[IPSUR-commits] r169 - pkg/IPSUR/inst/doc www/book www/rcmdrplugin
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Fri Jan 29 20:49:03 CET 2010
Author: gkerns
Date: 2010-01-29 20:49:01 +0100 (Fri, 29 Jan 2010)
New Revision: 169
Modified:
pkg/IPSUR/inst/doc/IPSUR.Rnw
www/book/installation.php
www/rcmdrplugin/installation.php
Log:
got IPSUR.lyx back up to speed and fixed installation links
Modified: pkg/IPSUR/inst/doc/IPSUR.Rnw
===================================================================
--- pkg/IPSUR/inst/doc/IPSUR.Rnw 2010-01-29 03:52:11 UTC (rev 168)
+++ pkg/IPSUR/inst/doc/IPSUR.Rnw 2010-01-29 19:49:01 UTC (rev 169)
@@ -32,7 +32,7 @@
{hyperref}
\hypersetup{pdftitle={Introduction to Probability and Statistics Using R},
pdfauthor={G. Jay Kerns},
- linkcolor=blue, citecolor=blue, urlcolor=blue}
+ linkcolor=blue, citecolor=black, urlcolor=blue}
\makeatletter
@@ -156,12 +156,11 @@
% make the input blue, output red
\DefineVerbatimEnvironment{Soutput}{Verbatim}{formatcom=\color{blue}}
\DefineVerbatimEnvironment{Sinput}{Verbatim}{fontshape=sl, formatcom=\color{red}}
-% make the output black
+% make the input/output black
%\DefineVerbatimEnvironment{Soutput}{Verbatim}{formatcom=\color{black}}
%\DefineVerbatimEnvironment{Sinput}{Verbatim}{fontshape=sl, formatcom=\color{black}}
-
% get rid of extra Sweave space
\fvset{listparameters={\setlength{\topsep}{0pt}}}
\renewenvironment{Schunk}{\vspace{\topsep}}{\vspace{\topsep}}
@@ -405,9 +404,11 @@
\noindent \bigskip{}
-\noindent Date: \today \vfill{}
+\noindent Date: \today
+\noindent \vfill{}
+
\cleardoublepage
\phantomsection
\pdfbookmark[1]{Contents}{table}
@@ -802,10 +803,10 @@
for your operating system:
\begin{description}
\item [{Microsoft~Windows:}] \url{http://cran.r-project.org/bin/windows/base/}
-\item [{MacOS:}] \url{http://cran.r-project/bin/macosx}
-\item [{Linux:}] \url{http://cran.r-project/bin/linux}
+\item [{MacOS:}] \url{http://cran.r-project.org/bin/macosx/}
+\item [{Linux:}] \url{http://cran.r-project.org/bin/linux/}
\end{description}
-On Windows, click the \inputencoding{latin9}\lstinline[showstringspaces=false]!.exe!\inputencoding{utf8}
+On MS-Windows, click the \inputencoding{latin9}\lstinline[showstringspaces=false]!.exe!\inputencoding{utf8}
program file to start installation. When it asks for \textquotedbl{}Customized
startup options\textquotedbl{}, specify \textsf{Yes}. In the next
window, be sure to select the SDI (single document interface) option;
@@ -818,7 +819,7 @@
With this option you can use \textsf{R} portably and without administrative
privileges. There is an entry in the \textsf{R} for Windows FAQ about
-this. Here is the procedure I use:
+this. Here is the procedure I use:
\begin{enumerate}
\item Download the Windows installer above and start installation as usual.
When it asks \emph{where} to install, navigate to the top-level directory
@@ -826,11 +827,11 @@
drive.
\item When it asks whether to modify the Windows registry, uncheck the box;
we do NOT want to tamper with the registry.
-\item After installation, change the name of the folder from {\textquotedbl{}}\inputencoding{latin9}\lstinline[showstringspaces=false]!R-x.y.z!\inputencoding{utf8}\textquotedbl{}
-to just plain {\textquotedbl{}}\inputencoding{latin9}\lstinline[showstringspaces=false]!R!\inputencoding{utf8}\textquotedbl{}.
