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@ -23,3 +23,4 @@ R-2.11.1.tar.gz
/R-3.2.3.tar.gz /R-3.2.3.tar.gz
/R-3.2.4-revised.tar.gz /R-3.2.4-revised.tar.gz
/R-3.3.0.tar.gz /R-3.3.0.tar.gz
/R-3.3.1.tar.gz

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R-FAQ.html
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@ -1,6 +1,6 @@
<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd"> <!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
<html> <html>
<!-- Created by GNU Texinfo 6.0, http://www.gnu.org/software/texinfo/ --> <!-- Created by GNU Texinfo 6.1, http://www.gnu.org/software/texinfo/ -->
<head> <head>
<title>R FAQ</title> <title>R FAQ</title>
@ -33,9 +33,8 @@ pre.smalldisplay {font-family: inherit; font-size: smaller}
pre.smallexample {font-size: smaller} pre.smallexample {font-size: smaller}
pre.smallformat {font-family: inherit; font-size: smaller} pre.smallformat {font-family: inherit; font-size: smaller}
pre.smalllisp {font-size: smaller} pre.smalllisp {font-size: smaller}
span.nocodebreak {white-space: nowrap}
span.nolinebreak {white-space: nowrap} span.nolinebreak {white-space: nowrap}
span.roman {font-family: serif; font-weight: normal} span.roman {font-family: initial; font-weight: normal}
span.sansserif {font-family: sans-serif; font-weight: normal} span.sansserif {font-family: sans-serif; font-weight: normal}
ul.no-bullet {list-style: none} ul.no-bullet {list-style: none}
body { body {
@ -129,9 +128,10 @@ p {
<h2>Frequently Asked Questions on R</h2> <h2>Frequently Asked Questions on R</h2>
<h3 style="text-align: center;">Version 3.2.2015-12-04</h3> <h3 style="text-align: center;">Version 2016-06-06</h3>
<h3 style="text-align: center;">Kurt Hornik</h3> <h3 style="text-align: center;">Kurt Hornik</h3>
<hr> <hr>
<a name="SEC_Contents"></a> <a name="SEC_Contents"></a>
<h2 class="contents-heading">Table of Contents</h2> <h2 class="contents-heading">Table of Contents</h2>
@ -249,6 +249,7 @@ p {
<li><a name="toc-Why-does-summary_0028_0029-report-strange-results-for-the-R_005e2-estimate-when-I-fit-a-linear-model-with-no-intercept_003f-1" href="#Why-does-summary_0028_0029-report-strange-results-for-the-R_005e2-estimate-when-I-fit-a-linear-model-with-no-intercept_003f">7.41 Why does summary() report strange results for the R^2 estimate when I fit a linear model with no intercept?</a></li> <li><a name="toc-Why-does-summary_0028_0029-report-strange-results-for-the-R_005e2-estimate-when-I-fit-a-linear-model-with-no-intercept_003f-1" href="#Why-does-summary_0028_0029-report-strange-results-for-the-R_005e2-estimate-when-I-fit-a-linear-model-with-no-intercept_003f">7.41 Why does summary() report strange results for the R^2 estimate when I fit a linear model with no intercept?</a></li>
<li><a name="toc-Why-is-R-apparently-not-releasing-memory_003f-1" href="#Why-is-R-apparently-not-releasing-memory_003f">7.42 Why is R apparently not releasing memory?</a></li> <li><a name="toc-Why-is-R-apparently-not-releasing-memory_003f-1" href="#Why-is-R-apparently-not-releasing-memory_003f">7.42 Why is R apparently not releasing memory?</a></li>
<li><a name="toc-How-can-I-enable-secure-https-downloads-in-R_003f-1" href="#How-can-I-enable-secure-https-downloads-in-R_003f">7.43 How can I enable secure https downloads in R?</a></li> <li><a name="toc-How-can-I-enable-secure-https-downloads-in-R_003f-1" href="#How-can-I-enable-secure-https-downloads-in-R_003f">7.43 How can I enable secure https downloads in R?</a></li>
<li><a name="toc-How-can-I-get-CRAN-package-binaries-for-outdated-versions-of-R_003f-1" href="#How-can-I-get-CRAN-package-binaries-for-outdated-versions-of-R_003f">7.44 How can I get CRAN package binaries for outdated versions of R?</a></li>
</ul></li> </ul></li>
<li><a name="toc-R-Programming-1" href="#R-Programming">8 R Programming</a> <li><a name="toc-R-Programming-1" href="#R-Programming">8 R Programming</a>
<ul class="no-bullet"> <ul class="no-bullet">
@ -333,7 +334,7 @@ Next: <a href="#Obtaining-this-document" accesskey="n" rel="next">Obtaining this
<a name="Legalese-1"></a> <a name="Legalese-1"></a>
<h3 class="section">1.1 Legalese</h3> <h3 class="section">1.1 Legalese</h3>
<p>This document is copyright &copy; 1998&ndash;2015 by Kurt <p>This document is copyright &copy; 1998&ndash;2016 by Kurt
Hornik. Hornik.
</p> </p>
<p>This document is free software; you can redistribute it and/or modify it <p>This document is free software; you can redistribute it and/or modify it
@ -391,14 +392,14 @@ Next: <a href="#Notation" accesskey="n" rel="next">Notation</a>, Previous: <a hr
<h3 class="section">1.3 Citing this document</h3> <h3 class="section">1.3 Citing this document</h3>
<p>In publications, please refer to this <acronym>FAQ</acronym> as Hornik <p>In publications, please refer to this <acronym>FAQ</acronym> as Hornik
(2015), &ldquo;The R <acronym>FAQ</acronym>&rdquo;, and give the above, (2016), &ldquo;The R <acronym>FAQ</acronym>&rdquo;, and give the above,
<em>official</em> <acronym>URL</acronym>: <em>official</em> <acronym>URL</acronym>:
</p> </p>
<div class="example"> <div class="example">
<pre class="example">@Misc{, <pre class="example">@Misc{,
author = {Kurt Hornik}, author = {Kurt Hornik},
title = {{R} {FAQ}}, title = {{R} {FAQ}},
year = {2015}, year = {2016},
url = {https://CRAN.R-project.org/doc/FAQ/R-FAQ.html} url = {https://CRAN.R-project.org/doc/FAQ/R-FAQ.html}
} }
</pre></div> </pre></div>
@ -568,12 +569,15 @@ Next: <a href="#How-can-R-be-obtained_003f" accesskey="n" rel="next">How can R b
<a name="What-is-the-current-version-of-R_003f-1"></a> <a name="What-is-the-current-version-of-R_003f-1"></a>
<h3 class="section">2.3 What is the current version of R?</h3> <h3 class="section">2.3 What is the current version of R?</h3>
<p>The current released version is 3.2.3. Based on this <p>R uses a &lsquo;major.minor.patchlevel&rsquo; numbering scheme. Based on this,
&lsquo;major.minor.patchlevel&rsquo; numbering scheme, there are two development there are the current release version of R (&lsquo;r-release&rsquo;) as well as two
versions of R, a patched version of the current release (&lsquo;r-patched&rsquo;) development versions of R, a patched version of the current release
and one working towards the next minor or eventually major (&lsquo;r-devel&rsquo;) (&lsquo;r-patched&rsquo;) and one working towards the next minor or eventually major
releases of R, respectively. Version r-patched is for bug fixes mostly. (&lsquo;r-devel&rsquo;) releases of R, respectively. New features are typically
New features are typically introduced in r-devel. introduced in r-devel, while r-patched is for bug fixes mostly.
</p>
<p>See <a href="https://CRAN.R-project.org/sources.html">https://CRAN.R-project.org/sources.html</a> for the current
versions of r-release, r-patched and r-devel.
</p> </p>
<hr> <hr>
<a name="How-can-R-be-obtained_003f"></a> <a name="How-can-R-be-obtained_003f"></a>
@ -927,11 +931,13 @@ Next: <a href="#What-mailing-lists-exist-for-R_003f" accesskey="n" rel="next">Wh
author = {{R Core Team}}, author = {{R Core Team}},
organization = {R Foundation for Statistical Computing}, organization = {R Foundation for Statistical Computing},
address = {Vienna, Austria}, address = {Vienna, Austria},
year = 2015, year = <var>YEAR</var>,
url = {https://www.R-project.org} url = {https://www.R-project.org}
} }
</pre></div> </pre></div>
<p>where <var>YEAR</var> is the release year of the version of R used and can
determined as <code>R.version$year</code>.
</p>
<p>Citation strings (or BibTeX entries) for R and R packages can also be <p>Citation strings (or BibTeX entries) for R and R packages can also be
obtained by <code>citation()</code>. obtained by <code>citation()</code>.
</p> </p>
@ -1050,6 +1056,9 @@ OS X, and MS Windows). <acronym>CRAN</acronym> also provides access to
documentation on R, existing mailing lists and the R Bug Tracking documentation on R, existing mailing lists and the R Bug Tracking
system. system.
