[IPSUR-commits] r110 - pkg/IPSUR/inst/doc
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Dec 30 23:52:45 CET 2009
Author: gkerns
Date: 2009-12-30 23:52:44 +0100 (Wed, 30 Dec 2009)
New Revision: 110
Modified:
pkg/IPSUR/inst/doc/IPSUR.Rnw
Log:
biblio stuff
Modified: pkg/IPSUR/inst/doc/IPSUR.Rnw
===================================================================
--- pkg/IPSUR/inst/doc/IPSUR.Rnw 2009-12-30 18:20:23 UTC (rev 109)
+++ pkg/IPSUR/inst/doc/IPSUR.Rnw 2009-12-30 22:52:44 UTC (rev 110)
@@ -528,13 +528,13 @@
Many proofs have been skipped entirely, and there is no rhyme or reason
to the current omissions. I will add more when I get a chance.
\item [{More~and~better~graphics:}] I have not used the \inputencoding{latin9}\lstinline[basicstyle={\ttfamily},breaklines=true,language=R]!ggplot2!\inputencoding{utf8}
-package because I do not know how to use it yet. It is on my to-do
-list.
+package \cite{Wickam2009} because I do not know how to use it yet.
+It is on my to-do list.
\item [{More~and~better~exercises:}] There are only a few exercises
in the first edition. I have not used the \inputencoding{latin9}\lstinline[basicstyle={\ttfamily},breaklines=true,language=R]!exams!\inputencoding{utf8}
-package, but I believe that it is a right way to move forward. As
-I learn more about what the package can do I would like to incorporate
-it into later editions of this book.
+package \cite{exams}, but I believe that it is a right way to move
+forward. As I learn more about what the package can do I would like
+to incorporate it into later editions of this book.
\end{description}
\section*{About This Document}
@@ -837,7 +837,7 @@
startup options\textquotedbl{}, specify \textsf{Yes}. In the next
window, be sure to select the SDI (single-window) option; this is
useful later when we discuss three dimensional plots with the \inputencoding{latin9}\lstinline[showstringspaces=false]!rgl!\inputencoding{utf8}
-package.
+package \cite{rgl}.
\subsection{Installing and Loading Add-on Packages}
@@ -1003,10 +1003,9 @@
I used this it but I remember liking it very much when I did. One
thing that stood out was that the user could drag-and-drop datasets
for plots. See here for more information \url{http://wiener.math.csi.cuny.edu/pmg/}
-\item [{Rattle~(\inputencoding{latin9}\lstinline[basicstyle={\ttfamily}]!rattle!\inputencoding{utf8})}] is
-a data mining toolkit which is designed to manage/analyze very large
-data sets, but it provides enough other general functionality to merit
-mention here.
+\item [{Rattle}] is a data mining toolkit which is designed to manage/analyze
+very large data sets, but it provides enough other general functionality
+to merit mention here. See \cite{rattle} for more information.
\item [{Deducer}] is relatively new and shows promise from what I have
seen, but I have not actually used it in the classroom yet.
\end{description}
@@ -1838,7 +1837,7 @@
data. We construct a stem and leaf diagram in \textsf{R} with the
\inputencoding{latin9}\lstinline[showstringspaces=false]!stem.leaf!\inputencoding{utf8}
function from the \inputencoding{latin9}\lstinline[showstringspaces=false]!aplpack!\inputencoding{utf8}
-package.
+package \cite{aplpack}.
\end{example}
<<>>=
library(aplpack)
@@ -1958,7 +1957,8 @@
\paragraph*{Pareto Diagrams }
These can be done with the \textsf{R} Commander, or with the \inputencoding{latin9}\lstinline[showstringspaces=false]!pareto.chart!\inputencoding{utf8}
-function at the console (from the package \inputencoding{latin9}\lstinline[showstringspaces=false]!qcc!\inputencoding{utf8}).
+function from the \inputencoding{latin9}\lstinline[showstringspaces=false]!qcc!\inputencoding{utf8}package
+\cite{qcc}.
