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Expand Up @@ -4,7 +4,7 @@ END-INFO-DIR-ENTRY

R FAQ
Frequently Asked Questions on R
Version 1.7-40, 2003-09-12
Version 1.7-42, 2003-09-16
ISBN 3-901167-51-X
Kurt Hornik

Expand Down Expand Up @@ -175,7 +175,7 @@ Feedback is of course most welcome.
Features specific to the Windows and Mac OS 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 Macintosh FAQ/DOC"
(http://cran.r-project.org/bin/macos/rmac-FAQ.html). If you have
(http://cran.R-project.org/bin/macos/rmac-FAQ.html). If you have
information on Mac or Windows systems that you think should be added to
this document, please let me know.

Expand Down Expand Up @@ -210,8 +210,8 @@ 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
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.
Expand All @@ -223,7 +223,7 @@ 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
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").

Expand Down Expand Up @@ -260,14 +260,14 @@ Sources, binaries and documentation for R can be obtained via CRAN, the

Sources are also available via anonymous rsync. Use

rsync -rC rsync.r-project.org::MODULE R
rsync -rC --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' option in the `rsync'
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/'.

Expand Down Expand Up @@ -351,7 +351,7 @@ 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>.
<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.
Expand All @@ -366,7 +366,7 @@ 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 to run under MacOS 8.6 to MacOS 9.1 or MacOS X natively.
The Mac version of R and the Mac binaries are maintained by Stefano Iacus
<Stefano.Iacus@r-project.org>.
<Stefano.Iacus@R-project.org>.

The "R for Macintosh FAQ/DOC"
(http://www.eco-dip.unimi.it/R/rmac-FAQ.html) has more details.
Expand All @@ -389,7 +389,7 @@ 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
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'.
Expand Down Expand Up @@ -496,7 +496,7 @@ Statistics_, *5*, 299-314. *Note Citing R::.
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'
`http://www.R-project.org/doc/bib/R.bib'

2.8 Citing R
============
Expand All @@ -516,42 +516,50 @@ To cite R in publications, use
2.9 What mailing lists exist for R?
===================================

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

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

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

`R-help'
The `main' R mailing list, for announcements about the development of R
and the availability of new code, including new or enhanced contributed
packages, questions and answers about problems and solutions using R,
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 and pre-testing of
new versions. It is meant for those who maintain an active position in
the development of R.

`r-help'
The `main' R mailing list, for announcements about the development of R
and the availability of new code, questions and answers about problems
and solutions using R, 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.

Note that the r-announce list is gatewayed into r-help, so you don't need
to subscribe to both of them.
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.

Send email to <r-help@lists.r-project.org> to reach everyone on the
r-help mailing list. To subscribe (or unsubscribe) to this list send
Send email to <R-help@lists.R-project.org> to reach everyone on the
R-help mailing list. To subscribe (or unsubscribe) to this list send
`subscribe' (or `unsubscribe') in the _body_ of the message (not in the
subject!) to <r-help-request@lists.r-project.org>. Information about the
subject!) to <R-help-request@lists.R-project.org>. Information about the
list can be obtained by sending an email with `info' as its contents to
<r-help-request@lists.r-project.org>.
<R-help-request@lists.R-project.org>.

Subscription and posting to the other lists is done analogously, with
`r-help' replaced by `r-announce' and `r-devel', respectively.
`R-help' replaced by `R-announce', `R-packages', and `R-devel',
respectively.

Subscriptions to `r-help' and `r-devel' are also available in digest
format, see the `doc/html/mail.html' file in CRAN for more information.
Subscriptions to the R-help and R-devel mailing lists are also available
in digest (plain or MIME) format, see the `doc/html/mail.html' file in CRAN
for more information.

It is recommended that you send mail to r-help rather than only to the R
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.
Expand All @@ -566,7 +574,7 @@ in a monthly schedule via the `doc/html/mail.html' file in CRAN.
Searchable archives of the lists are available via
`http://maths.newcastle.edu.au/~rking/R/'.

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

2.10 What is CRAN?
Expand All @@ -578,22 +586,22 @@ 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/'
`http://cran.R-project.org/'

and is currently being mirrored daily at

`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
`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
Paran�, Brazil)
`http://cran.ch.r-project.org/' (ETH Z�rich, Switzerland)
`http://cran.de.r-project.org/' (APP, Germany)
`http://cran.dk.r-project.org/' (SunSITE, Denmark)
`http://cran.hu.r-project.org/' (Semmelweis U, Hungary)
`http://cran.uk.r-project.org/' (U of Bristol, United
`http://cran.ch.R-project.org/' (ETH Z�rich, Switzerland)
`http://cran.de.R-project.org/' (APP, Germany)
`http://cran.dk.R-project.org/' (SunSITE, Denmark)
`http://cran.hu.R-project.org/' (Semmelweis U, Hungary)
`http://cran.uk.R-project.org/' (U of Bristol, United
Kingdom)
`http://cran.us.r-project.org/' (U of Wisconsin, USA)
`http://cran.za.r-project.org/' (Rhodes U, South Africa)
`http://cran.us.R-project.org/' (U of Wisconsin, USA)
`http://cran.za.R-project.org/' (Rhodes U, South Africa)

Please use the CRAN site closest to you to reduce network load.

Expand All @@ -605,8 +613,8 @@ 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
`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
Expand Down Expand Up @@ -880,12 +888,12 @@ 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 very large piece of
memory and uses it to store the objects. R performs its own memory
management of this piece of memory. 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.
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
Expand Down Expand Up @@ -1420,6 +1428,9 @@ distributions of R.)
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.

Expand Down Expand Up @@ -2115,6 +2126,12 @@ distributions of R.)
*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.

*sm*
Software linked to the book "Applied Smoothing Techniques for Data
Analysis: The Kernel Approach with S-PLUS Illustrations" by A. W.
Expand Down Expand Up @@ -2541,11 +2558,7 @@ 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'.

Frank Harrell <fharrell@virginia.edu> has made R ports of his *Design*
and *Hmisc* packages available via
`http://hesweb1.med.virginia.edu/biostat/s/library/r/'.

More code has been posted to the r-help mailing list, and can be
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?
Expand Down Expand Up @@ -2619,6 +2632,8 @@ at the R prompt.
grid The Grid Graphics Package
lattice Lattice Graphics
lqs Resistant Regression and Covariance Estimation
methods Formal Methods and Classes
mle Maximum likelihood estimation
mgcv Multiple smoothing parameter estimation and GAMs by GCV
modreg Modern Regression: Smoothing and Local Methods
mva Classical Multivariate Analysis
Expand All @@ -2631,7 +2646,7 @@ at the R prompt.
splines Regression Spline Functions and Classes
stepfun Step Functions, including Empirical Distributions
survival Survival analysis, including penalised likelihood
tcltk Interface to Tcl/Tk
tcltk Tcl/Tk Interface
tools Tools for Package Development and Administration
ts Time series functions

Expand Down Expand Up @@ -2697,7 +2712,7 @@ 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
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.
Expand All @@ -2706,7 +2721,7 @@ other writeups, ideas lists, and CVS miscellanea.
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>.
Kurt Hornik <Kurt.Hornik@R-project.org>.

6 R and Emacs
*************
Expand Down Expand Up @@ -3231,7 +3246,7 @@ non-orthogonal design (i.e., most unbalanced designs) these comparisons are
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
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
Expand Down Expand Up @@ -3458,11 +3473,11 @@ 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/'.
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 perhaps be sent to the
package maintainer rather than to r-bugs.
package maintainer rather than to R-bugs.

10 Acknowledgments
******************
Expand Down

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