This document contains answers to some of the most frequently asked questions about R.
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.
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.
You can also obtain the R FAQ from the doc/FAQ subdirectory of a
CRAN site (What is CRAN?).
In publications, please refer to this FAQ as Hornik (1999), "The R FAQ" and give the above, official URL.
Everything should be pretty standard. R> is used for the R
prompt, and a $ for the shell prompt (where applicable).
Feedback is of course most welcome.
In particular, note that I do not have access to Windows or Mac systems. Features specific to the Windows port of R are described in the "Frequently Asked Questions for R for Windows". If you have information on Windows or Mac systems that you think should be added to this document, please let me know.
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 (see What is S?) and Sussman's Scheme. Whereas the resulting language is very similar in appearance to S, the underlying implementation and semantics are derived from Scheme. See What are the differences between R and S?, for a discussion of the differences between R and S.
R was initially written by Ross Ihaka and Robert Gentleman, who are Senior Lecturers 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, Peter Dalgaard, Robert Gentleman, Kurt Hornik, Ross Ihaka, Friedrich Leisch, Thomas Lumley, Martin Maechler, Guido Masarotto, Paul Murrell, Brian Ripley, Duncan Temple Lang, and Luke Tierney.
R has a home page at http://stat.auckland.ac.nz/r/r.html. It is free software distributed under a GNU-style copyleft, and an official part of the GNU project ("GNU S").
R is being developed for the Unix, Windows and Mac families of operating systems.
The current version of R will configure and build under a number of
common Unix platforms including i386-freebsd, i386-linux, ppc-linux,
mips-sgi-irix, alpha-linux, alpha-dec-osf4, rs6000-ibm-aix,
hppa-hp-hpux, sparc-linux, and sparc-sun-solaris, see the file
PLATFORMS in the R distribution for more information.
If you know about other platforms, please drop us a note.
The current stable Unix/Windows version is 0.90.0, the unstable one is 0.99.0. Typically, new features are introduced in the development versions; updates of stable versions are for bug fixes mostly. The version for the Mac is pre-alpha.
Sources, binaries and documentation for R can be obtained via CRAN, the "Comprehensive R Archive Network" (see What is CRAN?).
If binaries are available for your platform (see 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 What machines does R run on?). The file INSTALL that comes with the
R distribution contains instructions.
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
documentation. If this is not available on your system, you can obtain
precompiled documentation files via CRAN.
In the simplest case, untar the R source code, cd 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
font-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 obtain a dvi version of the R manual. This
creates the files Manual.dvi (a start of a manual) and
Reference.dvi (an R object reference index) in the
doc/manual subdirectory. These files can be previewed and
printed using standard programs such as xdvi and dvips.
(Note that they have to be built in the source tree.)
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
${prefix}/man/man1
${prefix}/share/R
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.)
The bin/windows/windows-NT directory of a CRAN site contains the
latest binary distributions of R for 32 bit versions of MS Windows
(i.e., 95, 98 or NT), as well as binary distributions for a large number
of add-on packages from CRAN. The Windows version of R was created by
Robert Gentleman, and is now being developed and maintained by
Guido Masarotto and
Brian D. Ripley.
For most installations the installer rwinst.exe will be the
easiest tool to use.
See the R Windows FAQ for more details.
The Power Macintosh port is temporarily on hold, and currently no binary distribution is available. We hope that this will change soon.
The bin/linux directory contains Debian 2.1 packages for the i386
platform (now part of the Debian distribution and maintained by Doug
Bates) as well as Red Hat 5.1 packages for the alpha and sparc platforms
(maintained by Nassib Nasser and Vin Everett, respectively), Red Hat 6.0
packages for the i386 and alpha platforms (maintained by Martyn Plummer
and Naoki Takebayashi, respectively), S.u.S.E. 5.3/6.0/6.2 i386 packages
by Albrecht Gebhardt, and RPMs for the ppc platform by Alex Buerkle.
The bin/osf directory contains RPMs for alpha systems running
Digital Unix 4.0 by Albrecht Gebhardt.
No other binary distributions have thus far been made publically available.
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 HTML, and as hardcopy via LaTeX, see How can R be installed?. An up-to-date HTML version is always available for web browsing at http://stat.ethz.ch/R/manual/.
An earlier attempt at an R manual ("Notes on R: A Programming
Environment for Data Analysis and Graphics"), based on the "Notes on
S-PLUS" by Bill Venables and
David Smith, can be obtained as
Rnotes.tgz (LaTeX source) in a CRAN doc directory.
