fragile]
  \frametitle{User-Contributed Packages}

Packages not included in the base distribution can be installed directly
from the \R{} prompt. Currently, 
$\Sexpr{ncp}$ user contributed packages
covering almost all fields of statistical methodology are available.

<<AItR-rm, echo = FALSE, results = hide>>=
rm(ncp, colwidth, i)
@

A package is installed
by supplying the name of the package to the function \Rcmd{install.packages}.
For example the \Rpackage{sandwich} package can be downloaded and installed via
<<AItR-install-packages, echo = TRUE, eval = FALSE>>=
install.packages("sandwich")
@
The package functionality is available after \stress{attaching} the package
by
<<AItR-library, echo = TRUE, eval = FALSE>>=
library("sandwich")
@
A comprehensive list of available packages can be obtained from
\curl{http://CRAN.R-project.org/}

\end{frame}


\section{Help and Documentation \label{AItR:HDN}}
\index{Help system|(}

\begin{frame}[fragile]
  \frametitle{Help and Documentation}

Three different forms of documentation for the \R{} system for
statistical computing may be distinguished: 
\begin{itemize}
\item online help that comes with the
      base distribution or packages,
\item electronic manuals and 
\item publications work in the form of books etc.
\end{itemize}

The help system is a collection of manual pages describing each
user-visible function and data set that comes with \R{}.

\end{frame}

\begin{frame}[fragile]
  \frametitle{Getting Help in R}

A manual page is shown in a pager or web browser when the name
of the function we would like to get help for is supplied to the \Rcmd{help}
function
<<AItR-help, echo = TRUE, eval = FALSE>>=
help("mean")
@
or, for short,
\begin{Verbatim}
R> ?mean
\end{Verbatim}

The function \Rcmd{help.search} is helpful for searching within
manual pages. An overview on documented topics in an add-on package is given,
for example for the \Rpackage{sandwich} package, by
<<AItR-help-lib, echo = TRUE, eval = FALSE>>=
help(package = "sandwich")
@

\end{frame}

\begin{frame}[fragile]
  \frametitle{Package Vignettes}

Often a package comes along with an additional document describing the
package functionality and giving examples. Such a document is called a
\Rclass{vignette} and is viewed in a PDF viewer via
<<AItR-help-lib, echo = TRUE, eval = FALSE>>=
vignette("sandwich", package = "sandwich")
@
All R code contained in a vignette is available from
<<AItR-help-lib, echo = TRUE, eval = FALSE>>=
edit(vignette("sandwich"))
@

\end{frame}

\begin{frame}
  \frametitle{Written Documentation}

For the beginner, at least the first and the second document
of the following four manuals are mandatory:
\begin{description}
\item[An Introduction to R:] A more formal introduction to data analysis
                             with \R{} than this chapter.
\item[R Data Import/Export:] A very useful description of how to read and
                             write various external data formats.
\item[R Installation and Administration:] Hints for installing \R{} on
                                          special platforms.
\item[Writing R Extensions:] The authoritative source on how to write \R{}
                             programs and packages.
\end{description}

\end{frame}

\begin{frame}
  \frametitle{More Documentation on R}

Both printed and online publications are available, the most important ones
are \booktitle{Modern Applied Statistics with \S{}}
\booktitle{Introductory Statistics with \R{}},
\booktitle{\R{} Graphics}
and the \R{} Newsletter, freely available from
\curl{http://CRAN.R-project.org/doc/Rnews/}

In case the electronically available documentation and the answers to
frequently asked questions (FAQ), available from
\curl{http://CRAN.R-project.org/faqs.html}
have been consulted but a problem or question remains unsolved, the
\texttt{r-help} email list is the right place to get answers to well-thought-out
questions. Read the posting guide before starting to ask!

\end{frame}

\section{Data Objects in R} %%\R{}}

\begin{frame}[fragile]
  \frametitle{Data Objects: Forbes 2000 List}

\index{Forbes 2000 ranking|(}
The data handling and manipulation techniques will
be illustrated by means of a data set of $2000$ world leading companies, the
Forbes 2000 list for the year 2004 collected by \booktitle{Forbes Magazine}.

In a first step, we make the data available for computations within
\R. The \Rcmd{data} function searches for data objects of the specified
name (\Robject{"Forbes2000")}
in the package specified via the \Rarg{package} argument and
attaches the data object to the global environment:
\index{Forbes2000 data@\Robject{Forbes2000} data}
<<AItR-Forbes2000, echo = TRUE>>=
data("Forbes2000", package = "HSAUR2")
ls()
@

\end{frame}

\begin{frame}[fragile]
  \frametitle{Data Objects: Printing}

<<AItR-Forbes2000-print, echo = TRUE, eval = FALSE>>=
print(Forbes2000)
@
<<AItR-Forbes2000-print, echo = FALSE, eval = TRUE>>=
print(Forbes2000[1:3,])
cat("...\n")
@
will not be particularly helpful.