-(Even quicker: do this in step 1.)
-\item Download the following shortcut to the top-level of the USB drive,
-right beside the \inputencoding{latin9}\lstinline[showstringspaces=false]!R!\inputencoding{utf8}
+\item After installation, change the name of the folder from \inputencoding{latin9}\lstinline[showstringspaces=false]!R-x.y.z!\inputencoding{utf8}
+to just plain \inputencoding{latin9}\lstinline[showstringspaces=false]!R!\inputencoding{utf8}.
+(Even quicker: do this in step 1.)
+\item Download the following shortcut to the top-level directory of the
+USB drive, right beside the \inputencoding{latin9}\lstinline[showstringspaces=false]!R!\inputencoding{utf8}
folder, not inside the folder.
@@ -838,11 +839,11 @@
\url{http://ipsur.r-forge.r-project.org/book/download/R.exe}
\par\end{center}
-Use the downloaded shortcut to run \textsf{R}.
+Use the downloaded shortcut to run \textsf{R}.
\end{enumerate}
Steps 3 and 4 are not required but save you the trouble of navigating
-to the \inputencoding{latin9}\lstinline[showstringspaces=false]!/R-x.y.z/bin!\inputencoding{utf8}
+to the \inputencoding{latin9}\lstinline[showstringspaces=false]!R-x.y.z/bin!\inputencoding{utf8}
directory to double-click \inputencoding{latin9}\lstinline[showstringspaces=false]!Rgui.exe!\inputencoding{utf8}
every time you want to run the program. It is useless to create your
own shortcut to \inputencoding{latin9}\lstinline[showstringspaces=false]!Rgui.exe!\inputencoding{utf8}.
@@ -850,7 +851,7 @@
have a drive letter associated with them. So if you make your own
shortcut and plug your USB drive into some \emph{other} machine that
happens to assign your drive a different letter, then your shortcut
-will no longer be pointing to the right place.
+will no longer be pointing to the right place.
\subsection{Installing and Loading Add-on Packages\label{sub:Installing-and-Loading-packages}}
@@ -2024,7 +2025,7 @@
\paragraph*{Bar Graphs\label{par:Bar-Graphs}}
A bar graph is the analogue of a histogram for categorical data. A
-bar is displayed for each level of a factor, with the height of the
+bar is displayed for each level of a factor, with the heights of the
bars proportional to the frequencies of observations falling in the
respective categories. A disadvantage of bar graphs is that the levels
are ordered alphabetically (by default), which may sometimes obscure
@@ -2936,7 +2937,8 @@
It is sometimes useful to compare data sets with each other on a scale
that is independent of the measurement units. The \inputencoding{latin9}\lstinline[showstringspaces=false]!scale!\inputencoding{utf8}
function will rescale a numeric vector (or data frame) by subtracting
-the sample mean from each value (column) and/or
+the sample mean from each value (column) and/or by dividing each observation
+by the sample standard deviation.
\section{Multivariate Data and Data Frames\label{sec:multivariate-data}}
@@ -15641,8 +15643,9 @@
\begin{example}
\textbf{Standard error of the mean.\label{exa:Bootstrap-se-mean}}
In this example we illustrate the bootstrap by estimating the standard
-error of the sample mean, and we will do it in the special case that
-the underlying population is $\mathsf{norm}(\mathtt{mean}=3,\,\mathtt{sd}=1)$.
+error of the sample meanand we will do it in the special case that
+the underlying population is $\mathsf{norm}(\mathtt{mean}=3,\,\mathtt{sd}=1)$.
