START-INFO-DIR-ENTRY
* R FAQ: (R-FAQ).               The R statistical system FAQ.
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   R FAQ
Frequently Asked Questions on R
Version 1.9-24 2004-06-15
ISBN 3-900051-01-1
Kurt Hornik


Table of Contents
*****************


R FAQ

1 Introduction
  1.1 Legalese
  1.2 Obtaining this document
  1.3 Citing this document
  1.4 Notation
  1.5 Feedback

2 R Basics
  2.1 What is R?
  2.2 What machines does R run on?
  2.3 What is the current version of R?
  2.4 How can R be obtained?
  2.5 How can R be installed?
    2.5.1 How can R be installed (Unix)
    2.5.2 How can R be installed (Windows)
    2.5.3 How can R be installed (Macintosh)
  2.6 Are there Unix binaries for R?
  2.7 What documentation exists for R?
  2.8 Citing R
  2.9 What mailing lists exist for R?
  2.10 What is CRAN?
  2.11 Can I use R for commercial purposes?
  2.12 Why is R named R?
  2.13 What is the R Foundation?

3 R and S
  3.1 What is S?
  3.2 What is S-PLUS?
  3.3 What are the differences between R and S?
    3.3.1 Lexical scoping
    3.3.2 Models
    3.3.3 Others
  3.4 Is there anything R can do that S-PLUS cannot?
  3.5 What is R-plus?

4 R Web Interfaces

5 R Add-On Packages
  5.1 Which add-on packages exist for R?
    5.1.1 Add-on packages in R
    5.1.2 Add-on packages from CRAN
    5.1.3 Add-on packages from Omegahat
    5.1.4 Add-on packages from Bioconductor
    5.1.5 Other add-on packages
  5.2 How can add-on packages be installed?
  5.3 How can add-on packages be used?
  5.4 How can add-on packages be removed?
  5.5 How can I create an R package?
  5.6 How can I contribute to R?

6 R and Emacs
  6.1 Is there Emacs support for R?
  6.2 Should I run R from within Emacs?
  6.3 Debugging R from within Emacs

7 R Miscellanea
  7.1 Why does R run out of memory?
  7.2 Why does sourcing a correct file fail?
  7.3 How can I set components of a list to NULL?
  7.4 How can I save my workspace?
  7.5 How can I clean up my workspace?
  7.6 How can I get eval() and D() to work?
  7.7 Why do my matrices lose dimensions?
  7.8 How does autoloading work?
  7.9 How should I set options?
  7.10 How do file names work in Windows?
  7.11 Why does plotting give a color allocation error?
  7.12 How do I convert factors to numeric?
  7.13 Are Trellis displays implemented in R?
  7.14 What are the enclosing and parent environments?
  7.15 How can I substitute into a plot label?
  7.16 What are valid names?
  7.17 Are GAMs implemented in R?
  7.18 Why is the output not printed when I source() a file?
  7.19 Why does outer() behave strangely with my function?
  7.20 Why does the output from anova() depend on the order of factors in the model?
  7.21 How do I produce PNG graphics in batch mode?
  7.22 How can I get command line editing to work?
  7.23 How can I turn a string into a variable?
  7.24 Why do lattice/trellis graphics not work?
  7.25 How can I sort the rows of a data frame?
  7.26 Why does the help.start() search engine not work?

8 R Programming
  8.1 How should I write summary methods?
  8.2 How can I debug dynamically loaded code?
  8.3 How can I inspect R objects when debugging?
  8.4 How can I change compilation flags?

9 R Bugs
  9.1 What is a bug?
  9.2 How to report a bug

10 Acknowledgments


R FAQ
*****

1 Introduction
**************

This document contains answers to some of the most frequently asked
questions about R.

1.1 Legalese
============

This document is copyright (C) 1998-2004 by Kurt Hornik.

   This document is free software; you can redistribute it and/or modify it
under the terms of the GNU General Public License as published by the Free
Software Foundation; either version 2, or (at your option) any later
version.

   This document is distributed in the hope that it will be useful, but
WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License
for more details.

   A copy of the GNU General Public License is available via WWW at

     `http://www.gnu.org/copyleft/gpl.html'.

You can also obtain it by writing to the Free Software Foundation, Inc., 59
Temple Place -- Suite 330, Boston, MA 02111-1307, USA.

1.2 Obtaining this document
===========================

The latest version of this document is always available from

     `http://www.ci.tuwien.ac.at/~hornik/R/'

   From there, you can obtain versions converted to plain ASCII text, DVI,
GNU info, HTML, PDF, PostScript as well as the Texinfo source used for
creating all these formats using the GNU Texinfo system
(http://texinfo.org/).

   You can also obtain the R FAQ from the `doc/FAQ' subdirectory of a CRAN
site (*note What is CRAN?::).

1.3 Citing this document
========================

In publications, please refer to this FAQ as Hornik (2004), "The R FAQ",
and give the above, _official_ URL and the ISBN 3-900051-01-1.

1.4 Notation
============

Everything should be pretty standard.  `R>' is used for the R prompt, and a
`$' for the shell prompt (where applicable).

1.5 Feedback
============

Feedback is of course most welcome.

   In particular, note that I do not have access to Windows or Macintosh
systems.  Features specific to the Windows and Mac OS X ports of R are
described in the "R for Windows FAQ"
(http://www.stats.ox.ac.uk/pub/R/rw-FAQ.html) and the "R for Mac OS X FAQ
(http://cran.R-project.org/bin/macosx/RMacOSX-FAQ.html).  If you have
information on Macintosh or Windows systems that you think should be added
to this document, please let me know.

2 R Basics
**********

2.1 What is R?
==============

R is a system for statistical computation and graphics.  It consists of a
language plus a run-time environment with graphics, a debugger, access to
certain system functions, and the ability to run programs stored in script
files.

   The design of R has been heavily influenced by two existing languages:
Becker, Chambers & Wilks' S (*note What is S?::) and Sussman's Scheme
(http://www.cs.indiana.edu/scheme-repository/home.html).  Whereas the
resulting language is very similar in appearance to S, the underlying
implementation and semantics are derived from Scheme.  *Note What are the
differences between R and S?::, for further details.

   The core of R is an interpreted computer language which allows branching
and looping as well as modular programming using functions.  Most of the
user-visible functions in R are written in R.  It is possible for the user
to interface to procedures written in the C, C++, or FORTRAN languages for
efficiency.  The R distribution contains functionality for a large number
of statistical procedures.  Among these are: linear and generalized linear
models, nonlinear regression models, time series analysis, classical
parametric and nonparametric tests, clustering and smoothing.  There is
also a large set of functions which provide a flexible graphical
environment for creating various kinds of data presentations.  Additional
modules ("add-on packages") are available for a variety of specific
purposes (*note R Add-On Packages::).

   R was initially written by Ross Ihaka <Ross.Ihaka@R-project.org> and
Robert Gentleman <Robert.Gentleman@R-project.org> at the Department of
Statistics of the University of Auckland in Auckland, New Zealand.  In
addition, a large group of individuals has contributed to R by sending code
and bug reports.

   Since mid-1997 there has been a core group (the "R Core Team") who can
modify the R source code CVS archive.  The group currently consists of Doug
Bates, John Chambers, Peter Dalgaard, Robert Gentleman, Kurt Hornik,
Stefano Iacus, Ross Ihaka, Friedrich Leisch, Thomas Lumley, Martin
Maechler, Duncan Murdoch, Paul Murrell, Martyn Plummer, Brian Ripley,
Duncan Temple Lang, and Luke Tierney.

   R has a home page at `http://www.R-project.org/'.  It is free software
distributed under a GNU-style copyleft, and an official part of the GNU
project ("GNU S").

2.2 What machines does R run on?
================================

R is being developed for the Unix, Windows and Mac families of operating
systems.  Support for Mac OS Classic will end with the 1.7 series.

   The current version of R will configure and build under a number of
common Unix platforms including i386-freebsd, CPU-linux-gnu for the i386,
alpha, arm, hppa, ia64, m68k, powerpc, and sparc CPUs (see e.g.
`http://buildd.debian.org/build.php?&pkg=r-base'), i386-sun-solaris,
powerpc-apple-darwin, mips-sgi-irix, alpha-dec-osf4, rs6000-ibm-aix,
hppa-hp-hpux, and sparc-sun-solaris.

   If you know about other platforms, please drop us a note.

2.3 What is the current version of R?
=====================================

The current released version is 1.9.0.  Based on this
`major.minor.patchlevel' numbering scheme, there are two development
versions of R, working towards the next patch (`r-patched') and minor or
eventually major (`r-devel') releases of R, respectively.  Version
r-patched is for bug fixes mostly.  New features are typically introduced
in r-devel.

2.4 How can R be obtained?
==========================

Sources, binaries and documentation for R can be obtained via CRAN, the
"Comprehensive R Archive Network" (see *Note What is CRAN?::).

   Sources are also available via anonymous rsync.  Use

     rsync -rptC --delete rsync.R-project.org::MODULE R

to create a copy of the source tree specified by MODULE in the subdirectory
`R' of the current directory, where MODULE specifies one of the three
existing flavors of the R sources, and can be one of `r-release' (current
released version), `r-patched' (patched released version), and `r-devel'
(development version).  The rsync trees are created directly from the
master CVS archive and are updated hourly.  The `-C' and in the `rsync'
command is to cause it to skip the CVS directories.  Further information on
`rsync' is available at `http://rsync.samba.org/rsync/'.

   Note that the sources available via rsync do not include the recommended
packages, whereas these are included in the tarballs of released versions.
To install the appropriate sources for the recommended packages, run
`./tools/rsync-recommended' from the top-level of the R sources that you
pulled by rsync.

   The sources of the development version are also available via anonymous
CVS.  See `http://anoncvs.R-project.org' for more information.

2.5 How can R be installed?
===========================

2.5.1 How can R be installed (Unix)
-----------------------------------

If binaries are available for your platform (see *Note Are there Unix
binaries for R?::), you can use these, following the instructions that come
with them.

   Otherwise, you can compile and install R yourself, which can be done
very easily under a number of common Unix platforms (see *Note What
machines does R run on?::).  The file `INSTALL' that comes with the R
distribution contains a brief introduction, and the "R Installation and
Administration" guide (*note What documentation exists for R?::) has full
details.

   Note that you need a FORTRAN compiler or `f2c' in addition to a C
compiler to build R.  Also, you need Perl version 5 to build the R object
documentations.  (If this is not available on your system, you can obtain a
PDF version of the object reference manual via CRAN.)

   In the simplest case, untar the R source code, change to the directory
thus created, and issue the following commands (at the shell prompt):

     $ ./configure
     $ make

   If these commands execute successfully, the R binary and a shell script
front-end called `R' are created and copied to the `bin' directory.  You
can copy the script to a place where users can invoke it, for example to
`/usr/local/bin'.  In addition, plain text help pages as well as HTML and
LaTeX versions of the documentation are built.

   Use `make dvi' to create DVI versions of the R manuals, such as
`refman.dvi' (an R object reference index) and `R-exts.dvi', the "R
Extension Writers Guide", in the `doc/manual' subdirectory.  These files
can be previewed and printed using standard programs such as `xdvi' and
`dvips'.  You can also use `make pdf' to build PDF (Portable Document
Format) version of the manuals, and view these using e.g. Acrobat.  Manuals
written in the GNU Texinfo system can also be converted to info files
suitable for reading online with Emacs or stand-alone GNU Info; use `make
info' to create these versions (note that this requires `makeinfo' version
4).

   Finally, use `make check' to find out whether your R system works
correctly.

   You can also perform a "system-wide" installation using `make install'.
By default, this will install to the following directories:

`${prefix}/bin'
     the front-end shell script

`${prefix}/man/man1'
     the man page

`${prefix}/lib/R'
     all the rest (libraries, on-line help system, ...).  This is the "R
     Home Directory" (`R_HOME') of the installed system.

In the above, `prefix' is determined during configuration (typically
`/usr/local') and can be set by running `configure' with the option

     $ ./configure --prefix=/where/you/want/R/to/go

(E.g., the R executable will then be installed into
`/where/you/want/R/to/go/bin'.)

   To install DVI, info and PDF versions of the manuals, use `make
install-dvi', `make install-info' and `make install-pdf', respectively.

2.5.2 How can R be installed (Windows)
--------------------------------------

The `bin/windows' directory of a CRAN site contains binaries for a base
distribution and a large number of add-on packages from CRAN to run on
Windows 95, 98, ME, NT4, 2000, and XP (at least) on Intel and clones (but
not on other platforms).  The Windows version of R was created by Robert
Gentleman, and is now being developed and maintained by Duncan Murdoch
<murdoch@stats.uwo.ca> and Brian D. Ripley <Brian.Ripley@R-project.org>.

   For most installations the Windows installer program will be the easiest
tool to use.

   See the "R for Windows FAQ"
(http://www.stats.ox.ac.uk/pub/R/rw-FAQ.html) for more details.

2.5.3 How can R be installed (Macintosh)
----------------------------------------

The `bin/macosx' directory of a CRAN site contains a standard Apple
installer package named `RAqua.pkg.sit' compressed in Aladdin Stuffit
format.  Once downloaded, uncompressed and executed, the installer will
install the current non-developer release of R.  RAqua is a native Mac OS X
Darwin version of R with an Aqua GUI.  Inside `bin/macosx/X.Y' there are
prebuilt binary packages to be used with RAqua corresponding to the "X.Y"
release of R. The installation of these packages is available through the
"Package" menu of the RAqua GUI.  This port of R for Mac OS X is maintained
by Stefano Iacus <Stefano.Iacus@R-project.org>.  The "R for Mac OS X FAQ
(http://cran.R-project.org/bin/macosx/RMacOSX-FAQ.html) has more details.

   The `bin/macos' directory of a CRAN site contains bin-hexed (`hqx') and
stuffit (`sit') archives for a base distribution and a large number of
add-on packages of R 1.7.1 to run under Mac OS 8.6 to Mac OS 9.2.2.  This
port of R for Macintosh is no longer supported.

2.6 Are there Unix binaries for R?
==================================

The `bin/linux' directory of a CRAN site contains Debian
stable/testing/unstable packages for the i386 platform (now part of the
Debian distribution and maintained by Dirk Eddelbuettel), Mandrake
9.1/9.2/10.0 i386 packages by Michele Alzetta, Red Hat 7.x/8.x/9/Fedora1
i386, 7.x alpha, and Fedora1 x86_64 packages by Martyn Plummer, Naoki
Takebayashi, and James Henstridge, respectively, SuSE 7.3/8.0/8.1/8.2 i386
and 9.0/9.1 i586 packages by Detlef Steuer, and VineLinux 2.6 i386 packages
by Susunu Tanimura.

   The Debian packages can be accessed through APT, the Debian package
maintenance tool.  Simply add the line

     deb http://cran.R-project.org/bin/linux/debian DISTRIBUTION main

(where DISTRIBUTION is either `stable' or `testing'; feel free to use a
CRAN mirror instead of the master) to the file `/etc/apt/sources.list'.
Once you have added that line the programs `apt-get', `apt-cache', and
`dselect' (using the apt access method) will automatically detect and
install updates of the R packages.

   No other binary distributions are currently publically available.

2.7 What documentation exists for R?
====================================

Online documentation for most of the functions and variables in R exists,
and can be printed on-screen by typing `help(NAME)' (or `?NAME') at the R
prompt, where NAME is the name of the topic help is sought for.  (In the
case of unary and binary operators and control-flow special forms, the name
may need to be be quoted.)

   This documentation can also be made available as one reference manual
for on-line reading in HTML and PDF formats, and as hardcopy via LaTeX, see
*Note How can R be installed?::.  An up-to-date HTML version is always
available for web browsing at `http://stat.ethz.ch/R-manual/'.

   Printed copies of the R reference manual for some version(s) are
available from Network Theory Ltd, at
`http://www.network-theory.co.uk/R/base/'.  For each set of manuals sold,
the publisher donates USD 10 to the R Foundation (*note What is the R
Foundation?::).

   The R distribution also comes with the following manuals.

   * "An Introduction to R" (`R-intro') includes information on data types,
     programming elements, statistical modeling and graphics.  This
     document is based on the "Notes on S-PLUS" by Bill Venables and David
     Smith.

   * "Writing R Extensions" (`R-exts') currently describes the process of
     creating R add-on packages, writing R documentation, R's system and
     foreign language interfaces, and the R API.

   * "R Data Import/Export" (`R-data') is a guide to importing and
     exporting data to and from R.

   * "The R Language Definition" (`R-lang'), a first version of the
     "Kernighan & Ritchie of R", explains evaluation, parsing, object
     oriented programming, computing on the language, and so forth.

   * "R Installation and Administration" (`R-admin').

   Books on R include

     P. Dalgaard (2002), "Introductory Statistics with R", Springer: New
     York, ISBN 0-387-95475-9.
     `http://www.biostat.ku.dk/~pd/ISwR.html'.

