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- Committer: Bazaar Package Importer
- Author(s): Dirk Eddelbuettel
- Date: 2011-02-03 16:10:05 UTC
- mfrom: (1.2.19 upstream)
- Revision ID: james.westby@ubuntu.com-20110203161005-g1bg3cd5mtu15uh3
Tags: 5.13-1
New upstream version released today
- files added:
- doc/refcard/refcard.pdf
- etc/useR-2006-ESS
- etc/useR-2006-ESS/Lab1
- etc/useR-2006-ESS/Lab1/auto
- etc/useR-2006-ESS/Lab2
- etc/useR-2006-ESS/Lab2/auto
- etc/useR-2006-ESS/R-examples
- etc/useR-2006-ESS/RefCards
- files modified:
- ANNOUNCE
added
removed
etc/useR-2006-ESS/useR-ESS.tex
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\documentclass{beamer}
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\mode<presentation>
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{
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\usetheme{Warsaw}
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\setbeamercovered{transparent}
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}
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\usepackage[english]{babel}
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\usepackage[latin1]{inputenc}
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\usepackage{times}
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\usepackage[T1]{fontenc}
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% Or whatever. Note that the encoding and the font should match. If T1
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% does not look nice, try deleting the line with the fontenc.
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\title[Emacs and R]{Emacs enhances data analysis and programming with R}
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\subtitle{ESS useR Short Course}
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\author[Rossini]{A.J.~Rossini}
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\institute[Novartis Pharma AG]
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{
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Modeling and Simulation \\
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Novartis Pharma AG \\
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Basel, Switzerland
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}
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\date[14.06.2006]
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{14.06.2006 / useR-2006}
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\subject{Talks}
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% This is only inserted into the PDF information catalog. Can be left
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% out.
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% Delete this, if you do not want the table of contents to pop up at
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% the beginning of each subsection:
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% \AtBeginSubsection[]
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% {
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% \begin{frame}<beamer>
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% \frametitle{Outline}
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% \tableofcontents[currentsection,currentsubsection]
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% \end{frame}
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% }
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\begin{document}
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\begin{frame}
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\titlepage
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\end{frame}
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\section{Introduction}
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\begin{frame}
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\frametitle{Outline}
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%% \tableofcontents[hideallsubsections]
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\begin{enumerate}
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\item Introduction (now, 15 minutes)
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\item Using Emacs (45 minutes)
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\item Using ESS (60 minutes)
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\item Exercise 1: ESS
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\item Exercise 2: Sweave
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\item Emacs extensions (30 minutes)
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\item Emacs Lisp (30 minutes)
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\item Discussion and Misc Topics (related Emacs tools, ESS extensions, future designs)
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\end{enumerate}
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\end{frame}
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\subsection[Goals]{Goals for Today}
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\begin{frame}
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\frametitle{\#1: Efficient Program Editing}
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\framesubtitle{Edit, and let the computer repeat}
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\begin{itemize}
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\item Weird archaic keystrokes are dominant
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\item Weird archaic keystrokes can make life easier
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\item Menus and toolbars help Emacs
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\item Knowing R and data analysis means we can enhance related activities.
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\item Folding editors, Object explorers
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\end{itemize}
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\end{frame}
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\begin{frame}
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\frametitle{\#2: Process Interaction}
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\framesubtitle{You enter text for the process, so edit\ldots}
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\begin{itemize}
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\item R vs. ``emacs -f R''
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\item Getting Help
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\item Approaches for interacting
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\item Practical Directory layout
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\end{itemize}
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\end{frame}
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\begin{frame}
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\frametitle{\#3: Emacs is Extended and Extensible}
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\framesubtitle{Lisp and other hackers are your friends}
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\begin{itemize}
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\item Introduction to Lisp and Emacs Lisp
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\item Lisp extends Emacs
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\item Design of ESS
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\item Future Extensions??
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\end{itemize}
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\end{frame}
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%% \begin{frame}
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%% \frametitle{Make Titles Informative.}
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%% You can create overlays\dots
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%% \begin{itemize}
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%% \item using the \texttt{pause} command:
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%% \begin{itemize}
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%% \item
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%% First item.
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%% \pause
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%% \item
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%% Second item.
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%% \end{itemize}
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%% \item
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%% using overlay specifications:
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%% \begin{itemize}
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%% \item<3->
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%% First item.
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%% \item<4->
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%% Second item.
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%% \end{itemize}
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%% \item
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%% using the general \texttt{uncover} command:
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%% \begin{itemize}
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%% \uncover<5->{\item
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%% First item.}
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%% \uncover<6->{\item
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%% Second item.}
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%% \end{itemize}
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%% \end{itemize}
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%% \end{frame}
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\begin{frame}
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\frametitle{Disclaimer}
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\begin{itemize}
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\item ESS (and Emacs) is many (different) things to different
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people.
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\item Even for R development, the variation in personal philosophies
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and approaches for use is extremely high (even in the Core
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development team).
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\item Religious issues focusing on Emacs should be discussed elsewhere
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(c.f. \url{http://www.dina.kvl.dk/~abraham/religion/})
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\end{itemize}
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\end{frame}
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\begin{frame} \frametitle{Demo!}
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\framesubtitle{It'll get boring before it gets better\ldots}
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\alert{Please note or comment on any part that you'd like covered later.}
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\end{frame}
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\subsection{Introducing Emacs}
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\begin{frame} \frametitle{Overview}
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\begin{itemize}
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\item Emacs is the extensible, customizable, self-documenting
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real-time display editor.
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\item One of the oldest and yet still most powerful display editors
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\item The name \textbf{Emacs} comes from Editor (or Extensible)
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MACroS. (source of other amusing acronym expansions)
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\item Originally written in 1976 as a set of extensions to TECO
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(Text Editor and COrrector). It has since evolved.