\end{frame}

\begin{frame}[fragile]
  \frametitle{Inspecting Data Objects}

Better look at a description of their structure:
<<AItR-Forbes2000-str, echo = TRUE, eval = FALSE>>=
str(Forbes2000)
@
<<AItR-Forbes2000-str, echo = FALSE, eval = TRUE>>=
str(Forbes2000, vec.len = 2)
@

\end{frame}

\begin{frame}[fragile]
  \frametitle{Data Objects: Forbes 2000}

For each observation, the following eight variables are available:
\begin{description}
\item[\Robject{rank}]: the ranking of the company,
\item[\Robject{name}]: the name of the company,
\item[\Robject{country}]: where the company is situated,
\item[\Robject{category}]: products the company produces,
\item[\Robject{sales}]: the amount of sales of the company,
                        US dollars,
\item[\Robject{profits}]: the profit of the company,
\item[\Robject{assets}]: the assets of the company,
\item[\Robject{marketvalue}]: the market value of the company.
\end{description}

\end{frame}

\begin{frame}[fragile]
  \frametitle{Data Objects: Forbes 2000}


A similar but more detailed description is available from the help page for the
\Robject{Forbes2000} object:
<<AItR-Forbes2000-help, echo = TRUE, eval = FALSE>>=
help("Forbes2000")
@
or
\begin{Verbatim}
R> ?Forbes2000
\end{Verbatim}
All information provided by \Rcmd{str} can be obtained by specialised
functions as well and we will now have a closer look at the most important
of these.

\end{frame}

\begin{frame}[fragile]
  \frametitle{Everything is an Object!}

The \R{} language is an object-oriented programming language,
\index{Object-oriented programming language}
so every object
is an instance of a class:
<<AItR-Forbes2000-df, echo = TRUE>>=
class(Forbes2000)
@

The dimensions of a \Rclass{data.frame} can be
extracted using the \Rcmd{dim} function
<<AItR-Forbes2000-dim, echo = TRUE>>=
dim(Forbes2000)
@
or via
<<AItR-Forbes2000-nrow-ncol, echo = TRUE>>=
nrow(Forbes2000)
ncol(Forbes2000)
@

\end{frame}

\begin{frame}[fragile]
  \frametitle{Data Frames: Assessing Variables}

The variable names are accessible from
<<AItR-Forbes2000-names, echo = TRUE>>=
names(Forbes2000)
@
The values of single variables can be extracted from the
\Robject{Forbes2000} object by their names
<<AItR-Forbes2000-rank, echo = TRUE>>=
class(Forbes2000[,"rank"])
@
Brackets \Robject{[]} always indicate a subset
\index{Subset} of a larger object. 

\end{frame}

\begin{frame}[fragile]
  \frametitle{Vectors}

The rankings for all $\Sexpr{nrow(Forbes2000)}$ companies are represented in a \Rclass{vector}
structure the length of which is given by
<<AItR-Forbes2000-length, echo = TRUE>>=
length(Forbes2000[,"rank"])
@
A \Rclass{vector} is the elementary structure for data handling in \R{} and is
a set of simple elements, all being objects of the same class. 
<<AItR-Forbes2000-one-to-three, echo = TRUE>>=
1:3
c(1,2,3)
seq(from = 1, to = 3, by = 1)
@

\end{frame}

\begin{frame}[fragile]
  \frametitle{Nominal Variables: Factors}

Nominal measurements are represented by \Rclass{factor} variables in \R,
such as the category of the company's business segment %%'
<<AItR-Forbes2000-category, echo = TRUE>>=
class(Forbes2000[,"category"])
@
Objects of class \Rclass{factor} and \Rclass{character} basically differ in
the way their values are stored internally.
In our case, there are
<<AItR-Forbes2000-nlevels, echo = TRUE>>=
nlevels(Forbes2000[,"category"])
@
different categories:
<<AItR-Forbes2000-levels, echo = TRUE, eval = FALSE>>=
levels(Forbes2000[,"category"])
@
<<AItR-Forbes2000-levels, echo = FALSE>>=
levels(Forbes2000[,"category"])[1:3]
cat("...\n")
@