     J. Fox (2002), "An R and S-PLUS Companion to Applied Regression", Sage
     Publications, ISBN 0-761-92280-6 (softcover) or 0-761-92279-2
     (hardcover),
     `http://socserv.socsci.mcmaster.ca/jfox/Books/Companion/'.

     J. Maindonald and J. Braun (2003), "Data Analysis and Graphics Using R:
     An Example-Based Approach", Cambridge University Press, ISBN
     0-521-81336-0,
     `http://wwwmaths.anu.edu.au/~johnm/'.

     S. M. Iacus and G. Masarotto (2002), "Laboratorio di statistica con
     R", McGraw-Hill, ISBN 88-386-6084-0 (in Italian),
     `http://www.ateneonline.it/LibroAteneo.asp?item_id=1436'.

The book

     W. N. Venables and B. D. Ripley (2002), "Modern Applied Statistics with
     S.  Fourth Edition".  Springer, ISBN 0-387-95457-0

has a home page at `http://www.stats.ox.ac.uk/pub/MASS4/' providing
additional material.  Its companion is

     W. N. Venables and B. D. Ripley (2000), "S Programming".  Springer,
     ISBN 0-387-98966-8

and provides an in-depth guide to writing software in the S language which
forms the basis of both the commercial S-PLUS and the Open Source R data
analysis software systems.  See
`http://www.stats.ox.ac.uk/pub/MASS3/Sprog/' for more information.

   In addition to material written specifically or explicitly for R,
documentation for S/S-PLUS (see *Note R and S::) can be used in combination
with this FAQ (*note What are the differences between R and S?::).
Introductory books include

     P. Spector (1994), "An introduction to S and S-PLUS", Duxbury Press.

     A. Krause and M. Olsen (2002), "The Basics of S-PLUS" (Third Edition).
     Springer, ISBN 0-387-95456-2

   The book

     J. C. Pinheiro and D. M. Bates (2000), "Mixed-Effects Models in S and
     S-PLUS", Springer, ISBN 0-387-98957-0

provides a comprehensive guide to the use of the *nlme* package for linear
and nonlinear mixed-effects models.  This has a home page at
`http://nlme.stat.wisc.edu/MEMSS/'.

   As an example of how R can be used in teaching an advanced introductory
statistics course, see

     D. Nolan and T. Speed (2000), "Stat Labs: Mathematical Statistics
     Through Applications", Springer Texts in Statistics, ISBN 0-387-98974-9

This integrates theory of statistics with the practice of statistics
through a collection of case studies ("labs"), and uses R to analyze the
data.  More information can be found at
`http://www.stat.Berkeley.EDU/users/statlabs/'.

   Last, but not least, Ross' and Robert's experience in designing and
implementing R is described in Ihaka & Gentleman (1996), "R: A Language for
Data Analysis and Graphics", _Journal of Computational and Graphical
Statistics_, *5*, 299-314.

   An annotated bibliography (BibTeX format) of R-related publications
which includes most of the above references can be found at

     `http://www.R-project.org/doc/bib/R.bib'

2.8 Citing R
============

To cite R in publications, use

     @Manual{,
       title        = {R: A language and environment for statistical
                       computing},
       author       = {{R Development Core Team}},
       organization = {R Foundation for Statistical Computing},
       address      = {Vienna, Austria},
       year         = 2004,
       note         = {ISBN 3-900051-00-3},
       url          = {http://www.R-project.org}
     }

2.9 What mailing lists exist for R?
===================================

Thanks to Martin Maechler <Martin.Maechler@R-project.org>, there are four
mailing lists devoted to R.

`R-announce'
     A moderated list for major announcements about the development of R and
     the availability of new code.

`R-packages'
     A moderated list for announcements on the availability of new or
     enhanced contributed packages.

`R-help'
     The `main' R mailing list, for discussion about problems and solutions
     using R, announcements (not covered by `R-announce' and `R-packages')
     about the development of R and the availability of new code,
     enhancements and patches to the source code and documentation of R,
     comparison and compatibility with S and S-PLUS, and for the posting of
     nice examples and benchmarks.

`R-devel'
     This list is for discussions about the future of R, proposals of new
     functionality, and pre-testing of new versions.  It is meant for those
     who maintain an active position in the development of R.

Convenient access to information on these lists, subscription, and archives
is provided by the web interface at
`http://www.stat.math.ethz.ch/mailman/listinfo/'.  One can also subscribe
(or unsubscribe) via email, e.g. to R-help by sending `subscribe' (or
`unsubscribe') in the _body_ of the message (not in the subject!) to
<R-help-request@lists.R-project.org>.

   Send email to <R-help@lists.R-project.org> to send a message to everyone
on the R-help mailing list.  Subscription and posting to the other lists is
done analogously, with `R-help' replaced by `R-announce', `R-packages', and
`R-devel', respectively.  Note that the R-announce and R-packages lists are
gatewayed into R-help.  Hence, you should subscribe to either of them only
in case you are not subscribed to R-help.

   It is recommended that you send mail to R-help rather than only to the R
Core developers (who are also subscribed to the list, of course).  This may
save them precious time they can use for constantly improving R, and will
typically also result in much quicker feedback for yourself.

   Of course, in the case of bug reports it would be very helpful to have
code which reliably reproduces the problem.  Also, make sure that you
include information on the system and version of R being used.  See *Note R
Bugs:: for more details.

   Please read the posting guide
(http://www.R-project.org/posting-guide.html) _before_ sending anything to
any mailing list.

   See `http://www.R-project.org/mail.html' for more information on the R
mailing lists.

   The R Core Team can be reached at <R-core@lists.R-project.org> for
comments and reports.

2.10 What is CRAN?
==================

The "Comprehensive R Archive Network" (CRAN) is a collection of sites which
carry identical material, consisting of the R distribution(s), the
contributed extensions, documentation for R, and binaries.

   The CRAN master site at TU Wien, Austria, can be found at the URL

     `http://cran.R-project.org/'

Daily mirrors are available at URLs including

     `http://cran.at.R-project.org/'  (TU Wien, Austria)
     `http://cran.au.R-project.org/'  (PlanetMirror, Australia)
     `http://cran.br.R-project.org/'  (Universidade Federal de
                                      Paraná, Brazil)
     `http://cran.ch.R-project.org/'  (ETH Zürich, Switzerland)
     `http://cran.dk.R-project.org/'  (SunSITE, Denmark)
     `http://cran.es.R-project.org/'  (Spanish National Research
                                      Network, Madrid, Spain)
     `http://cran.fr.R-project.org/'  (INRA, Toulouse, France)
     `http://cran.hu.R-project.org/'  (Semmelweis U, Hungary)
     `http://cran.pt.R-project.org/'  (Universidade do Porto,
                                      Portugal)
     `http://cran.uk.R-project.org/'  (U of Bristol, United
                                      Kingdom)
     `http://cran.us.R-project.org/'  (pair Networks, USA)
     `http://cran.za.R-project.org/'  (Rhodes U, South Africa)

See `http://cran.R-project.org/mirrors.html' for a complete list of
mirrors.  Please use the CRAN site closest to you to reduce network load.

   From CRAN, you can obtain the latest official release of R, daily
snapshots of R (copies of the current CVS trees), as gzipped and bzipped
tar files, a wealth of additional contributed code, as well as prebuilt
binaries for various operating systems (Linux, Mac OS Classic, Mac OS X,
and MS Windows).  CRAN also provides access to documentation on R, existing
mailing lists and the R Bug Tracking system.

   To "submit" to CRAN, simply upload to
`ftp://cran.R-project.org/incoming/' and send an email to
<cran@R-project.org>.  Note that CRAN generally does not accept submissions
of precompiled binaries due to security reasons.

     *Note:*  It is very important that you indicate the copyright
     (license) information (GPL, BSD, Artistic, ...)  in your submission.

   Please always use the URL of the master site when referring to CRAN.

2.11 Can I use R for commercial purposes?
=========================================

R is released under the GNU General Public License (GPL).  If you have any
questions regarding the legality of using R in any particular situation you
should bring it up with your legal counsel.  We are in no position to offer
legal advice.

   It is the opinion of the R Core Team that one can use R for commercial
purposes (e.g., in business or in consulting).  The GPL, like all Open
Source licenses, permits all and any use of the package.  It only restricts
distribution of R or of other programs containing code from R.  This is
made clear in clause 6 ("No Discrimination Against Fields of Endeavor") of
the Open Source Definition (http://www.opensource.org/docs/definition.html):

     The license must not restrict anyone from making use of the program in
     a specific field of endeavor.  For example, it may not restrict the
     program from being used in a business, or from being used for genetic
     research.

It is also explicitly stated in clause 0 of the GPL, which says in part

     Activities other than copying, distribution and modification are not
     covered by this License; they are outside its scope.  The act of
     running the Program is not restricted, and the output from the Program
     is covered only if its contents constitute a work based on the Program.

   Most add-on packages, including all recommended ones, also explicitly
allow commercial use in this way.  A few packages are restricted to
"non-commercial use"; you should contact the author to clarify whether
these may be used or seek the advice of your legal counsel.

   None of the discussion in this section constitutes legal advice.  The R
Core Team does not provide legal advice under any circumstances.

2.12 Why is R named R?
======================

The name is partly based on the (first) names of the first two R authors
(Robert Gentleman and Ross Ihaka), and partly a play on the name of the
Bell Labs language `S' (*note What is S?::).

2.13 What is the R Foundation?
==============================

The R Foundation is a not for profit organization working in the public
interest.  It was founded by the members of the R Core Team in order to
provide support for the R project and other innovations in statistical
computing, provide a reference point for individuals, instititutions or
commercial enterprises that want to support or interact with the R
development community, and to hold and administer the copyright of R
software and documentation.  See `http://www.R-project.org/foundation/' for
more information.

3 R and S
*********

3.1 What is S?
==============

S is a very high level language and an environment for data analysis and
graphics.  In 1998, the Association for Computing Machinery (ACM) presented
its Software System Award to John M. Chambers, the principal designer of S,
for

     the S system, which has forever altered the way people analyze,
     visualize, and manipulate data ...

     S is an elegant, widely accepted, and enduring software system, with
     conceptual integrity, thanks to the insight, taste, and effort of John
     Chambers.

   The evolution of the S language is characterized by four books by John
Chambers and coauthors, which are also the primary references for S.

   * Richard A. Becker and John M. Chambers (1984), "S.  An Interactive
     Environment for Data Analysis and Graphics," Monterey: Wadsworth and
     Brooks/Cole.

     This is also referred to as the "_Brown Book_", and of historical
     interest only.

   * Richard A. Becker, John M. Chambers and Allan R. Wilks (1988), "The New
     S Language," London: Chapman & Hall.

     This book is often called the "_Blue Book_", and introduced what is
     now known as S version 2.

   * John M. Chambers and Trevor J. Hastie (1992), "Statistical Models in
     S,"  London: Chapman & Hall.

     This is also called the "_White Book_", and introduced S version 3,
     which added structures to facilitate statistical modeling in S.

   * John M. Chambers (1998), "Programming with Data," New York: Springer,
     ISBN 0-387-98503-4
     (<http://cm.bell-labs.com/cm/ms/departments/sia/Sbook/>).

     This "_Green Book_" describes version 4 of S, a major revision of S
     designed by John Chambers to improve its usefulness at every stage of
     the programming process.

   See `http://cm.bell-labs.com/cm/ms/departments/sia/S/history.html' for
further information on "Stages in the Evolution of S".

   There is a huge amount of user-contributed code for S, available at the
S Repository (http://lib.stat.cmu.edu/S/) at CMU.

3.2 What is S-PLUS?
===================

S-PLUS is a value-added version of S sold by Insightful Corporation.  Based
on the S language, S-PLUS provides functionality in a wide variety of
areas, including robust regression, modern non-parametric regression, time
series, survival analysis, multivariate analysis, classical statistical
tests, quality control, and graphics drivers.  Add-on modules add
additional capabilities for wavelet analysis, spatial statistics, GARCH
models, and design of experiments.

   See the Insightful S-PLUS page
(http://www.insightful.com/products/splus/) for further information.

3.3 What are the differences between R and S?
=============================================

We can regard S as a language with three current implementations or
"engines", the "old S engine" (S version 3; S-PLUS 3.x and 4.x), the "new S
engine" (S version 4; S-PLUS 5.x and above), and R.  Given this
understanding, asking for "the differences between R and S" really amounts
to asking for the specifics of the R implementation of the S language,
i.e., the difference between the R and S _engines_.

   For the remainder of this section, "S" refers to the S engines and not
the S language.

3.3.1 Lexical scoping
---------------------

Contrary to other implementations of the S language, R has adopted the
evaluation model of Scheme.

   This difference becomes manifest when _free_ variables occur in a
function.  Free variables are those which are neither formal parameters
(occurring in the argument list of the function) nor local variables
(created by assigning to them in the body of the function).  Whereas S
(like C) by default uses _static_ scoping, R (like Scheme) has adopted
_lexical_ scoping.  This means the values of free variables are determined
by a set of global variables in S, but in R by the bindings that were in
effect at the time the function was created.

   Consider the following function:

     cube <- function(n) {
       sq <- function() n * n
       n * sq()
     }

   Under S, `sq()' does not "know" about the variable `n' unless it is
defined globally:

     S> cube(2)
     Error in sq():  Object "n" not found
     Dumped
     S> n <- 3
     S> cube(2)
     [1] 18

   In R, the "environment" created when `cube()' was invoked is also looked
in:

     R> cube(2)
     [1] 8

   As a more "interesting" real-world problem, suppose you want to write a
function which returns the density function of the r-th order statistic
from a sample of size n from a (continuous) distribution.  For simplicity,
we shall use both the cdf and pdf of the distribution as explicit
arguments.  (Example compiled from various postings by Luke Tierney.)

   The S-PLUS documentation for `call()' basically suggests the following:

     dorder <- function(n, r, pfun, dfun) {
       f <- function(x) NULL
       con <- round(exp(lgamma(n + 1) - lgamma(r) - lgamma(n - r + 1)))
       PF <- call(substitute(pfun), as.name("x"))
       DF <- call(substitute(dfun), as.name("x"))
       f[[length(f)]] <-
         call("*", con,
              call("*", call("^", PF, r - 1),
                   call("*", call("^", call("-", 1, PF), n - r),
                        DF)))
       f
     }

Rather tricky, isn't it?  The code uses the fact that in S, functions are
just lists of special mode with the function body as the last argument, and
hence does not work in R (one could make the idea work, though).

   A version which makes heavy use of `substitute()' and seems to work
under both S and R is

     dorder <- function(n, r, pfun, dfun) {
       con <- round(exp(lgamma(n + 1) - lgamma(r) - lgamma(n - r + 1)))
       eval(substitute(function(x) K * PF(x)^a * (1 - PF(x))^b * DF(x),
                       list(PF = substitute(pfun), DF = substitute(dfun),
                            a = r - 1, b = n - r, K = con)))
     }

(the `eval()' is not needed in S).

   However, in R there is a much easier solution:

     dorder <- function(n, r, pfun, dfun) {
       con <- round(exp(lgamma(n + 1) - lgamma(r) - lgamma(n - r + 1)))
       function(x) {
         con * pfun(x)^(r - 1) * (1 - pfun(x))^(n - r) * dfun(x)
       }
     }

This seems to be the "natural" implementation, and it works because the
free variables in the returned function can be looked up in the defining
environment (this is lexical scope).

   Note that what you really need is the function _closure_, i.e., the body
along with all variable bindings needed for evaluating it.  Since in the
above version, the free variables in the value function are not modified,
you can actually use it in S as well if you abstract out the closure
operation into a function `MC()' (for "make closure"):

     dorder <- function(n, r, pfun, dfun) {
       con <- round(exp(lgamma(n + 1) - lgamma(r) - lgamma(n - r + 1)))
       MC(function(x) {
            con * pfun(x)^(r - 1) * (1 - pfun(x))^(n - r) * dfun(x)
          },
          list(con = con, pfun = pfun, dfun = dfun, r = r, n = n))
     }

   Given the appropriate definitions of the closure operator, this works in
both R and S, and is much "cleaner" than a substitute/eval solution (or one
which overrules the default scoping rules by using explicit access to
evaluation frames, as is of course possible in both R and S).

