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- Committer: Bazaar Package Importer
- Author(s): Camm Maguire
- Date: 2004-11-11 00:51:43 UTC
- mfrom: (1.1.2 upstream)
- mto: This revision was merged to the branch mainline in revision 3.
- Revision ID: james.westby@ubuntu.com-20041111005143-wv1cih1h04xyrxrb
Tags: 5.2.3-3
* repair broken replace-regexp-in-string -> ess-replace-regexp-in-string
patch
* expand autoload functionality in emacsen-startup
patch
* expand autoload functionality in emacsen-startup
added
removed
doc/ess-intro-graphs.tex
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\documentclass{article}
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\newif\ifMM\MMtrue
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\MMfalse
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\newif\ifdraft
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% During writing: a draft:
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%\drafttrue
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% FINAL:
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\draftfalse \ifMM\drafttrue\fi
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\ifdraft %% generate tableofcontents down to the \paragraph
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\setcounter{tocdepth}{5}
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\fi
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%1. introduction
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% a) a statistician's needs
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% b) statistical analysis packages supported by ESS
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%2. emacs
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% a) buffers
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% b) key sequences
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% c) modes
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% 1) font-lock
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% 2) shell/comint
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% 3) ange-ftp/EFS/tramp
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% 4) vc/pcl-cvs
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%3. ESS
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% a) interactive
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% 1) S family
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% 2) SAS
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% b) batch
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% 1) SAS
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% 2) BUGS
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% 3) S family
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%4. ESS as an open-source project
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% a) origins
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% 1)S-mode
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% 2)SAS-mode
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% b) unification
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% 1)ESS-mode
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% 2)Emacs/XEmacs
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% 3)Unix/Windows/Mac
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%5. conclusion
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% a) summary
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% b) what's next for ESS
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% ESS internet resources
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% a) home page
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% b) ess-help
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% c) anonymous cvs
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% References
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%
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\ifdraft
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%%%
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\usepackage[authoryear,round]{natbib}
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%or (if you have an unshiny latex installation)
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%\newcommand{\citep}[1]{{\{\sf#1\}}}
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%%%
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\usepackage{alltt}
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%% Postscript fonts
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\usepackage{times}
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\usepackage{graphicx}
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%\DeclareGraphicsExtensions{.jpg,.pdf,.png,.mps,.ps}
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\DeclareGraphicsRule{.ps}{eps}{.ps.bb}{}
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\DeclareGraphicsRule{.ps.Z}{eps}{.ps.bb}{'/bin/zcat -c #1}
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%\graphicspath{{jcgs/}}
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%\usepackage{psfig}
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\ifx\pdfoutput\undefined
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%% Stuff wout hyperref
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\def\url#1{\stexttt{#1}} % To help fit in lines ?AJR: stextsf?
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\else
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\usepackage{hyperref}
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\fi
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%%---End of package requiring ---------- Own Definitions -------------
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\newcommand*{\regstrd}{$^{\mbox{\scriptsize{\textregistered}}}$}
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\newcommand*{\tm}{$^{\mbox{\scriptsize\sc tm}}$}
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\newcommand*{\SAS}{\textsc{SAS}}
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\newcommand*{\Splus}{\textsc{S-Plus}}
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\newcommand*{\XLispStat}{\textsc{XLispStat}}
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\newcommand*{\Stata}{\textsc{Stata}}
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\newcommand*{\Rgui}{\textsc{Rgui}}
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\newcommand*{\Perl}{\textsc{Perl}}
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\newcommand*{\Fortran}{\textsc{Fortran}}
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\newcommand*{\Scmt}[1]{\hbox{\qquad {\footnotesize \#\#} \textsl{#1}}}
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\newtheorem{defn}{Definition}[section]
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\newcommand{\stexttt}[1]{{\small\texttt{#1}}}
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\newcommand{\ssf}[1]{{\small\sf{#1}}}
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\newcommand{\elcode}[1]{\\{\stexttt{\hspace*{2em} #1}}\\}
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\rule{.25pt}{10pc}}
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\newcommand{\ESSfig}[1]{\centering{#1}}
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%% Use \begin{Comment} .. \end{Comment} for internal comments
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\ifdraft
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%%--------------------------------------------------------------- Start Text
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\title{Emacs Speaks Statistics (ESS): A multi-platform, multi-package
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intelligent environment for statistical analysis}
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%%For blinded submission:
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%\author{anonymous}
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%%For regular review:
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\author{A.J. Rossini \and Richard M. Heiberger \and Rodney A. Sparapani
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\and Martin M{\"a}chler \and Kurt Hornik \footnote{%
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%%
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A.J. Rossini is Research Assistant Professor in the Department of
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Biostatistics, University of Washington and Joint Assistant Member at
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the Fred Hutchinson Cancer Research Center, Seattle, WA, USA
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\url{mailto: rossini@u.washington.edu};
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%%
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Richard M. Heiberger is Professor in the Department of Statistics at
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Temple University, Philadelphia, PA, USA \url{mailto: rmh@temple.edu};
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%%
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Rodney A. Sparapani is Senior Biostatistician in the Center for Patient
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Care and Outcomes Research at the Medical College of Wisconsin,
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Milwaukee, WI, USA \url{mailto: rsparapa@mcw.edu};
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%%
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Martin M{\"a}chler is Senior Scientist and Lecturer in the Seminar for
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Statistics, ETH Zurich, Zurich, Switzerland
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\url{mailto: maechler@stat.math.ethz.ch};
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%%
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Kurt Hornik is Professor in the Institut f{\"u}r Statistik,
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Wirtschaftsuniversit{\"a}t Wien and the Institut f{\"u}r
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Wahrscheinlichkeitstheorie und Statistik, Technische Universit{\"a}t
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Wien, Vienna, Austria \url{mailto: Kurt.Hornik@r-project.org}}}
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%%\date{\today}
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\date{$ $Date: 2003/10/22 17:34:04 $ $\tiny Revision: 1.255$ $}
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\begin{document}
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%% To cite everything
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%%\nocite{*}
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\ifdraft
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\setcounter{page}{0}
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%%\newpage
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\tableofcontents
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\fi
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\maketitle
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\ifdraft{}%% large line skip -- not for draft
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\else%FINAL:
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\renewcommand{\baselinestretch}{1.5}
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%%- \baselineskip=2pc
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\fi
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\begin{abstract}
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Computer programming is an important component of statistics
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research and data analysis. This skill is necessary for using
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sophisticated statistical packages as well as for writing custom
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software for data analysis. Emacs Speaks Statistics (ESS) provides
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an intelligent and consistent interface between the user and
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software. ESS interfaces with SAS, S-PLUS, R, and other statistics
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packages under the Unix, Microsoft Windows, and Apple Mac operating
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systems. ESS extends the Emacs text editor and uses its many
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features to streamline the creation and use of statistical software.