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\end{itemize}
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\end{frame}
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\begin{frame} \frametitle{Pros and Cons for Emacs}
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\begin{itemize}
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\item \alert{Why use Emacs?} It is a powerful text editor which
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can be extended to be a general interface to a computer (everything can be done within it).
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\item It is highly portable (in its own way) across many platforms.
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\item \alert{Why do not use it?} It has a different user interface,
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which is understandable given its age (little change since 1985).
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\item It does not follow ``modern'' keybindings.
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\item People don't understand Lisp (otherwise, what they want to do
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could be done in Emacs)
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\end{itemize}
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\centerline{\alert{some people are allergic to it}}
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\end{frame}
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\begin{frame}
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\frametitle{On-line Resources}
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Links to links:
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\begin{itemize}
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\item Emacs Wiki: \url{http://www.emacswiki.org/}
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\item Emacs \url{http://www.gnu.org/software/emacs/}
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\item XEmacs \url{http://www.xemacs.org/}
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\item Emacs Lisp Library \url{http://www.damtp.cam.ac.uk/user/sje30/emacs/ell.html}
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\end{itemize}
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\end{frame}
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\begin{frame}
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\frametitle{The Emacsen Problem}
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\framesubtitle{different religions cause stress}
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There are many variants or dialects of Emacs (\textit{similar to the
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S language having AT\&T's S, Insightful's S-PLUS, and R-core's R})
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\begin{itemize}
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\item Emacs: ``classic version''
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\item XEmacs: ``experiments'' (GUIs, dynamic loading, packaging)
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\item SXEmacs: ``splinter'' (Unix-focus, streamlining XEmacs)
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\end{itemize}
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ESS support is best in order (Emacs, XEmacs, SXEmacs). Most active
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ESS developers use Emacs. Users seem to be split 50/50 between
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Emacs and XEmacs.\\
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No bug reports on SXEmacs\ldots
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\end{frame}
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\begin{frame}
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\frametitle{Installation}
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\framesubtitle{the bane of Emacs}
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Installation can be tricky:
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\begin{itemize}
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\item Linux: Emacs usually can be installed or is preinstalled
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\item Microsoft: XEmacs is easier to install, Emacs might be better
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supported.
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\item Mac OSX: Emacs, AquaEmacs; via Fink, or UCLA package, or\ldots
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(check on the list).
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\end{itemize}
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We aren't dealing with this here!
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\end{frame}
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\begin{frame} \frametitle{Editing methodology}
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\framesubtitle{Emacs resembles modern editors unlike dual-mode VI}
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\begin{itemize}
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\item Idea: every keystroke (or sequence of keystrokes) generates a
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list to evaluate (i.e. command, or lisp function with arguments).
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\item Pressing ``X'' evaluates the list (self-insert-command "X") (we'll talk about Lisp later)
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\item Modifiers extend the keyboard (CTL, SHIFT, ALT, pressed
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simultaneously, some such as ESC, META, and others are pressed
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first, released, and then followed by a key).
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\end{itemize}
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\end{frame}
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\subsection{Introducing ESS}
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\begin{frame}
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\frametitle{Overview}
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\framesubtitle{ESS augments Emacs for R}
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\begin{itemize}
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\item Emacs Speaks Statistics (or Emacs Statistical System)
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\item Oldest active statistically-focused OSS project (1989).
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\item Design goal: a consistent interface unifying batch and
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interactive data analysis styles.
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\item Novelty (at the time): process control, unified interface.
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\item String (stream) operations; ``cheap parser''.
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\item Supports R, S-PLUS, SAS, Stata, LispStat
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\item Current development team (n=6) spans the US and Europe.
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\end{itemize}
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\end{frame}
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\begin{frame} \frametitle{History}
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\begin{itemize}
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\item 3 branches: S-mode, SAS-mode, Stata-mode
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\item S-mode: 1989, 2 groups managing the project before (Bates/F
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Ritter/E Kademan, M Meyer, DM Smith (now Insightful)).
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R added in 1995 (Rossini/Maechler)
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\item SAS: '94, Tom Cook ('92, John Sall, SAS). Integrated '95-6, Rossini
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\item Stata-mode: 1997, Thomas Lumley. Added 1997 (Rossini).
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\item 1997: last major restructuring (``grand unification'')
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\item 2004: switch leaders: Maechler takes over
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\end{itemize}
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\alert{We are still suffering from the 1997 grand unification.}
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\end{frame}
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\begin{frame}
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\frametitle{Interactive Programming}
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\framesubtitle{Everything goes back to being Lisp}
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\begin{itemize}
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\item Interactive programming (as originating with Lisp): works
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extremely well for data analysis (Lisp being the original
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``programming with data'' language).
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\item Theories/methods for how to do this are reflected in styles
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for using ESS.
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\end{itemize}
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\alert{Good Statistical Analysis is on-line Interactive Programming}
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\end{frame}
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\begin{frame}
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\frametitle{Installation}
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\framesubtitle{We have to deal with this here, though\ldots}
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\begin{itemize}
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\item Fetch the ESS package (tar or zip-file)
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\item unpack
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\item add a line in \textbf{.emacs} to load the \textbf{ess-site.el} file.
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\item restart Emacs (or \textbf{M-x load-file /path/to/ess-site.el}).
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\end{itemize}
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\end{frame}
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\begin{frame}
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\frametitle{Review: Introduction}
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\begin{itemize}
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\item ESS is a program in Lisp to extend Emacs
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\item Characteristics: OSS, developed initially to make life easier;
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continued development supported research in enhanced data analysis
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interfaces.
