[Seqinr-commits] r2085 - www/src/mainmatter
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu Aug 3 21:59:12 CEST 2017
Author: jeanlobry
Date: 2017-08-03 21:59:12 +0200 (Thu, 03 Aug 2017)
New Revision: 2085
Modified:
www/src/mainmatter/introduction.pdf
www/src/mainmatter/introduction.rnw
www/src/mainmatter/introduction.tex
Log:
update 3.4-5
Modified: www/src/mainmatter/introduction.pdf
===================================================================
(Binary files differ)
Modified: www/src/mainmatter/introduction.rnw
===================================================================
--- www/src/mainmatter/introduction.rnw 2017-08-03 19:09:44 UTC (rev 2084)
+++ www/src/mainmatter/introduction.rnw 2017-08-03 19:59:12 UTC (rev 2085)
@@ -12,8 +12,10 @@
% BEGIN - DO NOT REMOVE THIS LINE
\newpage
-\section{About ACNUC}
+\section{About}
+\subsection{ACNUC}
+
\marginpar{
\includegraphics[width=\marginparwidth]{../figs/acnucbook1}\\
\tiny{Cover of ACNUC book vol. 1}
@@ -110,7 +112,7 @@
4 linear km of journals. That wouldn't be enough to store a printed
version of GenBank. Picture by Lionel Clouzeau.}
}
-\section{About R and CRAN}
+\subsection{\Rlogo{} and CRAN}
\Rlogo{} \cite{R, RfromR} is a \emph{libre} language and environment for statistical computing and graphics
which provides a wide variety of statistical and graphical techniques: linear and
@@ -151,7 +153,7 @@
listed at \texttt{http://cran.r-project.org/mirrors.html}, and can be directly
selected with the function \texttt{chooseCRANmirror()}.
-\section{About this document}
+\subsection{This document}
In the terminology of the \Rlogo{} project \cite{R, RfromR}, this document
is a package \emph{vignette}, which means that all code outputs present
@@ -167,7 +169,7 @@
home page at \url{http://seqinr.r-forge.r-project.org/.}
-\section{About sequin and \seqinr{}}
+\subsection{sequin and \seqinr{}}
Sequin is the well known sofware used to submit sequences to GenBank, \seqinr{}
\cite{seqinr} has definitively no connection with sequin. \seqinr{} is just a shortcut, with
@@ -180,7 +182,7 @@
a very good summary of a major functionality of the \seqinr{} package: to
provide an efficient access to sequence databases under R.
-\section{About getting started}
+\subsection{Getting started}
You need a computer connected to the Internet. First, install \Rlogo{} on your computer.
There are distributions for Linux, Mac and Windows users
@@ -204,7 +206,7 @@
To get help on a specific function, say \texttt{aaa()}, just prefix its name
with a question mark, as in \texttt{?aaa} and press enter.
-\section{About running R in batch mode}
+\subsection{Running \Rlogo{} in batch mode}
Although \Rlogo{} is usually run in an interactive mode, some data pre-processing
and analyses could be too long. You can run your \Rlogo{} code in batch mode
@@ -233,7 +235,7 @@
like \texttt{load("mybigdata.RData")}).
-\section{About the learning curve}
+\section{The learning curve}
\subsection*{Introduction}
@@ -400,6 +402,7 @@
of \Rlogo{}~outputs (including graphics) in a \LaTeX~document. In the same spirit, there
is a package called \texttt{xtable} \cite{xtable} to coerce \Rlogo{}~data into \LaTeX~tables.
+\clearpage
\SweaveInput{../config/sessionInfo.rnw}
% END - DO NOT REMOVE THIS LINE
Modified: www/src/mainmatter/introduction.tex
===================================================================
--- www/src/mainmatter/introduction.tex 2017-08-03 19:09:44 UTC (rev 2084)
+++ www/src/mainmatter/introduction.tex 2017-08-03 19:59:12 UTC (rev 2085)
@@ -48,8 +48,10 @@
% BEGIN - DO NOT REMOVE THIS LINE
\newpage
-\section{About ACNUC}
+\section{About}
+\subsection{ACNUC}
+
\marginpar{
\includegraphics[width=\marginparwidth]{../figs/acnucbook1}\\
\tiny{Cover of ACNUC book vol. 1}
@@ -164,7 +166,7 @@
4 linear km of journals. That wouldn't be enough to store a printed
version of GenBank. Picture by Lionel Clouzeau.}
}
-\section{About R and CRAN}
+\subsection{\Rlogo{} and CRAN}
\Rlogo{} \cite{R, RfromR} is a \emph{libre} language and environment for statistical computing and graphics
which provides a wide variety of statistical and graphical techniques: linear and
@@ -183,13 +185,13 @@
listed at \texttt{http://cran.r-project.org/mirrors.html}, and can be directly
selected with the function \texttt{chooseCRANmirror()}.
-\section{About this document}
+\subsection{This document}
In the terminology of the \Rlogo{} project \cite{R, RfromR}, this document
is a package \emph{vignette}, which means that all code outputs present
here were actually obtained by runing them.
The examples given thereafter were run under \texttt{R version 3.4.1 (2017-06-30)}
-on Thu Aug 3 20:42:51 2017 with Sweave \cite{Sweave}. There is a section at the end of
+on Thu Aug 3 21:58:01 2017 with Sweave \cite{Sweave}. There is a section at the end of
each chapter called \textbf{Session Informations} that gives details about
packages and package versions that were involved\footnote{
Previous versions of \Rlogo{} and packages are available on CRAN mirrors,
@@ -199,7 +201,7 @@
home page at \url{http://seqinr.r-forge.r-project.org/.}
-\section{About sequin and \seqinr{}}
+\subsection{sequin and \seqinr{}}
Sequin is the well known sofware used to submit sequences to GenBank, \seqinr{}
\cite{seqinr} has definitively no connection with sequin. \seqinr{} is just a shortcut, with
@@ -212,7 +214,7 @@
a very good summary of a major functionality of the \seqinr{} package: to
provide an efficient access to sequence databases under R.
-\section{About getting started}
+\subsection{Getting started}
You need a computer connected to the Internet. First, install \Rlogo{} on your computer.
There are distributions for Linux, Mac and Windows users
@@ -243,7 +245,7 @@
To get help on a specific function, say \texttt{aaa()}, just prefix its name
with a question mark, as in \texttt{?aaa} and press enter.
-\section{About running R in batch mode}
+\subsection{Running \Rlogo{} in batch mode}
Although \Rlogo{} is usually run in an interactive mode, some data pre-processing
and analyses could be too long. You can run your \Rlogo{} code in batch mode
@@ -272,7 +274,7 @@
like \texttt{load("mybigdata.RData")}).
-\section{About the learning curve}
+\section{The learning curve}
\subsection*{Introduction}
@@ -450,6 +452,7 @@
of \Rlogo{}~outputs (including graphics) in a \LaTeX~document. In the same spirit, there
is a package called \texttt{xtable} \cite{xtable} to coerce \Rlogo{}~data into \LaTeX~tables.
+\clearpage
\section*{Session Informations}
@@ -476,7 +479,7 @@
There were two compilation steps:
\begin{itemize}
- \item \Rlogo{} compilation time was: Thu Aug 3 20:43:01 2017
+ \item \Rlogo{} compilation time was: Thu Aug 3 21:58:14 2017
\item \LaTeX{} compilation time was: \today
\end{itemize}
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