   For R, `MC()' simply is

     MC <- function(f, env) f

(lexical scope!), a version for S is

     MC <- function(f, env = NULL) {
       env <- as.list(env)
       if (mode(f) != "function")
         stop(paste("not a function:", f))
       if (length(env) > 0 && any(names(env) == ""))
         stop(paste("not all arguments are named:", env))
       fargs <- if(length(f) > 1) f[1:(length(f) - 1)] else NULL
       fargs <- c(fargs, env)
       if (any(duplicated(names(fargs))))
         stop(paste("duplicated arguments:", paste(names(fargs)),
              collapse = ", "))
       fbody <- f[length(f)]
       cf <- c(fargs, fbody)
       mode(cf) <- "function"
       return(cf)
     }

   Similarly, most optimization (or zero-finding) routines need some
arguments to be optimized over and have other parameters that depend on the
data but are fixed with respect to optimization.  With R scoping rules,
this is a trivial problem; simply make up the function with the required
definitions in the same environment and scoping takes care of it.  With S,
one solution is to add an extra parameter to the function and to the
optimizer to pass in these extras, which however can only work if the
optimizer supports this.

   Lexical scoping allows using function closures and maintaining local
state.  A simple example (taken from Abelson and Sussman) is obtained by
typing `demo("scoping")' at the R prompt.  Further information is provided
in the standard R reference "R: A Language for Data Analysis and Graphics"
(*note What documentation exists for R?::) and in Robert Gentleman and Ross
Ihaka (2000), "Lexical Scope and Statistical Computing", _Journal of
Computational and Graphical Statistics_, *9*, 491-508.

   Lexical scoping also implies a further major difference.  Whereas S
stores all objects as separate files in a directory somewhere (usually
`.Data' under the current directory), R does not.  All objects in R are
stored internally.  When R is started up it grabs a piece of memory and
uses it to store the objects.  R performs its own memory management of this
piece of memory, growing and shrinking its size as needed.  Having
everything in memory is necessary because it is not really possible to
externally maintain all relevant "environments" of symbol/value pairs.
This difference also seems to make R _faster_ than S.

   The down side is that if R crashes you will lose all the work for the
current session.  Saving and restoring the memory "images" (the functions
and data stored in R's internal memory at any time) can be a bit slow,
especially if they are big.  In S this does not happen, because everything
is saved in disk files and if you crash nothing is likely to happen to
them.  (In fact, one might conjecture that the S developers felt that the
price of changing their approach to persistent storage just to accommodate
lexical scope was far too expensive.)  Hence, when doing important work,
you might consider saving often (see *Note How can I save my workspace?::)
to safeguard against possible crashes.  Other possibilities are logging
your sessions, or have your R commands stored in text files which can be
read in using `source()'.

     *Note:*  If you run R from within Emacs (see *Note R and Emacs::), you
     can save the contents of the interaction buffer to a file and
     conveniently manipulate it using `ess-transcript-mode', as well as
     save source copies of all functions and data used.

3.3.2 Models
------------

There are some differences in the modeling code, such as

   * Whereas in S, you would use `lm(y ~ x^3)' to regress `y' on `x^3', in
     R, you have to insulate powers of numeric vectors (using `I()'), i.e.,
     you have to use `lm(y ~ I(x^3))'.

   * The glm family objects are implemented differently in R and S.  The
     same functionality is available but the components have different
     names.

   * Option `na.action' is set to `"na.omit"' by default in R, but not set
     in S.

   * Terms objects are stored differently.  In S a terms object is an
     expression with attributes, in R it is a formula with attributes.  The
     attributes have the same names but are mostly stored differently.  The
     major difference in functionality is that a terms object is
     subscriptable in S but not in R.  If you can't imagine why this would
     matter then you don't need to know.

   * Finally, in R `y~x+0' is an alternative to `y~x-1' for specifying a
     model with no intercept.  Models with no parameters at all can be
     specified by `y~0'.

3.3.3 Others
------------

Apart from lexical scoping and its implications, R follows the S language
definition in the Blue and White Books as much as possible, and hence
really is an "implementation" of S.  There are some intentional differences
where the behavior of S is considered "not clean".  In general, the
rationale is that R should help you detect programming errors, while at the
same time being as compatible as possible with S.

   Some known differences are the following.

   * In R, if `x' is a list, then `x[i] <- NULL' and `x[[i]] <- NULL'
     remove the specified elements from `x'.  The first of these is
     incompatible with S, where it is a no-op.  (Note that you can set
     elements to `NULL' using `x[i] <- list(NULL)'.)

   * In S, the functions named `.First' and `.Last' in the `.Data'
     directory can be used for customizing, as they are executed at the
     very beginning and end of a session, respectively.

     In R, the startup mechanism is as follows.  R first sources the system
     startup file ``$R_HOME'/library/base/R/Rprofile'.  Then, it searches
     for a site-wide startup profile unless the command line option
     `--no-site-file' was given.  The name of this file is taken from the
     value of the `R_PROFILE' environment variable.  If that variable is
     unset, the default is ``$R_HOME'/etc/Rprofile.site'
     (``$R_HOME'/etc/Rprofile' in versions prior to 1.4.0).  This code is
     loaded in package *base*.  Then, unless `--no-init-file' was given, R
     searches for a file called `.Rprofile' in the current directory or in
     the user's home directory (in that order) and sources it into the user
     workspace.  It then loads a saved image of the user workspace from
     `.RData' in case there is one (unless `--no-restore' was specified).
     If needed, the functions `.First()' and `.Last()' should be defined in
     the appropriate startup profiles.

   * In R, `T' and `F' are just variables being set to `TRUE' and `FALSE',
     respectively, but are not reserved words as in S and hence can be
     overwritten by the user.  (This helps e.g. when you have factors with
     levels `"T"' or `"F"'.)  Hence, when writing code you should always
     use `TRUE' and `FALSE'.

   * In R, `dyn.load()' can only load _shared objects_, as created for
     example by `R CMD SHLIB'.

   * In R, `attach()' currently only works for lists and data frames, but
     not for directories.  (In fact, `attach()' also works for R data files
     created with `save()', which is analogous to attaching directories in
     S.)  Also, you cannot attach at position 1.

   * Categories do not exist in R, and never will as they are deprecated now
     in S.  Use factors instead.

   * In R, `For()' loops are not necessary and hence not supported.

   * In R, `assign()' uses the argument `envir=' rather than `where=' as in
     S.

   * The random number generators are different, and the seeds have
     different length.

   * R passes integer objects to C as `int *' rather than `long *' as in S.

   * R has no single precision storage mode.  However, as of version 0.65.1,
     there is a single precision interface to C/FORTRAN subroutines.

   * By default, `ls()' returns the names of the objects in the current
     (under R) and global (under S) environment, respectively.  For example,
     given

          x <- 1; fun <- function() {y <- 1; ls()}

     then `fun()' returns `"y"' in R and `"x"' (together with the rest of
     the global environment) in S.

   * R allows for zero-extent matrices (and arrays, i.e., some elements of
     the `dim' attribute vector can be 0).  This has been determined a
     useful feature as it helps reducing the need for special-case tests for
     empty subsets.  For example, if `x' is a matrix, `x[, FALSE]' is not
     `NULL' but a "matrix" with 0 columns.  Hence, such objects need to be
     tested for by checking whether their `length()' is zero (which works
     in both R and S), and not using `is.null()'.

   * Named vectors are considered vectors in R but not in S (e.g.,
     `is.vector(c(a = 1:3))' returns `FALSE' in S and `TRUE' in R).

   * Data frames are not considered as matrices in R (i.e., if `DF' is a
     data frame, then `is.matrix(DF)' returns `FALSE' in R and `TRUE' in S).

   * R by default uses treatment contrasts in the unordered case, whereas S
     uses the Helmert ones.  This is a deliberate difference reflecting the
     opinion that treatment contrasts are more natural.

   * In R, the argument of a replacement function which corresponds to the
     right hand side must be named `value'.  E.g., `f(a) <- b' is evaluated
     as `a <- "f<-"(a, value = b)'.  S always takes the last argument,
     irrespective of its name.

   * In S, `substitute()' searches for names for substitution in the given
     expression in three places: the actual and the default arguments of
     the matching call, and the local frame (in that order).  R looks in
     the local frame only, with the special rule to use a "promise" if a
     variable is not evaluated.  Since the local frame is initialized with
     the actual arguments or the default expressions, this is usually
     equivalent to S, until assignment takes place.

   * In S, the index variable in a `for()' loop is local to the inside of
     the loop.  In R it is local to the environment where the `for()'
     statement is executed.

   * In S, `tapply(simplify=TRUE)' returns a vector where R returns a
     one-dimensional array (which can have named dimnames).

   * In S(-PLUS) the C locale is used, whereas in R the current operating
     system locale is used for determining which characters are
     alphanumeric and how they are sorted.  This affects the set of valid
     names for R objects (for example accented chars may be allowed in R)
     and ordering in sorts and comparisons (such as whether `"aA" < "Bb"' is
     true or false).  From version 1.2.0 the locale can be (re-)set in R by
     the `Sys.setlocale()' function.

   * In S, `missing(ARG)' remains `TRUE' if ARG is subsequently modified;
     in R it doesn't.

   * From R version 1.3.0, `data.frame' strips `I()' when creating (column)
     names.

   * In R, the string `"NA"' is not treated as a missing value in a
     character variable.  Use `as.character(NA)' to create a missing
     character value.

   * R disallows repeated formal arguments in function calls.

   * In S, `dump()', `dput()' and `deparse()' are essentially different
     interfaces to the same code.  In R from version 2.0.0, this is only
     true if the same values are passed in the `forDisplay' and `useSource'
     arguments, but by default they are not.  By default `dump()' tries to
     write code that will evaluate to reproduce the object, whereas
     `dput()' and `deparse()' default to options for producing deparsed
     code that is readable.


   There are also differences which are not intentional, and result from
missing or incorrect code in R.  The developers would appreciate hearing
about any deficiencies you may find (in a written report fully documenting
the difference as you see it).  Of course, it would be useful if you were
to implement the change yourself and make sure it works.

3.4 Is there anything R can do that S-PLUS cannot?
==================================================

Since almost anything you can do in R has source code that you could port
to S-PLUS with little effort there will never be much you can do in R that
you couldn't do in S-PLUS if you wanted to.  (Note that using lexical
scoping may simplify matters considerably, though.)

   R offers several graphics features that S-PLUS does not, such as finer
handling of line types, more convenient color handling (via palettes),
gamma correction for color, and, most importantly, mathematical annotation
in plot texts, via input expressions reminiscent of TeX constructs.  See
the help page for `plotmath', which features an impressive on-line example.
More details can be found in Paul Murrell and Ross Ihaka (2000), "An
Approach to Providing Mathematical Annotation in Plots", _Journal of
Computational and Graphical Statistics_, *9*, 582-599.

3.5 What is R-plus?
===================

There is no such thing.

4 R Web Interfaces
******************

*Rweb* is developed and maintained by Jeff Banfield
<jeff@math.montana.edu>.  The Rweb Home Page
(http://www.math.montana.edu/Rweb/) provides access to all three versions
of Rweb--a simple text entry form that returns output and graphs, a more
sophisticated Javascript version that provides a multiple window
environment, and a set of point and click modules that are useful for
introductory statistics courses and require no knowledge of the R language.
All of the Rweb versions can analyze Web accessible datasets if a URL is
provided.

   The paper "Rweb: Web-based Statistical Analysis", providing a detailed
explanation of the different versions of Rweb and an overview of how Rweb
works, was published in the Journal of Statistical Software
(`http://www.stat.ucla.edu/journals/jss/v04/i01/').

   Ulf Bartel <ulfi@cs.tu-berlin.de> is working on *R-Online*, a simple
on-line programming environment for R which intends to make the first steps
in statistical programming with R (especially with time series) as easy as
possible.  There is no need for a local installation since the only
requirement for the user is a JavaScript capable browser.  See
`http://osvisions.com/r-online/' for more information.

   David Firth <http://www.warwick.ac.uk/go/dfirth> has written *CGIwithR*,
an R add-on package available from CRAN.  It provides some simple
extensions to R to facilitate running R scripts through the CGI interface
to a web server.  It is easily installed using Apache under Linux and in
principle should run on any platform that supports R and a web server
provided that the installer has the necessary security permissions.

   *Rcgi* is a CGI WWW interface to R by MJ Ray <mjr@dsl.pipex.com>.  It
had the ability to use "embedded code": you could mix user input and code,
allowing the HTML author to do anything from load in data sets to enter
most of the commands for users without writing CGI scripts.  Graphical
output was possible in PostScript or GIF formats and the executed code was
presented to the user for revision.  However, it is not clear if the
project is still active.  Currently, a modified version of *Rcgi* by Mai
Zhou <mai@ms.uky.edu> (actually, two versions: one with (bitmap) graphics
and one without) as well as the original code are available from
`http://www.ms.uky.edu/~statweb'.

5 R Add-On Packages
*******************

5.1 Which add-on packages exist for R?
======================================

5.1.1 Add-on packages in R
--------------------------

The R distribution comes with the following packages:

*base*
     Base R functions and datasets.

*graphics*
     R functions for base graphics.

*grid*
     A rewrite of the graphics layout capabilities, plus some support for
     interaction.

*methods*
     Formally defined methods and classes for R objects, plus other
     programming tools, as described in the Green Book.

*splines*
     Regression spline functions and classes.

*stats*
     R statistical functions.

*stats4*
     Statistical functions using S4 classes.

*tcltk*
     Interface and language bindings to Tcl/Tk GUI elements.

*tools*
     Tools for package development and administration.

*utils*
     R utility functions.
   These "base packages" were substantially reorganized in R 1.9.  The
former *base* was split into the four packages *base*, *graphics*, *stats*,
and *utils*.  Packages *ctest*, *eda*, *modreg*, *mva*, *nls*, *stepfun*
and *ts* were merged into *stats*, package *lqs* returned to the
recommended package *MASS*, and package *mle* moved to *stats4*.

5.1.2 Add-on packages from CRAN
-------------------------------

The following packages are available from the CRAN `src/contrib' area.
(Packages denoted as _Recommended_ are to be included in all binary
distributions of R.)

*AlgDesign*
     Algorithmic experimental designs.  Calculates exact and approximate
     theory experimental designs for D, A, and I criteria.

*AnalyzeFMRI*
     Functions for I/O, visualisation and analysis of functional Magnetic
     Resonance Imaging (fMRI) datasets stored in the ANALYZE format.

*Bhat*
     Functions for general likelihood exploration (MLE, MCMC, CIs).

*BradleyTerry*
     Specify and fit the Bradley-Terry model and structured versions.

*BsMD*
     Bayes screening and model discrimination follow-up designs.

*CDNmoney*
     Components of Canadian monetary aggregates.

*CGIwithR*
     Facilities for the use of R to write CGI scripts.

*CircStats*
     Circular Statistics, from "Topics in Circular Statistics" by S. Rao
     Jammalamadaka and A. SenGupta, 2001, World Scientific.

*CoCoAn*
     Constrained Correspondence Analysis.

*DAAG*
     Various data sets used in examples and exercises in "Data Analysis and
     Graphics Using R" by John H. Maindonald and W. John Brown, 2003.

*DBI*
     A common database interface (DBI) class and method definitions.  All
     classes in this package are virtual and need to be extended by the
     various DBMS implementations.

*DCluster*
     A set of functions for the detection of spatial clusters of diseases
     using count data.

*Davies*
     Functions for the Davies quantile function and the Generalized Lambda
     distribution.

*Design*
     Regression modeling, testing, estimation, validation, graphics,
     prediction, and typesetting by storing enhanced model design attributes
     in the fit.  Design is a collection of about 180 functions that assist
     and streamline modeling, especially for biostatistical and
     epidemiologic applications.  It also contains new functions for binary
     and ordinal logistic regression models and the Buckley-James multiple
     regression model for right-censored responses, and implements
     penalized maximum likelihood estimation for logistic and ordinary
     linear models.  Design works with almost any regression model, but it
     was especially written to work with logistic regression, Cox
     regression, accelerated failure time models, ordinary linear models,
     and the Buckley-James model.

*Devore5*
     Data sets and sample analyses from "Probability and Statistics for
     Engineering and the Sciences (5th ed)" by Jay L. Devore, 2000, Duxbury.

*Devore6*
     Data sets and sample analyses from "Probability and Statistics for
     Engineering and the Sciences (6th ed)" by Jay L. Devore, 2003, Duxbury.

*EMV*
     Estimation of missing values in a matrix by a k-th nearest neighboors
     algorithm.

*GRASS*
     An interface between the GRASS geographical information system and R,
     based on starting R from within the GRASS environment and chosen
     LOCATION_NAME and MAPSET.  Wrapper and helper functions are provided
     for a range of R functions to match the interface metadata structures.

*GenKern*
     Functions for generating and manipulating generalised binned kernel
     density estimates.

*GeneTS*
     A package for analysing multiple gene expression time series data.
     Currently, implements methods for cell cycle analysis and for inferring
     large sparse graphical Gaussian models.

*HI*
     Simulation from distributions supported by nested hyperplanes.

*HighProbability*
     Estimation of the alternative hypotheses having frequentist or Bayesian
     probabilities at least as great as a specified threshold, given a list
     of p-values.