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ESS understands the syntax for each data analysis language it works
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with and provides consistent display and editing features across
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packages. ESS assists in the interactive or batch execution by the
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statistics packages of statements written in their languages. Some
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statistics packages can be run as a subprocess of Emacs, allowing
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the user to work directly from the editor and thereby retain a
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consistent and constant look-and-feel. We discuss how ESS works and
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how it increases statistical programming efficiency.
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\end{abstract}
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\noindent Keywords: Data Analysis, Programming,
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S, \SAS, \Splus, R, \XLispStat, \Stata, BUGS, Open Source Software,
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Cross-platform User Interface.
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\section{Introduction}
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\label{sec:introduction}
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Most statistical research activities, particularly data analysis and
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communication, involve some form of computing. The computer user
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interface is thus placed in the central role of facilitating
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statistical tasks. While presentation of character and graphical
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information is the most visual component of a user interface,
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perhaps a more critical component is how the computer interprets user
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input. A familiar, well-understood set of input behaviors can provide
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large gains in efficiency. This paper introduces Emacs Speaks
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Statistics (ESS) \citep{ESS}, a software package which provides a
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common interface to a variety of statistical packages on the most
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common computing platforms.
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ESS is an interface to statistical packages that provides tools which
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facilitate both statistical software development and data analysis.
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ESS provides assistance with both writing and evaluation of analysis
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code for both interactive and batch statistical packages. ESS
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currently supports the S family of languages (including S
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\citep{BecRCW88,ChaJH92,ChaJ98}, \Splus\regstrd\ \citep{Splus}, and R
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\citep{ihak:gent:1996,R}; \SAS\regstrd\ \citep{SAS:8}; \Stata\
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\citep{Stata:7.0}; \XLispStat\ \citep{Tier90} and its extensions Arc
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\citep{Cook:Weisberg:1999} and ViSta \citep{youn:fald:mcfa:1992}; BUGS
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\citep{BUGS}; and Omegahat \citep{DTLang:2000}. ESS can be extended
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to accommodate most statistical packages which provide either an
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interactive command-line or process batch files for instructions.
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We start by describing the Emacs text editor, the underlying platform
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on which ESS is built. Next, we discuss how ESS enhances a
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statistician's daily activities by presenting its features and showing
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how it facilitates statistical computing. We conclude with a short history
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of the development of ESS.
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% and conclude with future extensions and related work.
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\section{Emacs}
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\label{sec:emacs}
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Emacs is a mature, powerful, and extensible text editing system which
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is freely available, under the GNU General Public License (GPL), for a
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large number of platforms, including most Unix\regstrd
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distributions, Microsoft Windows\regstrd\ and Apple Mac\tm\ OS. There
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are two open-source implementations of Emacs: GNU Emacs
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\citep{GNU-Emacs} and XEmacs \citep{XEmacs}. Emacs shares many
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features with word processors, and some characteristics with operating
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systems, including many facilities which go beyond ordinary text
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editing. More important to our goals, Emacs can control and interact
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with other programs.
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\paragraph{Keyboard and Mouse Input.}
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When Emacs was originally written, character-based terminals were the
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most advanced method of computer access. Common Emacs commands were
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mapped to key sequences, creating keyboard shortcuts for convenience.
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Over the last decade, Emacs has been extended to use graphical
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windowing systems, such as X11\tm, Microsoft Windows, and Apple Mac
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OS, which allow additional forms of input, for example using a mouse,
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and which encourage multiple applications to share a single display.
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Presently, Emacs is more often used with a GUI, with commands bound to
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mouse actions, but having commands also associated with key sequences
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is an important ergonomic and time-saving feature. Emacs menus and
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toolbars on the display screen allow mouse access to frequently used
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actions and provide a graphical alternative when the user does not
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know or can not recall a key sequence; these are also subject to
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user-customization.
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\paragraph{Buffers give Emacs control.}
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Emacs buffers are the interface between the user and computer. They
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can be considered to be a collection of scratch pads that both the
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user and computer can read, write, and respond to. The user can
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simultaneously edit many files and control numerous programs by
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opening multiple buffers. With disk files, the working copy of the
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opened file is placed in an Emacs buffer where it can be viewed and
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edited either by the user or automatically by Emacs or another program
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under the control of Emacs. Emacs can save a backup of the contents
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to disk at specified intervals. Emacs presents buffer contents in
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ways which optimize reading and navigation activities. One example of
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program control is the embedding of the interactive operating system
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command line interpreter, called a shell, within Emacs. Variations on
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this theme are used to control programs such as statistical packages
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which take input from and provide output to the command-line. The
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resulting buffers provide a copy of the entire transcript of the
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interaction, which can be edited and searched while the program
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executes.
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\paragraph{Major and Minor Modes.}
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Emacs capabilities are extended by loading
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%% AJR: If we remove ``or byte-compiled'' we need to remove ``text'',
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%% since it is wrong.
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%% text
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%% or byte-compiled
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files containing commands and functions written in Emacs Lisp (elisp)
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\citep{RChassell1999}, which is a dialect of Lisp
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\citep{PGraham:1996}. Emacs commands can be called interactively by
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pressing a key sequence mapped to the command or by name.
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%% AJR: this is actually true for M-x long-command-not-bound-to-keys,
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%% but I'm not telling anyone this!
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% Rodney: I don't understand what the problem is with telling them.
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The most important extensions to Emacs take the form of modes, which
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provide specific enhancements to the editing behavior.
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Major modes provide a customized environment consisting of mapped key
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sequences and associated commands for performing tasks such as file
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editing, reading mail, or browsing disk directories. Only one major
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mode can be active for a given buffer at any time. Major modes also
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can be written to intelligently control other programs such as
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statistics packages. Major modes for file editing are often
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determined by the file type or extension, i.e. the characters at the
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end of the file name that follow a period like \stexttt{txt},
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\stexttt{s}, or \stexttt{sas}. Examples of this kind of major mode are
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\stexttt{ESS[S]} and \stexttt{ESS[SAS]}. Major modes understand a
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file's syntax and grammar and therefore provide intelligent
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actions such as automatic indentation; navigation in units of
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characters, words, lines, sentences, paragraphs, function definitions,
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and pages; syntax-based fontification and colorization; and
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reformatting based on programmed conventions.
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Minor modes provide complementary services that that are applicable
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across major modes. Many minor modes can be active at once. For
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example, \stexttt{font-lock-mode} allows Emacs to highlight, with
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fonts or colors, the syntax of a programming language whose
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characteristics are described within a major mode like
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\stexttt{ESS[S]}. The \stexttt{overwrite-mode} determines whether
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typed characters replace the existing text or are inserted at the
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cursor. Minor modes can emulate the key sequences used by another
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editor such as \stexttt{vi}. In addition, they can be used to perform
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version control operations and many other operations which are nearly
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identical across file types.
