The R Project SVN R

@node Legalese

@node Legalese

@section Legalese

@section Legalese

Copyright @copyright{} 1998--2020 @I{Kurt Hornik} @*

Copyright @copyright{} 1998--2020 @I{Kurt Hornik} @*

This document is free software; you can redistribute it and/or modify it

This document is free software; you can redistribute it and/or modify it

under the terms of the @acronym{GNU} General Public License as published

under the terms of the @acronym{GNU} General Public License as published

by the Free Software Foundation; either version 2, or (at your option)

by the Free Software Foundation; either version 2, or (at your option)

any later version.

any later version.

@I{John Chambers},

@I{John Chambers},

@I{Peter Dalgaard},

@I{Peter Dalgaard},

@I{Robert Gentleman},

@I{Robert Gentleman},

@I{Kurt Hornik},

@I{Kurt Hornik},

@I{Ross Ihaka},

@I{Ross Ihaka},

@I{Michael Lawrence},

@I{Michael Lawrence},

@I{Uwe Ligges},

@I{Uwe Ligges},

@I{Thomas Lumley},

@I{Thomas Lumley},

@I{Martin Maechler},

@I{Martin Maechler},

@I{Sebastian Meyer},

@I{Sebastian Meyer},

@I{Luke Tierney},

@I{Luke Tierney},

@I{Heather Turner}, and

@I{Heather Turner}, and

@I{Simon Urbanek},

@I{Simon Urbanek},

@end display

@end display

@noindent

@noindent

@I{Martin Morgan} up to June 2021,

@I{Martin Morgan} up to June 2021,

R has a home page at @url{https://www.R-project.org/}.  It is

R has a home page at @url{https://www.R-project.org/}.  It is

@url{https://www.gnu.org/philosophy/free-sw.html, free software}

@url{https://www.gnu.org/philosophy/free-sw.html, free software}

distributed under a @acronym{GNU}-style

distributed under a @acronym{GNU}-style

@url{https://www.gnu.org/copyleft/copyleft.html, copyleft}, and an

@url{https://www.gnu.org/copyleft/copyleft.html, copyleft}, and an

@c 2009-01-11

@c 2009-01-11

@c (Architecture: i386, OS: FreeBSD 7.1-PRERELEASE, Vendor: PC-BSD)

@c (Architecture: i386, OS: FreeBSD 7.1-PRERELEASE, Vendor: PC-BSD)

@c i386-freebsd,

@c i386-freebsd,

@c but all recent reports are on x86_64

@c but all recent reports are on x86_64

@c </COMMENT>

@c </COMMENT>

@c mips-sgi-irix,

@c mips-sgi-irix,

@c </FIXME>

@c </FIXME>

@I{i386-pc-solaris},

@I{i386-pc-solaris},

@I{rs6000-ibm-aix},

@I{rs6000-ibm-aix},

@I{x86_64-apple-darwin},

@I{x86_64-apple-darwin},

@I{x86_64-unknown-openbsd}.

@I{x86_64-unknown-openbsd}.

@c and according to @email{jlindsey@@luc.ac.be, Jim Lindsey} also on

@c and according to @email{jlindsey@@luc.ac.be, Jim Lindsey} also on

@c Mac, Amiga and Atari under m68k-linux.

@c Mac, Amiga and Atari under m68k-linux.

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

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

@node What is the current version of R?

@node What is the current version of R?

@section What is the current version of R?

@section What is the current version of R?

R uses a `major.minor.patchlevel' numbering scheme.  Based on this,

R uses a `major.minor.patchlevel' numbering scheme.  Based on this,

there are the current release version of R (`r-release') as well as two

there are the current release version of R (`r-release') as well as two

development versions of R, a patched version of the current release

development versions of R, a patched version of the current release

(`r-patched') and one working towards the next minor or eventually major

(`r-patched') and one working towards the next minor or eventually major

(`r-devel') releases of R, respectively.  New features are typically

(`r-devel') releases of R, respectively.  New features are typically

Books on R by R Core Team members include

Books on R by R Core Team members include

@quotation

@quotation

@I{John M. Chambers} (2008),

@I{John M. Chambers} (2008),

@I{Springer}, New York, ISBN 978-0-387-75935-7,

@I{Springer}, New York, ISBN 978-0-387-75935-7,

@url{https://johnmchambers.su.domains/Rbook/}.

@url{https://johnmchambers.su.domains/Rbook/}.

@I{Peter Dalgaard} (2008),

@I{Peter Dalgaard} (2008),

``Introductory Statistics with R'',

``Introductory Statistics with R'',

``Mixed-Effects Models in S and S-Plus''.

``Mixed-Effects Models in S and S-Plus''.

@I{Springer}, ISBN 0-387-98957-0.