\end{frame}

\begin{frame}[fragile]
  \frametitle{Summarizing Factors}

As a simple summary statistic,
the frequencies of the levels of such a \Rclass{factor} variable can be
found from
<<AItR-Forbes2000-table, echo = TRUE, eval = FALSE>>=
table(Forbes2000[,"category"])
@
<<AItR-Forbes2000-table, echo = FALSE>>=
table(Forbes2000[,"category"])[1:3]
cat("...\n")
@

\end{frame}

\begin{frame}[fragile]
  \frametitle{Numeric Variables}

The sales, assets, profits and market value variables are of type
\Robject{numeric}
<<AItR-Forbes2000-sales, echo = TRUE>>=
class(Forbes2000[,"sales"])
@
and simple summary statistics such as the mean, median and range can be
found from
<<AItR-Forbes2000-numsum, echo = TRUE>>=
median(Forbes2000[,"sales"])
mean(Forbes2000[,"sales"])
range(Forbes2000[,"sales"])
@

\end{frame}

\begin{frame}[fragile]
  \frametitle{Summary Statistics}

The \Rcmd{summary} method can be applied to
a numeric vector to give a set of useful summary statistics namely
the minimum, maximum, mean, median and the $25\%$ and $75\%$ quartiles;
for example
<<AItR-Forbes2000-summary, echo = TRUE>>=
summary(Forbes2000[,"sales"])
@

\end{frame}

\section{Data Import and Export}
\index{Data import and export|(}

\begin{frame}[fragile]
  \frametitle{Data Import}

The most frequent data formats the data analyst is confronted with are 
\begin{itemize}
\item comma separated files,
\item \EXCEL{} spreadsheets,
\item files in \SPSS{} format and
\item a variety of \SQL{} data base engines.
\end{itemize}
Querying data bases is a non-trivial task and requires additional knowledge
about querying languages and we therefore refer to the \booktitle{\R{} Data
Import/Export} manual.

\end{frame}

<<AItR-Forbes2000-files, echo = FALSE>>=
pkgpath <- system.file(package = "HSAUR2")
mywd <- getwd()
filep <- file.path(pkgpath, "rawdata")
setwd(filep)
@

\begin{frame}[fragile]
  \frametitle{Comma-separated Files}

When the variables are separated by commas and each row begins with a name
(a text format typically created by \EXCEL{}), we can read in the data as
follows using the \Rcmd{read.table} function
<<AItR-Forbes2000-read.table, echo = TRUE>>=
csvForbes2000 <- read.table("Forbes2000.csv",
    header = TRUE, sep = ",", row.names = 1)
@
The function \Rcmd{read.table} by default guesses the class of each variable from the
specified file. 

Files in \SPSS{} format are read in a way similar to reading comma separated files, using the
function \Rcmd{read.spss} from package \Rpackage{foreign}.

\end{frame}

\begin{frame}[fragile]
  \frametitle{Data Export}

A comma separated file
readable by \EXCEL{} can be constructed from a \Rclass{data.frame} object via
<<AItR-Forbes2000-write.table, echo = TRUE>>=
write.table(Forbes2000, file = "Forbes2000.csv", 
    sep = ",", col.names = NA)
@
The function \Rcmd{write.csv} is one alternative.

Alternatively, when data should be saved for later processing in \R{} only,
\R{} objects of arbitrary kind can be stored into an external binary file via
<<AItR-Forbes2000-save, echo = TRUE>>=
save(Forbes2000, file = "Forbes2000.rda")
@
<<AItR-Forbes2000-RODBC, echo = FALSE>>= 
setwd(mywd)
@

\end{frame}


\section{Basic Data Manipulation \label{AItR:BDM}}

\begin{frame}[fragile]
  \frametitle{More on Data Frames}

\index{Data manipulation|(}

Internally, a \Rclass{data.frame} is a \Rclass{list} of vectors
of a common length $n$, the number of rows of the table. Each of those vectors
represents the measurements of one variable and we can access such a variable by its name
<<AItR-Forbes2000-vector-companies, echo = TRUE>>=
companies <- Forbes2000[,"name"]
@
A subset of the elements of the
vector \Robject{companies} can be extracted using the \Rcmd{[]} subset
operator:
<<AItR-Forbes2000-vector-indexing, echo = TRUE>>=
companies[1:3]
@
\end{frame}

\begin{frame}[fragile]
  \frametitle{Subset Indexing}

In contrast to indexing with positive integers, negative indexing returns
all elements which are \stress{not} part of the index vector given in brackets. For
example, all companies except those with numbers four to two-thousand, i.e.,
the top three companies, are again
<<AItR-Forbes2000-vector-negative-indexing, echo = TRUE>>=
companies[-(4:2000)]
@