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\item Emacs has strengths and weaknesses; these are usually
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different than percieved strengths and weaknesses.
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\end{itemize}
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\end{frame}
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\section{Using Emacs}
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\subsection{Overview: Emacs}
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\begin{frame} \frametitle{Goals}
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\begin{itemize}
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\item use of Emacs to edit files
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\item filesystem interaction
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\end{itemize}
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\end{frame}
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\subsection{Getting Started}
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\begin{frame}[fragile]
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\frametitle{Starting (X)Emacs}
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\framesubtitle{trivial but essential}
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\alert{emacs} can be used instead of \alert{xemacs}.
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\begin{verbatim}
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xemacs <filename> run xemacs, edit <filename>
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xemacs -nw run xemacs in _text_ mode
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(nw="No Window"; useful for
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slow remote connections)
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\end{verbatim}
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\begin{itemize}
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\item Once started, no need for more.
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\item \alert{Only run one Emacs session}. This is a cardinal rule,
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do not violate it.
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(c.f.\hyperlink{keystrokes:fileloading}{\beamerbutton{file-loading section}})
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\end{itemize}
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\end{frame}
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\begin{frame}[fragile]
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\frametitle{Breaking and Quitting!}
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\framesubtitle{essential knowledge}
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\label{emacs:basics}
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\begin{itemize}
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\item Decide you were wrong while Emacs works: \verb+C-g+ (universal break)
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\item Quit and terminate: \verb+C-x C-c+ (will usually prompt you
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for any files which are modified but not saved)
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\end{itemize}
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\end{frame}
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\begin{frame}[fragile]
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\frametitle{Understanding Keystrokes.}
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\begin{itemize}
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\item \verb+[tab]+ is the TAB (indent) key.
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\item \verb+[return]+ is the Return (carriage return, enter) key.
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\item \textbf{C-h} means press \alert{control key} AND ``\alert{h}'' key at same time.
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\item \textbf{ESC-h} means press \alert{ESC key} THEN ``\alert{h}''
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\item \textbf{M-h} means press \alert{ALT key} AND ``\alert{h}''
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\item \textbf{M-C-h} means press Meta or Alt while pressing h. OR
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(if no meta/alt): ESC THEN (control and h keys together).
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\end{itemize}
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Older keyboards (and sometimes older Macs) without ALT or Meta lead
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to confusion between ESC and Meta, but ideally they should be different.
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\end{frame}
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\begin{frame} \frametitle{Stopping Activity}
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\framesubtitle{you need to know this\ldots}
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\alert{C-g} stops the current Emacs activity to the best of its ability.
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\end{frame}
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\begin{frame}
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\frametitle{Windows and Frames}
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\begin{itemize}
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\item Window: a different view on (usually) a different buffer within the same application
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\item Frame: a different window/application in the windowing system.
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\end{itemize}
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\end{frame}
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\begin{frame}[fragile]
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\frametitle{File suffices drive mode setup}
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\framesubtitle{Use the right file name formats:}
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\begin{itemize}
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\item \verb+.S+, such as \verb+critical_simulation.S+
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\item \verb+.R+, such as \verb+speedy_simulation.R+
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\end{itemize}
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There are other ways to force a file to be edited in a particular
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mode, but at this point, keep it simple.
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\end{frame}
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\begin{frame}
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\frametitle{Commands}
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Emacs has a single command-entry mode. There are 2 approaches for commands:
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\begin{itemize}
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\item \textbf{M-x (command-name)}
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\item keystrokes/toolbars/menus (which implement the above)
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\end{itemize}
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\end{frame}
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\subsection{Keystrokes}
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\begin{frame}
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\frametitle{Learning the Strokes.}
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\begin{itemize}
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\item forced practice: painful but fast. Keep a copy of the
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reference cards nearby! (usually 2-3 days of severe pain,
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followed by bliss).
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\item accelerators and menus can help: but they quickly become a crutch.
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\item Consider working through the tutorial (\textbf{C-h t}).
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\end{itemize}
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\alert{this is a major issue for speed typists converting to/from
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Emacs usage.}
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\end{frame}
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\begin{frame}[fragile]
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\frametitle{Loading Files}
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\label{keystrokes:fileloading}
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\begin{itemize}
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\item \verb+C-x C-f+ (load new file, \textbf{not} deleting old)
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\item \verb+C-x 4 C-f+ (load new file in different window)
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\item \verb+C-x 5 C-f+ (load new file in different frame)
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\end{itemize}
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(c.f. \hyperlink{emacs:basics}{\beamerbutton{basics}})
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\end{frame}
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\begin{frame}[fragile]
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\frametitle{Changing Active Buffer (edit file)}
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To edit (operate on) another file:
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\begin{itemize}
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\item \verb+C-x b+ (switch to new buffer in same window)
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\item \verb+C-x 4 b+ (replaces current file in different window)
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\item \verb+C-x 5 b+ (replaces current file in different frame)
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\end{itemize}
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Buffers represent the files you are editing (explain).
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\end{frame}
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\begin{frame}
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\frametitle{Review of Common Keystrokes}
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\framesubtitle{Demo and pain}
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\end{frame}
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\subsection{In Any Emacs Buffer}
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\begin{frame}[fragile] \frametitle{Moving Around}
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\begin{verbatim}
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C-v Move forward one screenful
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M-v Move backward one screenful
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C-l Clear and redraw screen
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M- -> Meta-<right> - moves forward a word
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M- <- Meta-<left> - moves back a word
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M- |^ Meta-<up> - move up a paragraph
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M- V Meta-<down> - move down a paragraph
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M- < Meta-<less than> - move to file start
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M- > Meta-<greater than> - move to file end
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\end{verbatim}
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\end{frame}
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\begin{frame}[fragile] \frametitle{Cut and Paste}
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\begin{verbatim}
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C-d _D_elete
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C-k _K_ill from the cursor position to
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end of line
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C-y Recover/Paste (_Y_ank) killed text
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(repeat to copy)
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M-y recover former killed text (after C-y).