@I{Springer}, ISBN 0-387-98957-0.

@end quotation

@end quotation

Last, but not least, Ross' and Robert's experience in designing and

Last, but not least, Ross' and Robert's experience in designing and

@emph{Journal of Computational and Graphical Statistics}, @strong{5}, 299--314

@emph{Journal of Computational and Graphical Statistics}, @strong{5}, 299--314

(@doi{10.1080/10618600.1996.10474713}).

(@doi{10.1080/10618600.1996.10474713}).

@node Citing R

@node Citing R

@section Citing R

@section Citing R

@item R-packages

@item R-packages

A moderated list for announcements on the availability of new or

A moderated list for announcements on the availability of new or

enhanced contributed packages.

enhanced contributed packages.

@item R-help

@item R-help

The `main' R mailing list, for discussion about problems and solutions

The `main' R mailing list, for discussion about problems and solutions

@c about the development of R and the availability of new code.

@c about the development of R and the availability of new code.

@c enhancements and patches to the source code and documentation of R,

@c enhancements and patches to the source code and documentation of R,

@c comparison and compatibility with S and @SPLUS{}, and for the posting of

@c comparison and compatibility with S and @SPLUS{}, and for the posting of

@c nice examples and benchmarks.

@c nice examples and benchmarks.

@item R-devel

@item R-devel

This is also called the ``@emph{White Book}'', and introduced S version

This is also called the ``@emph{White Book}'', and introduced S version

3, which added structures to facilitate statistical modeling in S.

3, which added structures to facilitate statistical modeling in S.

@item

@item

``Programming with Data,''

``Programming with Data,''

New York: @I{Springer},

New York: @I{Springer},

ISBN 0-387-98503-4

ISBN 0-387-98503-4

(@url{https://johnmchambers.su.domains/Sbook/}).

(@url{https://johnmchambers.su.domains/Sbook/}).

@c @example

@c @example

@c jackknife.S.lm <- function(lmobj) @{

@c jackknife.S.lm <- function(lmobj) @{

@c   n <- length(resid(lmobj))

@c   n <- length(resid(lmobj))

@c   jval <- sapply(1:n,

@c   jval <- sapply(1:n,

@c                  lmobj = lmobj)

@c                  lmobj = lmobj)

@c   (n - 1) * (n - 1) * var(jval) / n

@c   (n - 1) * (n - 1) * var(jval) / n

@c @}

@c @}

@c @end example

@c @end example

a character vector index looks only for exact matches (whereas @code{[[}

a character vector index looks only for exact matches (whereas @code{[[}

and @code{$} allow partial matches).  In S, @code{[} allows partial

and @code{$} allow partial matches).  In S, @code{[} allows partial

matches.

matches.

@item

@item

x2)}.  However, beware of named arguments since S's @code{atan(x = a, y

x2)}.  However, beware of named arguments since S's @code{atan(x = a, y

= b)} is equivalent to R's @code{atan2(y = a, x = b)} with the meanings

= b)} is equivalent to R's @code{atan2(y = a, x = b)} with the meanings

of @code{x} and @code{y} interchanged.  (R used to have undocumented

of @code{x} and @code{y} interchanged.  (R used to have undocumented

support for a two-argument @code{atan} with positional arguments, but

support for a two-argument @code{atan} with positional arguments, but

this has been withdrawn to avoid further confusion.)

this has been withdrawn to avoid further confusion.)

R offers several graphics features that @SPLUS{} does not, such as finer

R offers several graphics features that @SPLUS{} does not, such as finer

handling of line types, more convenient color handling (via palettes),

handling of line types, more convenient color handling (via palettes),

gamma correction for color, and, most importantly, mathematical

gamma correction for color, and, most importantly, mathematical

annotation in plot texts, via input expressions reminiscent of @TeX{}

annotation in plot texts, via input expressions reminiscent of @TeX{}

constructs.  See the help page for @code{plotmath}, which features an

constructs.  See the help page for @code{plotmath}, which features an

@I{Paul Murrell} and @I{Ross Ihaka} (2000),

@I{Paul Murrell} and @I{Ross Ihaka} (2000),

@emph{Journal of Computational and Graphical Statistics}, @strong{9}, 582--599

@emph{Journal of Computational and Graphical Statistics}, @strong{9}, 582--599

(@doi{10.1080/10618600.2000.10474900}).

(@doi{10.1080/10618600.2000.10474900}).

@node What is R-plus?

@node What is R-plus?

@section What is R-plus?

@section What is R-plus?

interaction.

interaction.

@item methods

@item methods

Formally defined methods and classes for R objects, plus other

Formally defined methods and classes for R objects, plus other

programming tools, as described in the Green Book.

programming tools, as described in the Green Book.

@item parallel

@item parallel

and random-number generation (added in R 2.14.0).

and random-number generation (added in R 2.14.0).