%
\begin{figure}
@@ -2517,7 +2517,7 @@
\subsection{How to do it with \textsf{R}}
The \inputencoding{latin9}\lstinline[showstringspaces=false]!e1071!\inputencoding{utf8}
-package has the \inputencoding{latin9}\lstinline[showstringspaces=false]!skewness!\inputencoding{utf8}
+package \cite{Dimitriadoue1071} has the \inputencoding{latin9}\lstinline[showstringspaces=false]!skewness!\inputencoding{utf8}
function for the sample skewness and the \inputencoding{latin9}\lstinline[showstringspaces=false]!kurtosis!\inputencoding{utf8}
function for the sample excess kurtosis. Both functions have a \inputencoding{latin9}\lstinline[showstringspaces=false]!na.rm!\inputencoding{utf8}
argument which is \inputencoding{latin9}\lstinline[showstringspaces=false]!FALSE!\inputencoding{utf8}
@@ -3483,7 +3483,7 @@
\subsection{How to do it with \textsf{R}}
Most of the probability work in this book is done with the \inputencoding{latin9}\lstinline[showstringspaces=false]!prob!\inputencoding{utf8}
-package \cite{Kernsprob2009}. A sample space is (usually) represented
+package \cite{Kernsprob}. A sample space is (usually) represented
by a \emph{data frame}, that is, a rectangular collection of variables
(see Section BLANK). Each row of the data frame corresponds to an
outcome of the experiment. The data frame choice is convenient both
@@ -3517,7 +3517,7 @@
function in the \inputencoding{latin9}\lstinline[showstringspaces=false]!base!\inputencoding{utf8}
package, \inputencoding{latin9}\lstinline[showstringspaces=false]!combn!\inputencoding{utf8}
in the \inputencoding{latin9}\lstinline[showstringspaces=false]!combinat!\inputencoding{utf8}
-package, and \inputencoding{latin9}\lstinline[showstringspaces=false]!permsn!\inputencoding{utf8}
+package \cite{combinat}, and \inputencoding{latin9}\lstinline[showstringspaces=false]!permsn!\inputencoding{utf8}
in the \inputencoding{latin9}\lstinline[showstringspaces=false]!prob!\inputencoding{utf8}
package%
\footnote{The seasoned \textsf{R} user can get the job done without the convenience
@@ -5996,7 +5996,7 @@
@
As easy as this is, it is even easier to do with the \inputencoding{latin9}\lstinline[showstringspaces=false]!distrEx!\inputencoding{utf8}
-package \cite{Ruckdeschel2006}. We define a random variable \inputencoding{latin9}\lstinline[showstringspaces=false]!X!\inputencoding{utf8}
+package \cite{Ruckdescheldistr}. We define a random variable \inputencoding{latin9}\lstinline[showstringspaces=false]!X!\inputencoding{utf8}
as an object, then compute things from the object such as mean, variance,
and standard deviation with the functions \inputencoding{latin9}\lstinline[showstringspaces=false]!E!\inputencoding{utf8},
\inputencoding{latin9}\lstinline[showstringspaces=false]!var!\inputencoding{utf8},
@@ -6262,8 +6262,9 @@
\begin{example}
Another way to do Example BLANK is with the \inputencoding{latin9}\lstinline[basicstyle={\ttfamily}]!distr!\inputencoding{utf8}
-family of packages. They use an object oriented approach to random
-variables, that is, a random variable is stored in an object \inputencoding{latin9}\lstinline[basicstyle={\ttfamily}]!X!\inputencoding{utf8},
+family of packages \cite{Ruckdescheldistr}. They use an object oriented
+approach to random variables, that is, a random variable is stored
+in an object \inputencoding{latin9}\lstinline[basicstyle={\ttfamily}]!X!\inputencoding{utf8},
and then questions about the random variable translate to functions
on and involving \inputencoding{latin9}\lstinline[basicstyle={\ttfamily}]!X!\inputencoding{utf8}.
Random variables with distributions from the \inputencoding{latin9}\lstinline[basicstyle={\ttfamily}]!base!\inputencoding{utf8}
@@ -7558,7 +7559,7 @@
Compare this answer to what we found in Example BLANK. Now let us
try expectation with the \inputencoding{latin9}\lstinline[showstringspaces=false]!distrEx!\inputencoding{utf8}
-package:
+package \cite{Ruckdescheldistr}:
<<>>=
library(distrEx)
@@ -8265,7 +8266,7 @@
There is some support of moments and moment generating functions for
some continuous probability distributions included in the \inputencoding{latin9}\lstinline[basicstyle={\ttfamily}]!actuar!\inputencoding{utf8}
-package \cite{Dutang2008}. The convention is \inputencoding{latin9}\lstinline[basicstyle={\ttfamily}]!m!\inputencoding{utf8}
+package \cite{Dutangactuar}. The convention is \inputencoding{latin9}\lstinline[basicstyle={\ttfamily}]!m!\inputencoding{utf8}
in front of the distribution name for raw moments, and \inputencoding{latin9}\lstinline[basicstyle={\ttfamily}]!mgf!\inputencoding{utf8}
in front of the distribution name for the moment generating function.