</p> </p>
<p>Since March 2016, &ldquo;old&rdquo; material is made available from a central
<acronym>CRAN</acronym> archive server (<a href="https://CRAN-archive.R-project.org/">https://CRAN-archive.R-project.org/</a>).
</p>
<p>Please always use the <acronym>URL</acronym> of the master site when referring to <p>Please always use the <acronym>URL</acronym> of the master site when referring to
<acronym>CRAN</acronym>. <acronym>CRAN</acronym>.
</p> </p>
@ -1233,9 +1242,7 @@ the programming process.
<p>See <a href="http://statweb.stanford.edu/~jmc4/papers/96.7.ps">http://statweb.stanford.edu/~jmc4/papers/96.7.ps</a> <p>See <a href="http://statweb.stanford.edu/~jmc4/papers/96.7.ps">http://statweb.stanford.edu/~jmc4/papers/96.7.ps</a>
for further information on the &ldquo;Evolution of the S Language&rdquo;. for further information on the &ldquo;Evolution of the S Language&rdquo;.
</p> </p>
<p>There is a huge amount of user-contributed code for S, available at the
<a href="http://lib.stat.cmu.edu/S/">S Repository</a> at <acronym>CMU</acronym>.
</p>
<hr> <hr>
<a name="What-is-S_002dPLUS_003f"></a> <a name="What-is-S_002dPLUS_003f"></a>
@ -1803,8 +1810,8 @@ and a web server provided that the installer has the necessary security
permissions. David&rsquo;s paper &ldquo;CGIwithR: Facilities for Processing Web permissions. David&rsquo;s paper &ldquo;CGIwithR: Facilities for Processing Web
Forms Using R&rdquo; was published in the Journal of Statistical Software Forms Using R&rdquo; was published in the Journal of Statistical Software
(<a href="http://www.jstatsoft.org/v08/i10/">http://www.jstatsoft.org/v08/i10/</a>). The package is now (<a href="http://www.jstatsoft.org/v08/i10/">http://www.jstatsoft.org/v08/i10/</a>). The package is now
maintained by <a href="mailto:duncan@wald.ucdavis.edu">Duncan Temple Lang</a> and maintained by <a href="mailto:duncan@wald.ucdavis.edu">Duncan Temple Lang</a>.
has a web page at <a href="http://www.omegahat.org/CGIwithR/">http://www.omegahat.org/CGIwithR/</a>. and has a web page at <a href="http://www.omegahat.net/CGIwithR/">http://www.omegahat.net/CGIwithR/</a>.
</p> </p>
<p>Jeff Horner is working on the R/Apache Integration Project which embeds <p>Jeff Horner is working on the R/Apache Integration Project which embeds
@ -2075,12 +2082,12 @@ Next: <a href="#Add_002don-packages-from-Bioconductor" accesskey="n" rel="next">
<a name="Add_002don-packages-from-Omegahat-1"></a> <a name="Add_002don-packages-from-Omegahat-1"></a>
<h4 class="subsection">5.1.3 Add-on packages from Omegahat</h4> <h4 class="subsection">5.1.3 Add-on packages from Omegahat</h4>
<p>The <a href="http://www.omegahat.org/">Omega Project for Statistical <p>The <a href="http://www.omegahat.net/">Omega Project for Statistical
Computing</a> provides a variety of open-source software for statistical Computing</a> provides a variety of open-source software for statistical
applications, with special emphasis on web-based software, Java, the applications, with special emphasis on web-based software, Java, the
Java virtual machine, and distributed computing. A <acronym>CRAN</acronym> style Java virtual machine, and distributed computing. A <acronym>CRAN</acronym> style
R package repository is available via <a href="http://www.omegahat.org/R/">http://www.omegahat.org/R/</a>. R package repository is available via <a href="http://www.omegahat.net/R/">http://www.omegahat.net/R/</a>.
See <a href="http://www.omegahat.org/">http://www.omegahat.org/</a> for information on most R packages See <a href="http://www.omegahat.net/">http://www.omegahat.net/</a> for information on most R packages
available from the Omega project. available from the Omega project.
</p> </p>
<hr> <hr>
@ -2565,6 +2572,8 @@ Next: <a href="#R-Programming" accesskey="n" rel="next">R Programming</a>, Previ
</td></tr> </td></tr>
<tr><td align="left" valign="top">&bull; <a href="#How-can-I-enable-secure-https-downloads-in-R_003f">How can I enable secure https downloads in R?</a>:</td><td>&nbsp;&nbsp;</td><td align="left" valign="top"> <tr><td align="left" valign="top">&bull; <a href="#How-can-I-enable-secure-https-downloads-in-R_003f">How can I enable secure https downloads in R?</a>:</td><td>&nbsp;&nbsp;</td><td align="left" valign="top">
</td></tr> </td></tr>
<tr><td align="left" valign="top">&bull; <a href="#How-can-I-get-CRAN-package-binaries-for-outdated-versions-of-R_003f">How can I get CRAN package binaries for outdated versions of R?</a>:</td><td>&nbsp;&nbsp;</td><td align="left" valign="top">
</td></tr>
</table> </table>
@ -3464,12 +3473,12 @@ Next: <a href="#How-can-I-capture-or-ignore-errors-in-a-long-simulation_003f" ac
<a name="Why-doesn_0027t-R-think-these-numbers-are-equal_003f-1"></a> <a name="Why-doesn_0027t-R-think-these-numbers-are-equal_003f-1"></a>
<h3 class="section">7.31 Why doesn&rsquo;t R think these numbers are equal?</h3> <h3 class="section">7.31 Why doesn&rsquo;t R think these numbers are equal?</h3>
<p>The only numbers that can be represented exactly in R&rsquo;s numeric type <p>The only numbers that can be represented exactly in R&rsquo;s numeric type are
are integers and fractions whose denominator is a power of 2. Other integers and fractions whose denominator is a power of 2. All other
numbers have to be rounded to (typically) 53 binary digits accuracy. As a numbers are internally rounded to (typically) 53 binary digits accuracy.
result, two floating point numbers will not reliably be equal unless they As a result, two floating point numbers will not reliably be equal
have been computed by the same algorithm, and not always even then. For unless they have been computed by the same algorithm, and not always
example even then. For example
</p> </p>
<div class="example"> <div class="example">
<pre class="example">R&gt; a &lt;- sqrt(2) <pre class="example">R&gt; a &lt;- sqrt(2)
@ -3477,6 +3486,8 @@ R&gt; a * a == 2
[1] FALSE [1] FALSE
R&gt; a * a - 2 R&gt; a * a - 2
[1] 4.440892e-16 [1] 4.440892e-16
R&gt; print(a * a, digits = 18)
[1] 2.00000000000000044
</pre></div> </pre></div>
<p>The function <code>all.equal()</code> compares two objects using a numeric <p>The function <code>all.equal()</code> compares two objects using a numeric
@ -3484,17 +3495,32 @@ tolerance of <code>.Machine$double.eps ^ 0.5</code>. If you want much greater
accuracy than this you will need to consider error propagation accuracy than this you will need to consider error propagation
carefully. carefully.
</p> </p>
<p>A discussion with many easily followed examples is in Appendix G
&ldquo;Computational Precision and Floating Point Arithmetic&rdquo;, pages
753&ndash;771 of <em>Statistical Analysis and Data Display: An Intermediate
Course with Examples in R</em>, Richard M. Heiberger and Burt Holland
(Springer 2015, second edition). This appendix is a free download from
<a href="http://link.springer.com/content/pdf/bbm%3A978-1-4939-2122-5%2F1.pdf">http://link.springer.com/content/pdf/bbm%3A978-1-4939-2122-5%2F1.pdf</a>.
</p>
<p>For more information, see e.g. David Goldberg (1991), &ldquo;What Every <p>For more information, see e.g. David Goldberg (1991), &ldquo;What Every
Computer Scientist Should Know About Floating-Point Arithmetic&rdquo;, Computer Scientist Should Know About Floating-Point Arithmetic&rdquo;,
<em>ACM Computing Surveys</em>, <strong>23/1</strong>, 5&ndash;48, also available via <em>ACM Computing Surveys</em>, <strong>23/1</strong>, 5&ndash;48, also available via
<a href="http://www.validlab.com/goldberg/paper.pdf">http://www.validlab.com/goldberg/paper.pdf</a>. <a href="http://www.validlab.com/goldberg/paper.pdf">http://www.validlab.com/goldberg/paper.pdf</a>.
</p> </p>
<p>To quote from &ldquo;The Elements of Programming Style&rdquo; by Kernighan and <p>Here is another example, this time using addition:
Plauger:
</p> </p>
<blockquote> <div class="example">
<p><em>10.0 times 0.1 is hardly ever 1.0</em>. <pre class="example">R&gt; .3 + .6 == .9
</p></blockquote> [1] FALSE
R&gt; .3 + .6 - .9
[1] -1.110223e-16
R&gt; print(matrix(c(.3, .6, .9, .3 + .6)), digits = 18)
[,1]
[1,] 0.299999999999999989
[2,] 0.599999999999999978
[3,] 0.900000000000000022
[4,] 0.899999999999999911
</pre></div>
<hr> <hr>
@ -3888,7 +3914,7 @@ actually used memory as well as unused memory that cannot be released.