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\paragraph{Network Support.}
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Emacs allows transparent access to remote files over a network. This
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means that the user views, edits, and saves files on a remote machine
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exactly as if they were on the local machine. Mechanisms for both
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open (\stexttt{ange-ftp} and \stexttt{EFS} use ftp) and secure
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(\stexttt{tramp} uses scp or ssh) access are available. Emacs can
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also monitor and control remote processes running in a shell buffer.
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\paragraph{Editing Extensions.}
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Most programming and documentation tasks consist of editing text.
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These tasks can be enhanced by contextual highlighting and recognition
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of special reserved words appropriate to the programming language in
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use. In addition, Emacs also supports folding, outlining, tags, and
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bookmarks, all of which assist with maneuvering around a file. Emacs
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shares many features with word processing programs and cooperates with
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markup-language document preparation systems such as \LaTeX,
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\textsc{html}, or \textsc{xml}.
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Tracking changes to a text file made by multiple users, potentially in
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different locations, is the job of source-code control programs.
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Emacs interacts with standard source-code control programs such as CVS, RCS,
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and SCCS through minor modes such as \stexttt{vc-mode}. These
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source-code control systems facilitate documenting and tracking edits and
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changes to a file. More importantly, they allow for branching and
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merging of versions so that material present in an older version of
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the file can be recovered and inserted into a newer version in a
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fairly easy manner.
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Comparison of files, two or three drafts of a paper for example, is
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simplified by \stexttt{ediff}.
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An example is shown in Figure \ref{f.ediff}.
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The lines that are similar are highlighted in the two
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buffers, one for each file, and the specific words that mismatch are
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highlighted in a contrasting color. \stexttt{ediff} has many tools
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for working with the differences in files and in entire directories.
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When combined with the patch utility or a source-code control system,
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it provides the user with the ability to insert, delete or modify only
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the differing portions of text files.
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\begin{figure}[tbp]
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\ESSfig{\includegraphics[angle=270,width=\textwidth]{ediff-sas}}
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%\url{http://software.biostat.washington.edu/ess/doc/figures/ediff-sas.gif}
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\caption{Ediff of two versions of a file.}
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\label{f.ediff}
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\end{figure}
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% Rodney: You can't just mention complex functionality like etags and
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% speedbar. We would need to introduce these packages. Since they
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% aren't critical to ESS at this time, let's ignore them.
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Emacs has many other important features. Emacs provides file-manager
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capabilities, such as \stexttt{dired} (discussed in Major and Minor
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Modes above) and \stexttt{speedbar}, both of which interface to the
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computer's directory structure. Emacs stores the complete history of
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commands issued in an editing session, allowing a flexible and fairly
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complete undo capability. More importantly, for modes which control
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processes, the process input history is stored for recall as well as
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for later editing for printing or re-use. Emacs also includes web
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browsers, mail/newsgroup readers, and spell checking.
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In addition to being an extremely powerful editor, Emacs also
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includes capabilities usually found in an operating system. Thus, it
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provides a strong foundation for constructing an integrated
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development environment focused on the needs of statisticians. Emacs'
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power, flexibility, portability, and extensibility make it a solid
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platform on which to construct a statistical analysis user interface.
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\section{ESS extends Emacs}
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\label{sec:ess-extends-emacs}
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Statistical programming is the writing of computer programs for data
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analysis and processing. These programs might be written in a
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computer language that requires a compiler, such as \Fortran\ or C.
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But, more likely, they are written in a statistical analysis language
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that only requires an interpreter such as R, \SAS, \Stata, or \XLispStat.
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General purpose languages such as \Fortran, C/C++, Java, and PERL
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have integrated development environments which facilitate writing and
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debugging code.
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ESS extends Emacs to provide an integrated development environment for
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statistical languages. It offers a single
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interface for a variety of statistical computing tasks including
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interactive data analysis and statistical programming.
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ESS is able to provide a functional and extensible interface
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which is uniform and consistent across multiple statistical packages.
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This is done by adding shortcuts and features for accelerated editing
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of files as well as by interacting with the particular statistical
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packages to provide, for example, control of input/output, assistance
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with evaluation, and specialized parsing of help files.
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ESS supports the S family (S, \Splus, and R) interactively. \SAS\ and
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BUGS are also well supported for batch processing. \Stata\ and
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\XLispStat\ (including ARC and ViSta) are supported through
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highlighting and process-interfacing.
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\subsection{Features and capabilities}
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\label{sec:ESS:features}
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\paragraph{Syntactic highlighting and indentation of source code.}
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The programmers task is eased when language constructs (such as
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reserved words, function calls, strings, and comments) are visually
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identifiable and when lines of code are automatically indented to a
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depth appropriate to their context (e.g., if--then clauses, loops).
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ESS provides both of these to the programmer by including a
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description of the syntax of each supported statistical language in
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the form used by \stexttt{font-lock-mode}.
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Figure \ref{f.font} shows an example of font-locking a complicated S
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statement. The top panel shows an \stexttt{if} statement with a long
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expression in the condition and a multi-line consequence. The keyword
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\stexttt{if} is shown in purple, the string \stexttt{"deltat"} in
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RosyBrown. The comments are in red. Everything else is in the
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standard font. The consequence is indented and the continuations of
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the consequence are further indented. The matching parentheses are
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shown in green. The cursor is indicated by a solid box. In the
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bottom panel, we replaced the matching parenthesis with an unbalanced
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bracket. Emacs immediately marks that with the paren-mismatch font,
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bright purple in this example. On a black and white terminal we would
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use bold, underline, italic, and reverse-video, rather than colors, to
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distinguish the fonts.
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% Figure \ref{f.font} shows a black-and-white example of font-locking a
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% complicated S statement. The top panel shows an \stexttt{if}
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% statement with a long expression in the condition and a multi-line
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% consequence. The keyword \stexttt{if} is shown in an underlined font,
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% the string \stexttt{"deltat"} in an italic underlined font. The
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% comments are in an italic font. Everything else is in the standard
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% font. The consequence is indented and the continuations of the
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% consequence are further indented. The matching parentheses are marked
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% by a bold foreground and a shaded background. The cursor is indicated
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% by a solid box. In the bottom panel we replaced the matching
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% parenthesis with an unbalanced bracket. Emacs immediately marks that
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% with the paren-mismatch font, bright purple on
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% a color terminal.
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The font selection and the indentation depth are automatically
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supplied by Emacs as the lines are typed. The user has several
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options for mapping of colors or fonts to each of the syntactic types.