At the time of this writing, the following distributions are supported:
@@ -8815,7 +8816,7 @@
To do the continuous case we could use the computer algebra utilities
of \inputencoding{latin9}\lstinline[showstringspaces=false]!Yacas!\inputencoding{utf8}
and the associated \textsf{R} package \inputencoding{latin9}\lstinline[showstringspaces=false]!Ryacas!\inputencoding{utf8}
-. See Section BLANK for another example where the \inputencoding{latin9}\lstinline[showstringspaces=false]!Ryacas!\inputencoding{utf8}
+\cite{ryacas}. See Section BLANK for another example where the \inputencoding{latin9}\lstinline[showstringspaces=false]!Ryacas!\inputencoding{utf8}
package appears.
@@ -9118,9 +9119,10 @@
\subsection{How to do it with \textsf{R}}
Use package \inputencoding{latin9}\lstinline[basicstyle={\ttfamily}]!mvtnorm!\inputencoding{utf8}
-\cite{Genz2009} or \inputencoding{latin9}\lstinline[basicstyle={\ttfamily}]!mnormt!\inputencoding{utf8}%
+\cite{Genzmvtnorm} or \inputencoding{latin9}\lstinline[basicstyle={\ttfamily}]!mnormt!\inputencoding{utf8}
+\cite{mnormt}%
\footnote{Another way to do this is with the \texttt{curve3d} function in the
-\texttt{emdbook} package. It looks like this:
+\texttt{emdbook} package \cite{emdbook}. It looks like this:
\begin{lyxcode}
library(emdbook);~library(mvtnorm)~~~\#~note:~the~order~matters
@@ -9198,7 +9200,7 @@
Here is another way to do it%
\footnote{Another way to do the plot is with the \inputencoding{latin9}\lstinline[basicstyle={\ttfamily}]!scatterplot3d!\inputencoding{utf8}
function in the \inputencoding{latin9}\lstinline[basicstyle={\ttfamily}]!scatterplot3d!\inputencoding{utf8}
-package \cite{Ligges2003}. It looks like this:
+package \cite{Liggesscatterplot3d}. It looks like this:
\begin{lyxcode}
library(scatterplot3d)
@@ -9766,9 +9768,9 @@
\subsection{How to do it with \textsf{R}}
The \inputencoding{latin9}\lstinline[showstringspaces=false]!TeachingDemos!\inputencoding{utf8}
-package \cite{Snow2009} has \inputencoding{latin9}\lstinline[showstringspaces=false]!clt.examp!\inputencoding{utf8}
+package \cite{Snowteachingdemos} has \inputencoding{latin9}\lstinline[showstringspaces=false]!clt.examp!\inputencoding{utf8}
and the \inputencoding{latin9}\lstinline[showstringspaces=false]!distrTeach!\inputencoding{utf8}
-\cite{Ruckdeschel2006} package has \inputencoding{latin9}\lstinline[showstringspaces=false]!illustrateCLT!\inputencoding{utf8}.
+\cite{Ruckdescheldistr} package has \inputencoding{latin9}\lstinline[showstringspaces=false]!illustrateCLT!\inputencoding{utf8}.
Try the following at the command line (output omitted):
<<eval = FALSE>>=
@@ -10537,7 +10539,7 @@
\end{example}
There is functionality in the \inputencoding{latin9}\lstinline[basicstyle={\ttfamily},showstringspaces=false]!distrTest!\inputencoding{utf8}
-package \cite{Ruckdeschel2006} to calculate theoretical MLEs; we
+package \cite{Ruckdescheldistr} to calculate theoretical MLEs; we
will skip examples of these for the time being.
@@ -11001,7 +11003,7 @@
\section{Other Topics}
-I am thinking about fitdistr from the MASS package.
+I am thinking about fitdistr from the MASS package \cite{Venables2002}.
Mention mle from the stats4 package
@@ -12231,7 +12233,7 @@
We may plot the confidence and prediction intervals with one fell
swoop using the \inputencoding{latin9}\lstinline[showstringspaces=false]!ci.plot!\inputencoding{utf8}
function from the \inputencoding{latin9}\lstinline[showstringspaces=false]!HH!\inputencoding{utf8}
-package \cite{Heiberger2009}. The graph is displayed in Figure \ref{fig:Scatter-cars-CIPI}.