+
Of course, we do not really need a bootstrap distribution here because
from Section \ref{sec:sampling-from-normal-dist} we know that $\Xbar\sim\mathsf{norm}(\mathtt{mean}=3,\,\mathtt{sd}=1/\sqrt{n})$,
but we proceed anyway to investigate how the bootstrap performs when
@@ -15792,9 +15795,9 @@
\end{example}
\begin{example}
-\textbf{The boot package in }\texttt{\textbf{R}}\textbf{.} It turns
-out that there are many bootstrap procedures and commands already
-built into base \texttt{R}, in the \inputencoding{latin9}\lstinline[showstringspaces=false]!boot!\inputencoding{utf8}
+\textbf{The boot package in }\texttt{\textbf{R}}. It turns out that
+there are many bootstrap procedures and commands already built into
+base \texttt{R}, in the \inputencoding{latin9}\lstinline[showstringspaces=false]!boot!\inputencoding{utf8}
package. Further, inside the \inputencoding{latin9}\lstinline[showstringspaces=false]!boot!\inputencoding{utf8}
package there is even a function called \inputencoding{latin9}\lstinline[showstringspaces=false]!boot!\inputencoding{utf8}\index{boot@\texttt{boot}}.
The basic syntax is of the form:\inputencoding{latin9}
@@ -15884,7 +15887,7 @@
into the function \inputencoding{latin9}\lstinline[showstringspaces=false]!boot.ci!\inputencoding{utf8}.
\begin{example}
\label{exa:percentile-interval-median-first}\textbf{Percentile interval
-for the expected value of the median.} We will try the naive approach
+for the expected value of the median.} Wee will try the naive approach
where we generate the resamples and calculate the percentile interval
by hand.
@@ -15899,8 +15902,8 @@
\end{example}
\begin{example}
-Confidence interval for expected value of the median, $2^{\mathrm{nd}}$
-try. Now we will do it the right way with the \inputencoding{latin9}\lstinline[showstringspaces=false]!boot!\inputencoding{utf8}
+\textbf{Confidence interval for expected value of the median, $2^{\mathrm{nd}}$
+try.} Now we will do it the right way with the \inputencoding{latin9}\lstinline[showstringspaces=false]!boot!\inputencoding{utf8}
function.
<<>>=
@@ -16517,8 +16520,8 @@
See \inputencoding{latin9}\lstinline[showstringspaces=false]!?read.spss!\inputencoding{utf8}
for the available options to customize the file import. Note that
-the R Commander will import many of the common file types with a menu
-driven interface.
+the \textsf{R} Commander will import many of the common file types
+with a menu driven interface.
\subsection{Importing a Data Frame}
@@ -16550,22 +16553,20 @@
\subsection{Sorting Data}
We can sort a vector with the \inputencoding{latin9}\lstinline[showstringspaces=false,tabsize=2]!sort!\inputencoding{utf8}
+function. Normally we have a data frame of several columns (variables)
+and many, many rows (observations). The goal is to shuffle the rows
+so that they are ordered by the values of one or more columns. This
+is done with the \inputencoding{latin9}\lstinline[showstringspaces=false,tabsize=2]!order!\inputencoding{utf8}
function.
-Normally we have a data frame of several columns (variables) and many,
-many rows (observations). The goal is to shuffle the rows so that
-they are ordered by the values of one or more columns. This is done
-with the \inputencoding{latin9}\lstinline[showstringspaces=false,tabsize=2]!order!\inputencoding{utf8}
-function.
-
For example, we may sort all of the rows of the \inputencoding{latin9}\lstinline[showstringspaces=false,tabsize=2]!Puromycin!\inputencoding{utf8}
data (in ascending order) by the variable \inputencoding{latin9}\lstinline[showstringspaces=false,tabsize=2]!conc!\inputencoding{utf8}
-with the following:
+with the following:
<<>>=
Tmp <- Puromycin[order(Puromycin$conc), ]
head(Tmp)
-@
+@
We can accomplish the same thing with the command
@@ -16574,15 +16575,15 @@
@
We can sort by more than one variable. To sort first by \inputencoding{latin9}\lstinline[showstringspaces=false,tabsize=2]!state!\inputencoding{utf8}
-and then next by \inputencoding{latin9}\lstinline[showstringspaces=false,tabsize=2]!conc!\inputencoding{utf8}
-do
+and next by \inputencoding{latin9}\lstinline[showstringspaces=false,tabsize=2]!conc!\inputencoding{utf8}
+do
<<eval = FALSE>>=
with(Puromycin, Puromycin[order(state, conc), ])
@
If we would like to sort a numeric variable in descending order then
-we put a minus sign in front of it.