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We selected
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% black-and-white font-mapping for display here. On a color terminal
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% we might use
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purple for the keywords, red for comments, green for matching parens,
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and inverse-video purple for mismatched parens. Emacs makes default
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choices of colors and ESS provides several other optional schemes.
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\begin{figure}[tbp]%h
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\ESSfig{%
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\includegraphics[angle=270,width=\textwidth]{font-cor-s}
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\includegraphics[angle=270,width=\textwidth]{font-incor-s}%
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}
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%\url{http://software.biostat.washington.edu/ess/doc/figures/font-cor-s.jpg}
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%\url{http://software.biostat.washington.edu/ess/doc/figures/font-incor-s.jpg}
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\caption{We illustrate here with fonts and colors appropriate for a
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color display. On a black and white terminal we would use bold,
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underline, italic, and reverse-video. On a color terminal we
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would use a selection of colors.}
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\label{f.font}
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\end{figure}
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Since S syntax is similar to that of C, ESS uses the Emacs tools for
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reformatting S code to match particular styles. Common C format styles,
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as well as locally customized styles, are defined by specifying the indentation
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level for nested statements, location of open-braces (at the end or at the
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beginning of a line), indentation offsets for if-then-else constructs,
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and similar characteristics.
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Syntax highlighting can be used to help enforce coding
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standards. Figure \ref{f.hilock} illustrates a standard for
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\SAS\ programming that says all \stexttt{PROC} statements must use the
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\stexttt{DATA=datasetname} option.
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\begin{figure}[tbp]
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\ESSfig{\includegraphics[angle=270,width=\textwidth]{hilock-sas}}
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%\url{http://software.biostat.washington.edu/ess/doc/figures/hilock-sas.gif}
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\caption{Enforce coding standards. The standard here is
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that all \stexttt{PROC} statements must use the
510
\stexttt{DATA=datasetname} option. Lines that satisfy the
511
standard turn green, lines that don't turn red.
512
Ambiguous ones turn yellow.}
513
\label{f.hilock}
514
\end{figure}
515
516
\paragraph{Process interaction.}
517
Emacs has historically referred to processes under its control as
518
``inferior'', accounting for the name inferior ESS (\stexttt{iESS}) to
519
denote the mode for interfacing with the statistical package. Figure
520
\ref{f.ess-demo} shows the S language program \stexttt{ess-demo.s} in
521
the top buffer in \stexttt{ESS[S]} mode and the executing R process in
522
the bottom buffer \stexttt{*R*}. The \stexttt{iESS} major mode of the
523
\stexttt{*R*} buffer is crafted for command-line editing. This mode
524
remembers and uses the command history, allowing for the recall and
525
searching of previously entered commands. Filename completion for
526
local directories is also available.
527
528
\begin{figure}[tb]
529
\ESSfig{\includegraphics[angle=270,width=\textwidth]{ess-demo}}
530
%\url{http://software.biostat.washington.edu/ess/doc/figures/ess-demo.jpg}
531
\caption{Line-by-line execution of a command file. The cursor is
532
placed on a line in the \stexttt{ESS[S]} buffer and then with a single
533
key sequence
534
the line is sent to the \stexttt{*R*} buffer for
535
execution. The output of the package goes directly to the
536
editable \stexttt{*R*} buffer.}
537
\label{f.ess-demo}
538
\end{figure}
539
540
\paragraph{Source-level Debugging.}
541
ESS facilitates the editing of source code files, sets of commands
542
written for a statistical analysis package, and allows the user to
543
load and error-check small sections of source code into the package.
544
This is done through several mechanisms. First, the presence of
545
unbalanced parentheses or mismatched/unterminated quotes is
546
immediately evident with syntactic highlighting of the source code.
547
Second, functions are provided for simple and consistent execution of
548
user-specified or natural units of the code (function definitions in S
549
or \XLispStat, \stexttt{PROC \dots\ RUN;} sections in \SAS). An
550
error-free evaluation lets the user execute the next section of code;
551
if errors arise, the user edits the current unit and re-evaluates.
552
Once the code is verified, an entire buffer, or file, of code can be
553
sent to the package as a unit. This file can also be used as a batch
554
file for routine analysis at a later time. Finally, output from the
555
statistics package is normally captured directly by Emacs and placed
556
into a buffer from where it can be edited and searched. Particular
557
forms of output such as requests for help pages and log-file output
558
can be diverted into special buffers with modes crafted to facilitate
559
reading. These modes include tools for automatically placing the
560
cursor on the first \stexttt{ERROR}, for example in \SAS\ and S.
561
562
\paragraph{Interactive transcripts.}
563
A transcript records all commands entered by the analyst and the
564
corresponding text-based responses such as tables and comments
565
generated by the statistics package during an interactive statistical
566
analysis session. Once a transcript file is generated, for example by
567
saving an \stexttt{iESS} buffer, \stexttt{transcript-mode} assists
568
with reuse of part or all of the entered commands. ESS understands
569
the transcript's syntax, especially the potential prompt patterns used
570
during the interactive analysis. ESS provides tools to facilitate
571
editing and re-evaluating the commands directly from the saved
572
transcript. This is useful both for demonstration of techniques and
573
for reconstruction and auditing of data analyses. Special ESS
574
functions can ``clean'' S language transcripts by isolating all input
575
lines and placing them in a new S language source file. Transcript
576
cleaning facilitates the use of an exploratory interactive analysis
577
session to construct functions and batch files for routine analysis of
578
similar data sets.
579
580
\paragraph{Remote access to statistics packages.}
581
ESS provides transparent facilities for editing files and running
582
programs which might reside on numerous remote machines during the
583
same session. The remote machine could be a different platform than
584
the local machine.
585
586
\paragraph{Manipulating and Editing Objects (S family).}
587
For languages in the S family, ESS provides object-name completion of
588
both user- and system-defined functions and data. ESS can dump and
589
save objects (user- and system-generated) into formatted text files,
590
and reload them (possibly after editing).
591
592
\paragraph{Help File Editing (R).}
593
ESS provides an R documentation mode (\stexttt{Rd-mode}) which assists
594
in writing help files for R functions, objects, and other topics worth
595
documenting. \stexttt{Rd-mode} provides the ability to view and
596
execute code embedded in the help file in the same manner as ESS
597
handles code from any S language source file. It provides syntax
598
highlighting and the ability to submit code directly to a running ESS
599
process, either R or \Splus, for evaluation and debugging. This
600
latter feature is useful for ensuring that code developed using R runs
601
under \Splus.