+package \cite{Heibergerhh}. The graph is displayed in Figure \ref{fig:Scatter-cars-CIPI}.
%
\begin{figure}
\begin{centering}
@@ -12626,7 +12628,7 @@
We do it in \textsf{R} with the \inputencoding{latin9}\lstinline[showstringspaces=false]!bptest!\inputencoding{utf8}
function from the \inputencoding{latin9}\lstinline[showstringspaces=false]!lmtest!\inputencoding{utf8}
-package \cite{Zeileis2002}.
+package \cite{Zeileislmtest}.
<<>>=
library(lmtest)
@@ -13175,8 +13177,8 @@
instead of a simple scatterplot we use a scatterplot matrix which
is made with the \inputencoding{latin9}\lstinline[showstringspaces=false]!splom!\inputencoding{utf8}
function in the \inputencoding{latin9}\lstinline[showstringspaces=false]!lattice!\inputencoding{utf8}
-package \cite{Sarkar2009} as shown below. The plot is shown in Figure
-BLANK.
+package \cite{Sarkarlattice} as shown below. The plot is shown in
+Figure BLANK.
%
\begin{figure}
@@ -13235,10 +13237,10 @@
ordinary plane and we can look at it with a 3D scatterplot.
One way to do this is with the \textsf{R} Commander in the \inputencoding{latin9}\lstinline[showstringspaces=false]!Rcmdr!\inputencoding{utf8}
-package. It has a 3D scatterplot option under the \textsf{Graphs}
-menu. It is especially great because the resulting graph is dynamic;
-it can be moved around with the mouse, zoomed, \emph{etc}. But that
-particular display does not translate well to a printed book.
+package \cite{Foxrcmdr}. It has a 3D scatterplot option under the
+\textsf{Graphs} menu. It is especially great because the resulting
+graph is dynamic; it can be moved around with the mouse, zoomed, \emph{etc}.
+But that particular display does not translate well to a printed book.
Another way to do it is with the \inputencoding{latin9}\lstinline[showstringspaces=false]!scatterplot3d!\inputencoding{utf8}
function in the \inputencoding{latin9}\lstinline[showstringspaces=false]!scatterplot3d!\inputencoding{utf8}
@@ -14272,7 +14274,7 @@
There are other -- shorter -- ways to plot regression lines by groups,
namely the \inputencoding{latin9}\lstinline[showstringspaces=false]!scatterplot!\inputencoding{utf8}
function in the \inputencoding{latin9}\lstinline[showstringspaces=false]!car!\inputencoding{utf8}
-package and the \inputencoding{latin9}\lstinline[showstringspaces=false]!xyplot!\inputencoding{utf8}
+\cite{car} package and the \inputencoding{latin9}\lstinline[showstringspaces=false]!xyplot!\inputencoding{utf8}
function in the \inputencoding{latin9}\lstinline[showstringspaces=false]!lattice!\inputencoding{utf8}
package. We elected to introduce the reader to the above approach
since many advanced plots in \textsf{R} are done in a similar, consecutive
@@ -15127,7 +15129,7 @@
This chapter is still under substantial revision. Look for it in the
Second Edition. In the meantime, you can preview any released drafts
with the development version of the \inputencoding{latin9}\lstinline[showstringspaces=false]!IPSUR!\inputencoding{utf8}
-package whcih is available from \textsf{R}-Forge:
+package which is available from \textsf{R}-Forge:
<<eval = FALSE>>=
install.packages("IPSUR", repos="http://R-Forge.R-project.org")
@@ -15141,7 +15143,7 @@
This chapter is still under substantial revision. Look for it in the
Second Edition. In the meantime, you can preview any released drafts
with the development version of the \inputencoding{latin9}\lstinline[showstringspaces=false]!IPSUR!\inputencoding{utf8}
-package whcih is available from \textsf{R}-Forge:
+package which is available from \textsf{R}-Forge:
<<eval = FALSE>>=
install.packages("IPSUR", repos="http://R-Forge.R-project.org")
@@ -15155,7 +15157,7 @@
This chapter is still under substantial revision. Look for it in the
Second Edition. In the meantime, you can preview any released drafts
with the development version of the \inputencoding{latin9}\lstinline[showstringspaces=false]!IPSUR!\inputencoding{utf8}
-package whcih is available from \textsf{R}-Forge:
+package which is available from \textsf{R}-Forge:
<<eval = FALSE>>=
install.packages("IPSUR", repos="http://R-Forge.R-project.org")
@@ -15344,7 +15346,7 @@
more work: we would usually like to repeat each row of \inputencoding{latin9}\lstinline[showstringspaces=false]!A!\inputencoding{utf8}
exactly the number of times shown in the \inputencoding{latin9}\lstinline[showstringspaces=false]!Freq!\inputencoding{utf8}
column. The \inputencoding{latin9}\lstinline[showstringspaces=false]!reshape!\inputencoding{utf8}
-package has the function \inputencoding{latin9}\lstinline[showstringspaces=false]!untable!\inputencoding{utf8}
+package \cite{Wickhamreshape} has the function \inputencoding{latin9}\lstinline[showstringspaces=false]!untable!\inputencoding{utf8}
designed for that very purpose:
<<>>=
@@ -16237,7 +16239,7 @@
which stands for {}``open document text''.