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Repeat to go back through stack).
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C-x u _U_ndo
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\end{verbatim}
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\end{frame}
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\begin{frame}[fragile] \frametitle{Loading / Saving Files}
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\begin{verbatim}
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C-x C-f _F_ind a file
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C-x C-s _S_ave the file
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If you find a second file with C-x C-f,
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the first file remains inside Emacs.
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You can switch back to it by finding it
480
again with C-x C-b. This way you can get
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quite a number of files inside Emacs.
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\end{verbatim}
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\end{frame}
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\begin{frame}[fragile] \frametitle{Managing Buffers and Windows}
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\begin{verbatim}
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C-x 0 Move between windows
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(Oh, not Zero!)
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C-x 1 One window
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(i.e., kill all other windows).
492
C-x b Switch to new _b_uffer
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C-x C-b List _b_uffers
494
\end{verbatim}
495
\end{frame}
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\begin{frame}[fragile] \frametitle{Search and Replace}
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\begin{verbatim}
500
M-x (then) replace-string
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Replace string
502
M-x (then) query-replace-string
503
Will ask you, for each match,
504
if you really want to replace
505
the old string with the new one.
506
C-s _S_earch forward (repeat to
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reuse past search strings)
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C-r Search _R_everse (repeat to
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reuse past search strings)
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\end{verbatim}
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\end{frame}
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\begin{frame}[fragile] \frametitle{Misc Emacs Actions}
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\begin{verbatim}
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C-h or C-h ? _H_elp
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C-h c (command) _H_elp on this _c_ommand
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C-u 8 (character or command)
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Repeat character/command 8 times
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C-g Stop, unhang.
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C-x C-c Stop and exit (_c_lose) Emacs
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\end{verbatim}
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\end{frame}
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\begin{frame}
529
\frametitle{Point and Mark}
530
\framesubtitle{critical concepts to learn}
531
532
\begin{itemize}
533
\item Point: where the cursor is.
534
\item Mark: a location that you've decided (actively or inactively)
535
is important.
536
\item Example: Move cursor somewhere. \textbf{M-x set-mark} or
537
\textbf{C-(space)}.
538
\item Exchange point and mark: \textbf{M-x
539
exchange-point-and-mark} or \textbf{C-x C-x}.
540
\end{itemize}
541
\end{frame}
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\subsection{Review: Using Emacs}
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\begin{frame}
546
\frametitle{Review}
547
\framesubtitle{Emacs}
548
\begin{itemize}
549
\item \textbf{C-g} stops emacs activity and returns to edit mode; \textbf{C-x C-c} quits
550
\item Try to use the keyboard and not the mouse, menus, or toolbars.
551
\item Keypresses are simply commands.
552
\item Biggest user headache? Differenting commands and text entry
553
\item Buffers represent the files you are editing. Morally, they
554
are the files themselves (with important exceptions).
555
\end{itemize}
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\end{frame}
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\section{Using ESS}
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\subsection{Overview: ESS}
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\begin{frame}
564
\frametitle{Overview: ESS}
565
This section should provide an overview for
566
\begin{itemize}
567
\item editing
568
\item interaction with R
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\item facilitating help
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\item reusing transcripts
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\item Sweave support
572
\end{itemize}
573
and finally, \alert{putting it all together}
574
\end{frame}
575
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\subsection{Editing}
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\begin{frame}[fragile]
579
\frametitle{Coding Style}
580
\framesubtitle{Indentation makes code readable}
581
582
Comment conventions:
583
\begin{enumerate}
584
\item \verb+#+ gets moved to the right-side of the line
585
\item \verb+##+ is placed at the current indentation level
586
\item \verb+###+ is placed flush-left.
587
\end{enumerate}
588
\end{frame}
589
590
\begin{frame}[fragile]
591
\frametitle{Indentation Example}
592
\begin{verbatim}
593
my.x <- rnorm(10)
594
### This is flush
595
## but this is at level
596
# this is right
597
\end{verbatim}
598
\end{frame}
599
600
601
\begin{frame}[fragile]
602
\frametitle{Editing, ESS adds\ldots}
603
\begin{itemize}
604
\item Automatic fontification, indentation
605
\end{itemize}
606
If R is running in another buffer:
607
\begin{itemize}
608
\item evaluation of lines (C-c C-n), regions (C-c C-r), functions
609
(C-c C-f), and buffers (C-c C-b)
610
\item help output in other buffers (and via command, C-c C-v)
611
\item Object (data, function) completion
612
\begin{itemize}
613
\item \verb+C-c [tab]+
614
\item \verb+[tab]+ (sometimes).