<a name="How-can-I-enable-secure-https-downloads-in-R_003f"></a> <a name="How-can-I-enable-secure-https-downloads-in-R_003f"></a>
<div class="header"> <div class="header">
<p> <p>
Previous: <a href="#Why-is-R-apparently-not-releasing-memory_003f" accesskey="p" rel="prev">Why is R apparently not releasing memory?</a>, Up: <a href="#R-Miscellanea" accesskey="u" rel="up">R Miscellanea</a> &nbsp; [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p> Next: <a href="#How-can-I-get-CRAN-package-binaries-for-outdated-versions-of-R_003f" accesskey="n" rel="next">How can I get CRAN package binaries for outdated versions of R?</a>, Previous: <a href="#Why-is-R-apparently-not-releasing-memory_003f" accesskey="p" rel="prev">Why is R apparently not releasing memory?</a>, Up: <a href="#R-Miscellanea" accesskey="u" rel="up">R Miscellanea</a> &nbsp; [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
</div> </div>
<a name="How-can-I-enable-secure-https-downloads-in-R_003f-1"></a> <a name="How-can-I-enable-secure-https-downloads-in-R_003f-1"></a>
<h3 class="section">7.43 How can I enable secure https downloads in R?</h3> <h3 class="section">7.43 How can I enable secure https downloads in R?</h3>
@ -3909,8 +3935,10 @@ this is done automatically for such URLs as from R 3.2.2.
The requisite code to add to <samp>.Rprofile</samp> or <samp>Rprofile.site</samp> is: The requisite code to add to <samp>.Rprofile</samp> or <samp>Rprofile.site</samp> is:
</p> </p>
<div class="example"> <div class="example">
<pre class="example">options(download.file.method = &quot;wininet&quot;, url.method = &quot;wininet&quot;) <span class="roman">(Windows)</span> <pre class="example">options(download.file.method = &quot;wininet&quot;, url.method = &quot;wininet&quot;)
options(download.file.method = &quot;libcurl&quot;, url.method = &quot;libcurl&quot;) <span class="roman">(Linux and OS X)</span> <span class="roman">(Windows)</span>
options(download.file.method = &quot;libcurl&quot;, url.method = &quot;libcurl&quot;)
<span class="roman">(Linux and OS X)</span>
</pre></div> </pre></div>
<p>(Method <code>&quot;wininet&quot;</code> is the default on Windows as from R 3.2.2.) <p>(Method <code>&quot;wininet&quot;</code> is the default on Windows as from R 3.2.2.)
@ -3924,7 +3952,28 @@ OS X. It is possible that system versions of <code>&quot;libcurl&quot;</code>,
<code>&quot;libcurl&quot;</code> with <acronym>HTTPS</acronym> support is required except on <code>&quot;libcurl&quot;</code> with <acronym>HTTPS</acronym> support is required except on
Windows. Windows.
</p> </p>
<hr>
<a name="How-can-I-get-CRAN-package-binaries-for-outdated-versions-of-R_003f"></a>
<div class="header">
<p>
Previous: <a href="#How-can-I-enable-secure-https-downloads-in-R_003f" accesskey="p" rel="prev">How can I enable secure https downloads in R?</a>, Up: <a href="#R-Miscellanea" accesskey="u" rel="up">R Miscellanea</a> &nbsp; [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
</div>
<a name="How-can-I-get-CRAN-package-binaries-for-outdated-versions-of-R_003f-1"></a>
<h3 class="section">7.44 How can I get CRAN package binaries for outdated versions of R?</h3>
<p>Since March 2016, Windows and OS X binaries of <acronym>CRAN</acronym> packages for old
versions of R (released more than 5 years ago) are made available from a
central <acronym>CRAN</acronym> archive server instead of the <acronym>CRAN</acronym> mirrors. To get
these, one should set the <acronym>CRAN</acronym> &ldquo;mirror&rdquo; element of the <code>repos</code>
option accordingly, by something like
</p><div class="example">
<pre class="example">local({r &lt;- getOption(&quot;repos&quot;)
r[&quot;CRAN&quot;] &lt;- &quot;http://CRAN-archive.R-project.org&quot;
options(repos = r)
})
</pre></div>
<p>(see <code>?options</code> for more information).
</p>
<hr> <hr>
<a name="R-Programming"></a> <a name="R-Programming"></a>
<div class="header"> <div class="header">

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@ -1,8 +1,8 @@
<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd"> <!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
<html> <html>
<!-- This manual is for R, version 3.2.3 (2015-12-10). <!-- This manual is for R, version 3.3.1 (2016-06-21).
Copyright (C) 2000-2015 R Core Team Copyright (C) 2000-2016 R Core Team
Permission is granted to make and distribute verbatim copies of this Permission is granted to make and distribute verbatim copies of this
manual provided the copyright notice and this permission notice are manual provided the copyright notice and this permission notice are
@ -17,7 +17,7 @@ Permission is granted to copy and distribute translations of this manual
into another language, under the above conditions for modified versions, into another language, under the above conditions for modified versions,
except that this permission notice may be stated in a translation except that this permission notice may be stated in a translation
approved by the R Core Team. --> approved by the R Core Team. -->
<!-- Created by GNU Texinfo 6.0, http://www.gnu.org/software/texinfo/ --> <!-- Created by GNU Texinfo 6.1, http://www.gnu.org/software/texinfo/ -->
<head> <head>
<title>R Data Import/Export</title> <title>R Data Import/Export</title>
@ -51,9 +51,8 @@ pre.smalldisplay {font-family: inherit; font-size: smaller}
pre.smallexample {font-size: smaller} pre.smallexample {font-size: smaller}
pre.smallformat {font-family: inherit; font-size: smaller} pre.smallformat {font-family: inherit; font-size: smaller}
pre.smalllisp {font-size: smaller} pre.smalllisp {font-size: smaller}
span.nocodebreak {white-space: nowrap}
span.nolinebreak {white-space: nowrap} span.nolinebreak {white-space: nowrap}
span.roman {font-family: serif; font-weight: normal} span.roman {font-family: initial; font-weight: normal}
span.sansserif {font-family: sans-serif; font-weight: normal} span.sansserif {font-family: sans-serif; font-weight: normal}
ul.no-bullet {list-style: none} ul.no-bullet {list-style: none}
body { body {
@ -241,9 +240,9 @@ Next: <a href="#Acknowledgements" accesskey="n" rel="next">Acknowledgements</a>
<p>This is a guide to importing and exporting data to and from R. <p>This is a guide to importing and exporting data to and from R.
</p> </p>
<p>This manual is for R, version 3.2.3 (2015-12-10). <p>This manual is for R, version 3.3.1 (2016-06-21).
</p> </p>
<p>Copyright &copy; 2000&ndash;2015 R Core Team <p>Copyright &copy; 2000&ndash;2016 R Core Team
</p> </p>
<blockquote> <blockquote>
<p>Permission is granted to make and distribute verbatim copies of this <p>Permission is granted to make and distribute verbatim copies of this
@ -372,13 +371,13 @@ here.
<p>There are packages to allow functionality developed in languages such as <p>There are packages to allow functionality developed in languages such as
<code>Java</code>, <code>perl</code> and <code>python</code> to be directly integrated <code>Java</code>, <code>perl</code> and <code>python</code> to be directly integrated
with R code, making the use of facilities in these languages even with R code, making the use of facilities in these languages even
more appropriate. (See the <a href="https://CRAN.R-project.org/package=rJava"><strong>rJava</strong></a> package from <acronym>CRAN</acronym> and more appropriate. (See the <a href="https://CRAN.R-project.org/package=rJava"><strong>rJava</strong></a> package from <acronym>CRAN</acronym>
the <strong>SJava</strong>, <strong>RSPerl</strong> and <strong>RSPython</strong> packages from the and the <strong>SJava</strong>, <strong>RSPerl</strong> and <strong>RSPython</strong> packages from the
Omegahat project, <a href="http://www.omegahat.org">http://www.omegahat.org</a>.) Omegahat project, <a href="http://www.omegahat.net">http://www.omegahat.net</a>.)
</p> </p>
<a name="index-Unix-tools"></a> <a name="index-Unix-tools"></a>
<a name="index-AWK"></a> <a name="index-awk"></a>
<a name="index-perl"></a> <a name="index-perl"></a>
<p>It is also worth remembering that R like S comes from the Unix <p>It is also worth remembering that R like S comes from the Unix
tradition of small re-usable tools, and it can be rewarding to use tools tradition of small re-usable tools, and it can be rewarding to use tools
@ -428,8 +427,7 @@ on their computers for that purpose). However, this is not always
possible, and <a href="#Importing-from-other-statistical-systems">Importing from other statistical systems</a> discusses possible, and <a href="#Importing-from-other-statistical-systems">Importing from other statistical systems</a> discusses
what facilities are available to access such files directly from R. what facilities are available to access such files directly from R.