Further documentation on R and the R API are currently being written.
In the absence of an R manual, documentation for S/S-PLUS (see R and S) can be used in combination with this FAQ (see What are the differences between R and S?). We recommend
W. N. Venables and B. D. Ripley (1999), "Modern Applied Statistics with S-PLUS. Third Edition". Springer, ISBN 0-387-98825-4.
which has a home page at http://www.stats.ox.ac.uk/pub/MASS3/ providing additional material, in particular "R Complements" which describe how to use the book with R. These complements provide both descriptions of some of the differences between R and S-PLUS, and the modifications needed to run the examples in the book. Its companion volume on "S Programming", due in about April 2000, will provide 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.
More introductory books are
P. Spector (1994), "An introduction to S and S-PLUS", Duxbury Press.A. Krause and M. Olsen (1997), "The Basics of S and S-PLUS", Springer.
Last, but not least, Ross' and Robert's experience in designing and implementing R is described in:
@article{,
author = {Ross Ihaka and Robert Gentleman},
title = {R: A Language for Data Analysis and Graphics},
journal = {Journal of Computational and Graphical Statistics},
year = 1996,
volume = 5,
number = 3,
pages = {299--314}
}
To cite R in publications, use the above Ihaka & Gentleman (1996), "R: A Language for Data Analysis and Graphics", Journal of Computational and Graphical Statistics, 5, 299-314.
Thanks to Martin Maechler, there are three mailing lists devoted to R.
r-announce
r-devel
r-help
Note that the r-announce list is gatewayed into r-help, so you don't need to subscribe to both of them.
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 list can be obtained by sending an email with
info as its contents to
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.
It is recommended that you send mail to r-help rather than only to the R 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 R Bugs for more details.
Archives of the above three mailing lists are made available on the net
in a monthly schedule via the doc/mail/mail.html file in CRAN.
An HTML archive of the lists are available via
http://www.ens.gu.edu.au/robertk/R/.
The R Core Team can be reached at r-core@lists.r-project.org for comments and reports.
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 can be found at the URL
http://cran.r-project.org/ (Austria)
(which is the same as http://cran.at.r-project.org/) and is currently being mirrored daily at
http://cran.dk.r-project.org/ (Denmark) http://cran.it.r-project.org/ (Italy) http://cran.ch.r-project.org/ (Switzerland) http://cran.uk.r-project.org/ (United Kingdom) http://cran.us.r-project.org/ (USA/Wisconsin)
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 or as two gzipped tar files (ready for 1.4M floppies), a wealth of additional contributed code, as well as prebuilt binaries for various operating systems (Linux, Nextstep, MacOS, MSWin) and pre-formatted help pages. 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 wwwadmin@cran.r-project.org.
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.
S is a very high level language and an environment for data analysis and graphics. S was written by Richard A. Becker, John M. Chambers, and Allan R. Wilks of AT&T Bell Laboratories Statistics Research Department.
The primary references for S are two books by the creators of S.
This book is often called the "Blue Book".
This is also called the "White Book".
Version 4 of S, a major revision of S designed by John Chambers to improve its usefulness at every stage of the programming process, is described in "Programming with Data" by John M. Chambers (1998), Springer: New York, ISBN 0-387-98503-4.
In 1998, the Association for Computing Machinery presented its Software System Award to John Chambers for the design of the S system. The ACM citation stated that "S 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." See http://netlib.bell-labs.com/cm/ms/departments/sia/S/index.html for "Stages in the Evolution of S".
There is a huge amount of user-contributed code for S, available at the S Repository at CMU.
The "Frequently Asked Questions about S" contains further information about S, but is not up-to-date.
S-PLUS is a value-added version of S sold by Statistical Sciences, Inc. (now a division of Mathsoft, Inc.). 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 MathSoft S-PLUS page for further information.
Whereas the developers of R have tried to stick to the S language as defined in "The New S Language" (Blue Book, see What is S?), they have 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" (see What documentation exists for R?) and a paper on
"Lexical Scope and Statistical Computing" by Robert Gentleman and Ross
Ihaka which can be obtained from the doc/misc directory of a CRAN
site and will appear in the Journal of Computational and Graphical
Statistics around the beginning of 2000.
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.
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.) R is
still in a beta stage, and may crash from time to time. Hence, for
important work you should consider saving often (see How can I save my workspace?). 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 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.