@item splines

@item splines

Regression spline functions and classes.

Regression spline functions and classes.

@item stats

@item stats

R statistical functions.

R statistical functions.

open development software project for the analysis and comprehension of

open development software project for the analysis and comprehension of

genomic data.  Most Bioconductor components are distributed as R add-on

genomic data.  Most Bioconductor components are distributed as R add-on

packages.  Initially most of the

packages.  Initially most of the

@url{https://bioconductor.org/packages/release/BiocViews.html#___Software,

@url{https://bioconductor.org/packages/release/BiocViews.html#___Software,

Bioconductor software packages}

Bioconductor software packages}

project has matured, the functional scope of the software packages

project has matured, the functional scope of the software packages

broadened to include the analysis of all types of genomic data, such as

broadened to include the analysis of all types of genomic data, such as

SAGE, sequence, or SNP data.  In addition, there are metadata

SAGE, sequence, or SNP data.  In addition, there are metadata

(annotation, CDF and probe) and experiment data packages.  See

(annotation, CDF and probe) and experiment data packages.  See

@url{https://bioconductor.org/install/} for available packages and a

@url{https://bioconductor.org/install/} for available packages and a

@example

@example

library()

library()

@end example

@end example

@noindent

@noindent

This produces something like

This produces something like

@quotation

@quotation

@cartouche

@cartouche

@noindent

@noindent

we obtain:

we obtain:

@example

@example

R> test1()

R> test1()

R> test2()

R> test2()

3 3.141593

3 3.141593

@end example

@end example

What is really used is the @emph{global} value of @code{.Options}, and

What is really used is the @emph{global} value of @code{.Options}, and

tick marks, and @code{xpd = TRUE} to allow for text outside the plot

tick marks, and @code{xpd = TRUE} to allow for text outside the plot

region.  You can adjust the value of the @code{0.25} offset as required

region.  You can adjust the value of the @code{0.25} offset as required

to move the axis labels up or down relative to the x axis.  See

to move the axis labels up or down relative to the x axis.  See

@code{?par} for more information.

@code{?par} for more information.

@I{Paul Murrell} (2003),

@I{Paul Murrell} (2003),

``Integrating grid Graphics Output with Base Graphics Output'',

``Integrating grid Graphics Output with Base Graphics Output'',

@emph{R News}, @strong{3/2}, 7--12.

@emph{R News}, @strong{3/2}, 7--12.

@node Why is read.table() so inefficient?

@node Why is read.table() so inefficient?

Course with Examples in R}, @I{Richard M. Heiberger} and @I{Burt Holland}

Course with Examples in R}, @I{Richard M. Heiberger} and @I{Burt Holland}

(@I{Springer} 2015, second edition).

(@I{Springer} 2015, second edition).

This appendix is a free download from

This appendix is a free download from

@url{https://link.springer.com/content/pdf/bbm:978-1-4939-2122-5/1.pdf}.

@url{https://link.springer.com/content/pdf/bbm:978-1-4939-2122-5/1.pdf}.

``What Every Computer Scientist Should Know About Floating-Point Arithmetic'',

``What Every Computer Scientist Should Know About Floating-Point Arithmetic'',

also available via

also available via

@c As of 2020-09-25, redirects to https without valid certificate ...

@c As of 2020-09-25, redirects to https without valid certificate ...

@c @url{http://www.validlab.com/goldberg/paper.pdf}.

@c @url{http://www.validlab.com/goldberg/paper.pdf}.

@c See <https://en.wikipedia.org/wiki/IEEE_754>:

@c See <https://en.wikipedia.org/wiki/IEEE_754>:

@url{https://docs.oracle.com/cd/E19957-01/806-3568/ncg_goldberg.html}.

@url{https://docs.oracle.com/cd/E19957-01/806-3568/ncg_goldberg.html}.

@end example

@end example

@node Why are p-values not displayed when using lmer()?

@node Why are p-values not displayed when using lmer()?

@section Why are @math{p}-values not displayed when using @code{lmer()}?

@section Why are @math{p}-values not displayed when using @code{lmer()}?

r-help list, which can be reviewed at

r-help list, which can be reviewed at

@uref{https://stat.ethz.ch/pipermail/r-help/2006-May/094765.html}.

@uref{https://stat.ethz.ch/pipermail/r-help/2006-May/094765.html}.

@node Why are there unwanted borders

@node Why are there unwanted borders

@section Why are there unwanted borders, lines or grid-like artifacts when viewing a plot saved to a PS or PDF file?

@section Why are there unwanted borders, lines or grid-like artifacts when viewing a plot saved to a PS or PDF file?

smoothing and line art smoothing.

smoothing and line art smoothing.

Disable line art smoothing.