602
603
\paragraph{Cooperation across Multiple Tools.}
604
Statistical packages are intended for either general statistical
605
analyses or for specialized forms of statistical analyses. The
606
specialized statistical packages can be far more efficient for their
607
intended activities, but this is balanced by their inability to
608
perform a wide range of general statistical functions. Tightly
609
coupled inter-operability between general and specialized packages
610
rarely exists, but such a facility is often desired. For example, a
611
general purpose package such as R does not perform Bayesian analyses
612
as easily as BUGS does. On the other hand, BUGS lacks breadth in the
613
range of analyses and results it can generate. For this reason, BUGS
614
is often distributed with R packages, like the diagnostic packages
615
CODA and BOA, which assist with importing and analyzing the results in
616
R. Another point of contention is the difference in the interfaces
617
between general packages and specialized packages. ESS helps by
618
providing a single point of contact to both tools, though the typical
619
interfaces (interactive for R, batch for BUGS) are different.
620
621
%\item[Rodney:] I can't speak for everyone, but the BUGS users I know are
622
% .. lots deleted by AJR
623
%will make sense. Besides, the most pressing need for me is to get
624
%ESS-elsewhere to work with ESS[BUGS] rather than creating inferior-BUGS.
625
626
%\item[Rich:] How does making ``ESS-elsewhere work with ESS[BUGS]'' differ
627
%from ``creating inferior-BUGS''? My question is predicated on the assumption
628
%that ESS-elsewhere is a (generalized) minor-mode that makes the location
629
%of the program irrelevant.
630
%See my ESS-elsewhere quibble below.
631
632
%\item[Rodney:] It's the whole batch BUGS vs. interactive BUGS thing. Batch
633
%BUGS with ESS-elsewhere; interactive BUGS with inferior-BUGS which does not
634
%and will never exist. If you want to call ``inferior-ESS'' ``ESS-elsewhere''
635
%why do you need two different names? ``inferior-ESS'' is a terrible name
636
%so the change would be fine with me, but you can't have it both ways? Is
637
%this why you keep saying that ESS-elsewhere works for SAS? See
638
%response to quibble below.
639
640
%\item[Rich:]
641
%\stexttt{iESS[SAS]} was designed to mimic as well as possible \stexttt{iESS[S]}.
642
%I need to read doc/README.SAS to make sure all of its options are represented
643
%here. --- Not yet done.
644
%\end{description}
645
%\end{Comment}
646
647
\paragraph{Simplifying Keymap Differences.}
648
Simple conflicts between interfaces are exemplified by different key
649
sequences for editing tasks such as cut, copy, paste, beginning of
650
line, end of line, etc. These may be the most aggravating because our
651
fingers are typing ``instinctively'', but differences in interfaces
652
circumvent this learned behavior. ESS solves this problem by
653
providing a uniform interface to keyboard actions across the variety
654
of statistical packages that might be used. That is, the same key
655
sequences are used for cursor movement, evaluation, and basic tasks
656
such as loading files for editing.
657
658
\paragraph{Concurrent Use of Multiple Machines and Operating Systems.}
659
It can be useful to have multiple statistical processes running
660
simultaneously, either on a single machine or a variety of machines.
661
This capability assists with large-scale numerical simulations as well
662
as code design and testing across multiple versions of statistical
663
software packages.
664
665
\subsection{Interactive Processing.}
666
\label{sec:interactive}
667
668
The increased popularity of exploratory data analysis as well as the
669
advent of simple GUIs has made interactive data analysis an important
670
component to statistical practices.
671
ESS uses three different approaches for communicating with statistical
672
packages.
673
674
\paragraph{Inter-Process Communication.}
675
Packages that use the command-line interface are run as an inferior
676
process in an Emacs buffer, with the standard input and output of the
677
package redirected to the buffer. Packages that do not use the
678
command-line interface must be run as an independent process, possibly
679
with limited cooperation.
680
681
ESS can use the Windows DDE (Dynamic Data Exchange) protocol to
682
provide one-way communication directly to packages which function as a
683
DDE server. ESS can control the actions of the package, but it can not capture
684
the results directly. Transcripts must be physically copied to an
685
Emacs buffer to get the transcript editing features.
686
687
Statistical packages that use neither the standard input/standard
688
output protocol nor DDE can not be directly controlled by Emacs. But, ESS
689
can still provide an editing environment for these statistical languages. The
690
user must either manually cut and paste the edited code into the
691
package or save the edited files and run them in a batch environment.
692
The Microsoft Windows versions of \SAS, \Stata, and \XLispStat\ are
693
in this category.
694
695
One useful extension in ESS is relaxation of the requirement that the
696
statistics program be available on the local machine. ESS provides
697
both transparent editing of files and execution of statistics packages
698
on a remote machine with \stexttt{iESS[S]} or \stexttt{iESS[SAS]} (see
699
below). All the editing and interaction features described for the
700
local machine work equally well on the remote machine. The
701
interaction, including all the unique features of working with ESS,
702
appears to the user as if the program were running on the local
703
%rmh: The interaction ... appears ....
704
machine. If the X11 Windowing system is running on the local machine,
705
it is even possible to bring up visual displays and graphics from
706
remote Unix systems onto a local Microsoft Windows or Apple Mac
707
display.
708
709
\paragraph{Interactive S family}
710
ESS for S family statistical languages, \stexttt{iESS[S]},
711
replaces the \Splus\ Commands window or the R GUI window. In addition
712
to running the S family language process, \stexttt{iESS[S]} mode provides the
713
same editing features, including syntactic highlighting and
714
string-search, as the editing mode \stexttt{ESS[S]}. It also provides
715
an interactive history mechanism; transcript recording and editing;
716
and the ability to re-submit the contents of a multi-line command to
717
the executing process with a single keystroke. \stexttt{iESS[S]} is
718
used with S, \Splus, and R on Unix and with Sqpe and R on Windows.
719
720
The \Splus\ GUI on Windows can be a DDE server. There are two
721
advantages to using even this limited communication with the \Splus\
722
GUI through ESS. First, through \stexttt{ESS[S]} mode the user gets
723
the full editing capabilities of Emacs. Second, S language commands
724
% rmh: S, not \Splus, in both places. The {\it language} is S.
725
% The previous session could be R or ATT S. It is not restricted to \Splus.
726
are sent from the editing mode \stexttt{ESS[S]} buffer and from
727
transcript buffers from previous S sessions directly to the GUI
728
Commands window with the same Emacs key sequences as are used with ESS
729
on Unix. Hence the user can work in a powerful editing environment
730
and is protected from the delay and ergonomic challenges of using the
731
mouse for copy and paste operations across windows.
732
733
\paragraph{Interactive \SAS.}
734
\stexttt{iESS[SAS]} is a mode that allows text-based \stexttt{PROC} by
735
\stexttt{PROC} interaction with an inferior buffer running an
736
interactive \SAS\ session on either the local or a remote computer.