615
\end{itemize}
616
\item Filename completion: M-\[tab\]
617
\end{itemize}
618
\end{frame}
619
620
\begin{frame}[fragile]
621
\frametitle{R editing buffer}
622
\framesubtitle{Usually named for the file being edited}
623
(mode line says "ESS[S]")
624
\begin{verbatim}
625
C-c C-j Send line to R
626
C-c C-n Send line to R
627
and go to _n_ext line
628
C-c C-r Send highlighted _r_egion to R
629
C-c C-b Send whole _b_uffer to R
630
C-c C-f Send _f_unction surrounding
631
cursor to R
632
C-c C-v xxx get R help on "xxx"
633
\end{verbatim}
634
\end{frame}
635
636
\subsection{Interactive}
637
638
\begin{frame}
639
\frametitle{Run R}
640
\begin{itemize}
641
\item Within emacs
642
\item At the command line
643
\end{itemize}
644
\end{frame}
645
646
\begin{frame}[fragile]
647
\frametitle{R process within Emacs (on start)}
648
\framesubtitle{starting from the command line or launcher}
649
Replace the command \textbf{R} with one of:
650
\begin{verbatim}
651
emacs -f R run (x)emacs, starting R
652
xemacs -f R session
653
\end{verbatim}
654
adds a few nice features to the command interface. (follow with
655
\textbf{\&} to background the process; \verb+xemacs+ might also
656
work)
657
\end{frame}
658
659
\begin{frame}[fragile]
660
\frametitle{R process within Emacs (running emacs)}
661
\framesubtitle{Starting from a running emacs}
662
\begin{verbatim}
663
M-x R Start R process buffer
664
M-x R-mode Change mode of current buffer
665
for R code editing
666
\end{verbatim}
667
\end{frame}
668
669
\begin{frame}[fragile]
670
\frametitle{Evaluate file contents}
671
\framesubtitle{working from the editing (ESS) buffer}.
672
673
From a file of commands:
674
\begin{itemize}
675
\item Send current line to R: \verb+C-c C-j+
676
\item Send current function to R (assumes the cursor is in the
677
function body): \verb+C-c C-f+.
678
\item Send current region (highlighted) to R \verb+C-c C-r+
679
\item Send whole buffer/file to R \verb+C-c C-b+
680
\end{itemize}
681
\end{frame}
682
683
\begin{frame}[fragile]
684
\frametitle{Object and File completion}
685
Completion of objects (functions and data):
686
\begin{enumerate}
687
\item \verb+C-c [tab]+
688
\item \verb+[tab]+ (sometimes).
689
\end{enumerate}
690
\end{frame}
691
692
\begin{frame}
693
\frametitle{Dumping Objects}
694
\framesubtitle{Getting objects back}
695
(for modification, saving, eventual reloading):
696
\begin{enumerate}
697
\item \textbf{C-c C-d} dumps the named object into an editing buffer
698
\item Examples: today's date for use as a log file; (140606), ``lm''.
699
\item if object doesn't exist: create a blank buffer
700
\item if object exists: insert the object's textual representation (no comments)
701
\item The file will be stored in \textbf{/tmp/username.objectname.R}
702
(unless you want it elsewhere or named something else).
703
\end{enumerate}
704
Type commands into the edit file, evaluate them when desired, edit
705
as needed for correctness (and comment mistakes, with reasons for
706
them, for later reminders and documentation).
707
\end{frame}
708
709
\begin{frame}[fragile]
710
\frametitle{Commandline History}
711
\framesubtitle{ESS remembers what you've done}
712
Search command-line history ``manually'', matching on current input
713
\begin{enumerate}
714
\item backwards: \verb+M-p+
715
\item forwards: \verb+M-n+
716
\end{enumerate}
717
Complete current line based on command-line history:
718
\begin{enumerate}
719
\item backwards: \verb+\C-[uparrow]-p+
720
\item forwards: \verb+M-n+
721
\end{enumerate}
722
If you are reviewing old commands, to re-enter it (i.e. cursor on that line)
723
\verb+[return]+.
724
\end{frame}
725
726
\begin{frame}
727
\frametitle{Philosophy: Files are ``truth''}
728
\framesubtitle{Don't believe your .RData}
729
\begin{itemize}
730
\item This is a generally decent approach.
731
\item Saving objects in binary format in special files can be a
732
reasonable strategy
733
\item Work from an R file, \emph{submitting} commands to the R
734
process. This saves the source, and allows for structuring of the
735
input, along with having a transcript of the order of commands to
736
understand reproducibility aspects.
737
\end{itemize}
738
\end{frame}
739
740
\begin{frame}[fragile]
741
\frametitle{Working from R process}
742
\framesubtitle{from the process (inferior ESS, or iESS) buffer}
743
\alert{not usually recommended}
744
\begin{enumerate}
745
\item One improvement is to use a \verb+source()+-like facility. To
746
source a file into R (within ESS): \textbf{C-c C-l} (load file)
747
\item To find what the errors are (if any): \textbf{C-c `} (backquote).
748
\end{enumerate}
749
The latter will tell you what the error is. You'll have to go back
750
to the file (\textbf{C-x C-b} or use \textit{Buffers} menu item to
751
bring in back to the screen) and correct it.
752
\end{frame}
753
754
\begin{frame}[fragile]
755
\frametitle{Working from R buffer}
756
\framesubtitle{from the editing (ESS) buffer}
757
Better yet, use a file, and send material from the file straight to
758
the process. This works if the file ends in the proper suffix (and
759
hence, the mode at the bottom should say ``ESS''). The following is
760
possible:
761
\begin{itemize}
762
\item Send current line to R: \textbf{C-c C-j}
763
\item Send current function to R (assumes the cursor is in the
764
function body): \textbf{C-c C-f}
765
\item Send current region (highlighted) to R: \textbf{C-c C-r}
766
\item Send whole buffer/file to R: \textbf{C-c C-b}
767
\end{itemize}
768
\end{frame}
769
770
\begin{frame}
771
\frametitle{Philosophy: RData is true}
772
\framesubtitle{Editing objects without source}
773
\begin{itemize}
774
\item This is a dangerous approach; corruption of the RData file is
775
more difficult to fix using an editor or other external tools than
776
corruption of text files, usually.
777
\item Trusting .RData to have what you've done is rather suboptimal
778
strategy (quite prone to user mistakes)
779
\end{itemize}
780
\end{frame}
781
782
\begin{frame}
783
\frametitle{If you must use a command line\ldots}
784
\begin{itemize}
785
\item This style is useful for quick and dirty exercises/testing.