*Hmisc*
     Functions useful for data analysis, high-level graphics, utility
     operations, functions for computing sample size and power, importing
     datasets, imputing missing values, advanced table making, variable
     clustering, character string manipulation, conversion of S objects to
     LaTeX code, recoding variables, and bootstrap repeated measures
     analysis.

*HyperbolicDist*
     Basic functions for the hyperbolic distribution: probability density
     function, distribution function, quantile function, a routine for
     generating observations from the hyperbolic, and a function for fitting
     the hyperbolic distribution to data.

*ISwR*
     Data sets for "Introductory Statistics with R" by Peter Dalgaard,
     2002, Springer.

*Icens*
     Functions for computing the NPMLE for censored and truncated data.

*KMsurv*
     Data sets and functions for "Survival Analysis, Techniques for Censored
     and Truncated Data" by Klein and Moeschberger, 1997, Springer.

*KernSmooth*
     Functions for kernel smoothing (and density estimation) corresponding
     to the book "Kernel Smoothing" by M. P. Wand and M. C. Jones, 1995.
     _Recommended_.

*MASS*
     Functions and datasets from the main package of Venables and Ripley,
     "Modern Applied Statistics with S".  Contained in the `VR' bundle.
     _Recommended_.

*MCMCpack*
     Markov chain Monte Carlo (MCMC) package: functions for posterior
     simulation for a number of statistical models.

*MPV*
     Data sets from the book "Introduction to Linear Regression Analysis"
     by D. C. Montgomery, E. A. Peck, and C. G. Vining, 2001, John Wiley and
     Sons.

*Matrix*
     A Matrix package.

*NISTnls*
     A set of test nonlinear least squares examples from NIST, the U.S.
     National Institute for Standards and Technology.

*Oarray*
     Arrays with arbitrary offsets.

*PHYLOGR*
     Manipulation and analysis of phylogenetically simulated data sets (as
     obtained from PDSIMUL in package PDAP) and phylogenetically-based
     analyses using GLS.

*PTAk*
     A multiway method to decompose a tensor (array) of any order, as a
     generalisation of SVD also supporting non-identity metrics and
     penalisations.  Also includes some other multiway methods.

*R2HTML*
     Functions for exporting R objects & graphics in an HTML document.

*R2WinBUGS*
     Running WinBUGS from R: call a BUGS model, summarize inferences and
     convergence in a table and graph, and save the simulations in arrays
     for easy access in R.

*RArcInfo*
     Functions to import Arc/Info V7.x coverages and data.

*RColorBrewer*
     ColorBrewer palettes for drawing nice maps shaded according to a
     variable.

*RMySQL*
     An interface between R and the MySQL database system.

*RODBC*
     An ODBC database interface.

*ROracle*
     Oracle Database Interface driver for R.  Uses the ProC/C++ embedded
     SQL.

*RQuantLib*
     Provides access to (some) of the QuantLib functions from within R;
     currently limited to some Option pricing and analysis functions.  The
     QuantLib project aims to provide a comprehensive software framework for
     quantitative finance.

*RSQLite*
     Database Interface R driver for SQLite.  Embeds the SQLite database
     engine in R.

*RScaLAPACK*
     An interface to ScaLAPACK functions from R.

*RSvgDevice*
     A graphics device for R that uses the new w3.org XML standard for
     Scalable Vector Graphics.

*RUnit*
     Functions implementing a standard Unit Testing framework, with
     additional code inspection and report generation tools.

*RadioSonde*
     A collection of programs for reading and plotting SKEW-T,log p diagrams
     and wind profiles for data collected by radiosondes (the typical
     weather balloon-borne instrument).

*RandomFields*
     Creating random fields using various methods.

*Rcmdr*
     A platform-independent basic-statistics GUI (graphical user interface)
     for R, based on the *tcltk* package.

*RmSQL*
     An interface between R and the mSQL database system.

*Rmpi*
     An interface (wrapper) to MPI (Message-Passing Interface) APIs.  It
     also provides an interactive R slave environment in which distributed
     statistical computing can be carried out.

*Rwave*
     An environment for the time-frequency analysis of 1-D signals (and
     especially for the wavelet and Gabor transforms of noisy signals),
     based on the book "Practical Time-Frequency Analysis: Gabor and Wavelet
     Transforms with an Implementation in S" by Rene Carmona, Wen L. Hwang
     and Bruno Torresani, 1998, Academic Press.

*SASmixed*
     Data sets and sample linear mixed effects analyses corresponding to the
     examples in "SAS System for Mixed Models" by R. C. Littell, G. A.
     Milliken, W. W. Stroup and R. D. Wolfinger, 1996, SAS Institute.

*SIN*
     A SINful approach to selection of Gaussian Graphical Markov Models.

*SenSrivastava*
     Collection of datasets from "Regression Analysis, Theory, Methods and
     Applications" by A. Sen and M. Srivastava, 1990, Springer-Verlag.

*SoPhy*
     Soil Physics Tools: simulation of water flux and solute transport in
     soil.

*SparseLogReg*
     Sparse logistic regression.

*SparseM*
     Basic linear algebra for sparse matrices.

*StatDataML*
     Read and write StatDataML.

*SuppDists*
     Ten distributions supplementing those built into R (Inverse Gauss,
     Kruskal-Wallis, Kendall's Tau, Friedman's chi squared, Spearman's rho,
     maximum F ratio, the Pearson product moment correlation coefficiant,
     Johnson distributions, normal scores and generalized hypergeometric
     distributions).

*VLMC*
     Functions, classes & methods for estimation, prediction, and simulation
     (bootstrap) of VLMC (Variable Length Markov Chain) models.

*VaR*
     Methods for calculation of Value at Risk (VaR).

*XML*
     Facilities for reading XML documents and DTDs.

*abind*
     Combine multi-dimensional arrays.

*acepack*
     ACE (Alternating Conditional Expectations) and AVAS (Additivity and
     VAriance Stabilization for regression) methods for selecting regression
     transformations.

*adapt*
     Adaptive quadrature in up to 20 dimensions.

*ade4*
     Multivariate data analysis and graphical display.

*agce*
     Analysis of growth curve experiments.

*akima*
     Linear or cubic spline interpolation for irregularly gridded data.

*amap*
     Another Multidimensional Analysis Package.

*anm*
     Analog model for statistical/empirical downscaling.

*ape*
     Analyses of Phylogenetics and Evolution, providing functions for
     reading and plotting phylogenetic trees in parenthetic format
     (standard Newick format), analyses of comparative data in a
     phylogenetic framework, analyses of diversification and
     macroevolution, computing distances from allelic and nucleotide data,
     reading nucleotide sequences from GenBank via internet, and several
     tools such as Mantel's test, computation of minimum spanning tree, or
     the population parameter theta based on various approaches.

*ash*
     David Scott's ASH routines for 1D and 2D density estimation.

*assist*
     A suite of functions implementing smoothing splines.

*asypow*
     A set of routines that calculate power and related quantities utilizing
     asymptotic likelihood ratio methods.

*aws*
     Functions to perform adaptive weights smoothing.

*bayesmix*
     Bayesian mixture models of univariate Gaussian distributions using
     JAGS.

*betareg*
     Beta regression for modeling rates and proportions.

*bim*
     Bayesian interval mapping diagnostics:  functions to interpret QTLCart
     and Bmapqtl samples.

*bindata*
     Generation of correlated artificial binary data.

*blighty*
     Function for drawing the coastline of the United Kingdom.

*boa*
     Bayesian Output Analysis Program for MCMC.

*boolean*
     Boolean logit and probit: a procedure for testing Boolean hypotheses.

*boot*
     Functions and datasets for bootstrapping from the book "Bootstrap
     Methods and Their Applications" by A. C. Davison and D. V. Hinkley,
     1997, Cambridge University Press.  _Recommended_.

*bootstrap*
     Software (bootstrap, cross-validation, jackknife), data and errata for
     the book "An Introduction to the Bootstrap" by B. Efron and R.
     Tibshirani, 1993, Chapman and Hall.

*bqtl*
     QTL mapping toolkit for inbred crosses and recombinant inbred lines.
     Includes maximum likelihood and Bayesian tools.

*brlr*
     Bias-reduced logistic regression: fits logistic regression models by
     maximum penalized likelihood.

*car*
     Companion to Applied Regression, containing functions for applied
     regession, linear models, and generalized linear models, with an
     emphasis on regression diagnostics, particularly graphical diagnostic
     methods.

*cat*
     Analysis of categorical-variable datasets with missing values.

*cclust*
     Convex clustering methods, including k-means algorithm, on-line update
     algorithm (Hard Competitive Learning) and Neural Gas algorithm (Soft
     Competitive Learning) and calculation of several indexes for finding
     the number of clusters in a data set.

*cfa*
     Analysis of configuration frequencies.

*chron*
     A package for working with chronological objects (times and dates).

*circular*
     Circular statistics, from "Topics in Circular Statistics" by Rao
     Jammalamadaka and A. SenGupta, 2001, World Scientific.

*class*
     Functions for classification (k-nearest neighbor and LVQ).  Contained
     in the `VR' bundle.  _Recommended_.

*classPP*
     Projection Pursuit for supervised classification.

*clim.pact*
     Climate analysis and downscaling for monthly and daily data.

*clines*
     Calculates Contour Lines.

*cluster*
     Functions for cluster analysis.  _Recommended_.

*cmprsk*
     Estimation, testing and regression modeling of subdistribution
     functions in competing risks.

*cobs*
     Constrained B-splines: qualitatively constrained (regression) smoothing
     via linear programming.

*coda*
     Output analysis and diagnostics for Markov Chain Monte Carlo (MCMC)
     simulations.

*combinat*
     Combinatorics utilities.

*concord*
     Measures of concordance and reliability.

*conf.design*
     A series of simple tools for constructing and manipulating confounded
     and fractional factorial designs.

*covRobust*
     Robust covariance estimation via nearest neighbor cleaning.

*cramer*
     Routine for the multivariate nonparametric Cramer test.

*crossdes*
     Functions for the construction and randomization of balanced carryover
     balanced designs, to check given designs for balance, and for
     simulation studies on the validity of two randomization procedures.

*date*
     Functions for dealing with dates.  The most useful of them accepts a
     vector of input dates in any of the forms `8/30/53', `30Aug53', `30
     August 1953', ..., `August 30 53', or any mixture of these.

*dblcens*
     Calculates the NPMLE of the survival distribution for doubly censored
     data.

*deal*
     Bayesian networks with continuous and/or discrete variables can be
     learned and compared from data.

*debug*
     Debugger for R functions, with code display, graceful error recovery,
     line-numbered conditional breakpoints, access to exit code, flow
     control, and full keyboard input.

*deldir*
     Calculates the  Delaunay triangulation and the Dirichlet or Voronoi
     tesselation (with respect to the entire plane) of a planar point set.

*diamonds*
     Functions for illustrating aperture-4 diamond partitions in the plane,
     or on the surface of an octahedron or icosahedron, for use as analysis
     or sampling grids.

*dichromat*
     Color schemes for dichromats: collapse red-green distinctions to
     simulate the effects of colour-blindness.

*digest*
     Two functions for the creation of "hash" digests of arbitrary R
     objects using the md5 and sha-1 algorithms permitting easy comparison
     of R language objects.

*diptest*
     Compute Hartigan's dip test statistic for unimodality.

*dispmod*
     Functions for modelling dispersion in GLMs.

*distr*
     An object orientated implementation of distributions and some
     additional functionality.

*dr*
     Functions, methods, and datasets for fitting dimension reduction
     regression, including pHd and inverse regression methods SIR and SAVE.

*dse*
     Dynamic System Estimation, a multivariate time series package.
     Contains *dse1* (the base system, including multivariate ARMA and state
     space models), *dse2* (extensions for evaluating estimation
     techniques, forecasting, and for evaluating forecasting model),
     *tframe* (functions for writing code that is independent of the
     representation of time). and *setRNG* (a mechanism for generating the
     same random numbers in S and R).

*dynamicGraph*
     Interactive graphical tool for manipulating graphs.

*e1071*
     Miscellaneous functions used at the Department of Statistics at TU Wien
     (E1071), including moments, short-time Fourier transforms, Independent
     Component Analysis, Latent Class Analysis, support vector machines, and
     fuzzy clustering, shortest path computation, bagged clustering, and
     some more.

*effects*
     Graphical and tabular effect displays, e.g., of interactions, for
     linear and generalised linear models.

*eha*
     A package for survival and event history analysis.

*ellipse*
     Package for drawing ellipses and ellipse-like confidence regions.

*emme2*
     Functions to read from and write to an EMME/2 databank.

*emplik*
     Empirical likelihood ratio for means/quantiles/hazards from possibly
     right censored data.

*energy*
     E-statistics (energy) tests for comparing distributions: multivariate
     normality, Poisson test, multivariate k-sample test for equal
     distributions, hierarchical clustering by e-distances.

*evd*
     Functions for extreme value distributions.  Extends simulation,
     distribution, quantile and density functions to univariate, bivariate
     and (for simulation) multivariate parametric extreme value
     distributions, and provides fitting functions which calculate maximum
     likelihood estimates for univariate and bivariate models.

*evdbayes*
     Functions for the bayesian analysis of extreme value models, using MCMC
     methods.

*evir*
     Extreme Values in R: Functions for extreme value theory, which may be
     divided into the following groups; exploratory data analysis, block
     maxima, peaks over thresholds (univariate and bivariate), point
     processes, gev/gpd distributions.

*exactLoglinTest*
     Monte Carlo exact tests for log-linear models.

*exactRankTests*
     Computes exact p-values and quantiles using an implementation of the
     Streitberg/Roehmel shift algorithm.

*fastICA*
     Implementation of FastICA algorithm to perform Independent Component
     Analysis (ICA) and Projection Pursuit.

*fda*
     Functional Data Analysis: analysis of data where the basic observation
     is a function of some sort.

*fdim*
     Functions for calculating fractal dimension.

*fields*
     A collection of programs for curve and function fitting with an
     emphasis on spatial data.  The major methods implemented include cubic
     and thin plate splines, universal Kriging and Kriging for large data
     sets.  The main feature is that any covariance function implemented in
     R can be used for spatial prediction.

*flexmix*
     Flexible Mixture Modeling: a general framework for finite mixtures of
     regression models using the EM algorithm.

*foreign*
     Functions for reading and writing data stored by statistical software
     like Minitab, SAS, SPSS, Stata, etc.  _Recommended_.

*fork*
     Functions for handling multiple processes: simple wrappers around the
     Unix process management API calls.

*fortunes*
     R fortunes.

*forward*
     Forward search approach to robust analysis in linear and generalized
     linear regression models.

*fpc*
     Fixed point clusters, clusterwise regression and discriminant plots.

*fracdiff*
     Maximum likelihood estimation of the parameters of a fractionally
     differenced ARIMA(p,d,q) model (Haslett and Raftery, Applied
     Statistics, 1989).

*ftnonpar*
     Features and strings for nonparametric regression.

*g.data*
     Create and maintain delayed-data packages (DDP's).

*gafit*
     Genetic algorithm for curve fitting.

*gap*
     Genetic analysis package for both population and family data.

*gbm*
     Generalized Boosted Regression Models: implements extensions to Freund
     and Schapire's AdaBoost algorithm and J. Friedman's gradient boosting
     machine.  Includes regression methods for least squares, absolute loss,
     logistic, Poisson, Cox proportional hazards partial likelihood, and
     AdaBoost exponential loss.

*gclus*
     Clustering Graphics.  Orders panels in scatterplot matrices and
     parallel coordinate displays by some merit index.

*gee*
     An implementation of the Liang/Zeger generalized estimating equation
     approach to GLMs for dependent data.

*geepack*
     Generalized estimating equations solver for parameters in mean, scale,
     and correlation structures, through mean link, scale link, and
     correlation link.  Can also handle clustered categorical responses.

*genetics*
     Classes and methods for handling genetic data.  Includes classes to
     represent genotypes and haplotypes at single markers up to multiple
     markers on multiple chromosomes, and functions for allele frequencies,
     flagging homo/heterozygotes, flagging carriers of certain alleles,
     computing disequlibrium, testing Hardy-Weinberg equilibrium, ...

*geoR*
     Functions to perform geostatistical data analysis including model-based
     methods.

*geoRglm*
     Functions for inference in generalised linear spatial models.

*ggm*
     Functions for defining directed acyclic graphs and undirected graphs,
     finding induced graphs and fitting Gaussian Markov models.

*gld*
     Basic functions for the generalised (Tukey) lambda distribution.

*gllm*
     Routines for log-linear models of incomplete contingency tables,
     including some latent class models via EM and Fisher scoring
     approaches.

*glmmML*
     A Maximum Likelihood approach to generalized linear models with random
     intercept.

*gpclib*
     General polygon clipping routines for R based on Alan Murta's C
     library.

*gpls*
     Classification using generalized partial least squares for two-group
     and multi-group (more than 2 group) classification.