For Excel spreadsheets, the available methods are summarized in For Excel spreadsheets, the available methods are summarized in
<a href="#Reading-Excel-spreadsheets">Reading Excel spreadsheets</a>. For ODS spreadsheets from Open <a href="#Reading-Excel-spreadsheets">Reading Excel spreadsheets</a>.
Office, see the Omegahat package<a name="DOCF1" href="#FOOT1"><sup>1</sup></a> <strong>ROpenOffice</strong>.
</p> </p>
<p>In a few cases, data have been stored in a binary form for compactness <p>In a few cases, data have been stored in a binary form for compactness
and speed of access. One application of this that we have seen several and speed of access. One application of this that we have seen several
@ -471,7 +469,7 @@ intro.dat: UTF-8 Unicode (with BOM) text
<p>Modern Unix-alike systems, including OS X, are likely to produce <p>Modern Unix-alike systems, including OS X, are likely to produce
UTF-8 files. Windows may produce what it calls &lsquo;Unicode&rsquo; files UTF-8 files. Windows may produce what it calls &lsquo;Unicode&rsquo; files
(<code>UCS-2LE</code> or just possibly <code>UTF-16LE</code><a name="DOCF2" href="#FOOT2"><sup>2</sup></a>). Otherwise most files will be in a (<code>UCS-2LE</code> or just possibly <code>UTF-16LE</code><a name="DOCF1" href="#FOOT1"><sup>1</sup></a>). Otherwise most files will be in a
8-bit encoding unless from a Chinese/Japanese/Korean locale (which have 8-bit encoding unless from a Chinese/Japanese/Korean locale (which have
a wide range of encodings in common use). It is not possible to a wide range of encodings in common use). It is not possible to
automatically detect with certainty which 8-bit encoding (although automatically detect with certainty which 8-bit encoding (although
@ -622,7 +620,7 @@ and <code>write.table</code> has a <code>fileEncoding</code> argument to make th
easier. easier.
</p> </p>
<p>The hard part is to know what file encoding to use. For use on Windows, <p>The hard part is to know what file encoding to use. For use on Windows,
it is best to use what Windows calls &lsquo;Unicode&rsquo;<a name="DOCF3" href="#FOOT3"><sup>3</sup></a>, that is <code>&quot;UTF-16LE&quot;</code>. Using UTF-8 is a good way it is best to use what Windows calls &lsquo;Unicode&rsquo;<a name="DOCF2" href="#FOOT2"><sup>2</sup></a>, that is <code>&quot;UTF-16LE&quot;</code>. Using UTF-8 is a good way
to make portable files that will not easily be confused with any other to make portable files that will not easily be confused with any other
encoding, but even OS X applications (where UTF-8 is the system encoding, but even OS X applications (where UTF-8 is the system
encoding) may not recognize them, and Windows applications are most encoding) may not recognize them, and Windows applications are most
@ -685,12 +683,9 @@ graphical displays, mathematics and so on.
<p>although it does not require it. <p>although it does not require it.
</p> </p>
<p>The <a href="https://CRAN.R-project.org/package=XML"><strong>XML</strong></a> package provides general facilities for reading and <p>The <a href="https://CRAN.R-project.org/package=XML"><strong>XML</strong></a> package provides general facilities for reading and
writing <acronym>XML</acronym> documents within R. A description of the writing <acronym>XML</acronym> documents within R.
facilities of the <a href="https://CRAN.R-project.org/package=XML"><strong>XML</strong></a> package is outside the scope of this Package <a href="https://CRAN.R-project.org/package=StatDataML"><strong>StatDataML</strong></a> on <acronym>CRAN</acronym> is one example building
document: see the package&rsquo;s Web page at on <a href="https://CRAN.R-project.org/package=XML"><strong>XML</strong></a>.
<a href="http://www.omegahat.org/RSXML">http://www.omegahat.org/RSXML</a> for details and examples. Package
<a href="https://CRAN.R-project.org/package=StatDataML"><strong>StatDataML</strong></a> on <acronym>CRAN</acronym> is one example building on
<a href="https://CRAN.R-project.org/package=XML"><strong>XML</strong></a>.
</p> </p>
<p>NB: <a href="https://CRAN.R-project.org/package=XML"><strong>XML</strong></a> is available as a binary package for Windows, normally <p>NB: <a href="https://CRAN.R-project.org/package=XML"><strong>XML</strong></a> is available as a binary package for Windows, normally
from the &lsquo;CRAN extras&rsquo; repository (which is selected by default on from the &lsquo;CRAN extras&rsquo; repository (which is selected by default on
@ -856,7 +851,7 @@ indicate missing cases in a regular layout.
columns as character vectors and then tries to select a suitable class columns as character vectors and then tries to select a suitable class
for each variable in the data frame. It tries in turn <code>logical</code>, for each variable in the data frame. It tries in turn <code>logical</code>,
<code>integer</code>, <code>numeric</code> and <code>complex</code>, moving on if any <code>integer</code>, <code>numeric</code> and <code>complex</code>, moving on if any
entry is not missing and cannot be converted.<a name="DOCF4" href="#FOOT4"><sup>4</sup></a> entry is not missing and cannot be converted.<a name="DOCF3" href="#FOOT3"><sup>3</sup></a>
If all of these fail, the variable is converted to a factor. If all of these fail, the variable is converted to a factor.
</p> </p>
<p>Arguments <code>colClasses</code> and <code>as.is</code> provide greater control. <p>Arguments <code>colClasses</code> and <code>as.is</code> provide greater control.
@ -1490,7 +1485,7 @@ Next: <a href="#R-interface-packages" accesskey="n" rel="next">R interface packa
<a href="http://www.ibm.com/db2">IBM&rsquo;s DB2</a>; <a href="http://www.ibm.com/db2">IBM&rsquo;s DB2</a>;
<a href="https://www.microsoft.com/SQL/default.mspx">Microsoft <acronym>SQL</acronym> <a href="https://www.microsoft.com/SQL/default.mspx">Microsoft <acronym>SQL</acronym>
Server</a> on Windows) and academic and small-system databases (such as Server</a> on Windows) and academic and small-system databases (such as
MySQL<a name="DOCF5" href="#FOOT5"><sup>5</sup></a>, PostgreSQL, Microsoft MySQL<a name="DOCF4" href="#FOOT4"><sup>4</sup></a>, PostgreSQL, Microsoft
Access, &hellip;), the former marked out by much greater emphasis on data Access, &hellip;), the former marked out by much greater emphasis on data
security features. The line is blurring, with MySQL and PostgreSQL security features. The line is blurring, with MySQL and PostgreSQL
having more and more high-end features, and free &lsquo;express&rsquo; versions having more and more high-end features, and free &lsquo;express&rsquo; versions
@ -3014,7 +3009,7 @@ Previous: <a href="#Function-and-variable-index" accesskey="p" rel="prev">Functi
<tr><td></td><th align="left">Index Entry</th><td>&nbsp;</td><th align="left"> Section</th></tr> <tr><td></td><th align="left">Index Entry</th><td>&nbsp;</td><th align="left"> Section</th></tr>
<tr><td colspan="4"> <hr></td></tr> <tr><td colspan="4"> <hr></td></tr>
<tr><th><a name="Concept-index_cp_letter-A">A</a></th><td></td><td></td></tr> <tr><th><a name="Concept-index_cp_letter-A">A</a></th><td></td><td></td></tr>
<tr><td></td><td valign="top"><a href="#index-AWK">AWK</a>:</td><td>&nbsp;</td><td valign="top"><a href="#Introduction">Introduction</a></td></tr> <tr><td></td><td valign="top"><a href="#index-awk">awk</a>:</td><td>&nbsp;</td><td valign="top"><a href="#Introduction">Introduction</a></td></tr>
<tr><td colspan="4"> <hr></td></tr> <tr><td colspan="4"> <hr></td></tr>
<tr><th><a name="Concept-index_cp_letter-B">B</a></th><td></td><td></td></tr> <tr><th><a name="Concept-index_cp_letter-B">B</a></th><td></td><td></td></tr>
<tr><td></td><td valign="top"><a href="#index-Binary-files">Binary files</a>:</td><td>&nbsp;</td><td valign="top"><a href="#Binary-files">Binary files</a></td></tr> <tr><td></td><td valign="top"><a href="#index-Binary-files">Binary files</a>:</td><td>&nbsp;</td><td valign="top"><a href="#Binary-files">Binary files</a></td></tr>
@ -3163,23 +3158,19 @@ Previous: <a href="#Function-and-variable-index" accesskey="p" rel="prev">Functi
<h4 class="footnotes-heading">Footnotes</h4> <h4 class="footnotes-heading">Footnotes</h4>
<h3><a name="FOOT1" href="#DOCF1">(1)</a></h3> <h3><a name="FOOT1" href="#DOCF1">(1)</a></h3>
<p>Currently not available from
that repository but as a source package for download from
<a href="http://www.omegahat.org/ROpenOffice/">http://www.omegahat.org/ROpenOffice/</a>.</p>
<h3><a name="FOOT2" href="#DOCF2">(2)</a></h3>
<p>the <p>the
distinction is subtle, distinction is subtle,
<a href="https://en.wikipedia.org/wiki/UTF-16/UCS-2">https://en.wikipedia.org/wiki/UTF-16/UCS-2</a>, and the use of <a href="https://en.wikipedia.org/wiki/UTF-16/UCS-2">https://en.wikipedia.org/wiki/UTF-16/UCS-2</a>, and the use of
surrogate pairs is very rare.</p> surrogate pairs is very rare.</p>
<h3><a name="FOOT3" href="#DOCF3">(3)</a></h3> <h3><a name="FOOT2" href="#DOCF2">(2)</a></h3>
<p>Even then, <p>Even then,
Windows applications may expect a Byte Order Mark which the Windows applications may expect a Byte Order Mark which the
implementation of <code>iconv</code> used by R may or may not add depending implementation of <code>iconv</code> used by R may or may not add depending
on the platform.</p> on the platform.</p>
<h3><a name="FOOT4" href="#DOCF4">(4)</a></h3> <h3><a name="FOOT3" href="#DOCF3">(3)</a></h3>
<p>This is normally <p>This is normally
fast as looking at the first entry rules out most of the possibilities.</p> fast as looking at the first entry rules out most of the possibilities.</p>
<h3><a name="FOOT5" href="#DOCF5">(5)</a></h3> <h3><a name="FOOT4" href="#DOCF4">(4)</a></h3>
<p>and forks, notably MariaDB.</p> <p>and forks, notably MariaDB.</p>
</div> </div>
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<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd"> <!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
<html> <html>
<!-- This manual is for R, version 3.2.3 (2015-12-10). <!-- This manual is for R, version 3.3.1 (2016-06-21).