737
\stexttt{iESS[SAS]} mode works by redirecting standard input and
738
output from \SAS\ to ESS. Currently, the \stexttt{iESS[SAS]} mode can
739
run on any computer, but the \SAS\ process it is controlling must be
740
running on a Unix machine. This process is very efficient for dial-up
741
network connections to a remote computer with \SAS\ installed. The
742
resulting interface is similar to the SAS character terminal
743
interface, but with Emacs key sequences.
744
745
%Rodney: What is this paragraph about? I'm going to comment it out
746
%because I don't recognize what it is supposed to be. Maybe somebody
747
%can fix it later.
748
%
749
% rmh: Round umpteen. Yes, this is redundant with the third paragraph
750
% of interprocess communication. I still want it here. Try this rephrasing.
751
%
752
\stexttt{ESS[SAS]} mode can be used in conjunction with the \SAS\
753
Display Manager to allow simultaneous access to Emacs for editing
754
\SAS\ language code and to the \SAS\ mouse-based interfaces to the
755
graphical routines and help system.
756
757
%%%%% AJR: WHY IS THIS SUBSTANTIALLY DIFFERENT THAN BATCH? I KNOW ITS
758
%%%%% SLIGHTLY DIFFERENT, BUT SUBSTANTIALLY?
759
%%%%% rmh: this is a form of interaction, not batch. I restored the
760
%%%%% first paragraph with some expansion.
761
%\paragraph{\SAS---Interactive cooperation with the \SAS\ Display Manager.}
762
%ESS users who write data analysis code in \stexttt{ESS[SAS]} mode in Emacs
763
%often need to work with the \SAS\ Display Manager's
764
%mouse-based interface to the graphical
765
%routines, the help system, and other non-text-based features.
766
%%The authors of ESS prefer the Emacs environment for
767
%%the text-file interaction with \SAS, that is with editing and
768
%%managing input command files and output listing and log files,
769
%%even on computer systems which run
770
%%the \SAS\ Display Manager environment.
771
%In this situation, the user
772
%designs the command file in \stexttt{ESS[SAS]} mode and highlights
773
%regions to be forwarded to \SAS\ for processing.
774
%%
775
%% Rodney: I don't see this as a feature of either ESS or emacs. And,
776
%% what the authors prefer is certainly not germane.
777
%%
778
%%
779
%% rmh: This is my preferred mode for interacting with SAS. I tried another
780
%% rephrasing. It {\it is} a feature of ESS. ESS is able to provide ESS[SAS]
781
%% mode for the text processing (.sas .lst. log files) and simultaneously
782
%% let the user have interactive graphical access.
783
%%This can be done by either:
784
%%\begin{enumerate}
785
%%\item copying and pasting the marked regions to the \SAS\ Editor window
786
%% and then pressing the \stexttt{RUN} button. Highlighted sections of
787
%% the \SAS\ Listing window are brought back to Emacs to be read in the
788
%% \stexttt{ESSlst} mode editing environment.
789
%%\item submitting the marked region for Batch File Processing (see the
790
%% next section) but using the mapped key sequences to append to the log
791
%% and listing files instead of replacing them.
792
%%\end{enumerate}
793
794
\subsection{Batch File Processing.}
795
\label{sec:batch-file}
796
797
Batch file processing with statistical analysis packages is a better
798
choice than interactive processing when the execution times are longer
799
than the user is willing to wait as well as for regularly updated
800
statistical reports and figures. ESS provides a means to shorten the
801
debugging cycle for writing code intended for batch evaluation by
802
containing the whole process, both writing and evaluation, within
803
Emacs.
804
805
\paragraph{Batch \SAS.}
806
\label{sec:sas-batch}
807
808
\SAS\ is a popular choice for processing and analyzing large amounts
809
of data. However, interactive \SAS\ is rarely used in these situations
810
due to the length of time involved. Instead, a file containing \SAS\
811
commands is created and \SAS\ executes these commands in the background,
812
or batch, while the user moves on to other activities.
813
814
ESS facilitates \SAS\ batch with \stexttt{ESS[SAS]}, the mode for files
815
with the \stexttt{sas} extension. ESS defines \SAS\ syntax so that
816
\stexttt{font-lock-mode} can highlight statements, procedures,
817
functions, macros, datasets, comments and character string literals in
818
\SAS\ programs. Optionally, the same language features are
819
highlighted in the \SAS\ log with the addition of log notes, warnings
820
and error messages.
821
822
For files with the \stexttt{sas} extension, ESS binds the function
823
keys in \stexttt{ESS[SAS]} mode to match the definitions used by \SAS\
824
Display Manager. These definitions are optionally available in all
825
modes. They are particularly useful when viewing \SAS\ log and
826
listing files (with extensions of \stexttt{log} and \stexttt{lst}
827
respectively).
828
829
Only one function key press is needed to submit a \SAS\ batch process.
830
Other function keys open the \SAS\ program, the \SAS\ log and the
831
\SAS\ listing buffers. When accessed in this manner, the \SAS\ log
832
and \SAS\ listing buffers are automatically updated since they may
833
have been appended or over-written by the \SAS\ batch process. In
834
addition, the \SAS\ log is searched for error messages and the error
835
messages, if any, are sequentially displayed with consecutive key
836
presses.
837
838
Another function key opens a \SAS\ permanent dataset for editing or
839
viewing. An option is provided so that the tab and return keys
840
operate in typewriter fashion like they do in \SAS\ Display Manager.
841
This option also defines a key to move the cursor to a previous
842
tab-stop and delete any characters between its present position and
843
the tab-stop. This is a \SAS\ Display Manager feature that is not
844
typically available in Emacs.
845
846
The \SAS\ batch process runs on the computer where the \SAS\ program
847
resides. This is important because any \SAS\ permanent datasets
848
referenced in a \SAS\ program only exist on the computer running \SAS.
849
If the \SAS\ program resides on a remote computer, then the
850
log and listing are also accessed remotely. The net result is that
851
running \SAS\ batch on remote computers is nearly transparent to the
852
ESS user.
853
854
%\begin{Comment}
855
%Rich's version:
856
%\end{Comment}
857
%The \SAS\ batch process can run on the same computer on which the
858
%emacs session is running or it can run on a remote computer. For
859
%remote jobs, files are transparently saved (with ftp or scp or kermit)
860
%and the batch process is transparently submitted through a telnet or
861
%ssh connection.
862
863
%\begin{Comment}
864
%Rich: I have some terminology quibbles here with how the term
865
%``ESS-elsewhere'' is used with SAS BATCH. I think of S-elsewhere or
866
%ESS-elsewhere as a trick to make a \stexttt{telnet-mode} buffer think
867
%it is \stexttt{iESS-mode} buffer.
868
869
%I don't think of file saving, editing, and retrieval as an example
870
%of ESS-elsewhere. Neither is submission of the remote job;
871
%that is just an ordinary shell command in an ordinary shell buffer.