786
\item Transcripts can be cleaned and edited to record the salient
787
points of the sesssion.
788
\end{itemize}
789
\end{frame}
790
791
\subsection{Putting it together}
792
793
\begin{frame}
794
\frametitle{Begin ESS/Emacs/R}
795
\begin{enumerate}
796
\item Start XEmacs (in a terminal window, enter \textbf{xemacs \&})
797
\item Start R (\textbf{M-x R}).
798
\item Load a file (\textbf{C-x C-f} \textit{filename})
799
\end{enumerate}
800
\end{frame}
801
802
\begin{frame}[fragile]
803
\frametitle{Data Analysis Example}
804
Demo.
805
\end{frame}
806
807
\begin{frame}[fragile] \frametitle{Function Editing}
808
\begin{enumerate}
809
\item demo.R: evaluate.
810
\item Try editing existing functions: \textbf{my.test.function} and
811
\textbf{that}, by \textbf{C-c C-d this}. Remember that you should
812
be able to complete the name using \textit{ajr.t}\textbf{SPACE}
813
(i.e. Control-C, then SPACE key). Generally, completion of
814
variables and functions can be done using \textbf{C-c [tab]} in the
815
editing buffer, and \textbf{SPACE} in the command entry area (at
816
the very bottom of the Emacs screen/window).
817
\end{enumerate}
818
\end{frame}
819
820
\subsection{Special Facilities and Activties}
821
822
\begin{frame}
823
\frametitle{Navigating Help Buffers}
824
\begin{itemize}
825
\item To get help on a function (help(``lm'')) without
826
spoiling your input line: \textbf{C-c C-v}
827
\item Navigation of sections: ``n'' next section, ``p'' prev section.
828
\item evaluation of example: ``l'' (eval line) ``r'' eval region.
829
\item searching: ``/'' isearch forward
830
\item kill-buffer and go \textit{back}: ``x''
831
\end{itemize}
832
See menu items
833
\end{frame}
834
835
\begin{frame}
836
\frametitle{Using Transcripts}
837
\framesubtitle{for teaching, reproduction, and audits}
838
\begin{itemize}
839
\item Transcript suffix: .Rt
840
\item Stepping through entries:
841
\item Cleaning transcripts: \textbf{M-x ess-transcript-clean-buffer}
842
\item Cleaning transcripts: \textbf{M-x ess-transcript-DO-clean-region} (even when read-only toggled)
843
\end{itemize}
844
\end{frame}
845
846
\begin{frame}
847
\frametitle{Using Multiple Processes}
848
\framesubtitle{For when you want to multitask}
849
ESS supports multiple processes. This is useful for
850
\begin{itemize}
851
\item testing on multiple versions of R
852
\item testing on R and S-PLUS (and S4, if one still has a copy)
853
\item inefficient multiprocessing
854
\end{itemize}
855
\end{frame}
856
857
\begin{frame}
858
\frametitle{Using Remote Processes}
859
\framesubtitle{loading other people's computers}
860
Since we are capturing/using R text I/O, local or remote is not an
861
issue (running R in an Emacs shell, logged in (shell account via
862
telnet, ssh, rlogin) to another machine)
863
\begin{itemize}
864
\item \textbf{M-x ESS-remote}
865
\item follow instructions
866
\end{itemize}
867
\end{frame}
868
869
\begin{frame}[fragile]
870
\frametitle{Customizing ESS}
871
See (commented out) example customizations in ess-site.el (assuming
872
that the lisp files are installed:
873
\begin{verbatim}
874
M-x locate-library [return] ess-site [return]
875
\end{verbatim}
876
will help. Also,
877
\begin{verbatim}
878
M-x customize-group [return] ess
879
\end{verbatim}
880
helps to review possible customizations (this is an alternative to
881
editing the \textbf{\~{}/.emacs} file for setting customizing
882
variables).
883
\end{frame}
884
885
\subsection{Sweave Support}
886
887
\begin{frame}
888
\frametitle{Overview: Sweave}
889
Sweave originated from the Literate Data Analysis philosophy which
890
in itself was the idea of applying Literate Programming to the
891
specialized programming discipline \emph{interactive data analysis}.
892
893
Support for editing Noweb files existed within ESS 4 years before
894
Sweave, but Sweave is a ``Killer App''.
895
\end{frame}
896
897
\begin{frame}
898
\frametitle{Documents as Programs}
899
\begin{itemize}
900
\item Every electronic document is a ``computer program'' (sometimes
901
at a primitive level) for some rendering device or program (such
902
as: Microsoft Word; Postscript printers; Adobe Acrobat Reader;
903
Emacs)
904
\item This is the general theory behind the WWW, as well as the
905
so-called \emph{Semantic Web}.
906
\end{itemize}
907
\end{frame}
908
909
\begin{frame}
910
\frametitle{Literate Programming}
911
A programming methodology devised by Donald Knuth in the late 70s,
912
early 80s, which mixes computer programs doing mathematics with
913
mathematical documentation (formulas, theorems, algorithms).
914
915
2 operations:
916
\begin{itemize}
917
\item Tangling: translating document into undocumented computer source code for
918
compiling.
919
\item Weaving: translating document into documentation for the source code.
920
\end{itemize}
921
The original tool was called Web (predates the \textit{World-Wide-Web}).
922
\end{frame}
923
924
\begin{frame} \frametitle{Literate Statistical Practice}
925
\framesubtitle{or \emph{Literate Data Analysis:}}
926
The application of literate programming to statistics; recognizing
927
that statistical data analysis is a specialized programming activity
928
with different characteristics than systems programming or
929
applications programming.
