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%%\newcommand{\Rpackage}[1]{\hbox{\rm\textit{#1}}}
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\newcommand{\Rarg}[1]{\texttt{#1}}
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\newcommand{\booktitle}[1]{`#1'} %%'

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\newcommand{\Cov}{\mathsf{Cov}}   
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\newcommand{\N}{\mathcal{N}}   
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\usepackage{amstext}

%%% links
\usepackage{hyperref}

\hypersetup{%
  pdftitle = {A Handbook of Statistical Analyses Using R},
  pdfsubject = {Book},
  pdfauthor = {Brian S. Everitt and Torsten Hothorn},
  colorlinks = {true},
  linkcolor = {blue},
  citecolor = {blue},
  urlcolor = {red},
  hyperindex = {true},
  linktocpage = {true},
}


%%% captions & tables
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%%\usepackage[format=hang,margin=10pt,labelfont=bf]{caption}
%% </FIMXE>
\usepackage{longtable}
\usepackage{rotating}

%%% R symbol in chapter 1
\usepackage{wrapfig}

%%% Bibliography
\usepackage[round,comma]{natbib}
\renewcommand{\refname}{References \addcontentsline{toc}{chapter}{References}}
\citeindexfalse

%%% texi2dvi complains that \newblock is undefined, hm...
\def\newblock{\hskip .11em plus .33em minus .07em}

%%% Example sections
\newcounter{exercise}[chapter]
\setcounter{exercise}{0}
\newcommand{\exercise}{\item{\stepcounter{exercise} Ex.
                       \arabic{chapter}.\arabic{exercise} }}


%% URLs
\newcommand{\curl}[1]{\begin{center} \url{#1} \end{center}}

%%% for manual corrections
%\renewcommand{\baselinestretch}{2}

%%% plot sizes
\setkeys{Gin}{width=0.95\textwidth}

%%% color
\usepackage{color}

%%% hyphenations
\hyphenation{drop-out}

%%% new bidirectional quotes need 
\usepackage[utf8]{inputenc}
\begin{document}

%% Title page

\title{A Handbook of Statistical Analyses Using \R}

\author{Brian S. Everitt and Torsten Hothorn}

\maketitle
%%\VignetteIndexEntry{Errata}
\setcounter{chapter}{15}


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

<<setup, echo = FALSE, results = hide>>=
rm(list = ls())
s <- search()[-1]
s <- s[-match(c("package:base", "package:stats", "package:graphics", "package:grDevices",
                "package:utils", "package:datasets", "package:methods", "Autoloads"), s)]
if (length(s) > 0) sapply(s, detach, character.only = TRUE)
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HSAURpkg <- require("HSAUR")
if (!HSAURpkg) stop("cannot load package ", sQuote("HSAUR"))
rm(HSAURpkg)
a <- Sys.setlocale("LC_ALL", "C")
book <- TRUE
refs <- cbind(c("AItR", "SI", "CI", "ANOVA", "MLR", "GLM", 
                "DE", "RP", "SA", "ALDI", "ALDII", "MA", "PCA", 
                "MDS", "CA"), 1:15)
ch <- function(x, book = TRUE) {
    ch <- refs[which(refs[,1] == x),]
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        return(paste("Chapter~\\\\ref{", ch[1], "}", sep = ""))
    } else {
        return(paste("Chapter~\\\\ref{", ch[2], "}", sep = ""))
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}
@

\pagestyle{headings}

\chapter[Errata]{Errata}

The document gives a list of typos, errors, inconsistencies etc. which have been spotted. 
Moreover, small numeric output differences which are due to updated packages are reported here.
To get a full list of differences run \Rcmd{R CMD check HSAUR} on the source package. 
All issues marked with \textbf{R1}, \textbf{R2} etc have been silently fixed 
in first reprint, second reprint etc.

\section*{Preface}

Typo in name of vignette for Chapter 1, should read
<<pre-vignette, echo = TRUE, eval = FALSE>>=
vignette("Ch_introduction_to_R", package = "HSAUR")
@
and
<<pre-vignette, echo = TRUE, eval = FALSE>>=
edit(vignette("Ch_introduction_to_R", package = "HSAUR"))
@
As of version 1.0-3, only the correctly named vignette is available (\textbf{R1}).

\section{Introduction to R}

\begin{itemize}
\item Type at page 11: `.' needs to be double-quoted in \Rcmd{list.files} (\textbf{R1})
\item Typo at page 20 (Ex. 1.5): number of companies, not number of countries (\textbf{R1}).

\end{itemize}

\section{Simple Inference}

Typo at page 31, code line 4: use argument \Rcmd{varwidth = TRUE}, not \Rcmd{var.width = TRUE} (\textbf{R1}).

\section{Conditional Inference}

\begin{itemize}
\item The names of the test statistics in the output have been changed from \Rcmd{T} to \Rcmd{Z} 
or \Rcmd{chi-squared} throughout the chapter (\textbf{R1}).