872
%M-x SAS probably is an example of ESS-elsewhere, but I
873
%designed it before I thought of the ESS-elsewhere concept.
874
875
%The initial idea behind S-elsewhere was to run an interactive S or S-Plus
876
%session on a remote computer in telnet (or equivalent) buffer. The trick
877
%was to make the \stexttt{telnet-mode} buffer accept C-c C-n and
878
%related commands from the \stexttt{S-mode} buffers. Hence I had to
879
%make the \stexttt{telnet-mode} buffer think it is \stexttt{iESS-mode}
880
%buffer. The ``elsewhere'' part of the name is entirely related to a
881
%different start up procedure. Once the connection is made, there is
882
%{\em no} difference visible to the user. The buffer shows itself to
883
%be an ordinary \stexttt{iESS} buffer. Tony generalized S-elsewhere
884
%to ESS-elsewhere to allow other languages than S to be used
885
%interactively.
886
887
%I have been using ESS for SAS remote BATCH for years, ever since you
888
%and I started working on this together. We initially defined
889
%ess-sas-submit-method to encapsulate the location of the sas process.
890
%Except for a few lines of elisp to get the connection started, the user
891
%behavior has been identical whether the SAS process is on the same or
892
%different machine. Since we are not interactively talking to the SAS
893
%process in an inferior-ESS buffer I don't see this as ESS-elsewhere.
894
895
%Rodney: Remote submissions of SAS batch jobs never worked. I only got
896
%it to work a couple of weeks ago. The problem was with the cd command.
897
%You need to ignore the beginning and end of the expanded buffer name
898
%that are the ange-ftp/EFS/tramp stubs which tell Emacs what the remote
899
%username and hostname are. I find the batch usage of ESS-elsewhere
900
%entirely consistent with the interactive behavior. OTOH, I don't find
901
%the terminology particularly illuminating. I think ESS-remote or
902
%ESS-net would be more meaningful.
903
%\end{Comment}
904
905
\paragraph{Batch BUGS.}
906
BUGS software performs Markov Chain Monte Carlo integration. There is
907
an interactive capability, but it is not often used since the analyses
908
can be very time-consuming. Most BUGS programs are executed as batch
909
processes. ESS facilitates BUGS batch with \stexttt{ESS[BUGS]}, the
910
mode for files with the \stexttt{bug} extension. ESS provides 4
911
features. First, BUGS syntax is described to allow for proper
912
fontification of statements, distributions, functions, commands and
913
comments in BUGS model files, command files and log files. Second,
914
ESS creates templates for the command file from the model file so that
915
a BUGS batch process can be defined by a single file. Third, ESS
916
provides a BUGS batch script that allows ESS to set BUGS batch
917
parameters. Finally, key sequences are defined to create a command
918
file and submit a BUGS batch process.
919
920
\paragraph{Batch S family.}
921
ESS provides 2 facilities for batch processing of S family language files.
922
The first is to execute the contents of a file using buffer-evaluation. This
923
differs from interactive processing only by the number of commands
924
being evaluated; errors can be found by examining the resulting
925
transcript. The second is the load-source mechanism, which provides a
926
means of jumping to errors in the source file, but doesn't display the
927
evaluated commands in the transcript. These mechanisms provide
928
different tools for debugging the source files.
929
930
\section{History of ESS}
931
\label{sec:ESS:history}
932
933
ESS is built on Emacs, the editing system for which Richard Stallman
934
won a MacArthur Foundation Fellowship in 1990. Emacs has a long
935
history of being a programmer's editor. Many statisticians got their
936
first taste of the power of Emacs with \Fortran\ mode which was
937
introduced in 1986. As statisticians' preferences changed from
938
generalist compiled languages such as \Fortran\ to specialist
939
statistical analysis packages like S and \SAS, Emacs modes soon
940
followed.
941
942
The ESS environment is built on the open-source projects of
943
many contributors, dating back over 10 years.
944
Doug Bates and Ed Kademan wrote S-mode in 1989 to edit S and \Splus\
945
files in GNU Emacs. Frank Ritter and Mike Meyer added features,
946
creating version 2. Meyer and David Smith made further contributions,
947
creating version 3. For version 4, David Smith provided significant
948
enhancements to allow for powerful process interaction.
949
950
John Sall wrote GNU Emacs macros for \SAS\ source code around 1990.
951
Tom Cook added functions to submit jobs, review listing and log files,
952
and produce basic views of a dataset, thus creating a SAS-mode which was
953
distributed in 1994.
954
955
In 1994, A.J. Rossini extended S-mode to support XEmacs. Together
956
with extensions written by Martin M{\"a}chler, this became version
957
4.7 and supported S, \Splus, and R.
958
In 1995, Rossini extended SAS-mode to work with XEmacs.
959
960
In 1997, Rossini merged S-mode and SAS-mode into a single Emacs
961
package for statistical programming; the product of this marriage was
962
called ESS version 5. Richard M. Heiberger designed the inferior mode
963
for interactive \SAS\ and SAS-mode was further integrated into ESS.
964
Thomas Lumley's Stata mode, written around 1996, was also folded into
965
ESS. More changes were made to support additional statistical
966
languages, particularly \XLispStat.
967
968
ESS initially worked only with Unix statistics packages that used
969
standard-input and standard-output for both the command-line interface
970
and batch processing. ESS could not communicate with statistical
971
packages that did not use this protocol. This changed in 1998 when
972
Brian Ripley demonstrated use of the Windows Dynamic Data Exchange
973
(DDE) protocol with ESS. Heiberger then used DDE to provide
974
interactive interfaces for Windows versions of \Splus. In 1999,
975
Rodney A. Sparapani and Heiberger implemented \SAS\ batch for ESS, which
976
relies on files rather than standard-input/standard-output, on Unix,
977
Windows and Mac. In 2001, Sparapani added BUGS batch file processing
978
to ESS for Unix and Windows.
979
980
This history is summarized in Table \ref{tab:timeline}.