There are some differences in the modeling code, such as
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)).
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.
Apart from lexical scoping and its implications, R follows the S language definition in the Blue Book 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.
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).)
.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--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--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. It also loads a saved image
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.
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.
dyn.load() can only load shared libraries, as
created for example by R SHLIB.
attach() currently only works for lists and data frames
(not for directories). Also, you cannot attach at position 1.
For() loops are not necessary and hence not supported.
assign() uses the argument envir= rather than
where= as in S.
int * rather than long *
as in S.
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.
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().
is.vector(c(a = 1:3)) returns FALSE in S and TRUE
in R).
DF is a
data frame, then is.matrix(DF) returns FALSE in R and
TRUE in S).
value. E.g., fun(a) <-
b is evaluated as (fun<-)(a, value = b).
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.
eval(EXPR, sys.parent()) does not work. Instead, one
should use eval(EXPR, sys.frame(sys.parent())), which also works
in S.
for() loop is local to the inside
of the loop. In R it is local to the environment where the for()
statement is executed.
tapply(simplify=TRUE) returns a vector where R returns a
one-dimensional array (which can have named dimnames).
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.
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. Unfortunately, this feature still is mostly undocumented. The paper "An Approach to Providing Mathematical Annotation in Plots" by Paul Murrell and Ross Ihaka, which will soon appear in the Journal of Computational and Graphical Statistics, has more details on this.
Rcgi is a CGI WWW interface to R by Mark J Ray. Recent version have the ability to use "embedded code": you can 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 is possible in PostScript or GIF formats and the executed code is presented to the user for revision.
Demo and download are available from http://www.mth.uea.ac.uk/~h089/Rcgi/.
Rweb is developed and maintained by Jeff Banfield. The Rweb Home Page 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.
A paper on Rweb, 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/).
The R distribution comes with the following extra packages:
The following packages are available from the CRAN src/contrib
area.
VR.
VR.
8/30/53,
30Aug53, 30 August 1953, ..., August 30 53, or
any mixture of these.
VR.
VR.
.dta files.
See CRAN src/contrib/INDEX 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
More code has been posted to the r-help mailing list, and can be obtained from the mailing list archive.
(Unix only.) The add-on packages on CRAN come as gzipped tar files (which may contain more than one package). First "unpack" the files of interest. If you have GNU tar, you can use tar zxf name, otherwise you can use gunzip -c name | tar xf -.
Let pkgdir_1, ..., pkgdir_n be the (relative or
absolute) path names of the packages to be installed. (In the simplest
case, the unpacking creates a single package directory, and its name is
used.) To install to the default R directory tree (the library
subdirectory of R_HOME), type
$ R INSTALL pkgdir_1 ... pkgdir_n
at the shell prompt. To install to another tree (e.g., your private one), use
$ R INSTALL -l lib pkgdir_1 ... pkgdir_n
where lib gives the path to the library tree to install to.
As of R version 0.65.1, you no longer need to explicitly unpack for installing; i.e., you can do R INSTALL /path/to/pkg_ver.tar.gz.
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 $HOME/lib/R and a
public site-wide tree in /usr/local/lib/R/site, put
R_LIBS="$HOME/lib/R:/usr/local/lib/R/site"; export R_LIBS
into your (Bourne) shell profile or your ~/.Renviron file.
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':
MASS Main package of Venables and Ripley's MASS
base The R base package
class Functions for classification
cluster Functions for clustering
ctest Classical tests
date Functions for handling dates
eda Exploratory Data Analysis
gee Generalized Estimating Equation models
lme Linear mixed effects library
locfit Local regression, likelihood and density estimation
lqs Resistant regression and covariance estimation
modreg Modern regression: smoothing and local methods
mva Classical Multivariate Analysis
nls Nonlinear regression
nnet Software for feed-forward neural networks with a single
hidden layer and for multinomial log-linear models.
splines Regression spline functions and classes
stepfun Step functions, including empirical distributions
survival5 Survival analysis
ts Time series functions
You can "load" the installed package pkg by
library(pkg)
You can then find out which functions it provides by typing one of
help(package = pkg) library(help = pkg)
You can unload the loaded package pkg by
detach("package:pkg")
To remove the packages pkg_1, ..., pkg_n from the default library or the library lib, do
$ R REMOVE pkg_1 ... pkg_n
or
$ R REMOVE -l lib pkg_1 ... pkg_n
respectively.