930
931
(realization prototype: ESS-Noweb and Sweave).
932
\end{frame}
933
934
\begin{frame} \frametitle{ESS enhances Sweave}
935
\begin{itemize}
936
\item context specific modes (doc: latex, html, muse; code: R, etc).
937
\item chunk and thread evaluation.
938
\item functions for processing Sweave files.
939
\end{itemize}
940
\end{frame}
941
942
\begin{frame}
943
\frametitle{Evaluation}
944
\framesubtitle{Chunks and Threads}
945
\begin{itemize}
946
\item eval-chunk (run code inside a code chunk)
947
\item eval-thread (run code inside a series of code chunks)
948
\end{itemize}
949
\end{frame}
950
951
\begin{frame}
952
\frametitle{Accelerated Sweave Development }
953
\begin{itemize}
954
\item ESS has specialized support
955
\item use Makefiles (editor-neutral approach)
956
\item \textbf{M-x ess-makeSweave} or \textbf{M-n s}
957
\item \textbf{M-x ess-makeLatex} or \textbf{M-n l}
958
\item \textbf{M-x ess-makePS} or \textbf{M-n p}
959
\item \textbf{M-x ess-makePDF} or \textbf{M-n P}
960
\item \textbf{M-x ess-insert-Sexpr} or \textbf{M-n x}
961
\end{itemize}
962
\end{frame}
963
964
\subsection{Review: ESS}
965
966
\begin{frame}
967
\frametitle{Review: Using ESS}
968
\begin{itemize}
969
\item ESS for R has 4 modes: editing, interactive, transcript, help.
970
\item Focus on learning to use keystrokes rather than mouse.
971
\end{itemize}
972
\end{frame}
973
974
\section{Emacs is Extended}
975
976
\begin{frame}
977
\frametitle{Packages and Extensions.}
978
Emacs has many modes:
979
\begin{itemize}
980
\item language-specific markup (programming, markup)
981
\item editor behavior (spell checking, pending delete, folding,
982
editor emulation (vi, brief))
983
\item IDE capabilities (object explorers, completers)
984
\item database (edb)
985
\item communication (mail, news, www, rdf)
986
\item sub (inferior) process control (telnet, R, \ldots)
987
\item publication (text mode conversion)
988
\item version control interfaces
989
\item anything you can program!
990
\end{itemize}
991
\end{frame}
992
993
\begin{frame}
994
\frametitle{Relevant to Data analysis and R}
995
\begin{itemize}
996
\item folding modes (outline; however, the newer version, allout,
997
stomps on R-mode)
998
\item object explorers (ecb)
999
\item documentation modes
1000
\begin{itemize}
1001
\item specialized: latex, html, rtf
1002
\item generic: muse, \ldots (idea: simple markup which translates to
1003
html, latex, texinfo, etc).
1004
\end{itemize}
1005
\end{itemize}
1006
\end{frame}
1007
1008
\begin{frame}
1009
\frametitle{Dired}
1010
A directory/file explorer and navigator.
1011
\end{frame}
1012
1013
\begin{frame}
1014
\frametitle{Emacs Code Browser}
1015
\begin{itemize}
1016
\item ESS integrates to support R
1017
\item Extension/customization: through imenu support.
1018
\item file-level navigation and objects, editing history of files,
1019
files in current directory, directory tree.
1020
\end{itemize}
1021
(demo with R-examples/FCS.R)
1022
\end{frame}
1023
1024
\begin{frame}
1025
\frametitle{Muse}
1026
\framesubtitle{a mode for documentation and notes}
1027
\begin{itemize}
1028
\item Wiki-like editing, hyperlinks, within text.
1029
\item simple format
1030
\item Supports generation of latex, pdf, (x)html, xml.
1031
\end{itemize}
1032
\end{frame}
1033
1034
\begin{frame}
1035
\frametitle{Planner: Task management}
1036
\framesubtitle{getting organized and tracking activity}
1037
\begin{itemize}
1038
\item Plain-text task management and organization
1039
\item Supports many common time-management approaches (GTD, ).
1040
\item Extremely customizeable
1041
\end{itemize}
1042
\end{frame}
1043
1044
\subsection{LaTeX Extensions}
1045
1046
\begin{frame}
1047
\frametitle{LaTeX Support}
1048
\framesubtitle{nearly WYSIWYG}
1049
\begin{itemize}
1050
\item AUC-TeX: latex document support
1051
\item BiBTeX-mode and RefTeX: citation management
1052
\item X-Symbol: native display of mathematical symbols
1053
\item tex-preview: You can see what you will get (YCSWYWG)
1054
\end{itemize}
1055
\end{frame}
1056
1057
\section{Lisp and Emacs Lisp}
1058
1059
\begin{frame}
1060
\frametitle{Customizing Emacs}
1061
\framesubtitle{Sometimes with Lisp}
1062
\begin{itemize}
1063
\item Critical components for customizing Emacs: current best
1064
practices suggest that you customize via ``M-x customize''. (this
1065
is a recent (last 5 years) change!).
1066
\item However, adding Lisp commands to your \textbf{.emacs} file is
1067
still very useful (and sometimes required).
1068
\item Note that commas denote comments (from the comma until the end
1069
of the line).
1070
\end{itemize}
1071
\end{frame}
1072
1073
\subsection{Introduction to Lisp}
1074
1075
\begin{frame}[fragile]
1076
\frametitle{Lisp}
1077
Lisp (LISt Processor) is different than most high-level computing
1078
languages, and similar to Emacs, it is very old (1956). Lisp is
1079
built on lists of things which might be evaluated:
1080
\begin{verbatim}
1081
(function data1 data2 data3)
1082
\end{verbatim}
1083
or ``quoted'':
1084
\begin{verbatim}
1085
'(function data1 data2 data3)
1086
\end{verbatim}
1087
The difference is important -- lists of data (the second) are not
1088
functions applied to data (the first).