*grasper*
     Generalized Regression Analysis and Spatial Predictions for R.

*gregmisc*
     Miscellaneous functions written/maintained by Gregory R. Warnes.

*gridBase*
     Integration of base and grid graphics.

*gss*
     A comprehensive package for structural multivariate function estimation
     using smoothing splines.

*gstat*
     multivariable geostatistical modelling, prediction and simulation.
     Includes code for variogram modelling; simple, ordinary and universal
     point or block (co)kriging, sequential Gaussian or indicator
     (co)simulation, and map plotting functions.

*gtkDevice*
     GTK graphics device driver that may be used independently of the
     R-GNOME interface and can be used to create R devices as embedded
     components in a GUI using a Gtk drawing area widget, e.g., using RGtk.

*hapassoc*
     Likelihood inference of trait associations with SNP haplotypes and
     other attributes using the EM Algorithm.

*haplo.score*
     Score tests for association of traits with haplotypes when linkage
     phase is ambiguous.

*haplo.stats*
     Statistical analysis of haplotypes with traits and covariates when
     linkage phase is ambiguous.

*hdf5*
     Interface to the NCSA HDF5 library.

*hett*
     Functions for the fitting and summarizing of heteroscedastic
     t-regression.

*hier.part*
     Hierarchical Partitioning: variance partition of a multivariate data
     set.

*homals*
     Homogeneity Analysis (HOMALS) package with optional Tcl/Tk interface.

*httpRequest*
     Implements HTTP Request protocols (GET, POST, and multipart POST
     requests).

*hwde*
     Models and tests for departure from Hardy-Weinberg equilibrium and
     independence between loci.

*ifs*
     Iterated Function Systems distribution function estimator.

*impute*
     Imputation for microarray data (currently KNN only).

*ineq*
     Inequality, concentration and poverty measures, and Lorenz curves
     (empirical and theoretic).

*ipred*
     Improved predictive models by direct and indirect bootstrap aggregation
     in classification and regression as well as resampling based estimators
     of prediction error.

*ismev*
     Functions to support the computations carried out in "An Introduction
     to Statistical Modeling of Extreme Values;' by S. Coles, 2001,
     Springer.  The functions may be divided into the following groups;
     maxima/minima, order statistics, peaks over thresholds and point
     processes.

*its*
     An S4 class for handling irregular time series.

*kernlab*
     Kernel-based machine learning methods including support vector
     machines.

*klaR*
     Miscellaneous functions for classification and visualization developed
     at the Department of Statistics, University of Dortmund.

*knnTree*
     Construct or predict with k-nearest-neighbor classifiers, using
     cross-validation to select k, choose variables (by forward or
     backwards selection), and choose scaling (from among no scaling,
     scaling each column by its SD, or scaling each column by its MAD).
     The finished classifier will consist of a classification tree with one
     such k-nn classifier in each leaf.

*knncat*
     Nearest-neighbor classification with categorical variables.

*kza*
     Kolmogorov-Zurbenko Adpative filter for locating change points in a
     time series.

*labstatR*
     Functions for the book "Laboratorio di statistica con R" by S. M.
     Iacus and G. Masarotto, 2002, McGraw-Hill.  Function names and
     documentation in Italian.

*lars*
     Least Angle Regression, Lasso and Forward Stagewise: efficient
     procedures for fitting an entire lasso sequence with the cost of a
     single least squares fit.

*lasso2*
     Routines and documentation for solving regression problems while
     imposing an L1 constraint on the estimates, based on the algorithm of
     Osborne et al. (1998)

*lattice*
     Lattice graphics, an implementation of Trellis Graphics functions.
     _Recommended_.

*lazy*
     Lazy learning for local regression.

*ldDesign*
     Design of experiments for detection of linkage disequilibrium,

*leaps*
     A package which performs an exhaustive search for the best subsets of a
     given set of potential regressors, using a branch-and-bound algorithm,
     and also performs searches using a number of less time-consuming
     techniques.

*lgtdl*
     A set of methods for longitudinal data objects.

*linprog*
     Solve linear programming/linear optimization problems by using the
     simplex algorithm.

*lme4*
     Fit linear and generalized linear mixed-effects models.

*lmeSplines*
     Fit smoothing spline terms in Gaussian linear and nonlinear
     mixed-effects models.

*lmm*
     Linear mixed models.

*lmtest*
     A collection of tests on the assumptions of linear regression models
     from the book "The linear regression model under test" by W. Kraemer
     and H. Sonnberger, 1986, Physica.

*locfit*
     Local Regression, likelihood and density estimation.

*logistf*
     Firth's bias reduced logistic regression approach with penalized
     profile likelihood based confidence intervals for parameter estimates.

*logspline*
     Logspline density estimation.

*lokern*
     Kernel regression smoothing with adaptive local or global plug-in
     bandwidth selection.

*lpSolve*
     Functions that solve general linear/integer problems, assignment
     problems, and transportation problems via interfacing Lp_solve.

*lpridge*
     Local polynomial (ridge) regression.

*mAr*
     Estimation of multivariate AR models through a computationally
     efficient stepwise least-squares algorithm.

*magic*
     A variety of methods for creating magic squares of any order greater
     than 2, and various magic hypercubes.

*mapdata*
     Supplement to package *maps*, providing the larger and/or
     higher-resolution databases.

*mapproj*
     Map Projections: converts latitude/longitude into projected
     coordinates.

*maps*
     Draw geographical maps.  Projection code and larger maps are in
     separate packages.

*maptools*
     Set of tools for manipulating and reading geographic data, in
     particular ESRI shapefiles.

*maptree*
     Functions with example data for graphing and mapping models from
     hierarchical clustering and classification and regression trees.

*mathgraph*
     Tools for constructing and manipulating objects from a class of
     directed and undirected graphs.

*maxstat*
     Maximally selected rank and Gauss statistics with several p-value
     approximations.

*mcgibbsit*
     Warnes and Raftery's MCGibbsit MCMC diagnostic.

*mclust*
     Model-based cluster analysis: the 2002 version of MCLUST.

*mda*
     Code for mixture discriminant analysis (MDA), flexible discriminant
     analysis (FDA), penalized discriminant analysis (PDA), multivariate
     additive regression splines (MARS), adaptive back-fitting splines
     (BRUTO), and penalized regression.

*meanscore*
     Mean Score method for missing covariate data in logistic regression
     models.

*merror*
     Accuracy and precision of measurements.

*mgcv*
     Routines for GAMs and other genralized ridge regression problems with
     multiple smoothing parameter selection by GCV or UBRE.  _Recommended_.

*mimR*
     An R interface to MIM for graphical modeling in R.

*mix*
     Estimation/multiple imputation programs for mixed categorical and
     continuous data.

*mixreg*
     Functions to fit mixtures of regressions.

*mlbench*
     A collection of artificial and real-world machine learning benchmark
     problems, including the Boston housing data.

*mmlcr*
     Mixed-mode latent class regression (also known as mixed-mode mixture
     model regression or mixed-mode mixture regression models) which can
     handle both longitudinal and one-time responses.

*moc*
     Fits a variety of mixtures models for multivariate observations with
     user-difined distributions and curves.

*mscalib*
     Calibration and filtering of MALDI-TOF Peptide Mass Fingerprint data.

*msm*
     Functions for fitting continuous-time Markov multi-state models to
     categorical processes observed at arbitrary times, optionally with
     misclassified responses, and covariates on transition or
     misclassification rates.

*muhaz*
     Hazard function estimation in survival analysis.

*multcomp*
     Multiple comparison procedures for the one-way layout.

*multidim*
     Multidimensional descriptive statistics: factorial methods and
     classification.

*multinomRob*
     Overdispersed multinomial regression using robust (LQD and tanh)
     estimation.

*multiv*
     Functions for hierarchical clustering, partitioning, bond energy
     algorithm, Sammon mapping, PCA and correspondence analysis.

*mvbutils*
     Utilities by Mark V. Bravington for project organization, editing and
     backup, sourcing, documentation (formal and informal), package
     preparation, macro functions, and more.

*mvnmle*
     ML estimation for multivariate normal data with missing values.

*mvnormtest*
     Generalization of the Shapiro-Wilk test for multivariate variables.

*mvpart*
     Multivariate partitioning.

*mvtnorm*
     Multivariate normal and t distributions.

*ncdf*
     Interface to Unidata netCDF data files.

*ncomplete*
     Functions to perform the regression depth method (RDM) to binary
     regression to approximate the minimum number of observations that can
     be removed such that the reduced data set has complete separation.

*negenes*
     Estimating the number of essential genes in a genome on the basis of
     data from a random transposon mutagenesis experiment, through the use
     of a Gibbs sampler.

*nlme*
     Fit and compare Gaussian linear and nonlinear mixed-effects models.
     _Recommended_.

*nlmeODE*
     Combine the *nlme* and *odesolve* packages for mixed-effects modelling
     using differential equations.

*nlrq*
     Nonlinear quantile regression.

*nnet*
     Software for single hidden layer perceptrons ("feed-forward neural
     networks"), and for multinomial log-linear models.  Contained in the
     `VR' bundle.  _Recommended_.

*nor1mix*
     One-dimensional normal mixture models classes, for, e.g., density
     estimation or clustering algorithms research and teaching; providing
     the widely used Marron-Wand densities.

*norm*
     Analysis of multivariate normal datasets with missing values.

*normalp*
     A collection of utilities for normal of order p distributions (General
     Error Distributions).

*nortest*
     Five omnibus tests for the composite hypothesis of normality.

*noverlap*
     Functions to perform the regression depth method (RDM) to binary
     regression to approximate the amount of overlap, i.e., the minimal
     number of observations that need to be removed such that the reduced
     data set has no longer overlap.

*npmc*
     Nonparametric Multiple Comparisons:  provides simultaneous rank test
     procedures for the one-way layout without presuming a certain
     distribution.

*nprq*
     Nonparametric and sparse quantile regression methods.

*odesolve*
     An interface for the Ordinary Differential Equation (ODE) solver lsoda.
     ODEs are expressed as R functions.

*orientlib*
     Representations, conversions and display of orientation SO(3) data.

*oz*
     Functions for plotting Australia's coastline and state boundaries.

*pamr*
     Pam: Prediction Analysis for Microarrays.

*pan*
     Multiple imputation for multivariate panel or clustered data.

*panel*
     Functions and datasets for fitting models to Panel data.

*pastecs*
     Package for Analysis of Space-Time Ecological Series.

*pcurve*
     Fits a principal curve to a numeric multivariate dataset in arbitrary
     dimensions.  Produces diagnostic plots.  Also calculates Bray-Curtis
     and other distance matrices and performs multi-dimensional scaling and
     principal component analyses.

*pear*
     Periodic Autoregression Analysis.

*permax*
     Functions intended to facilitate certain basic analyses of DNA array
     data, especially with regard to comparing expression levels between two
     types of tissue.

*pgam*
     Poisson-Gamma Additive Models.

*pheno*
     Some easy-to-use functions for time series analyses of (plant-)
     phenological data sets.

*phyloarray*
     Software to process data from phylogenetic or identification
     microarrays.

*pinktoe*
     Converts S trees to HTML/Perl files for interactive tree traversal.

*pixmap*
     Functions for import, export, plotting and other manipulations of
     bitmapped images.

*pls.pcr*
     Multivariate regression by PLS and PCR.

*polspline*
     Routines for the polynomial spline fitting routines hazard regression,
     hazard estimation with flexible tails, logspline, lspec, polyclass, and
     polymars, by C. Kooperberg and co-authors.

*polynom*
     A collection of functions to implement a class for univariate
     polynomial manipulations.

*pps*
     Functions to select samples using PPS (probability proportional to
     size) sampling, for stratified simple random sampling, and to compute
     joint inclusion probabilities for Sampford's method of PPS sampling.

*prabclus*
     Distance based parametric bootstrap tests for clustering, mainly
     thought for presence-absence data (clustering of species distribution
     maps).  Jaccard and Kulczynski distance measures, clustering of MDS
     scores, and nearest neighbor based noise detection.

*princurve*
     Fits a principal curve to a matrix of points in arbitrary dimension.

*pspline*
     Smoothing splines with penalties on order m derivatives.

*psy*
     Various procedures used in psychometry: Kappa, ICC, Cronbach alpha,
     screeplot, PCA and related methods.

*qcc*
     Quality Control Charts.  Shewhart quality control charts for
     continuous, attribute and count data.  Cusum and EWMA charts.
     Operating characteristic curves.  Process capability analysis.  Pareto
     chart and cause-and-effect chart.

*qtl*
     Analysis of experimental crosses to identify QTLs.

*quadprog*
     For solving quadratic programming problems.

*quantreg*
     Quantile regression and related methods.

*qvcalc*
     Functions to compute quasi-variances and associated measures of
     approximation error.

*race*
     Implementation of some racing methods for the empirical selection of
     the best.

*randomForest*
     Breiman's random forest classifier.

*rbugs*
     Functions to prepare files needed for running BUGS in batch mode, and
     running BUGS from R.  Support for Linux systems with Wine is
     emphasized.

*ref*
     Functions for creating references, reading from and writing ro
     references and a memory efficient refdata type that transparently
     encapsulates matrices and data frames.

*regress*
     Fitting Gaussian linear models where the covariance structure is a
     linear combination of known matrices by maximising the residual log
     likelihood.  Can be used for multivariate models and random effects
     models.

*relimp*
     Functions to facilitate inference on the relative importance of
     predictors in a linear or generalized linear model.

*rgdal*
     Provides bindings to Frank Warmerdam's Geospatial Data Abstraction
     Library (GDAL).

*rgenoud*
     R version of GENetic Optimization Using Derivatives.

*rgl*
     3D visualization device system (OpenGL).

*rimage*
     Functions for image processing, including Sobel filter, rank filters,
     fft, histogram equalization, and reading JPEG files.

*rlecuyer*
     R interface to RNG with multiple streams.

*rmeta*
     Functions for simple fixed and random effects meta-analysis for
     two-sample comparison of binary outcomes.

*rpart*
     Recursive PARTitioning and regression trees.  _Recommended_.

*rpart.permutation*
     Permutation tests of rpart models.

*rpvm*
     R interface to PVM (Parallel Virtual Machine).  Provides interface to
     PVM APIs, and examples and documentation for its use.

*rqmcmb2*
     Markov chain marginal bootstrap for quantile regression.

*rsprng*
     Provides interface to SPRNG (Scalable Parallel Random Number
     Generators) APIs, and examples and documentation for its use.

*sampfling*
     Implements a modified version of the Sampford sampling algorithm.
     Given a quantity assigned to each unit in the population, samples are
     drawn with probability proportional to te product of the quantities of
     the units included in the sample.

*sandwich*
     Model-robust standard error estimators for time series and longitudinal
     data.

*sca*
     Simple Component Analysis.

*scatterplot3d*
     Plots a three dimensional (3D) point cloud perspectively.

*seacarb*
     Calculates parameters of the seawater carbonate system.

*seao*
     Simple Evolutionary Algorithm Optimization.

*seao.gui*
     Simple Evolutionary Algorithm Optimization: graphical user interface.

*segmented*
     Functions to estimate break-points of segmented relationships in
     regression models (GLMs).

*sem*
     Functions for fitting general linear Structural Equation Models (with
     observed and unobserved variables) by the method of maximum likelihood
     using the RAM approach.

*seqmon*
     Sequential monitoring of clinical trials.

*session*
     Functions for interacting with, saving and restoring R sessions.

*setRNG*
     Set (normal) random number generator and seed.

*sfsmisc*
     Utilities from Seminar fuer Statistik ETH Zurich.

*sgeostat*
     An object-oriented framework for geostatistical modeling.

*shapefiles*
     Functions to read and write ESRI shapefiles.

*shapes*
     Routines for the statistical analysis of shapes, including procrustes
     analysis, displaying shapes and principal components, testing for mean
     shape difference, thin-plate spline transformation grids and edge
     superimposition methods.

*simpleboot*
     Simple bootstrap routines.

*skewt*
     Density, distribution function, quantile function and random generation
     for the skewed t distribution of Fernandez and Steel.

*sm*
     Software linked to the book "Applied Smoothing Techniques for Data
     Analysis:  The Kernel Approach with S-PLUS Illustrations" by A. W.
     Bowman and A. Azzalini (1997), Oxford University Press.

*sma*
     Functions for exploratory (statistical) microarray analysis.

*smoothSurv*
     Survival regression with smoothed error distribution.

*sn*
     Functions for manipulating skew-normal probability distributions and
     for fitting them to data, in the scalar and the multivariate case.

*sna*
     A range of tools for social network analysis, including node and
     graph-level indices, structural distance and covariance methods,
     structural equivalence detection, p* modeling, and network
     visualization.

*snow*
     Simple Network of Workstations: support for simple parallel computing
     in R.

*som*
     Self-Organizing Maps (with application in gene clustering).