Copyright (C) 1990 W. N. Venables Copyright (C) 1990 W. N. Venables
@ -10,7 +10,7 @@ Copyright (C) 1997 R. Gentleman & R. Ihaka
Copyright (C) 1997, 1998 M. Maechler Copyright (C) 1997, 1998 M. Maechler
Copyright (C) 1999-2015 R Core Team Copyright (C) 1999-2016 R Core Team
Permission is granted to make and distribute verbatim copies of this Permission is granted to make and distribute verbatim copies of this
manual provided the copyright notice and this permission notice are manual provided the copyright notice and this permission notice are
@ -25,7 +25,7 @@ Permission is granted to copy and distribute translations of this manual
into another language, under the above conditions for modified versions, into another language, under the above conditions for modified versions,
except that this permission notice may be stated in a translation except that this permission notice may be stated in a translation
approved by the R Core Team. --> approved by the R Core Team. -->
<!-- Created by GNU Texinfo 6.0, http://www.gnu.org/software/texinfo/ --> <!-- Created by GNU Texinfo 6.1, http://www.gnu.org/software/texinfo/ -->
<head> <head>
<title>An Introduction to R</title> <title>An Introduction to R</title>
@ -59,9 +59,8 @@ pre.smalldisplay {font-family: inherit; font-size: smaller}
pre.smallexample {font-size: smaller} pre.smallexample {font-size: smaller}
pre.smallformat {font-family: inherit; font-size: smaller} pre.smallformat {font-family: inherit; font-size: smaller}
pre.smalllisp {font-size: smaller} pre.smalllisp {font-size: smaller}
span.nocodebreak {white-space: nowrap}
span.nolinebreak {white-space: nowrap} span.nolinebreak {white-space: nowrap}
span.roman {font-family: serif; font-weight: normal} span.roman {font-family: initial; font-weight: normal}
span.sansserif {font-family: sans-serif; font-weight: normal} span.sansserif {font-family: sans-serif; font-weight: normal}
ul.no-bullet {list-style: none} ul.no-bullet {list-style: none}
body { body {
@ -404,13 +403,13 @@ analysis, classification, clustering, ...).
<p>This manual provides information on data types, programming elements, <p>This manual provides information on data types, programming elements,
statistical modelling and graphics. statistical modelling and graphics.
</p> </p>
<p>This manual is for R, version 3.2.3 (2015-12-10). <p>This manual is for R, version 3.3.1 (2016-06-21).
</p> </p>
<p>Copyright &copy; 1990 W. N. Venables<br> <p>Copyright &copy; 1990 W. N. Venables<br>
Copyright &copy; 1992 W. N. Venables &amp; D. M. Smith<br> Copyright &copy; 1992 W. N. Venables &amp; D. M. Smith<br>
Copyright &copy; 1997 R. Gentleman &amp; R. Ihaka<br> Copyright &copy; 1997 R. Gentleman &amp; R. Ihaka<br>
Copyright &copy; 1997, 1998 M. Maechler<br> Copyright &copy; 1997, 1998 M. Maechler<br>
Copyright &copy; 1999&ndash;2015 R Core Team Copyright &copy; 1999&ndash;2016 R Core Team
</p> </p>
<blockquote> <blockquote>
<p>Permission is granted to make and distribute verbatim copies of this <p>Permission is granted to make and distribute verbatim copies of this
@ -7425,8 +7424,8 @@ are designed to complement textbooks. Some (the <em>recommended</em>
packages) are distributed with every binary distribution of R. Most packages) are distributed with every binary distribution of R. Most
are available for download from <acronym>CRAN</acronym> are available for download from <acronym>CRAN</acronym>
(<a href="https://CRAN.R-project.org/">https://CRAN.R-project.org/</a> and its mirrors) and other (<a href="https://CRAN.R-project.org/">https://CRAN.R-project.org/</a> and its mirrors) and other
repositories such as Bioconductor (<a href="https://www.bioconductor.org/">https://www.bioconductor.org/</a>) repositories such as Bioconductor (<a href="https://www.bioconductor.org/">https://www.bioconductor.org/</a>).
and Omegahat (<a href="http://www.omegahat.org/">http://www.omegahat.org/</a>). The <em>R FAQ</em> and Omegahat (<a href="http://www.omegahat.net/">http://www.omegahat.net/</a>). The <em>R FAQ</em>
contains a list of CRAN packages current at the time of release, but the contains a list of CRAN packages current at the time of release, but the
collection of available packages changes very frequently. collection of available packages changes very frequently.
</p> </p>
@ -8604,15 +8603,15 @@ used by the inbuilt command line editor: this used to happen on OS X.
file <samp>README.Rterm</samp> for command-line editing under file <samp>README.Rterm</samp> for command-line editing under
<code>Rterm.exe</code>. <code>Rterm.exe</code>.
</p> </p>
<p>When using R with <strong>readline</strong> capabilities, the functions <p>When using R with GNU<a name="DOCF28" href="#FOOT28"><sup>28</sup></a> <strong>readline</strong> capabilities, the functions described
described below are available, as well as others (probably) documented below are available, as well as others (probably) documented in
in <code>man readline</code> or <code>info readline</code> on your system. <code>man readline</code> or <code>info readline</code> on your system.
</p> </p>
<p>Many of these use either Control or Meta characters. Control <p>Many of these use either Control or Meta characters. Control
characters, such as <kbd>Control-m</kbd>, are obtained by holding the characters, such as <kbd>Control-m</kbd>, are obtained by holding the
<tt class="key">CTRL</tt> down while you press the <tt class="key">m</tt> key, and are written as <tt class="key">CTRL</tt> down while you press the <tt class="key">m</tt> key, and are written as
<kbd>C-m</kbd> below. Meta characters, such as <kbd>Meta-b</kbd>, are typed by <kbd>C-m</kbd> below. Meta characters, such as <kbd>Meta-b</kbd>, are typed by
holding down <tt class="key">META</tt><a name="DOCF28" href="#FOOT28"><sup>28</sup></a> and pressing <tt class="key">b</tt>, and written as <kbd>M-b</kbd> holding down <tt class="key">META</tt><a name="DOCF29" href="#FOOT29"><sup>29</sup></a> and pressing <tt class="key">b</tt>, and written as <kbd>M-b</kbd>
in the following. If your terminal does not have a <tt class="key">META</tt> key in the following. If your terminal does not have a <tt class="key">META</tt> key
enabled, you can still type Meta characters using two-character enabled, you can still type Meta characters using two-character
sequences starting with <kbd>ESC</kbd>. Thus, to enter <kbd>M-b</kbd>, you could sequences starting with <kbd>ESC</kbd>. Thus, to enter <kbd>M-b</kbd>, you could
@ -8620,6 +8619,9 @@ type <tt class="key">ESC</tt><tt class="key">b</tt>. The <kbd>ESC</kbd> charact
allowed on terminals with real Meta keys. Note that case is significant allowed on terminals with real Meta keys. Note that case is significant
for Meta characters. for Meta characters.
</p> </p>
<p>Some but not all versions<a name="DOCF30" href="#FOOT30"><sup>30</sup></a> of <strong>readline</strong>
will recognize resizing of the terminal window so this is best avoided.