A package consists of a subdirectory containing the files
DESCRIPTION, INDEX, and TITLE, and the
subdirectories R, data, exec, inst,
man and src (some of which can be missing).
The DESCRIPTION file contains basic information about the package
in the following format:
Package: e1071
Version: 0.7-3
Author: Compiled by Fritz Leisch <Friedrich.Leisch@ci.tuwien.ac.at>.
Description: Miscellaneous functions used at the Department of
Statistics at TU Wien (E1071).
Depends:
License: GPL version 2 or later
The license field should contain an explicit statement or a well-known
abbreviation (such as GPL, LGPL, BSD and
Artistic), maybe followed by a reference to the actual license
file. It is very important that you include this information!
Otherwise, it may not even be legally correct for others to distribute
copies of the package.
The TITLE file contains a line giving the name of the package
and a brief description. INDEX contains a line for each
sufficiently interesting object in the package, giving its name and a
description (functions such as print methods not usually called
explicitly might not be included). Note that you can automatically
create this file using something like R CMD Rdindex man/*.Rd >
INDEX provided that Perl is available on your system.
The R subdirectory contains code files. The code files to be
installed must start with a (lower- or uppercase) letter and have one of
the extensions .R, .S, .q, .r, or .s.
We recommend using .R, as this extension seems to be not used by
any other software. It should be possible to read in the files using
source(), so R objects must be created by assignments. Note that
there has to be no connection between the name of the file and the R
objects created by it. If necessary, one of these files (historically
zzz.R) should use library.dynam() inside
.First.lib() to load compiled code.
The man subdirectory should contain documentation files for the
objects in the package. The documentation files to be installed must
also start with a (lower- or uppercase) letter and have the extension
.Rd (the default) or .rd.
C or FORTRAN source and optionally a Makefile for the compiled
code is in src. Note that the Makefile most likely is not
needed.
The data subdirectory is for additional data files the package
makes available for loading using data(). Currently, data files
can have one of three types as indicated by their extension: plain R
code (.R or .r), tables (.tab, .txt, or
.csv), or save() images (.RData or .rda).
The subdirectory should contain a 00Index file that describes
the datasets available.
The contents of the inst subdirectory will be copied recursively
to the installation directory.
Finally, exec could contain additional executables the package
needs, typically Shell or Perl scripts. This mechanism is currently not
used by any package, and still experimental.
You can also provide (Bourne) shell scripts configure and
cleanup for configuration before installation (such as checking
for additional software that might be needed by the package), and
removing the files created in this process. See the add-on package
e1071 on CRAN for an example of this mechanism.
See the documentation for library() for more information.
The web page http://www.biostat.washington.edu/~thomas/Rlib.html maintained by Thomas Lumley provides information on porting S packages to R.
See What is CRAN?, for information on uploading a package to CRAN.
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 What is S?); Generalized Additive Models (gam) and some of the nonlinear modeling code are not there yet.
See also the PROJECTS file in the top level R source directory.
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.
There is an Emacs package which provides a standard interface between statistical programs and statistical processes called ESS ("Emacs Speaks Statistics"). 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), SAS, Stata, SPSS dialects (SPSS, Fiasco) and SCA.
ESS grew out of the desire 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 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 versions of ESS are available from http://ess.stat.wisc.edu/pub/ESS/ or ftp://ess.stat.wisc.edu/pub/ESS/, or via CRAN. 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.
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. This prompts you for the arguments; in particular, you can increase the memory size this way (see Why does R run out of memory?).
R (currently) uses a static memory model. This means that when it starts up, it asks the operating system to reserve a fixed amount of memory for it. The size of this chunk cannot be changed subsequently. Hence, it can happen that not enough memory was allocated, e.g., when trying to read large data sets into R.
In these cases, you should restart R with more memory available, using
the command line options --nsize and --vsize. To
understand these options, one needs to know that R maintains separate
areas for fixed and variable sized objects. The first of these is
allocated as an array of "cons cells" (Lisp programmers will know what
they are, others may think of them as the building blocks of the
language itself, parse trees, etc.), and the second are thrown on a
"heap". The --nsize option can be used to specify the number
of cons cells which R is to use (the default is 250000), and the
--vsize option to specify the size of the vector heap in bytes
(the default is 6 MB). Boths options must either be integers or
integers ending with M, K, or k meaning `Mega'
(2^20), (computer) `Kilo' (2^10), or regular `kilo' (1000).
E.g., to read in a table of 5000 observations on 40 numeric variables,
R --vsize 6M should do (which currently is the default).