*sound*
     A sound interface for R: Basic functions for dealing with `.wav' files
     and sound samples.

*spatial*
     Functions for kriging and point pattern analysis from "Modern Applied
     Statistics with S" by W. Venables and B. Ripley.  Contained in the
     `VR' bundle.  _Recommended_.

*spatialCovariance*
     Computation of spatial covariance matrices for data on rectangles using
     one dimensional numerical integration and analytic results.

*spatstat*
     Data analysis and modelling of two-dimensional point patterns,
     including multitype points and spatial covariates.

*spc*
     Statistical Process Control: evaluation of control charts by means of
     the zero-state, steady-state ARL (Average Run Length), setting up
     control charts for given in-control ARL, and plotting of the related
     figures.

*spdep*
     A collection of functions to create spatial weights matrix objects from
     polygon contiguities, from point patterns by distance and tesselations,
     for summarising these objects, and for permitting their use in spatial
     data analysis; a collection of tests for spatial autocorrelation,
     including global Moran's I and Geary's C, local Moran's I, saddlepoint
     approximations for global and local Moran's I; and functions for
     estimating spatial simultaneous autoregressive (SAR) models.  (Was
     formerly the three packages: *spweights*, *sptests*, and *spsarlm*.)

*spe*
     Stochastic Proximity Embedding.

*splancs*
     Spatial and space-time point pattern analysis functions.

*statmod*
     Miscellaneous biostatistical modelling functions.

*strucchange*
     Various tests on structural change in linear regression models.

*subselect*
     A collection of functions which assess the quality of variable subsets
     as surrogates for a full data set, and search for subsets which are
     optimal under various criteria.

*supclust*
     Methodology for supervised grouping of predictor variables.

*survey*
     Summary statistics, generalized linear models, and general maximum
     likelihood estimation for stratified, cluster-sampled, unequally
     weighted survey samples.

*survival*
     Functions for survival analysis, including penalised likelihood.
     _Recommended_.

*survrec*
     Survival analysis for recurrent event data.

*svmpath*
     Computes the entire regularization path for the two-class svm
     classifier with essentialy the same cost as a single SVM fit.

*systemfit*
     Contains functions for fitting simultaneous systems of equations using
     Ordinary Least Sqaures (OLS), Two-Stage Least Squares (2SLS), and
     Three-Stage Least Squares (3SLS).

*tapiR*
     Tools for accessing (UK) parliamentary information in R.

*tensor*
     Tensor product of arrays.

*tkrplot*
     Simple mechanism for placing R graphics in a Tk widget.

*tree*
     Classification and regression trees.

*treeglia*
     Stem analysis functions for volume increment and carbon uptake
     assessment from tree-rings.

*tripack*
     A constrained two-dimensional Delaunay triangulation package.

*tseries*
     Package for time series analysis with emphasis on non-linear modelling.

*twostage*
     Functions for optimal design of two-stage-studies using the Mean Score
     method.

*udunits*
     Interface to Unidata's routines to convert units.

*urca*
     Unit root and cointegration tests for time series data.

*vardiag*
     Interactive variogram diagnostics.

*vcd*
     Functions and data sets based on the book "Visualizing Categorical
     Data" by Michael Friendly.

*vegan*
     Various help functions for vegetation scientists and community
     ecologists.

*verify*
     Construction of test suites using verify objects.

*waveslim*
     Basic wavelet routines for time series analysis.

*wavethresh*
     Software to perform 1-d and 2-d wavelet statistics and transforms.

*wle*
     Robust statistical inference via a weighted likelihood approach.

*xgobi*
     Interface to the XGobi and XGvis programs for graphical data analysis.

*xtable*
     Export data to LaTeX and HTML tables.

*zoo*
     A class with methods for totally ordered indexed observations such as
     irregular time series.

See CRAN `src/contrib/PACKAGES' for more information.

   There is also a CRAN `src/contrib/Devel' directory which contains
packages still "under development" or depending on features only present in
the current development versions of R.  Volunteers are invited to give
these a try, of course.  This area of CRAN currently contains

*Dopt*
     Finding D-optimal experimental designs.

*GLMMGibbs*
     Generalised Linear Mixed Models by Gibbs sampling.

*RPgSQL*
     Provides methods for accessing data stored in PostgreSQL tables.

*dseplus*
     Extensions to *dse*, the Dynamic Systems Estimation multivariate time
     series package.  Contains PADI, juice and monitoring extensions.

*ensemble*
     Ensembles of tree classifiers.

*runStat*
     Running median and mean.

*write.snns*
     Function for writing a SNNS pattern file from a data frame or matrix.

5.1.3 Add-on packages from Omegahat
-----------------------------------

The `src/contrib/Omegahat' Directory of a CRAN site contains yet unreleased
packages from the Omegahat Project for Statistical Computing
(http://www.omegahat.org/).  Currently, there are

*CORBA*
     Dynamic CORBA client/server facilities for R.  Connects to other
     CORBA-aware applications developed in arbitrary languages, on different
     machines and allows R functionality to be exported in the same way to
     other applications.

*OOP*
     OOP style classes and methods for R and S-PLUS.  Object references and
     class-based method definition are supported in the style of languages
     such as Java and C++.

*REmbeddedPostgres*
     Allows R functions and objects to be used to implement SQL functions --
     per-record, aggregate and trigger functions.

*REventLoop*
     An abstract event loop mechanism that is toolkit independent and can be
     used to to replace the R event loop.

*RGdkPixbuf*
     S language functions to access the facilities in the GdkPixbuf library
     for manipulating images.

*RGnumeric*
     A plugin for the Gnumeric spreadsheet that allows R functions to be
     called from cells within the sheet, automatic recalculation, etc.

*RGtk*
     Facilities in the S language for programming graphical interfaces using
     Gtk, the Gnome GUI toolkit.

*RGtkBindingGenerator*
     A meta-package which generates C and R code to provide bindings to a
     Gtk-based library.

*RGtkExtra*
     A collection of S functions that provide an interface to the widgets in
     the gtk+extra library such as the GtkSheet data-grid display, icon
     list, file list and directory tree.

*RGtkGlade*
     S language bindings providing an interface to Glade, the interactive
     Gnome GUI creator.

*RGtkHTML*
     A collection of S functions that provide an interface to creating and
     controlling an HTML widget which can be used to display HTML documents
     from files or content generated dynamically in S.

*RGtkViewers*
     A collection of tools for viewing different S objects, databases, class
     and widget hierarchies, S source file contents, etc.

*RJavaDevice*
     A graphics device for R that uses Java components and graphics.  APIs.

*RObjectTables*
     The C and S code allows one to define R objects to be used as elements
     of the search path with their own semantics and facilities for reading
     and writing variables.  The objects implement a simple interface via R
     functions (either methods or closures) and can access external data,
     e.g., in other applications, languages, formats, ...

*RSMethods*
     An implementation of S version 4 methods and classes for R, consistent
     with the basic material in "Programming with Data" by John M.
     Chambers, 1998, Springer NY.

*RSPerl*
     An interface from R to an embedded, persistent Perl interpreter,
     allowing one to call arbitrary Perl subroutines, classes and methods.

*RSPython*
     Allows Python programs to invoke S functions, methods, etc., and S code
     to call Python functionality.

*RXLisp*
     An interface to call XLisp-Stat functions from within R.

*SASXML*
     Example for reading XML files in SAS 8.2 manner.

*SJava*
     An interface from R to Java to create and call Java objects and
     methods.

*SLanguage*
     Functions and C support utilities to support S language programming
     that can work in both R and S-PLUS.

*SNetscape*
     Plugin for Netscape and JavaScript.

*SWinRegistry*
     Provides access from within R to read and write the Windows registry.

*SWinTypeLibs*
     Provides ways to extract type information from type libraries and/or
     DCOM objects that describes the methods, properties, etc. of an
     interface.

*SXalan*
     Process XML documents using XSL functions implemented in R and
     dynamically substituting output from R.

*Slcc*
     Parses C source code, allowing one to analyze and automatically
     generate interfaces from S to that code, including the table of
     S-accessible native symbols, parameter count and type information, S
     constructors from C objects, call graphs, etc.

*Sxslt*
     An extension module for libxslt, the XML-XSL document translator, that
     allows XSL functions to be implemented via R functions.

5.1.4 Add-on packages from Bioconductor
---------------------------------------

The Bioconductor Project (http://www.bioconductor.org) produces an open
source software framework that will assist biologists and statisticians
working in bioinformatics, with primary emphasis on inference using DNA
microarrays.  The following R packages are contained in the current release
of Bioconductor, with more packages under development.

*AnnBuilder*
     Assemble and process genomic annotation data, from databases such as
     GenBank, the Gene Ontology Consortium, LocusLink, UniGene, the UCSC
     Human Genome Project.

*Biobase*
     Object-oriented representation and manipulation of genomic data (S4
     class structure).

*Biostrings*
     Class definitions and generics for biological sequences along with
     pattern matching algorithms.

*DNAcopy*
     Segments DNA copy number data using circular binary segmentation to
     detect regions with abnormal copy number.

*DynDoc*
     Functionality to create and interact with dynamic documents, vignettes,
     and other navigable documents.

*EBarrays*
     Empirical Bayes tools for the analysis of replicated microarray data
     across multiple conditions.

*GOstats*
     Tools for manipulating GO and microarrays.

*GeneSpring*
     Functions and class definitions to be able to read and write GeneSpring
     specific data objects and convert them to Bioconductor objects.

*GeneTS*
     A package for analysing multiple gene expression time series data.
     Currently, implements methods for cell cycle analysis and for inferring
     large sparse graphical Gaussian models.

*Icens*
     Functions for computing the NPMLE for censored and truncated data.

*LPE*
     Significance analysis of microarray data with small number of
     replicates using the Local Pooled Error (LPE) method.

*MeasurementError.cor*
     Two-stage measurement error model for correlation estimation with
     smaller bias than the usual sample correlation.

*PROcess*
     Ciphergen SELDI-TOF processing.

*RBGL*
     An interface between the graph package and the Boost graph libraries,
     allowing for fast manipulation of graph objects in R.

*RMAGEML*
     Functionality to handle MAGEML documents.

*ROC*
     Receiver Operating Characteristic (ROC) approach for identifying genes
     that are differentially expressed in two types of samples.

*RSNPper*
     Interface to chip.org::SNPper for SNP-related data.

*RdbiPgSQL*
     Methods for accessing data stored in PostgreSQL tables.

*Rdbi*
     Generic framework for database access in R.

*Resourcerer*
     Read annotation data from TIGR Resourcerer or convert the annotation
     data into Bioconductor data package.

*Rgraphviz*
     An interface with Graphviz for plotting graph objects in R.

*Ruuid*
     Creates Universally Unique ID values (UUIDs) in R.

*SAGElyzer*
     Locates genes based on SAGE tags.

*SNAData*
     Data from the book "Social Network Analysis" by Wasserman & Faust
     (1999).

*aCGH*
     Classes and functions for Array Comparative Genomic Hybridization data.

*affy*
     Methods for Affymetrix Oligonucleotide Arrays.

*affyPLM*
     For fitting Probe Level Models.

*affycomp*
     Graphics toolbox for assessment of Affymetrix expression measures.

*affydata*
     Affymetrix data for demonstration purposes.

*affylmGUI*
     Graphical User Interface for affy analysis using package *limma*.

*affypdnn*
     Probe Dependent Nearest Neighbors (PDNN) for the affy package.

*altcdfenvs*
     Utilities to handle cdfenvs.

*annaffy*
     Functions for handling data from Bioconductor Affymetrix annotation
     data packages.

*annotate*
     Associate experimental data in real time to biological metadata from
     web databases such as GenBank, LocusLink and PubMed.  Process and store
     query results.  Generate HTML reports of analyses.

*arrayMagic*
     Utilities for quality control and processing for two-color cDNA
     microarray data.

*arrayQuality*
     Performing print-run and array level quality assessment.

*bim*
     Bayesian interval mapping diagnostics:  functions to interpret QTLCart
     and Bmapqtl samples.

*convert*
     Convert Microarray Data Objects.

*ctc*
     Tools to export and import Tree and Cluster to other programs.

*daMA*
     Functions for the efficient design of factorial two-color microarray
     experiments and for the statistical analysis of factorial microarray
     data.

*ecolitk*
     Metadata and tools to work with E. coli.

*edd*
     Expression density diagnostics: graphical methods and pattern
     recognition algorithms for distribution shape classification.

*exprExternal*
     Implementation of exprSet using externalVectors.

*externalVector*
     Basic class definitions and generics for external pointer based vector
     objects for R.

*factDesign*
     A set of tools for analyzing data from factorial designed microarray
     experiments.  The functions can be used to evaluate appropriate tests
     of contrast and perform single outlier detection.

*gcrma*
     Background adjustment using sequence information.

*genefilter*
     Tools for sequentially filtering genes using a wide variety of
     filtering functions.  Example of filters include: number of missing
     value, coefficient of variation of expression measures, ANOVA p-value,
     Cox model p-values.  Sequential application of filtering functions to
     genes.

*geneplotter*
     Graphical tools for genomic data, for example for plotting expression
     data along a chromosome or producing color images of expression data
     matrices.

*globaltest*
     Testing globally whether a group of genes is significantly related to
     some clinical variable of interest.

*goTools*
     Functions for description/comparison of oligo ID list using the Gene
     Ontology database.

*gpls*
     Classification using generalized partial least squares for two-group
     and multi-group classification.

*graph*
     Classes and tools for creating and manipulating graphs within R.

*hexbin*
     Binning functions, in particular hexagonal bins for graphing.

*impute*
     Imputation for microarray data (currently KNN only).

*limma*
     Linear models for microarray data.

*limmaGUI*
     Graphical User Interface for package *limma*.

*makecdfenv*
     Two functions.  One reads a Affymetrix chip description file (CDF) and
     creates a hash table environment containing the location/probe set
     membership mapping.  The other creates a package that automatically
     loads that environment.

*marray*
     Exploratory analysis for two-color spotted microarray data.

*marrayClasses*
     Class definitions for pre-normalized and normalized cDNA microarray
     data.  Basic methods for accessing/replacing, printing, and subsetting.

*marrayInput*
     Functions for reading microarray data into R from different image
     analysis output files, and probe and target description files.  Widgets
     are supplied to facilitate and automate data input and the creation of
     microarray specific R objects for storing these data.

*marrayNorm*
     Functions for location and scale normalization procedures based on
     robust local regression.

*marrayPlots*
     Functions for diagnostic plots for pre- and post-normalization cDNA
     microarray intensity data: boxplots, scatter-plots, color images.

*marrayTools*
     Miscellaneous functions used in the functional genomics core facility
     in UCB and UCSF.

*matchprobes*
     Tools for sequence matching of probes on arrays.

*multtest*
     Multiple testing procedures for controlling the family-wise error rate
     (FWER) and the false discovery rate (FDR).  Tests can be based on t-
     or F-statistics for one- and two-factor designs, and permutation
     procedures are available to estimate adjusted p-values.

*ontoTools*
     Graphs and sparse matrices for working with ontologies.

*pairseqsim*
     Pairwise sequence alignment and scoring algorithms for global, local
     and overlap alignment with affine gap penalty.

*pamr*
     Pam: Prediction Analysis for Microarrays.

*pickgene*
     Adaptive gene picking for microarray expression data analysis.

*prada*
     Tools for analyzing and navigating data from high-throughput
     phenotyping experiments based on cellular assays and fluorescent
     detection.

*qvalue*
     Q-value estimation for false discovery rate control.

*rama*
     Robust Analysis of MicroArrays: robust estimation of cDNA microarray
     intensities with replicates using a Bayesian hierarchical model.

*reposTools*
     Tools for dealing with file repositories and allow users to easily
     install, update, and distribute packages, vignettes, and other files.

*rhdf5*
     Storage and retrieval of large datasets using the HDF5 library and file
     format.

*siggenes*
     Identifying differentially expressed genes and estimating the False
     Discovery Rate (FDR) with both the Significance Analysis of Microarrays
     (SAM) and the Empirical Bayes Analyses of Microarrays (EBAM).

*simpleaffy*
     Very simple high level analysis of Affymetrix data.

*splicegear*
     A set of tools to work with alternative splicing.

*tkWidgets*
     Widgets in Tcl/Tk that provide functionality for Bioconductor packages.

*vsn*
     Calibration and variance stabilizing transformations for both
     Affymetrix and cDNA array data.

*webbioc*
     Integrated web interface for doing microarray analysis using several of
     the Bioconductor packages.

*widgetTools*
     Tools for creating Tcl/Tk widgets, i.e., small-scale graphical user
     interfaces.