The \inputencoding{latin9}\lstinline[showstringspaces=false]!odfWeave!\inputencoding{utf8}
-package provides a way to generate an \inputencoding{latin9}\lstinline[showstringspaces=false]!.odt!\inputencoding{utf8}
+package \cite{odfweave} provides a way to generate an \inputencoding{latin9}\lstinline[showstringspaces=false]!.odt!\inputencoding{utf8}
file with \textsf{R} input and output code automatically formatted
correctly and inserted in the correct places. In this way, one does
not need to worry about all of the trouble of typesetting \textsf{R}
@@ -17350,56 +17352,16 @@
\textbf{Publisher:} & G.~Jay Kerns\tabularnewline
\end{tabular}
-\bibliographystyle{plain}
-\cleardoublepage\addcontentsline{toc}{chapter}{\bibname}\bibliography{IPSUR}
-
-
-
-\chapter{Some References}
-\begin{itemize}
-\item Billingsley, Resnick, or Ash Dooleans-Dade.
-\item Calculus (say, Stewart or Apostol), Real Analysis (say, Rudin, Folland,
-or Carothers), or Measure Theory (Billingsley, Halmos, Dudley) fo
-\item A. Agresti and B.A. Coull, Approximate is better than \textquotedbl{}exact\textquotedbl{}
-for interval estimation of binomial proportions, \_American Statistician,\_
-{*}52{*}:119-126, 1998. For the score interval.
-\item Reference to Tabachnick \& Fidell.
-\item Venables, W. and Smith, D. (2005). An Introduction to \textsf{R}.
-\url{http://www.r-project.org/Manuals}.
-\item Bootstrap Confidence Intervals, Thomas J. DiCiccio and Bradley Efron,
-Statistical Science 1996, Vol. 11, No. 3, 189–228
-\item Torsten Hothorn, Kurt Hornik, Mark A. van de Wiel \& Achim Zeileis
-(2008). Implementing a class of permutation tests: The coin package,
-Journal of Statistical Software, 28(8), 1–23. http://www.jstatsoft.org/v28/i08/
-\item \url{http://www.rsscse.org.uk/ts/gtb/johnson3.pdf}
-\item \url{http://en.wikipedia.org/wiki/Mark_and_recapture}
-\item Forecasting, Time Series, and Regression, 4th Ed., Bowerman, O'Connell,
-and Koehler (Duxbury)
-\item Mathematical Statistics, Vol. I, 2nd Ed., Bickel and Doksum (Prentice
-Hall)
-\item Applied Linear Regression Models, 3rd Ed., Neter, Kutner, Nachtsheim,
-and Wasserman (Irwin)
-\item Introduction to Statistical Thought
-\item \textquotedbl{}Bootstrap Methods and Their Applications\textquotedbl{}
-by A. C. Davison and D. V. Hinkley (1997, CUP).
-\item emdbook
-\item mnormt
-\item Ryacas
-\item car
-\end{itemize}
-
-
-<<>>=
+<<echo=FALSE, results=hide, split=FALSE>>=
rm(.Random.seed)
save.image(file = "IPSUR.RData")
+Stangle(file="IPSUR.Rnw", output="IPSUR.R", annotate=TRUE)
@
+\bibliographystyle{plain}
+\cleardoublepage\addcontentsline{toc}{chapter}{\bibname}\nocite{*}
+\bibliography{IPSUR}
-\chapter{\textsf{R} Transcript}
-<<echo=FALSE, results=hide, split=FALSE>>=
-Stangle(file="IPSUR.Rnw", output="IPSUR.R", annotate=TRUE)
-@
-
\printindex{}
\end{document}
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