981
982
\begin{table}[tbp]
983
\centering
984
{\scriptsize
985
\begin{tabular}{c ll c ll}
986
\hline
987
Year \\
988
\hline
989
& \multicolumn{2}{c}{S-mode} && \multicolumn{2}{c}{SAS-mode} \\
990
\cline{2-3} \cline{5-6}
991
1989 & v.1 & (GNU Emacs, Unix, S/S+) && \\
992
1990 & & && & (GNU Emacs, Unix, SAS editing) \\
993
1991 & v.2 & (GNU Emacs, Unix, S/S+) && \\
994
1993 & v.3 & (GNU Emacs, Unix, S/S+) && \\
995
1994 & v.4 & (GNU Emacs/XEmacs, Unix, S/S+) && v.1 & (GNU Emacs, Unix, SAS batch) \\
996
1995 & v.4.7 & (GNU Emacs/XEmacs, Unix, S/S+/R) && v.2 & (GNU Emacs/XEmacs, Unix, SAS batch) \\
997
\cline{2-6}\\[-3.5ex]
998
\cline{2-6}
999
& \multicolumn{5}{c}{Emacs Speaks Statistics (ESS)} \\
1000
\cline{2-6}
1001
&\multicolumn{2}{c}{Emacs, Operating Systems} &&\multicolumn{2}{c}{Additional Functionality}\\
1002
\cline{2-3} \cline{5-6}
1003
1997 & v.5.0 & (GNU Emacs/XEmacs, Unix) &&& Stata, XLispStat, SAS interactive \\
1004
1998 & v.5.1.1 & (GNU Emacs/XEmacs, Unix/Windows) &&& S+elsewhere; Windows: S+/R\\
1005
1999 & v.5.1.10 & (GNU Emacs/XEmacs, Unix/Windows/Mac) &&& SAS batch; Omegahat \\
1006
2001 & v.5.1.19 & (GNU Emacs/XEmacs, Unix/Windows/Mac) &&& Unix/DOS: BUGS batch; Mac: R \\
1007
%% 2002 & v.5.1.20 & (Emacs/XEmacs, Unix/Windows/Mac) &&& Unix/DOS: BUGS batch, Mac: R \\
1008
%% 2002 & v.5.2 & (Emacs/XEmacs, Unix/Windows/Mac) &&& ? \\
1009
\hline
1010
\end{tabular}
1011
}
1012
\caption{History and Ancestors of ESS}
1013
\label{tab:timeline}
1014
\end{table}
1015
1016
1017
%\section{Future Work}
1018
1019
%%%There are two active areas of extensions for user environments. One
1020
%%%is to enhance the capabilities of the IDE for statistical practice;
1021
%%%this includes implementing such common IDE features as object
1022
%%%browsers, tool-tips, and interfacing cleaning. The other is to target
1023
%%%appropriate potentially useful programming methodologies for transfer
1024
%%%to statistical practice.
1025
%%%
1026
%%%Literate Programming methodologies \citep{Knuth:1992,NRamsey:1994} are
1027
%%%a natural fit for statistical practice. We refer to the application
1028
%%%to statistical analysis as Literate Statistical Practice
1029
%%%\citep{rossini:dsc:2001}. The tools used are Noweb
1030
%%%\citep{NRamsey:1994} and either \LaTeX, \textsc{html}, or \textsc{xml}
1031
%%%for documenting and explaining the analysis. This approach to
1032
%%%programming encourages the use of a literary documentation style to
1033
%%%explain the programming code for the data analysis. The program can
1034
%%%then be extracted from the documentation text for realizing the
1035
%%%statistical analysis.
1036
1037
%%future enhancement perhaps
1038
%%ESS provides the same ESS-elsewhere support for BUGS batch
1039
%%that it does for \SAS\ batch (see above).
1040
1041
%Important extensions which should be implemented in future
1042
%versions include class browsers, analysis templates, tool-tips, and
1043
%similar features. Class browsers can be thought of as a tree or
1044
%outline for presenting datasets, variables and functions in the
1045
%context of what they represent; this allows for rapid and appropriate
1046
%inspection. Analysis templates would allow statistics centers and
1047
%groups to provide standardized templates for initiating an analysis.
1048
1049
%Additional statistical packages can easily be added to ESS.
1050
1051
%%While most IDE features have been developed for object-oriented
1052
%%languages, the above also can apply to non-object oriented
1053
%%programming.
1054
1055
%ESS is one of the first Rapid Application Development (RAD)
1056
%environments intended for statisticians. It provides
1057
1058
1059
\section{Conclusion}
1060
\label{sec:concl}
1061
1062
ESS provides an enhanced, powerful interface for efficient interactive
1063
data analysis and statistical programming. It allows the user
1064
complete control over the communications among the files in which the
1065
analysis is specified, the statistical process doing the computation,
1066
and the output. Because all are within the same programming
1067
environment, and therefore are accessed with the same editing and
1068
searching concepts and the same key sequences, user efficiency is
1069
increased. It is completely customizable to satisfy individual
1070
desires for interface styles and can be extended to support other
1071
statistical languages and data analysis packages.
1072
1073
%\begin{Comment}
1074
%Rich: see my discussion of ESS-elsewhere terminology.
1075
1076
%What is the behavior for remote SAS that is new for 2002?
1077
1078
%Rodney: SAS batch now works and Kermit was added as a method of transfer.
1079
%\end{Comment}
1080
%ESS-elsewhere provides interactive and batch processing
1081
%with \SAS\ running on a remote machine that is accessed over a
1082
%network. This provides a powerful development environment for \SAS.
1083
1084
%%This
1085
%%includes support for syntax highlighting and template-based source file
1086
%%generation that provides the capability of specifying all the necessary
1087
%%parameters for a BUGS batch run in a single file.
1088
1089
\bibliographystyle{plainnat}
1090
\pdfbookmark[1]{References}{section.7}
1091
%\addcontentsline {toc}{section}{\numberline {}References}
1092
\bibliography{ess-intro-graphs}
1093
1094
\clearpage
1095
1096
\appendix
1097
\section{Appendix: ESS Resources on the Internet}
1098
%\addcontentsline {toc}{section}{\numberline {}ESS Resources on the Internet}
1099
\label{sec:access}
1100
1101
\paragraph{Latest Version.}
1102
1103
ESS is constantly in flux. New versions of statistical
1104
packages, Emacs and operating systems require new releases of ESS to
1105
support them. The latest stable version of ESS can be found on the web at
1106
\url{http://software.biostat.washington.edu/statsoft/ess/}. To get help
1107
with problems, send e-mail to \url{mailto: ess-help@stat.math.ethz.ch}.
1108
The latest development, hence unstable, version can be obtained by
1109
anonymous CVS. First type:
1110
1111
\stexttt{cvs -d
1112
:pserver:anoncvs@software.biostat.washington.edu:/var/anoncvs login}
1113
1114
You will be prompted for a password which is ``\stexttt{anoncvs}''.
1115
Then type:
1116
1117
\stexttt{cvs -d
1118
:pserver:anoncvs@software.biostat.washington.edu:/var/anoncvs co
1119
ess}
1120
1121
\paragraph{Additional documentation.}
1122
1123
An expanded version of the present paper is in \citep{RMHHS:2001}. A
1124
general introduction and usage instructions can be found in
1125
\citep{heiberger:dsc:2001}; in addition, one which is more focused on
1126
\SAS\ can be found in \citep{heiberger:philasugi:2001}. The
1127
documentation that comes with ESS provides details of its
1128
implementation as well as examples of its use.
1129
1130
\end{document}
1131
1132
1133
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1134
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1135
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1136
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