</p>
<a name="Editing-actions"></a> <a name="Editing-actions"></a>
<h3 class="appendixsection">C.2 Editing actions</h3> <h3 class="appendixsection">C.2 Editing actions</h3>
@ -8654,7 +8656,8 @@ re-submitted.
<dd><p>Go to the next command (forwards in the history). <dd><p>Go to the next command (forwards in the history).
</p></dd> </p></dd>
<dt><kbd>C-r <var>text</var></kbd></dt> <dt><kbd>C-r <var>text</var></kbd></dt>
<dd><p>Find the last command with the <var>text</var> string in it. <dd><p>Find the last command with the <var>text</var> string in it. This can be
cancelled by <code>C-g</code> (and on some versions of R by <code>C-c</code>).
</p></dd> </p></dd>
</dl> </dl>
@ -9589,9 +9592,17 @@ on most 64-bit versions of Windows.</p>
&lsquo;Emacs Speaks Statistics&rsquo; package; see the <acronym>URL</acronym> &lsquo;Emacs Speaks Statistics&rsquo; package; see the <acronym>URL</acronym>
<a href="http://ESS.R-project.org">http://ESS.R-project.org</a></p> <a href="http://ESS.R-project.org">http://ESS.R-project.org</a></p>
<h3><a name="FOOT28" href="#DOCF28">(28)</a></h3> <h3><a name="FOOT28" href="#DOCF28">(28)</a></h3>
<p>It is possible to build R using an
emulation of GNU <strong>readline</strong>, such as one based on NetBSD&rsquo;s
<strong>editline</strong>, it which case only a subset of the capabilities may
be provided.</p>
<h3><a name="FOOT29" href="#DOCF29">(29)</a></h3>
<p>On a PC keyboard this is usually the <p>On a PC keyboard this is usually the
Alt key, occasionally the &lsquo;Windows&rsquo; key. On a Mac keyboard normally no Alt key, occasionally the &lsquo;Windows&rsquo; key. On a Mac keyboard normally no
meta key is available.</p> meta key is available.</p>
<h3><a name="FOOT30" href="#DOCF30">(30)</a></h3>
<p>In particular, not versions 6.3 or
later: this is worked around as from R 3.4.0.</p>
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<html> <html>
<!-- This manual is for R, version 3.2.3 (2015-12-10). <!-- This manual is for R, version 3.3.1 (2016-06-21).
Copyright (C) 1999-2015 R Core Team Copyright (C) 1999-2016 R Core Team
Permission is granted to make and distribute verbatim copies of this Permission is granted to make and distribute verbatim copies of this
manual provided the copyright notice and this permission notice are manual provided the copyright notice and this permission notice are
@ -17,7 +17,7 @@ Permission is granted to copy and distribute translations of this manual
into another language, under the above conditions for modified versions, into another language, under the above conditions for modified versions,
except that this permission notice may be stated in a translation except that this permission notice may be stated in a translation
approved by the R Core Team. --> approved by the R Core Team. -->
<!-- Created by GNU Texinfo 6.0, http://www.gnu.org/software/texinfo/ --> <!-- Created by GNU Texinfo 6.1, http://www.gnu.org/software/texinfo/ -->
<head> <head>
<title>R Internals</title> <title>R Internals</title>
@ -51,9 +51,8 @@ pre.smalldisplay {font-family: inherit; font-size: smaller}
pre.smallexample {font-size: smaller} pre.smallexample {font-size: smaller}
pre.smallformat {font-family: inherit; font-size: smaller} pre.smallformat {font-family: inherit; font-size: smaller}
pre.smalllisp {font-size: smaller} pre.smalllisp {font-size: smaller}
span.nocodebreak {white-space: nowrap}
span.nolinebreak {white-space: nowrap} span.nolinebreak {white-space: nowrap}
span.roman {font-family: serif; font-weight: normal} span.roman {font-family: initial; font-weight: normal}
span.sansserif {font-family: sans-serif; font-weight: normal} span.sansserif {font-family: sans-serif; font-weight: normal}
ul.no-bullet {list-style: none} ul.no-bullet {list-style: none}
body { body {
@ -288,9 +287,9 @@ Next: <a href="#R-Internal-Structures" accesskey="n" rel="next">R Internal Struc
<p>This is a guide to the internal structures of R and coding standards for <p>This is a guide to the internal structures of R and coding standards for
the core team working on R itself. the core team working on R itself.
</p> </p>
<p>This manual is for R, version 3.2.3 (2015-12-10). <p>This manual is for R, version 3.3.1 (2016-06-21).
</p> </p>
<p>Copyright &copy; 1999&ndash;2015 R Core Team <p>Copyright &copy; 1999&ndash;2016 R Core Team
</p> </p>
<blockquote> <blockquote>
<p>Permission is granted to make and distribute verbatim copies of this <p>Permission is granted to make and distribute verbatim copies of this
@ -877,7 +876,7 @@ enclosure.
<p>There are additional places that &lsquo;variables&rsquo; can be looked up, called <p>There are additional places that &lsquo;variables&rsquo; can be looked up, called
&lsquo;user databases&rsquo; in comments in the code. These seem undocumented in &lsquo;user databases&rsquo; in comments in the code. These seem undocumented in
the R sources, but apparently refer to the <strong>RObjectTable</strong> package the R sources, but apparently refer to the <strong>RObjectTable</strong> package
at <a href="http://www.omegahat.org/RObjectTables/">http://www.omegahat.org/RObjectTables/</a>. at <a href="http://www.omegahat.net/RObjectTables/">http://www.omegahat.net/RObjectTables/</a>.
</p> </p>
<a name="index-base-environment"></a> <a name="index-base-environment"></a>
<a name="index-environment_002c-base"></a> <a name="index-environment_002c-base"></a>
@ -961,7 +960,7 @@ Next: <a href="#Hash-table" accesskey="n" rel="next">Hash table</a>, Previous: <
<a name="index-namespace"></a> <a name="index-namespace"></a>
<p>Namespaces are environments associated with packages (and once again <p>Namespaces are environments associated with packages (and once again
the base package is special and will be considered separately). A the base package is special and will be considered separately). A
package <code><var>pkg</var></code> with a namespace defines two environments package <code><var>pkg</var></code> defines two environments
<code>namespace:<var>pkg</var></code> and <code>package:<var>pkg</var></code>: it is <code>namespace:<var>pkg</var></code> and <code>package:<var>pkg</var></code>: it is
<code>package:<var>pkg</var></code> that can be <code>attach</code>ed and form part of <code>package:<var>pkg</var></code> that can be <code>attach</code>ed and form part of
the search path. the search path.
@ -1867,21 +1866,21 @@ Next: <a href="#Mechanics-of-S4-dispatch" accesskey="n" rel="next">Mechanics of
<a name="S4-methods-1"></a> <a name="S4-methods-1"></a>
<h4 class="subsection">1.12.3 S4 methods</h4> <h4 class="subsection">1.12.3 S4 methods</h4>
<p>Details of methods are stored in S4 objects of class <p>Details of the methods are stored in environments (typically hidden in the
<code>&quot;MethodsList&quot;</code>. They have a non-syntactic name of the form respective namespace) with a non-syntactic name of the form
<code>.__M__<var>generic</var>:<var>package</var></code> for all methods defined in the <code>.__T__<var>generic</var>:<var>package</var></code> containing objects of class
current environment for the named generic derived from a specific <code>MethodDefinition</code> for all methods defined in the current environment
package (which might be <code>.GlobalEnv</code>). for the named generic derived from a specific package (which might be <code>.GlobalEnv</code>).
</p> This is sometimes referred to as a &lsquo;methods table&rsquo;.
<p>There is also environment <code>.__T__<var>generic</var>:<var>package</var></code> which
has names the signatures of the methods defined, and values the
corresponding method functions. This is often referred to as a &lsquo;methods
table&rsquo;.
</p>
<p>When a package without a namespace is attached these objects become
visible on the search path. <code>library</code> calls
<code>methods:::cacheMetaData</code> to update the internal tables.
</p> </p>
<p>For example,
</p><div class="example">
<pre class="example"> length(nM &lt;- asNamespace(&quot;Matrix&quot;) ) # 941 for Matrix 1.2-6
length(meth &lt;- grep(&quot;^[.]__T__&quot;, names(nM), value=TRUE))# 107 generics with methods
length(meth.Ops &lt;- nM$`.__T__Ops:base‘) # 71 methods for the ’Ops' (group)generic
head(sort(names(meth.Ops))) ## &quot;abIndex#abIndex&quot; ... &quot;ANY#ddiMatrix&quot; &quot;ANY#ldiMatrix&quot; &quot;ANY#Matrix&quot;
</pre></div>
<p>During an R session there is an environment associated with each <p>During an R session there is an environment associated with each
non-primitive generic containing objects <code>.AllMTable</code>, non-primitive generic containing objects <code>.AllMTable</code>,
<code>.Generic</code>, <code>.Methods</code>, <code>.MTable</code>, <code>.SigArgs</code> and <code>.Generic</code>, <code>.Methods</code>, <code>.MTable</code>, <code>.SigArgs</code> and
@ -1895,8 +1894,8 @@ directive <code>exportMethods</code> will export all the methods defined in
the namespace for a specified generic: the code also adds to the list the namespace for a specified generic: the code also adds to the list
of generics any that are exported directly. For generics which are of generics any that are exported directly. For generics which are
listed via <code>exportMethods</code> or exported themselves, the listed via <code>exportMethods</code> or exported themselves, the
corresponding <code>&quot;MethodsList&quot;</code> and environment are exported and so corresponding environment is exported and so
will appear (as hidden objects) in the package environment. will appear (as hidden object) in the package environment.