\item Reference \cite{HSAUR:Hothorn:2006:AmStat} updated (\textbf{R1})
\end{itemize}

\section{Analysis of Variance}

Figure 4.3 had wrong line types in legend (Beef and Cereal interchanged) (\textbf{R2}).

\section{Multiple Linear Regression}

\begin{itemize}
\item
Page 74, Table 5.1: The values for \Robject{cloudcover} and \Robject{sne} had to be exchanged. 
The corresponding coefficients and Figures in this chapter change accordingly (\textbf{R1}).
\item 
Page 83: both \Rcmd{fitted} and \Rcmd{predict} can be used to compute fitted values, the later on
can be applied to new unseen data as well (\textbf{R1}).
\item Page 87: $\hat{y}_i$ instead of $\hat{y}$ in the definition of
      the standardized residual.
\end{itemize}


\section{Logistic Regression and Generalised Linear Models}

\begin{itemize}
\item page 97: predictions are to be computed for \Rcmd{plasma\_glm\_2},
               not \Rcmd{plasma\_glm\_1} (affects Figure~6.4) (\textbf{R2}).
\item Function \Rcmd{myplot} (page 100): the \Rcmd{vfont} argument in \Rcmd{text} has been changed 
to \Rcmd{family = "HersheySerif"} (the resulting plots remain the same) (\textbf{R1}).
\end{itemize}

\section{Density Estimation}

\begin{itemize}
\item Page 117: typo: in instead of is
\item Page 121: small numeric differences for the output of \Rcmd{optim}

\item update to \Rpackage{mclust} version 3.0-0 (new names of parameters in \Robject{mclust}
objects)

\end{itemize}

\section{Recursive Partitioning}

\begin{itemize}
\item Page 138: the probability for glaucoma is \Rcmd{predict(trees[[i]], newdata = GlaucomaM)[,1]}
      and the code for converting average class probabilities in factors has to be reverted, too.
      Affects Figure 8.4. (which is now in sync with the interpretation).
\item Page 139: small differences in \Rcmd{predtab} 
\item Page 140: small differences in table at bottom of this page
\item Reference \cite{HSAUR:Hothorn:2006:JCGS} updated (\textbf{R1})
\item Page 142, Ex. 8.1.: regression tree, not classification tree.
\end{itemize}

\section{Survival Analysis}

\begin{itemize}
\item The name of the test statistic in the output of \Rcmd{surv\_test} has been changed to
\Rcmd{chi-squared} (\textbf{R1}).
\item Denominator $s$ was missing from $h(t)$ (page 147) (\textbf{R2}).
\end{itemize}

\section{Analysing Longitudinal Data I}

Page 168, Figure 10.2: \Rcmd{summary} does not provide degrees of freedom and p-values 
in newer versions of \Rpackage{lme4}.

\section{Analysing Longitudinal Data II}

--nothing known--

\section{Meta-Analysis}

\begin{itemize}
\item Page 202: $\mu_i \sim \N(\mu, \tau^2)$, not $N(\mu, \tau^2)$ (\textbf{R2}).
\item Page 202: $W_i = 1/ (V_i + \hat{\tau}^2)$ since $V_i$ is the within-study variance.
\item Page 207: square for \Rcmd{selogs} was missing (\textbf{R2}).
\end{itemize}

\section{Principal Component Analysis}

--nothing known--

\section{Multidimensional Scaling}

In the formula for $b_{ij}$ on page 231 the last term in the 
parentheses should have a plus sign not a minus sign.

\section{Cluster Analysis}

\begin{itemize}
\item update to \Rpackage{mclust} version 3.0-0 (new plot method)
\item Page 248: the likelihood needs $|\Sigma_j|^{-1/2}$
\item Page 248: $W_j$ is a $q \times q$ matrix
\item Page 248: $\Sigma_j = \Sigma, j = 1, \dots, c$.
\item Page 248: 
\begin{eqnarray*}
l(\vartheta, \gamma) = -\frac{1}{2} \sum_{j = 1}^c \text{trace}(\W_j
\Sigma_j^{-1}) + n_j \log |\Sigma_j|
\end{eqnarray*}
\item Page 248: $\sum_{j = 1}^c n_j \log | \W_j  / n_j|$
\end{itemize}

\section*{Thanks}

We would like to thank the following people for pointing out errors, 
typos etc and for making suggestions for improvements:
\begin{itemize}
\item Tobias Verbeke
\item Brian D. Ripley
\item Yihui Xie
\item Mike Cheung
\item Lothar H{\"a}berle
\item Radoslav Harman
\end{itemize}

\bibliographystyle{LaTeXBibTeX/refstyle}
\bibliography{LaTeXBibTeX/HSAUR}   
\end{document}