5.1.5 Other add-on packages
---------------------------

Jim Lindsey <jlindsey@luc.ac.be> has written a collection of R packages for
nonlinear regression and repeated measurements, consisting of *event*
(event history procedures and models), *gnlm* (generalized nonlinear
regression models), *growth* (multivariate normal and
elliptically-contoured repeated measurements models), *repeated*
(non-normal repeated measurements models), *rmutil* (utilities for
nonlinear regression and repeated measurements), and *stable* (probability
functions and generalized regression models for stable distributions).  All
analyses in the new edition of his book "Models for Repeated Measurements"
(1999, Oxford University Press) were carried out using these packages.  Jim
has also started *dna*, a package with procedures for the analysis of DNA
sequences.  Jim's packages can be obtained from
`http://www.luc.ac.be/~jlindsey/rcode.html'.

   More code has been posted to the R-help mailing list, and can be
obtained from the mailing list archive.

5.2 How can add-on packages be installed?
=========================================

(Unix only.)  The add-on packages on CRAN come as gzipped tar files named
`PKG_VERSION.tar.gz', which may in fact be "bundles" containing more than
one package.  Provided that `tar' and `gzip' are available on your system,
type

     $ R CMD INSTALL /path/to/PKG_VERSION.tar.gz

at the shell prompt to install to the library tree rooted at the first
directory given in `R_LIBS' (see below) if this is set and non-null, and to
the default library (the `library' subdirectory of ``R_HOME'') otherwise.
(Versions of R prior to 1.3.0 installed to the default library by default.)

   To install to another tree (e.g., your private one), use

     $ R CMD INSTALL -l LIB /path/to/PKG_VERSION.tar.gz

where LIB gives the path to the library tree to install to.

   Even more conveniently, you can install and automatically update
packages from within R if you have access to CRAN.  See the help page for
`CRAN.packages()' for more information.

   You can use several library trees of add-on packages.  The easiest way
to tell R to use these is via the environment variable `R_LIBS' which
should be a colon-separated list of directories at which R library trees
are rooted.  You do not have to specify the default tree in `R_LIBS'.
E.g., to use a private tree in `$HOME/lib/R' and a public site-wide tree in
`/usr/local/lib/R-contrib', put

     R_LIBS="$HOME/lib/R:/usr/local/lib/R-contrib"; export R_LIBS

into your (Bourne) shell profile or even preferably, add the line

     R_LIBS="$HOME/lib/R:/usr/local/lib/R-contrib"

your `~/.Renviron' file.  (Note that no `export' statement is needed or
allowed in this file; see the on-line help for `Startup' for more
information.)

5.3 How can add-on packages be used?
====================================

To find out which additional packages are available on your system, type

     library()

at the R prompt.

   This produces something like

     Packages in `/home/me/lib/R':
     
     mystuff       My own R functions, nicely packaged but not documented
     
     Packages in `/usr/local/lib/R/library':
     
     KernSmooth    Functions for kernel smoothing for Wand & Jones (1995)
     MASS          Main Package of Venables and Ripley's MASS
     base          The R base package
     boot          Bootstrap R (S-Plus) Functions (Canty)
     class         Functions for Classification
     cluster       Functions for clustering (by Rousseeuw et al.)
     foreign       Read data stored by Minitab, S, SAS, SPSS, Stata, ...
     graphics      The R Graphics Package
     grid          The Grid Graphics Package
     lattice       Lattice Graphics
     methods       Formal Methods and Classes
     mgcv          Multiple smoothing parameter estimation and GAMs by GCV
     nlme          Linear and nonlinear mixed effects models
     nnet          Feed-forward Neural Networks and Multinomial Log-Linear
                   Models
     rpart         Recursive partitioning
     spatial       Functions for Kriging and Point Pattern Analysis
     splines       Regression Spline Functions and Classes
     stats         The R Stats Package
     stats4        Statistical functions using S4 classes
     survival      Survival analysis, including penalised likelihood
     tcltk         Tcl/Tk Interface
     tools         Tools for Package Development
     utils         The R Utils Package

   You can "load" the installed package PKG by

     library(PKG)

   You can then find out which functions it provides by typing one of

     library(help = PKG)
     help(package = PKG)

   You can unload the loaded package PKG by

     detach("package:PKG")

5.4 How can add-on packages be removed?
=======================================

Use

     $ R CMD REMOVE PKG_1 ... PKG_N

to remove the packages PKG_1, ..., PKG_N from the library tree rooted at
the first directory given in `R_LIBS' if this is set and non-null, and from
the default library otherwise.  (Versions of R prior to 1.3.0 removed from
the default library by default.)

   To remove from library LIB, do

     $ R CMD REMOVE -l LIB PKG_1 ... PKG_N

5.5 How can I create an R package?
==================================

A package consists of a subdirectory containing the files `DESCRIPTION' and
`INDEX', and the subdirectories `R', `data', `demo', `exec', `inst', `man',
`src', and `tests' (some of which can be missing).  Optionally the package
can also contain script files `configure' and `cleanup' which are executed
before and after installation.

   See section "Creating R packages" in `Writing R Extensions', for
details.  This manual is included in the R distribution, *note What
documentation exists for R?::, and gives information on package structure,
the configure and cleanup mechanisms, and on automated package checking and
building.

   R version 1.3.0 has added the function `package.skeleton()' which will
set up directories, save data and code, and create skeleton help files for
a set of R functions and datasets.

   *Note What is CRAN?::, for information on uploading a package to CRAN.

5.6 How can I contribute to R?
==============================

R is in active development and there is always a risk of bugs creeping in.
Also, the developers do not have access to all possible machines capable of
running R.  So, simply using it and communicating problems is certainly of
great value.

   One place where functionality is still missing is the modeling software
as described in "Statistical Models in S" (see *Note What is S?::);
Generalized Additive Models (*note Are GAMs implemented in R?::) and some
of the nonlinear modeling code are not there yet.

   The R Developer Page (http://developer.R-project.org/) acts as an
intermediate repository for more or less finalized ideas and plans for the
R statistical system.  It contains (pointers to) TODO lists, RFCs, various
other writeups, ideas lists, and CVS miscellanea.

   Many (more) of the packages available at the Statlib S Repository might
be worth porting to R.

   If you are interested in working on any of these projects, please notify
Kurt Hornik <Kurt.Hornik@R-project.org>.

6 R and Emacs
*************

6.1 Is there Emacs support for R?
=================================

There is an Emacs package called ESS ("Emacs Speaks Statistics") which
provides a standard interface between statistical programs and statistical
processes.  It is intended to provide assistance for interactive
statistical programming and data analysis.  Languages supported include: S
dialects (S 3/4, S-PLUS 3.x/4.x/5.x, and R), LispStat dialects (XLispStat,
ViSta) and SAS.  Stata and SPSS dialect (SPSS, PSPP) support is being
examined for possible future implementation

   ESS grew out of the need for bug fixes and extensions to S-mode 4.8
(which was a GNU Emacs interface to S/S-PLUS version 3 only).  The current
set of developers desired support for XEmacs, R, S4, and MS Windows.  In
addition, with new modes being developed for R, Stata, and SAS, it was felt
that a unifying interface and framework for the user interface would
benefit both the user and the developer, by helping both groups conform to
standard Emacs usage.  The end result is an increase in efficiency for
statistical programming and data analysis, over the usual tools.

   R support contains code for editing R source code (syntactic indentation
and highlighting of source code, partial evaluations of code, loading and
error-checking of code, and source code revision maintenance) and
documentation (syntactic indentation and highlighting of source code,
sending examples to running ESS process, and previewing), interacting with
an inferior R process from within Emacs (command-line editing, searchable
command history, command-line completion of R object and file names, quick
access to object and search lists, transcript recording, and an interface
to the help system), and transcript manipulation (recording and saving
transcript files, manipulating and editing saved transcripts, and
re-evaluating commands from transcript files).

   The latest stable version of ESS are available via CRAN or the ESS web
page (http://ESS.R-project.org/).  The HTML version of the documentation
can be found at `http://stat.ethz.ch/ESS/'.

   ESS comes with detailed installation instructions.

   For help with ESS, send email to <ESS-help@stat.ethz.ch>.

   Please send bug reports and suggestions on ESS to
<ESS-bugs@stat.math.ethz.ch>.  The easiest way to do this from is within
Emacs by typing `M-x ess-submit-bug-report' or using the [ESS] or [iESS]
pulldown menus.

6.2 Should I run R from within Emacs?
=====================================

Yes, _definitely_.  Inferior R mode provides a readline/history mechanism,
object name completion, and syntax-based highlighting of the interaction
buffer using Font Lock mode, as well as a very convenient interface to the
R help system.

   Of course, it also integrates nicely with the mechanisms for editing R
source using Emacs.  One can write code in one Emacs buffer and send whole
or parts of it for execution to R; this is helpful for both data analysis
and programming.  One can also seamlessly integrate with a revision control
system, in order to maintain a log of changes in your programs and data, as
well as to allow for the retrieval of past versions of the code.

   In addition, it allows you to keep a record of your session, which can
also be used for error recovery through the use of the transcript mode.

   To specify command line arguments for the inferior R process, use `C-u
M-x R' for starting R.

6.3 Debugging R from within Emacs
=================================

To debug R "from within Emacs", there are several possibilities.  To use
the Emacs GUD (Grand Unified Debugger) library with the recommended
debugger GDB, type `M-x gdb' and give the path to the R _binary_ as
argument.  At the `gdb' prompt, set `R_HOME' and other environment
variables as needed (using e.g.  `set env R_HOME /path/to/R/', but see also
below), and start the binary with the desired arguments (e.g., `run
--quiet').

   If you have ESS, you can do `C-u M-x R <RET> - d <SPC> g d b <RET>' to
start an inferior R process with arguments `-d gdb'.

   A third option is to start an inferior R process via ESS (`M-x R') and
then start GUD (`M-x gdb') giving the R binary (using its full path name)
as the program to debug.  Use the program `ps' to find the process number
of the currently running R process then use the `attach' command in gdb to
attach it to that process.  One advantage of this method is that you have
separate `*R*' and `*gud-gdb*' windows.  Within the `*R*' window you have
all the ESS facilities, such as object-name completion, that we know and
love.

   When using GUD mode for debugging from within Emacs, you may find it
most convenient to use the directory with your code in it as the current
working directory and then make a symbolic link from that directory to the
R binary.  That way `.gdbinit' can stay in the directory with the code and
be used to set up the environment and the search paths for the source, e.g.
as follows:

     set env R_HOME /opt/R
     set env R_PAPERSIZE letter
     set env R_PRINTCMD lpr
     dir /opt/R/src/appl
     dir /opt/R/src/main
     dir /opt/R/src/nmath
     dir /opt/R/src/unix

7 R Miscellanea
***************

7.1 Why does R run out of memory?
=================================

Versions of R prior to 1.2.0 used a _static_ memory model.  At startup, R
asked the operating system to reserve a fixed amount of memory for it.  The
size of this chunk could not be changed subsequently.  Hence, it could
happen that not enough memory was allocated, e.g., when trying to read
large data sets into R.  In such cases, it was necessary to restart R with
more memory available, as controlled by the command line options `--nsize'
and `--vsize'.

   R version 1.2.0 introduces a new "generational" garbage collector, which
will increase the memory available to R as needed.  Hence, user
intervention is no longer necessary for ensuring that enough memory is
available.

   The new garbage collector does not move objects in memory, meaning that
it is possible for the free memory to become fragmented so that large
objects cannot be allocated even when there is apparently enough memory for
them.

7.2 Why does sourcing a correct file fail?
==========================================

Versions of R prior to 1.2.1 may have had problems parsing files not ending
in a newline.  Earlier R versions had a similar problem when reading in
data files.  This should no longer happen.

7.3 How can I set components of a list to NULL?
===============================================

You can use

     x[i] <- list(NULL)

to set component `i' of the list `x' to `NULL', similarly for named
components.  Do not set `x[i]' or `x[[i]]' to `NULL', because this will
remove the corresponding component from the list.

   For dropping the row names of a matrix `x', it may be easier to use
`rownames(x) <- NULL', similarly for column names.

7.4 How can I save my workspace?
================================

`save.image()' saves the objects in the user's `.GlobalEnv' to the file
`.RData' in the R startup directory.  (This is also what happens after
`q("yes")'.)  Using `save.image(FILE)' one can save the image under a
different name.

7.5 How can I clean up my workspace?
====================================

To remove all objects in the currently active environment (typically
`.GlobalEnv'), you can do

     rm(list = ls(all = TRUE))

(Without `all = TRUE', only the objects with names not starting with a `.'
are removed.)

7.6 How can I get eval() and D() to work?
=========================================

Strange things will happen if you use `eval(print(x), envir = e)' or
`D(x^2, "x")'.  The first one will either tell you that "`x'" is not found,
or print the value of the wrong `x'.  The other one will likely return zero
if `x' exists, and an error otherwise.

   This is because in both cases, the first argument is evaluated in the
calling environment first.  The result (which should be an object of mode
`"expression"' or `"call"') is then evaluated or differentiated.  What you
(most likely) really want is obtained by "quoting" the first argument upon
surrounding it with `expression()'.  For example,

     R> D(expression(x^2), "x")
     2 * x

   Although this behavior may initially seem to be rather strange, is
perfectly logical.  The "intuitive" behavior could easily be implemented,
but problems would arise whenever the expression is contained in a
variable, passed as a parameter, or is the result of a function call.
Consider for instance the semantics in cases like

     D2 <- function(e, n) D(D(e, n), n)

or

     g <- function(y) eval(substitute(y), sys.frame(sys.parent(n = 2)))
     g(a * b)

   See the help page for `deriv()' for more examples.

7.7 Why do my matrices lose dimensions?
=======================================

When a matrix with a single row or column is created by a subscripting
operation, e.g., `row <- mat[2, ]', it is by default turned into a vector.
In a similar way if an array with dimension, say, 2 x 3 x 1 x 4 is created
by subscripting it will be coerced into a 2 x 3 x 4 array, losing the
unnecessary dimension.  After much discussion this has been determined to
be a _feature_.

   To prevent this happening, add the option `drop = FALSE' to the
subscripting.  For example,

     rowmatrix <- mat[2, , drop = FALSE]  # creates a row matrix
     colmatrix <- mat[, 2, drop = FALSE]  # creates a column matrix
     a <- b[1, 1, 1, drop = FALSE]        # creates a 1 x 1 x 1 array

   The `drop = FALSE' option should be used defensively when programming.
For example, the statement

     somerows <- mat[index, ]

will return a vector rather than a matrix if `index' happens to have length
1, causing errors later in the code.  It should probably be rewritten as

     somerows <- mat[index, , drop = FALSE]

7.8 How does autoloading work?
==============================

R has a special environment called `.AutoloadEnv'.  Using `autoload(NAME,
PKG)', where NAME and PKG are strings giving the names of an object and the
package containing it, stores some information in this environment.  When R
tries to evaluate NAME, it loads the corresponding package PKG and
reevaluates NAME in the new package's environment.

   Using this mechanism makes R behave as if the package was loaded, but
does not occupy memory (yet).

   See the help page for `autoload()' for a very nice example.

7.9 How should I set options?
=============================

The function `options()' allows setting and examining a variety of global
"options" which affect the way in which R computes and displays its
results.  The variable `.Options' holds the current values of these
options, but should never directly be assigned to unless you want to drive
yourself crazy--simply pretend that it is a "read-only" variable.

   For example, given

     test1 <- function(x = pi, dig = 3) {
       oo <- options(digits = dig); on.exit(options(oo));
       cat(.Options$digits, x, "\n")
     }
     test2 <- function(x = pi, dig = 3) {
       .Options$digits <- dig
       cat(.Options$digits, x, "\n")
     }

we obtain:

     R> test1()
     3 3.14
     R> test2()
     3 3.141593

   What is really used is the _global_ value of `.Options', and using
`options(OPT = VAL)' correctly updates it.  Local copies of `.Options',
either in `.GlobalEnv' or in a function environment (frame), are just
silently disregarded.

7.10 How do file names work in Windows?
=======================================

As R uses C-style string handling, `\' is treated as an escape character,
so that for example one can enter a newline as `\n'.  When you really need
a `\', you have to escape it with another `\'.

   Thus, in filenames use something like `"c:\\data\\money.dat"'.  You can
also replace `\' by `/' (`"c:/data/money.dat"').

7.11 Why does plotting give a color allocation error?
=====================================================

Sometimes plotting, e.g., when running `demo("image")', results in "Error:
color allocation error".  This is an X problem, and only indirectly related
to R.  It occurs when applications started prior to R have used all the
available colors.  (How many colors are available depends on the X
configuration; sometimes only 256 colors can be used.)

   One application which is notorious for "eating" colors is Netscape.  If
the problem occurs when Netscape is running, try (re)starting it with
either the `-no-install' (to use the default colormap) or the `-install'
(to install a private colormap) option.

   You could also set the `colortype' of `X11()' to `"pseudo.cube"' rather
than the default `"pseudo"'.  See the help page for `X11()' for more
information.