</p> </p>
<p>Methods for primitives which are internally S4 generic (see below) are <p>Methods for primitives which are internally S4 generic (see below) are
always exported, whether mentioned in the <samp>NAMESPACE</samp> file or not. always exported, whether mentioned in the <samp>NAMESPACE</samp> file or not.
@ -1910,7 +1909,7 @@ methods defined on generics in other packages. Since methods for a
generic could be imported from several different packages, the methods generic could be imported from several different packages, the methods
tables are merged. tables are merged.
</p> </p>
<p>When a package with a namespace is attached <p>When a package is attached
<code>methods:::cacheMetaData</code> is called to update the internal tables: <code>methods:::cacheMetaData</code> is called to update the internal tables:
only the visible methods will be cached. only the visible methods will be cached.
</p> </p>
@ -1939,7 +1938,7 @@ space there will be two functions called <code>myfn</code> on the search
paths, and which will be called depends on which search path is in use. paths, and which will be called depends on which search path is in use.
This is starkest for functions in the base namespace, where the This is starkest for functions in the base namespace, where the
original will be found ahead of the newly created function from any original will be found ahead of the newly created function from any
other package with a namespace. other package.
</p> </p>
<p>Primitive functions are treated quite differently, for efficiency <p>Primitive functions are treated quite differently, for efficiency
reasons: this results in different semantics. <code>setGeneric</code> is reasons: this results in different semantics. <code>setGeneric</code> is
@ -2527,6 +2526,7 @@ following groups of functions:
<pre class="example">abs sign sqrt <pre class="example">abs sign sqrt
floor ceiling floor ceiling
</pre><pre class="example"> </pre><pre class="example">
</pre><pre class="example">exp expm1 </pre><pre class="example">exp expm1
log2 log10 log1p log2 log10 log1p
cos sin tan cos sin tan
@ -2535,10 +2535,13 @@ cosh sinh tanh
acosh asinh atanh acosh asinh atanh
cospi sinpi tanpi cospi sinpi tanpi
</pre><pre class="example"> </pre><pre class="example">
</pre><pre class="example">gamma lgamma digamma trigamma </pre><pre class="example">gamma lgamma digamma trigamma
</pre><pre class="example"> </pre><pre class="example">
</pre><pre class="example">cumsum cumprod cummax cummin </pre><pre class="example">cumsum cumprod cummax cummin
</pre><pre class="example"> </pre><pre class="example">
</pre><pre class="example">Im Re Arg Conj Mod </pre><pre class="example">Im Re Arg Conj Mod
</pre></div> </pre></div>
@ -4510,8 +4513,8 @@ Default: -1.
<a name="index-_005fR_005fCHECK_005fXREFS_005fREPOSITORIES_005f"></a> <a name="index-_005fR_005fCHECK_005fXREFS_005fREPOSITORIES_005f"></a>
</dt> </dt>
<dd><p>If set to a non-empty value, a space-separated list of repositories to <dd><p>If set to a non-empty value, a space-separated list of repositories to
use to determine known packages. Default: empty, when the CRAN, use to determine known packages. Default: empty, when the CRAN
Omegahat and Bioconductor repositories known to R is used. and Bioconductor repositories known to R is used.
</p></dd> </p></dd>
<dt><code>_R_CHECK_SRC_MINUS_W_IMPLICIT_</code> <dt><code>_R_CHECK_SRC_MINUS_W_IMPLICIT_</code>
<a name="index-_005fR_005fCHECK_005fSRC_005fMINUS_005fW_005fIMPLICIT_005f"></a> <a name="index-_005fR_005fCHECK_005fSRC_005fMINUS_005fW_005fIMPLICIT_005f"></a>
@ -4617,13 +4620,15 @@ Default: false (but true for CRAN submission checks).
<a name="index-_005fR_005fCHECK_005fALWAYS_005fLOG_005fVIGNETTE_005fOUTPUT_005f"></a> <a name="index-_005fR_005fCHECK_005fALWAYS_005fLOG_005fVIGNETTE_005fOUTPUT_005f"></a>
</dt> </dt>
<dd><p>By default the output from running the R code in the vignettes is <dd><p>By default the output from running the R code in the vignettes is
kept only if there is an error. kept only if there is an error. As from R 3.2.4 this also applies to
the <samp>build_vignettes.log</samp> log from the re-building of vignettes.
Default: false. Default: false.
</p></dd> </p></dd>
<dt><code>_R_CHECK_CLEAN_VIGN_TEST_</code> <dt><code>_R_CHECK_CLEAN_VIGN_TEST_</code>
<a name="index-_005fR_005fCHECK_005fCLEAN_005fVIGN_005fTEST_005f"></a> <a name="index-_005fR_005fCHECK_005fCLEAN_005fVIGN_005fTEST_005f"></a>
</dt> </dt>
<dd><p>Should the <samp>vign_test</samp> directory be removed if the test is successful? <dd><p>Should the <samp>vign_test</samp> directory be removed if the test is
successful?
Default: true. Default: true.
</p></dd> </p></dd>
<dt><code>_R_CHECK_REPLACING_IMPORTS_</code> <dt><code>_R_CHECK_REPLACING_IMPORTS_</code>
@ -4633,7 +4638,7 @@ Default: true.
from auto-generated <samp>NAMESPACE</samp> files in other packages, but most from auto-generated <samp>NAMESPACE</samp> files in other packages, but most
often from importing the whole of a namespace rather than using often from importing the whole of a namespace rather than using
<code>importFrom</code>. <code>importFrom</code>.
Default: false (but true for CRAN submission checks). Default: true.
</p></dd> </p></dd>
<dt><code>_R_CHECK_UNSAFE_CALLS_</code> <dt><code>_R_CHECK_UNSAFE_CALLS_</code>
<a name="index-_005fR_005fCHECK_005fUNSAFE_005fCALLS_005f"></a> <a name="index-_005fR_005fCHECK_005fUNSAFE_005fCALLS_005f"></a>
@ -4835,6 +4840,14 @@ suggests and enhances.
Default: true (and true for CRAN submission checks). Default: true (and true for CRAN submission checks).
</p> </p>
</dd> </dd>
<dt><code>_R_CHECK_CODE_USAGE_WITH_ONLY_BASE_ATTACHED_</code>
<a name="index-_005fR_005fCHECK_005fCODE_005fUSAGE_005fWITH_005fONLY_005fBASE_005fATTACHED_005f"></a>
</dt>
<dd><p>If set, check code usage (via <a href="https://CRAN.R-project.org/package=codetools"><strong>codetools</strong></a>) with only the base
package attached.
Default: true.