Note that the information on where to find vectors and strings on the heap is stored using cons cells. Thus, it may also be necessary to allocate more space for cons cells in order to perform computations with very "large" variable-size objects.
You can find out the current memory consumption (the proportion of heap
and cons cells used) by typing gc() at the R prompt. This may
help you in finding out whether to increase --vsize or
--nsize. Note that following gcinfo(TRUE), automatic
garbage collection always prints memory use statistics.
As of version 0.62.3, R will tell you whether you ran out of cons or heap memory.
The defaults for --nsize and --vsize can be changed by
setting the environment variables R_NSIZE and R_VSIZE
respectively, perhaps most conveniently on Unix in the R environment
file (~/.Renviron by default).
When using read.table(), the memory requirements are in fact
higher than anticipated, because the file is first read in as one long
string which is then split again. Use scan() if possible in
case you run out of memory when reading in a large table.
R sometimes has problems parsing a file which does not end in a newline.
This can happen for example when Emacs is used for editing the file and
next-line-add-newlines is set to nil. To avoid the
problem, either set require-final-newline to a non-nil
value in one of your Emacs startup files, or make sure R-mode (see Is there Emacs support for R?) is used for editing R source files (which
locally ensures this setting).
Earlier R versions had a similar problem when reading in data files, but this should have been taken care of now.
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.
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.
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.)
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 pages for more examples.
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]
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.
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.
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").
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.
We expect R to be Y2K compliant when compiled and run on a Y2K compliant system. In particular R does not internally represent or manipulate dates as two-digit quantities. However, no guarantee of Y2K compliance is provided for R. R is free software and comes with no warranty whatsover.
R, like any other programming language, can be used to write programs and manipulate data in ways that are not Y2K compliant.
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.
According to Doug Bates, the secret of symbolic debugging of dynamically loaded code is to
dyn.load() to load your library.
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 executable. 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
In the C implementation underlying R, all objects are so-called SEXPs
(from Lisp's "S-expressions" which comes from "symbolic
expression"), which are pointers to data structures called SEXPRECs.
(See the file src/include/Rinternals.h in the R sources for the
definition of the SEXPREC type.) For example, let
R> DF <- data.frame(a = 1:3, b = 4:6)
By setting a breakpoint at do_get and typing get("DF") at
the R prompt, one can find out the address in memory of DF, e.g.
Value returned is $1 = (SEXPREC *) 0x40583e1c
(gdb) p *$1
$2 = {
sxpinfo = {type = 19, obj = 1, named = 1, gp = 0,
mark = 0, debug = 0, trace = 0, = 0},
attrib = 0x40583e80,
u = {
vecsxp = {
length = 2,
type = {c = 0x40634700 "0>X@D>X@0>X@", i = 0x40634700,
f = 0x40634700, z = 0x40634700, s = 0x40634700},
truelength = 1075851272,
},
primsxp = {offset = 2},
symsxp = {pname = 0x2, value = 0x40634700, internal = 0x40203008},
listsxp = {carval = 0x2, cdrval = 0x40634700, tagval = 0x40203008},
envsxp = {frame = 0x2, enclos = 0x40634700},
closxp = {formals = 0x2, body = 0x40634700, env = 0x40203008},
promsxp = {value = 0x2, expr = 0x40634700, env = 0x40203008}
}
}
(Debugger output reformatted for better legibility).
Using PrintValue() one can "inspect" the values of the various
elements of the SEXP, e.g.,
(gdb) p PrintValue($1->attrib) $names [1] "a" "b" $row.names [1] "1" "2" "3" $class [1] "data.frame" $3 = void
(Make sure, however, to use PrintValue() on SEXPs with the `obj'
bit turned on only.)
To find out where exactly the corresponding information is stored, one needs to go "deeper":
(gdb) set $a = $1->attrib (gdb) p $a->u.listsxp.tagval->u.symsxp.pname->u.vecsxp.type.c $4 = 0x405d40e8 "names" (gdb) p $a->u.listsxp.carval->u.vecsxp.type.s[1]->u.vecsxp.type.c $5 = 0x40634378 "b" (gdb) p $1->u.vecsxp.type.s[0]->u.vecsxp.type.i[0] $6 = 1 (gdb) p $1->u.vecsxp.type.s[1]->u.vecsxp.type.i[1] $7 = 5
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
.Internal(), .External(), .C() or .Fortran()
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.
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@lists.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.
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, 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 ...