7.12 How do I convert factors to numeric?
=========================================

It may happen that when reading numeric data into R (usually, when reading
in a file), they come in as factors.  If `f' is such a factor object, you
can use

     as.numeric(as.character(f))

to get the numbers back.  More efficient, but harder to remember, is

     as.numeric(levels(f))[as.integer(f)]

   In any case, do not call `as.numeric()' or their likes directly for the
task at hand (as `as.numeric()' or `unclass()' give the internal codes).

7.13 Are Trellis displays implemented in R?
===========================================

The recommended package *lattice* (which is based on another recommended
package, *grid*) provides graphical functionality that is compatible with
most Trellis commands.

   You could also look at `coplot()' and `dotchart()' which might do at
least some of what you want.  Note also that the R version of `pairs()' is
fairly general and provides most of the functionality of `splom()', and
that R's default plot method has an argument `asp' allowing to specify (and
fix against device resizing) the aspect ratio of the plot.

   (Because the word "Trellis" has been claimed as a trademark we do not
use it in R.  The name "lattice" has been chosen for the R equivalent.)

7.14 What are the enclosing and parent environments?
====================================================

Inside a function you may want to access variables in two additional
environments: the one that the function was defined in ("enclosing"), and
the one it was invoked in ("parent").

   If you create a function at the command line or load it in a package its
enclosing environment is the global workspace.  If you define a function
`f()' inside another function `g()' its enclosing environment is the
environment inside `g()'.  The enclosing environment for a function is
fixed when the function is created.  You can find out the enclosing
environment for a function `f()' using `environment(f)'.

   The "parent" environment, on the other hand, is defined when you invoke
a function.  If you invoke `lm()' at the command line its parent
environment is the global workspace, if you invoke it inside a function
`f()' then its parent environment is the environment inside `f()'.  You can
find out the parent environment for an invocation of a function by using
`parent.frame()' or `sys.frame(sys.parent())'.

   So for most user-visible functions the enclosing environment will be the
global workspace, since that is where most functions are defined.  The
parent environment will be wherever the function happens to be called from.
If a function `f()' is defined inside another function `g()' it will
probably be used inside `g()' as well, so its parent environment and
enclosing environment will probably be the same.

   Parent environments are important because things like model formulas
need to be evaluated in the environment the function was called from, since
that's where all the variables will be available.  This relies on the
parent environment being potentially different with each invocation.

   Enclosing environments are important because a function can use
variables in the enclosing environment to share information with other
functions or with other invocations of itself (see the section on lexical
scoping).  This relies on the enclosing environment being the same each
time the function is invoked.

   Scoping _is_ hard.  Looking at examples helps.  It is particularly
instructive to look at examples that work differently in R and S and try to
see why they differ.  One way to describe the scoping differences between R
and S is to say that in S the enclosing environment is _always_ the global
workspace, but in R the enclosing environment is wherever the function was
created.

7.15 How can I substitute into a plot label?
============================================

Often, it is desired to use the value of an R object in a plot label, e.g.,
a title.  This is easily accomplished using `paste()' if the label is a
simple character string, but not always obvious in case the label is an
expression (for refined mathematical annotation).  In such a case, either
use `parse()' on your pasted character string or use `substitute()' on an
expression.  For example, if `ahat' is an estimator of your parameter a of
interest, use

     title(substitute(hat(a) == ahat, list(ahat = ahat)))

(note that it is `==' and not `=').  There are more worked examples in the
mailing list achives.

7.16 What are valid names?
==========================

When creating data frames using `data.frame()' or `read.table()', R by
default ensures that the variable names are syntactically valid.  (The
argument `check.names' to these functions controls whether variable names
are checked and adjusted by `make.names()' if needed.)

   To understand what names are "valid", one needs to take into account
that the term "name" is used in several different (but related) ways in the
language:

  1. A _syntactic name_ is a string the parser interprets as this type of
     expression.  It consists of letters, numbers, and the dot and (for
     version of R at least 1.9.0) underscore characters, and starts with
     either a letter or a dot not followed by a number.  Reserved words are
     not syntactic names.

  2. An _object name_ is a string associated with an object that is
     assigned in an expression either by having the object name on the left
     of an assignment operation or as an argument to the `assign()'
     function.  It is usually a syntactic name as well, but can be any
     non-empty string if it is quoted (and it is always quoted in the call
     to `assign()').

  3. An _argument name_ is what appears to the left of the equals sign when
     supplying an argument in a function call (for example, `f(trim=.5)').
     Argument names are also usually syntactic names, but again can be
     anything if they are quoted.

  4. An _element name_ is a string that identifies a piece of an object (a
     component of a list, for example.)  When it is used on the right of
     the `$' operator, it must be a syntactic name, or quoted.  Otherwise,
     element names can be any strings.  (When an object is used as a
     database, as in a call to `eval()' or `attach()', the element names
     become object names.)

  5. Finally, a _file name_ is a string identifying a file in the operating
     system for reading, writing, etc.  It really has nothing much to do
     with names in the language, but it is traditional to call these
     strings file "names".

7.17 Are GAMs implemented in R?
===============================

There is a `gam()' function for Generalized Additive Models in package
*mgcv*, but it is not an exact clone of what is described in the White Book
(no `lo()' for example).  Package *gss* can fit spline-based GAMs too.  And
if you can accept regression splines you can use `glm()'.  For gaussian
GAMs you can use `bruto()' from package *mda*.

7.18 Why is the output not printed when I source() a file?
==========================================================

Most R commands do not generate any output. The command

     1+1

computes the value 2 and returns it; the command

     summary(glm(y~x+z, family=binomial))

fits a logistic regression model, computes some summary information and
returns an object of class `"summary.glm"' (*note How should I write
summary methods?::).

   If you type `1+1' or `summary(glm(y~x+z, family=binomial))' at the
command line the returned value is automatically printed (unless it is
`invisible()'), but in other circumstances, such as in a `source()'d file
or inside a function it isn't printed unless you specifically print it.

   To print the value use

     print(1+1)

or

     print(summary(glm(y~x+z, family=binomial)))

instead, or use `source(FILE, echo=TRUE)'.

7.19 Why does outer() behave strangely with my function?
========================================================

As the help for `outer()' indicates, it does not work on arbitrary
functions the way the `apply()' family does.  It requires functions that
are vectorized to work elementwise on arrays.  As you can see by looking at
the code, `outer(x, y, FUN)' creates two large vectors containing every
possible combination of elements of `x' and `y' and then passes this to
`FUN' all at once.  Your function probably cannot handle two large vectors
as parameters.

   If you have a function that cannot handle two vectors but can handle two
scalars, then you can still use `outer()' but you will need to wrap your
function up first, to simulate vectorized behavior.  Suppose your function
is

     foo <- function(x, y, happy) {
       stopifnot(length(x) == 1, length(y) == 1) # scalars only!
       (x + y) * happy
     }

If you define the general function

     wrapper <- function(x, y, my.fun, ...) {
       sapply(seq(along = x), FUN = function(i) my.fun(x[i], y[i], ...))
     }

then you can use `outer()' by writing, e.g.,

     outer(1:4, 1:2, FUN = wrapper, my.fun = foo, happy = 10)

7.20 Why does the output from anova() depend on the order of factors in the model?
==================================================================================

In a model such as `~A+B+A:B', R will report the difference in sums of
squares between the models `~1', `~A', `~A+B' and `~A+B+A:B'.  If the model
were `~B+A+A:B', R would report differences between `~1', `~B', `~A+B', and
`~A+B+A:B' . In the first case the sum of squares for `A' is comparing `~1'
and `~A', in the second case it is comparing `~B' and `~B+A'.  In a
non-orthogonal design (i.e., most unbalanced designs) these comparisons are
(conceptually and numerically) different.

   Some packages report instead the sums of squares based on comparing the
full model to the models with each factor removed one at a time (the famous
`Type III sums of squares' from SAS, for example).  These do not depend on
the order of factors in the model.  The question of which set of sums of
squares is the Right Thing provokes low-level holy wars on R-help from time
to time.

   There is no need to be agitated about the particular sums of squares
that R reports.  You can compute your favorite sums of squares quite
easily.  Any two models can be compared with `anova(MODEL1, MODEL2)', and
`drop1(MODEL1)' will show the sums of squares resulting from dropping
single terms.

7.21 How do I produce PNG graphics in batch mode?
=================================================

Under Unix, the `png()' device uses the X11 driver, which is a problem in
batch mode or for remote operation.  If you have Ghostscript you can use
`bitmap()', which produces a PostScript file then converts it to any bitmap
format supported by ghostscript.  On some installations this produces ugly
output, on others it is perfectly satisfactory.  In theory one could also
use Xvfb, which provides an X server with no display.

7.22 How can I get command line editing to work?
================================================

The Unix command-line interface to R can only provide the inbuilt command
line editor which allows recall, editing and re-submission of prior
commands provided that the GNU readline library is available at the time R
is configured for compilation.  Note that the `development' version of
readline including the appropriate headers is needed: users of Linux binary
distributions will need to install packages such as `libreadline-dev'
(Debian) or `readline-devel' (Red Hat).

7.23 How can I turn a string into a variable?
=============================================

If you have

     varname <- c("a", "b", "d")

you can do

     get(varname[1]) + 2

for

     a + 2

or

     assign(varname[1], 2 + 2)

for

     a <- 2 + 2

or

     eval(substitute(lm(y ~ x + variable),
                     list(variable = as.name(varname[1]))

for

     lm(y ~ x + a)

   At least in the first two cases it is often easier to just use a list,
and then you can easily index it by name

     vars <- list(a = 1:10, b = rnorm(100), d = LETTERS)
     vars[["a"]]

without any of this messing about.

7.24 Why do lattice/trellis graphics not work?
==============================================

The most likely reason is that you forgot to tell R to display the graph.
Lattice functions such as `xyplot()' create a graph object, but do not
display it (the same is true of Trellis graphics in S-PLUS).  The `print()'
method for the graph object produces the actual display.  When you use
these functions interactively at the command line, the result is
automatically printed, but in `source()' or inside your own functions you
will need an explicit `print()' statement.

7.25 How can I sort the rows of a data frame?
=============================================

To sort the rows within a data frame, with respect to the values in one or
more of the columns, simply use `order()'.

7.26 Why does the help.start() search engine not work?
======================================================

The browser-based search engine in `help.start()' utilizes a Java applet.
In order for this to function properly, a compatible version of Java must
installed on your system and linked to your browser, and both Java _and_
JavaScript need to be enabled in your browser.

   There have been a number of compatibility issues with versions of Java
and of browsers.  For further details please consult section "Enabling
search in HTML help" in `R Installation and Administration'.  This manual is
included in the R distribution, *note What documentation exists for R?::,
and its HTML version is linked from the HTML search page.

8 R Programming
***************

8.1 How should I write summary methods?
=======================================

Suppose you want to provide a summary method for class `"foo"'.  Then
`summary.foo()' should not print anything, but return an object of class
`"summary.foo"', _and_ you should write a method `print.summary.foo()'
which nicely prints the summary information and invisibly returns its
object.  This approach is preferred over having `summary.foo()' print
summary information and return something useful, as sometimes you need to
grab something computed by `summary()' inside a function or similar.  In
such cases you don't want anything printed.

8.2 How can I debug dynamically loaded code?
============================================

Roughly speaking, you need to start R inside the debugger, load the code,
send an interrupt, and then set the required breakpoints.

   See section "Finding entry points in dynamically loaded code" in
`Writing R Extensions'.  This manual is included in the R distribution,
*note What documentation exists for R?::.

8.3 How can I inspect R objects when debugging?
===============================================

The most convenient way is to call `R_PV' from the symbolic debugger.

   See section "Inspecting R objects when debugging" in `Writing R
Extensions'.

8.4 How can I change compilation flags?
=======================================

Suppose you have C code file for dynloading into R, but you want to use `R
CMD SHLIB' with compilation flags other than the default ones (which were
determined when R was built).  You could change the file
``R_HOME'/etc/Makeconf' to reflect your preferences.  If you are a Bourne
shell user, you can also pass the desired flags to Make (which is used for
controlling compilation) via the Make variable `MAKEFLAGS', as in

     MAKEFLAGS="CFLAGS=-O3" R CMD SHLIB *.c

9 R Bugs
********

9.1 What is a bug?
==================

If R executes an illegal instruction, or dies with an operating system
error message that indicates a problem in the program (as opposed to
something like "disk full"), then it is certainly a bug.  If you call
`.C()', `.Fortran()', `.External()' or `.Call()' (or `.Internal()')
yourself (or in a function you wrote), you can always crash R by using
wrong argument types (modes).  This is not a bug.

   Taking forever to complete a command can be a bug, but you must make
certain that it was really R's fault.  Some commands simply take a long
time.  If the input was such that you _know_ it should have been processed
quickly, report a bug.  If you don't know whether the command should take a
long time, find out by looking in the manual or by asking for assistance.

   If a command you are familiar with causes an R error message in a case
where its usual definition ought to be reasonable, it is probably a bug.
If a command does the wrong thing, that is a bug.  But be sure you know for
certain what it ought to have done.  If you aren't familiar with the
command, or don't know for certain how the command is supposed to work,
then it might actually be working right.  Rather than jumping to
conclusions, show the problem to someone who knows for certain.

   Finally, a command's intended definition may not be best for statistical
analysis.  This is a very important sort of problem, but it is also a
matter of judgment.  Also, it is easy to come to such a conclusion out of
ignorance of some of the existing features.  It is probably best not to
complain about such a problem until you have checked the documentation in
the usual ways, feel confident that you understand it, and know for certain
that what you want is not available.  If you are not sure what the command
is supposed to do after a careful reading of the manual this indicates a
bug in the manual.  The manual's job is to make everything clear.  It is
just as important to report documentation bugs as program bugs.  However,
we know that the introductory documentation is seriously inadequate, so you
don't need to report this.

   If the online argument list of a function disagrees with the manual, one
of them must be wrong, so report the bug.

9.2 How to report a bug
=======================

When you decide that there is a bug, it is important to report it and to
report it in a way which is useful.  What is most useful is an exact
description of what commands you type, starting with the shell command to
run R, until the problem happens.  Always include the version of R,
machine, and operating system that you are using; type `version' in R to
print this.

   The most important principle in reporting a bug is to report _facts_,
not hypotheses or categorizations.  It is always easier to report the
facts, but people seem to prefer to strain to posit explanations and report
them instead.  If the explanations are based on guesses about how R is
implemented, they will be useless; others will have to try to figure out
what the facts must have been to lead to such speculations.  Sometimes this
is impossible.  But in any case, it is unnecessary work for the ones trying
to fix the problem.

   For example, suppose that on a data set which you know to be quite large
the command

     R> data.frame(x, y, z, monday, tuesday)

never returns.  Do not report that `data.frame()' fails for large data
sets.  Perhaps it fails when a variable name is a day of the week.  If this
is so then when others got your report they would try out the
`data.frame()' command on a large data set, probably with no day of the
week variable name, and not see any problem.  There is no way in the world
that others could guess that they should try a day of the week variable
name.

   Or perhaps the command fails because the last command you used was a
method for `"["()' that had a bug causing R's internal data structures to
be corrupted and making the `data.frame()' command fail from then on.  This
is why others need to know what other commands you have typed (or read from
your startup file).

   It is very useful to try and find simple examples that produce
apparently the same bug, and somewhat useful to find simple examples that
might be expected to produce the bug but actually do not.  If you want to
debug the problem and find exactly what caused it, that is wonderful.  You
should still report the facts as well as any explanations or solutions.
Please include an example that reproduces the problem, preferably the
simplest one you have found.

   Invoking R with the `--vanilla' option may help in isolating a bug.
This ensures that the site profile and saved data files are not read.

   On Unix systems a bug report can be generated using the function
`bug.report()'.  This automatically includes the version information and
sends the bug to the correct address.  Alternatively the bug report can be
emailed to <R-bugs@R-project.org> or submitted to the Web page at
`http://bugs.R-project.org/'.

   Bug reports on contributed packages should be sent first to the package
maintainer, and only submitted to the R-bugs repository by package
maintainers, mentioning the package in the subject line.

   There is a section of the bug repository for suggestions for
enhancements for R labelled `wishlist'.  Suggestions can be submitted in
the same ways as bugs, but please ensure that the subject line makes clear
that this is for the wishlist and not a bug report, for example by starting
with `Wishlist:'.

   Comments on and suggestions for the Windows port of R should be sent to
<R-windows@R-project.org>.

10 Acknowledgments
******************

Of course, many many thanks to Robert and Ross for the R system, and to the
package writers and porters for adding to it.

   Special thanks go to Doug Bates, Peter Dalgaard, Paul Gilbert, Stefano
Iacus, Fritz Leisch, Jim Lindsey, Thomas Lumley, Martin Maechler, Brian D.
Ripley, Anthony Rossini, and Andreas Weingessel for their comments which
helped me improve this FAQ.

   More to some soon ...