\end{frame}

\begin{frame}[fragile]
  \frametitle{Data Frame Indexing}

Because \Rclass{data.frame}s have a concept of rows and
columns, we need to separate the subsets corresponding to rows and columns
by a comma. The statement
<<AItR-Forbes2000-top-three, echo = TRUE>>=
Forbes2000[1:3, c("name", "sales", "profits", 
    "assets")]
@
extracts four variables for the three largest companies. A
 single variable can be extracted from a \Rclass{data.frame} by
<<AItR-Forbes2000-list-extract, echo = TRUE>>=
companies <- Forbes2000$name
@

\end{frame}

\begin{frame}[fragile]
  \frametitle{Data Frame Ordering}

The three top selling companies are to be computed.
First, we need to compute the ordering of the companies' sales %%'
<<AItR-Forbes2000-sales, echo = TRUE>>=
order_sales <- order(Forbes2000$sales)
@
The three companies with the lowest sales are
<<AItR-Forbes2000-sales-small, echo = TRUE>>=
companies[order_sales[1:3]]
@
and the three top sellers are 
<<AItR-Forbes2000-order, echo = TRUE>>=
Forbes2000[order_sales[c(2000, 1999, 1998)], "name"]
@

\end{frame}

\begin{frame}[fragile]
  \frametitle{Data Frame Subsetting}

Another way of selecting vector elements is the use of a logical vector
being \Robject{TRUE} when the corresponding element is to be selected and
\Robject{FALSE} otherwise. 

The companies with assets of more than $1000$ billion US dollars are
<<AItR-Forbes2000-logical, echo = TRUE>>=
Forbes2000[Forbes2000$assets > 1000,
    c("name", "sales", "profits")]
table(Forbes2000$assets > 1000)
@

\end{frame}

\begin{frame}[fragile]
  \frametitle{Missing Values}

In \R, missing values are treated by a special symbol, \Robject{NA}, indicating
\index{NA symbol@\Robject{NA} symbol}
that this measurement is not available.
\index{Missing values}
The observations with profit information missing can be obtained
via
<<AItR-Forbes2000-NA, echo = TRUE>>=
na_profits <- is.na(Forbes2000$profits)
table(na_profits)
Forbes2000[na_profits, c("name", "profits")]
@

\end{frame}

\begin{frame}[fragile]
  \frametitle{Removing Missing Values}

We want to remove all observations with at least one missing value from a
\Rclass{data.frame} object. The function \Rcmd{complete.cases} takes a
\Rclass{data.frame} and returns a logical vector being \Robject{TRUE} when
the corresponding observation does not contain any missing value:
<<AItR-Forbes2000-complete-cases, echo = TRUE>>=
table(complete.cases(Forbes2000))
@

\end{frame}

\begin{frame}[fragile]
  \frametitle{Using subset}

Subsetting \Rclass{data.frame}s driven by logical expressions may induce a
lot of typing which can be avoided. The \Rcmd{subset} function takes a
\Rclass{data.frame} as first argument and a logical expression as second
argument:
<<AItR-Forbes2000-UK, echo = TRUE>>=
UKcomp <- subset(Forbes2000, 
    country == "United Kingdom")
dim(UKcomp)
@

\end{frame}

\section{Simple Summary Statistics}

\begin{frame}[fragile]
  \frametitle{str and summary}

Applying the \Rcmd{summary} method to the \Robject{Forbes2000}
<<AItR-Forbes2000-summary-output, echo = TRUE, eval = FALSE>>=
summary(Forbes2000)
@
<<AItR-Forbes2000-summary-output, echo = FALSE>>=
summary(Forbes2000[,1:3])
@

\end{frame}

\begin{frame}[fragile]
  \frametitle{apply and Friends}

The members of the \Rcmd{apply} family help to solve recurring tasks for each
element of a \Rclass{data.frame}, \Rclass{matrix}, \Rclass{list} or for each
level of a factor. 

We compare the profits in each of the 
$\Sexpr{nlevels(Forbes2000$category)}$ categories and first
compute the median profit for each category from
<<AItR-Forbes2000-tapply-category, echo = TRUE>>=
mprofits <- tapply(Forbes2000$profits, 
    Forbes2000$category, median, na.rm = TRUE)
@

\end{frame}

\begin{frame}[fragile]
  \frametitle{Sorting}

The three categories with highest median profit are computed from the vector
of sorted median profits
<<AItR-Forbes2000-mprofits, echo = TRUE>>=
rev(sort(mprofits))[1:3]
@
where \Rcmd{rev} rearranges the vector of median profits
\Rcmd{sort}ed from smallest to largest.