1089
\end{frame}
1090
1091
\begin{frame}[fragile]
1092
\frametitle{Evaluation}
1093
Lisp is built on lists of things which might be evaluated:
1094
\begin{verbatim}
1095
(function data1 data2 data3)
1096
\end{verbatim}
1097
or ``quoted'':
1098
\begin{verbatim}
1099
'(function data1 data2 data3)
1100
(list function data1 data2 data3)
1101
\end{verbatim}
1102
The difference is important -- lists of data (the second) are not
1103
functions applied to data (the first).
1104
\end{frame}
1105
1106
\begin{frame}[fragile]
1107
\frametitle{Defining Variables}
1108
\framesubtitle{Setting variables}
1109
\begin{verbatim}
1110
(setq <variable> <value>)
1111
\end{verbatim}
1112
Example:
1113
\begin{verbatim}
1114
(setq ess-source-directory
1115
"/home/rossini/R-src")
1116
\end{verbatim}
1117
\end{frame}
1118
1119
\begin{frame}[fragile]
1120
\frametitle{Defining on the fly}
1121
\begin{verbatim}
1122
(setq ess-source-directory
1123
(lambda () (file-name-as-directory
1124
(expand-file-name
1125
(concat (default-directory)
1126
ess-suffix "-src")))))
1127
\end{verbatim}
1128
(Lambda-expressions are anonymous functions, i.e. ``instant-functions'')
1129
\end{frame}
1130
1131
1132
\begin{frame}[fragile]
1133
\frametitle{Function Reuse}
1134
By naming the function, we could make the previous example reusable
1135
(if possible):
1136
\begin{verbatim}
1137
(defun my-src-directory ()
1138
(file-name-as-directory
1139
(expand-file-name
1140
(concat (default-directory)
1141
ess-suffix "-src"))))
1142
\end{verbatim}
1143
Example:
1144
\begin{verbatim}
1145
(setq ess-source-directory (my-src-directory))
1146
\end{verbatim}
1147
\end{frame}
1148
1149
\begin{frame}[fragile]
1150
\frametitle{Programming Emacs Lisp}
1151
1152
There are three general approaches to testing, evaluating, and
1153
deploying Emacs Lisp code.
1154
\begin{itemize}
1155
\item Loading files: \verb+M-x load-file <filename.el>+
1156
\item Using the \verb+*scratch*+ buffer
1157
\item \verb+ielm+ , an emacs-lisp REPL
1158
\end{itemize}
1159
Review the latter two
1160
\end{frame}
1161
1162
\begin{frame}[fragile]
1163
\frametitle{Playing in the scratch buffer.}
1164
\begin{enumerate}
1165
\item \verb+C-x b *scratch*+
1166
\item (display-time)\verb+C-j+
1167
\item (setq my-test ``asdf'')\verb+C-j+
1168
\item my-test\verb+C-j+
1169
\end{enumerate}
1170
\end{frame}
1171
1172
\begin{frame}
1173
\frametitle{ielm: command-line usage.}
1174
\begin{enumerate}
1175
\item M-x ielm
1176
\item follow the instructions for more information (similar to using
1177
R in interactive mode)
1178
\end{enumerate}
1179
\end{frame}
1180
1181
\subsection{Extending Emacs and ESS}
1182
1183
\begin{frame}
1184
\frametitle{Organization.}
1185
\framesubtitle{Structure of ESS}
1186
\begin{itemize}
1187
\item How ESS works
1188
\item Reading the code
1189
\item making extensions
1190
\end{itemize}
1191
\end{frame}
1192
1193
\begin{frame}
1194
\frametitle{Debugging.}
1195
\begin{itemize}
1196
\item Set options to ``debug on error'' and ``debug on signal''.
1197
Both bring up the stack-trace of the current status of the lisp
1198
program (nesting and variable values).
1199
\item Look for errors in loading to determine the path taken to the error
1200
\item more sophisticated debuggers exist.
1201
\end{itemize}
1202
\end{frame}
1203
1204
1205
\begin{frame}
1206
\frametitle{Idea generation: SLIME}
1207
\framesubtitle{Lisp IDE suggests ESS improvements}
1208
\begin{itemize}
1209
\item Use R subprocesses (old idea of DTL).
1210
\item Synchronize processes
1211
\end{itemize}
1212
\end{frame}
1213
1214
1215
\section{Discussion}
1216
1217
\begin{frame}
1218
\frametitle{Future?}
1219
\begin{itemize}
1220
\item Continued support for R within ESS
1221
\item Object and formating support
1222
\end{itemize}
1223
\end{frame}
1224
1225
1226
\begin{frame}
1227
\frametitle<presentation>{Summary}
1228
1229
% Keep the summary *very short*.
1230
\begin{itemize}
1231
\item
1232
Emacs takes time to learn, but rewards the user.
1233
\item
1234
ESS enhances R.
1235
\item
1236
Lisp is worth learning.
1237
\end{itemize}
1238
1239
% The following outlook is optional.
1240
\vskip0pt plus.5fill
1241
\begin{itemize}
1242
\item
1243
Outlook
1244
\begin{itemize}
1245
\item
1246
ESS is the oldest open-source statistics project; yet it can
1247
always be improved!
1248
\item
1249
Many possible extensions for supporting work modes for
1250
Statisticians and Data Analysts. More need implementation.
1251
\end{itemize}
1252
\end{itemize}
1253
\end{frame}
1254
1255
\end{document}
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