Disable line art smoothing.

@item Preview (macOS)

@item Preview (macOS)

There is an option in Preferences to enable/disable anti-aliasing of

There is an option in Preferences to enable/disable anti-aliasing of

text and line art.

text and line art.

@item @I{GSview} (cross platform)

@item @I{GSview} (cross platform)

There are settings for Text Alpha and Graphics Alpha.

There are settings for Text Alpha and Graphics Alpha.

Change Graphics Alpha from 4 bits to 1 bit to disable graphic

Change Graphics Alpha from 4 bits to 1 bit to disable graphic

anti-aliasing.

anti-aliasing.

@item @I{gv} (Unix-like X)

@item @I{gv} (Unix-like X)

@c graph.

@c graph.

@node How do I access the source code for a function?

@node How do I access the source code for a function?

@section How do I access the source code for a function?

@section How do I access the source code for a function?

a complete overview on how to access source code, see @I{Uwe Ligges} (2006),

a complete overview on how to access source code, see @I{Uwe Ligges} (2006),

``Help Desk: Accessing the sources'', @emph{R News}, @strong{6/4},

``Help Desk: Accessing the sources'', @emph{R News}, @strong{6/4},

43--45 (@url{https://CRAN.R-project.org/doc/Rnews/Rnews_2006-4.pdf}).

43--45 (@url{https://CRAN.R-project.org/doc/Rnews/Rnews_2006-4.pdf}).

@node Why does summary() report strange results for the R^2 estimate when I fit a linear model with no intercept?

@node Why does summary() report strange results for the R^2 estimate when I fit a linear model with no intercept?

bug has already been reported and/or fixed.  First, try the ``Show open

bug has already been reported and/or fixed.  First, try the ``Show open

bugs new-to-old'' or the search facility on

bugs new-to-old'' or the search facility on

@url{https://bugs.R-project.org/}.  Second, consult

@url{https://bugs.R-project.org/}.  Second, consult

@url{https://svn.R-project.org/R/trunk/doc/NEWS.Rd}, which

@url{https://svn.R-project.org/R/trunk/doc/NEWS.Rd}, which

records changes that will appear in the @emph{next} release of R,

records changes that will appear in the @emph{next} release of R,

Third, if possible try the current r-patched or r-devel version of R.

Third, if possible try the current r-patched or r-devel version of R.

If a bug has already been reported or fixed, please do not submit

If a bug has already been reported or fixed, please do not submit

further bug reports on it.  Finally, check carefully whether the bug is

further bug reports on it.  Finally, check carefully whether the bug is

with R, or a contributed package.  Bug reports on contributed packages

with R, or a contributed package.  Bug reports on contributed packages

should be sent first to the package maintainer, and only submitted to

should be sent first to the package maintainer, and only submitted to

For reports on R this will open the R Bugzilla page at

For reports on R this will open the R Bugzilla page at

@url{https://bugs.R-project.org/}: for a contributed package it will open

@url{https://bugs.R-project.org/}: for a contributed package it will open

the package's bug tracker Web page or help you compose an email to the

the package's bug tracker Web page or help you compose an email to the

maintainer.  Since 2016, only ``members'' (including all who have

maintainer.  Since 2016, only ``members'' (including all who have

previously submitted bugs) can submit new bugs on the R Bugzilla.  See

previously submitted bugs) can submit new bugs on the R Bugzilla.  See

@uref{https://www.r-project.org/bugs.html, Bug Reporting in R} for more

@uref{https://www.r-project.org/bugs.html, Bug Reporting in R} for more

information.

information.

There is a section of the bug repository for suggestions for

There is a section of the bug repository for suggestions for

enhancements for R labelled @samp{wishlist}.  Suggestions can be

enhancements for R labelled @samp{wishlist}.  Suggestions can be

@unnumbered Acknowledgments

@unnumbered Acknowledgments

Of course, many many thanks to Robert and Ross for the R system, and to

Of course, many many thanks to Robert and Ross for the R system, and to

the package writers and porters for adding to it.

the package writers and porters for adding to it.

@I{Paul Gilbert},

@I{Paul Gilbert},

@I{Stefano Iacus},

@I{Stefano Iacus},

@I{Fritz Leisch},

@I{Fritz Leisch},

@I{Jim Lindsey},

@I{Jim Lindsey},

@I{Thomas Lumley},

@I{Thomas Lumley},

@I{Martin Maechler},

@I{Martin Maechler},

@I{Brian D. Ripley},

@I{Brian D. Ripley},

@I{Andreas Weingessel}

@I{Andreas Weingessel}

for their comments which helped me improve this @acronym{FAQ}.

for their comments which helped me improve this @acronym{FAQ}.

@c FIXME:

@c FIXME:

More to come soon @dots{}

More to come soon @dots{}