+we put a minus sign in front of it.
<<>>=
Tmp <- with(Puromycin, Puromycin[order(-conc), ])
@@ -16602,9 +16603,8 @@
\section{Exporting Data\label{sec:Exporting-a-Data}}
-The basic function is \inputencoding{latin9}\lstinline[showstringspaces=false,tabsize=2]!write.table!\inputencoding{utf8}
-in the \inputencoding{latin9}\lstinline[showstringspaces=false,tabsize=2]!base!\inputencoding{utf8}
-package. The \inputencoding{latin9}\lstinline[showstringspaces=false,tabsize=2]!MASS!\inputencoding{utf8}
+The basic function is \inputencoding{latin9}\lstinline[showstringspaces=false,tabsize=2]!write.table!\inputencoding{utf8}.
+The \inputencoding{latin9}\lstinline[showstringspaces=false,tabsize=2]!MASS!\inputencoding{utf8}
package also has a \inputencoding{latin9}\lstinline[showstringspaces=false,tabsize=2]!write.matrix!\inputencoding{utf8}
function.
@@ -16612,13 +16612,12 @@
\section{Reshaping Data\label{sec:Reshaping-a-Data}}
\begin{itemize}
\item Aggregation
-\item Convert Tables to Data Frames and back
+\item Convert Tables to data frames and back
\end{itemize}
-\inputencoding{latin9}\lstinline[showstringspaces=false,tabsize=2]!rbind!\inputencoding{utf8}
-
+\inputencoding{latin9}\lstinline[showstringspaces=false,tabsize=2]!rbind!\inputencoding{utf8},
\inputencoding{latin9}\lstinline[showstringspaces=false,tabsize=2]!cbind!\inputencoding{utf8}
-\inputencoding{latin9}\lstinline[showstringspaces=false,tabsize=2]!ab[order(ab[ ,1]), ]!\inputencoding{utf8}
+\inputencoding{latin9}\lstinline[showstringspaces=false,tabsize=2]!ab[order(ab[,1]),]!\inputencoding{utf8}
\inputencoding{latin9}\lstinline[showstringspaces=false,tabsize=2]!complete.cases!\inputencoding{utf8}
@@ -18490,7 +18489,7 @@
\cleardoublepage
\phantomsection
\addcontentsline{toc}{chapter}{\bibname}
-%\nocite{*}
+%\nocite{*}
%\bibliography{IPSUR}
\bibliographystyle{plainurl}
Modified: www/book/installation.php
===================================================================
--- www/book/installation.php 2010-01-29 03:52:11 UTC (rev 168)
+++ www/book/installation.php 2010-01-29 19:49:01 UTC (rev 169)
@@ -49,7 +49,7 @@
<br />
MacOS X - <a href="http://cran.r-project.org/bin/macosx/">http://cran.r-project.org/bin/macosx/</a>
<br />
- Linux - <a href="http://cran.r-project.org/bin/linux/">http://cran.r-project/bin/linux</a>
+ Linux - <a href="http://cran.r-project.org/bin/linux/">http://cran.r-project.org/bin/linux/</a>
</div>
<ul><br />
<li>
Modified: www/rcmdrplugin/installation.php
===================================================================
--- www/rcmdrplugin/installation.php 2010-01-29 03:52:11 UTC (rev 168)
+++ www/rcmdrplugin/installation.php 2010-01-29 19:49:01 UTC (rev 169)
@@ -57,7 +57,7 @@
<br />
Linux -
<a href="http://cran.r-project.org/bin/linux/">
- http://cran.r-project/bin/linux
+ http://cran.r-project.org/bin/linux/
</a>
</div>
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