\end{frame}

\subsection{Simple Graphics}

\begin{frame}[fragile]
  \frametitle{Simple Graphics: Histograms}

The degree of skewness of a distribution can be investigated by constructing
histograms using the
\Rcmd{hist} function:
<<AItR-Forbes2000-marketvalue, echo = TRUE, eval = FALSE>>=
layout(matrix(1:2, nrow = 2))
hist(Forbes2000$marketvalue)
hist(log(Forbes2000$marketvalue))
@
\end{frame}

\begin{frame}[fragile]
\begin{center}
<<AItR-Forbes2000-marketvalue, echo = FALSE, fig = TRUE>>=
layout(matrix(1:2, nrow = 2))
hist(Forbes2000$marketvalue)
hist(log(Forbes2000$marketvalue))
@
\end{center}

\end{frame}

\begin{frame}[fragile]
  \frametitle{Simple Graphics: Scatterplots}

In \R, regression relationships are specified by
so-called \stress{model formulae} which may look
like
<<AItR-Forbes2000-formula, echo = TRUE>>=
fm <- marketvalue ~ sales
class(fm)
@
with the dependent variable on the left hand side and the independent
variable on the right hand side. The tilde separates left and right hand
side.

\end{frame}

\begin{frame}[fragile]
  \frametitle{Simple Graphics: Scatterplots}

\begin{center}
<<AItR-Forbes2000-marketvalue-sales, echo = TRUE, fig = TRUE>>=
plot(log(marketvalue) ~ log(sales), 
     data = Forbes2000, pch = ".")
@
\end{center}

\end{frame}

\begin{frame}

%%% R CMD build will receive an error from texi2dvi because of pdf version
%%% 1.4 used here -- exclude this piece of code

\begin{center}
<<AItR-Forbes2000-marketvalue-sales-shading, echo = FALSE, fig = FALSE, results = hide>>=
pdf("figures/marketvalue-sales.pdf", version = "1.4")
plot(log(marketvalue) ~ log(sales), data = Forbes2000,
     col = rgb(0,0,0,0.1), pch = 16)
dev.off()
@
\includegraphics{figures/marketvalue-sales}
\end{center}

\end{frame}

\begin{frame}[fragile]
  \frametitle{Simple Graphics: Boxplots}

<<AItR-Forbes2000-country-plot, echo = TRUE, eval = FALSE>>=
boxplot(log(marketvalue) ~ country, data =
    subset(Forbes2000, country %in% c("United Kingdom", 
           "Germany", "India", "Turkey")),
    ylab = "log(marketvalue)", varwidth = TRUE)
@

\end{frame}

\begin{frame}

\begin{center}
<<AItR-Forbes2000-country-plot, echo = FALSE, fig = TRUE>>=
tmp <- subset(Forbes2000, country %in% c("United Kingdom", "Germany",
                                          "India", "Turkey"))
tmp$country <- tmp$country[,drop = TRUE]
boxplot(log(marketvalue) ~ country, data = tmp,
        ylab = "log(marketvalue)", varwidth = TRUE)
@
\end{center}

\end{frame}

\section{Organising an Analysis}

\begin{frame}[fragile]
  \frametitle{Organising an Analysis}

<<AItR-analysis1, echo = FALSE, results = hide>>=
file.create("analysis.R")
@

ALWAYS maintain your R code for an analysis as a separate text
file collecting all steps necessary to perform a certain data analysis task!

Such an \R{} transcript file can be read by
<<AItR-analysis2, echo = TRUE, eval = FALSE>>=
source("analysis.R", echo = TRUE)
@
When all steps of a data analysis, i.e.,
data preprocessing, transformations, simple summary statistics and plots,
model building and inference as well as reporting, are collected in such
an \R{} transcript file, the analysis can be reproduced at any time! 

<<AItR-analysis3, echo = FALSE, results = hide>>=
file.remove("analysis.R")
@

\end{frame}

\begin{frame}[fragile]
  \frametitle{Exercises}

\begin{itemize}
\item Calculate the median profit for the companies in the United States and the
median profit for the companies in the UK, France and Germany.

\item Find all German companies with negative profit.

\item 
Which business category are most of the companies situated at the Bermuda
island working in?

\item
For the $50$ companies in the Forbes data set with the highest profits,
plot sales against assets (or some suitable transformation of each
variable), labelling each point with the appropriate country name which may
need to be abbreviated (using \Rcmd{abbreviate}) to avoid making the
plot look too `messy'. %%'

\item
Find the average value of sales for the companies in each country in
the Forbes data set, and find the number of countries in each country with
profits above $5$ billion US dollars.
\end{itemize}

\end{frame}

\end{document}