</p>
</dd>
<dt><code>_R_CHECK_EXIT_ON_FIRST_ERROR_</code> <dt><code>_R_CHECK_EXIT_ON_FIRST_ERROR_</code>
<a name="index-_005fR_005fCHECK_005fEXIT_005fON_005fFIRST_005fERROR_005f"></a> <a name="index-_005fR_005fCHECK_005fEXIT_005fON_005fFIRST_005fERROR_005f"></a>
</dt> </dt>
@ -5346,6 +5359,7 @@ Next: <a href="#Concept-index" accesskey="n" rel="next">Concept index</a>, Previ
<tr><td></td><td valign="top"><a href="#index-_005fR_005fCHECK_005fCODE_005fATTACH_005f"><code>_R_CHECK_CODE_ATTACH_</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Tools">Tools</a></td></tr> <tr><td></td><td valign="top"><a href="#index-_005fR_005fCHECK_005fCODE_005fATTACH_005f"><code>_R_CHECK_CODE_ATTACH_</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Tools">Tools</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-_005fR_005fCHECK_005fCODE_005fDATA_005fINTO_005fGLOBALENV_005f"><code>_R_CHECK_CODE_DATA_INTO_GLOBALENV_</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Tools">Tools</a></td></tr> <tr><td></td><td valign="top"><a href="#index-_005fR_005fCHECK_005fCODE_005fDATA_005fINTO_005fGLOBALENV_005f"><code>_R_CHECK_CODE_DATA_INTO_GLOBALENV_</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Tools">Tools</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-_005fR_005fCHECK_005fCODE_005fUSAGE_005fVIA_005fNAMESPACES_005f"><code>_R_CHECK_CODE_USAGE_VIA_NAMESPACES_</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Tools">Tools</a></td></tr> <tr><td></td><td valign="top"><a href="#index-_005fR_005fCHECK_005fCODE_005fUSAGE_005fVIA_005fNAMESPACES_005f"><code>_R_CHECK_CODE_USAGE_VIA_NAMESPACES_</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Tools">Tools</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-_005fR_005fCHECK_005fCODE_005fUSAGE_005fWITH_005fONLY_005fBASE_005fATTACHED_005f"><code>_R_CHECK_CODE_USAGE_WITH_ONLY_BASE_ATTACHED_</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Tools">Tools</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-_005fR_005fCHECK_005fCODOC_005fS4_005fMETHODS_005f"><code>_R_CHECK_CODOC_S4_METHODS_</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Tools">Tools</a></td></tr> <tr><td></td><td valign="top"><a href="#index-_005fR_005fCHECK_005fCODOC_005fS4_005fMETHODS_005f"><code>_R_CHECK_CODOC_S4_METHODS_</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Tools">Tools</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-_005fR_005fCHECK_005fCOMPACT_005fDATA_005f"><code>_R_CHECK_COMPACT_DATA_</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Tools">Tools</a></td></tr> <tr><td></td><td valign="top"><a href="#index-_005fR_005fCHECK_005fCOMPACT_005fDATA_005f"><code>_R_CHECK_COMPACT_DATA_</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Tools">Tools</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-_005fR_005fCHECK_005fCRAN_005fINCOMING_005f"><code>_R_CHECK_CRAN_INCOMING_</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Tools">Tools</a></td></tr> <tr><td></td><td valign="top"><a href="#index-_005fR_005fCHECK_005fCRAN_005fINCOMING_005f"><code>_R_CHECK_CRAN_INCOMING_</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Tools">Tools</a></td></tr>

19
R-lang.html
View File

@ -1,8 +1,8 @@
<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd"> <!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
<html> <html>
<!-- This manual is for R, version 3.2.3 (2015-12-10). <!-- This manual is for R, version 3.3.1 (2016-06-21).
Copyright (C) 2000-2015 R Core Team Copyright (C) 2000-2016 R Core Team
Permission is granted to make and distribute verbatim copies of this Permission is granted to make and distribute verbatim copies of this
manual provided the copyright notice and this permission notice are manual provided the copyright notice and this permission notice are
@ -17,7 +17,7 @@ Permission is granted to copy and distribute translations of this manual
into another language, under the above conditions for modified versions, into another language, under the above conditions for modified versions,
except that this permission notice may be stated in a translation except that this permission notice may be stated in a translation
approved by the R Core Team. --> approved by the R Core Team. -->
<!-- Created by GNU Texinfo 6.0, http://www.gnu.org/software/texinfo/ --> <!-- Created by GNU Texinfo 6.1, http://www.gnu.org/software/texinfo/ -->
<head> <head>
<title>R Language Definition</title> <title>R Language Definition</title>
@ -51,9 +51,8 @@ pre.smalldisplay {font-family: inherit; font-size: smaller}
pre.smallexample {font-size: smaller} pre.smallexample {font-size: smaller}
pre.smallformat {font-family: inherit; font-size: smaller} pre.smallformat {font-family: inherit; font-size: smaller}
pre.smalllisp {font-size: smaller} pre.smalllisp {font-size: smaller}
span.nocodebreak {white-space: nowrap}
span.nolinebreak {white-space: nowrap} span.nolinebreak {white-space: nowrap}
span.roman {font-family: serif; font-weight: normal} span.roman {font-family: initial; font-weight: normal}
span.sansserif {font-family: sans-serif; font-weight: normal} span.sansserif {font-family: sans-serif; font-weight: normal}
ul.no-bullet {list-style: none} ul.no-bullet {list-style: none}
body { body {
@ -342,9 +341,9 @@ Next: <a href="#Introduction" accesskey="n" rel="next">Introduction</a> &nbsp; [
parsing, object oriented programming, computing on the language, and so parsing, object oriented programming, computing on the language, and so
forth. forth.
</p> </p>
<p>This manual is for R, version 3.2.3 (2015-12-10). <p>This manual is for R, version 3.3.1 (2016-06-21).
</p> </p>
<p>Copyright &copy; 2000&ndash;2015 R Core Team <p>Copyright &copy; 2000&ndash;2016 R Core Team
</p> </p>
<blockquote> <blockquote>
<p>Permission is granted to make and distribute verbatim copies of this <p>Permission is granted to make and distribute verbatim copies of this
@ -1780,10 +1779,8 @@ Next: <a href="#repeat" accesskey="n" rel="next">repeat</a>, Previous: <a href="
<p>R has three statements that provide explicit <p>R has three statements that provide explicit
looping.<a name="DOCF3" href="#FOOT3"><sup>3</sup></a> They are <code>for</code>, <code>while</code> and looping.<a name="DOCF3" href="#FOOT3"><sup>3</sup></a> They are <code>for</code>, <code>while</code> and
<code>repeat</code>. The two built-in constructs, <code>next</code> and <code>repeat</code>. The two built-in constructs, <code>next</code> and
<code>break</code>, provide additional control over the evaluation. Each of <code>break</code>, provide additional control over the evaluation.
the three statements returns the value of the last statement that was R provides other functions for
evaluated. It is possible, although uncommon, to assign the result of
one of these statements to a symbol. R provides other functions for
implicit looping such as <code>tapply</code>, <code>apply</code>, and <code>lapply</code>. implicit looping such as <code>tapply</code>, <code>apply</code>, and <code>lapply</code>.
In addition many operations, especially arithmetic ones, are vectorized In addition many operations, especially arithmetic ones, are vectorized
so you may not need to use a loop. so you may not need to use a loop.

12
R.spec
View File

@ -81,8 +81,8 @@
%global macrosdir %(d=%{_rpmconfigdir}/macros.d; [ -d $d ] || d=%{_sysconfdir}/rpm; echo $d) %global macrosdir %(d=%{_rpmconfigdir}/macros.d; [ -d $d ] || d=%{_sysconfdir}/rpm; echo $d)
Name: R Name: R
Version: 3.3.0 Version: 3.3.1
Release: 10%{?dist} Release: 1%{?dist}
Summary: A language for data analysis and graphics Summary: A language for data analysis and graphics
URL: http://www.r-project.org URL: http://www.r-project.org
Source0: ftp://cran.r-project.org/pub/R/src/base/R-3/R-%{version}.tar.gz Source0: ftp://cran.r-project.org/pub/R/src/base/R-3/R-%{version}.tar.gz
@ -256,7 +256,7 @@ Provides: R-Matrix = 1.2.6
Obsoletes: R-Matrix < 0.999375-7 Obsoletes: R-Matrix < 0.999375-7
Provides: R-methods = %{version} Provides: R-methods = %{version}
Provides: R-mgcv = 1.8.12 Provides: R-mgcv = 1.8.12
Provides: R-nlme = 3.1.127 Provides: R-nlme = 3.1.128
Provides: R-nnet = 7.3.12 Provides: R-nnet = 7.3.12
Provides: R-parallel = %{version} Provides: R-parallel = %{version}
Provides: R-rpart = 4.1.10 Provides: R-rpart = 4.1.10
@ -264,7 +264,7 @@ Provides: R-spatial = 7.3.11
Provides: R-splines = %{version} Provides: R-splines = %{version}
Provides: R-stats = %{version} Provides: R-stats = %{version}
Provides: R-stats4 = %{version} Provides: R-stats4 = %{version}
Provides: R-survival = 2.39.2 Provides: R-survival = 2.39.4
Provides: R-tcltk = %{version} Provides: R-tcltk = %{version}
Provides: R-tools = %{version} Provides: R-tools = %{version}
Provides: R-utils = %{version} Provides: R-utils = %{version}
@ -1006,6 +1006,7 @@ R CMD javareconf \
%{_libdir}/R/library/nlme/html/ %{_libdir}/R/library/nlme/html/
%{_libdir}/R/library/nlme/INDEX %{_libdir}/R/library/nlme/INDEX
%{_libdir}/R/library/nlme/libs/ %{_libdir}/R/library/nlme/libs/
%{_libdir}/R/library/nlme/LICENCE
%{_libdir}/R/library/nlme/Meta/ %{_libdir}/R/library/nlme/Meta/
%{_libdir}/R/library/nlme/mlbook/ %{_libdir}/R/library/nlme/mlbook/
%{_libdir}/R/library/nlme/NAMESPACE %{_libdir}/R/library/nlme/NAMESPACE
@ -1136,6 +1137,9 @@ R CMD javareconf \
%{_libdir}/libRmath.a %{_libdir}/libRmath.a
%changelog %changelog
* Tue Jul 5 2016 Tom Callaway <spot@fedoraproject.org> - 3.3.1-1
- update to 3.3.1
* Sat Jun 11 2016 Tom Callaway <spot@fedoraproject.org> - 3.3.0-10 * Sat Jun 11 2016 Tom Callaway <spot@fedoraproject.org> - 3.3.0-10
- fix CAPABILITIES pathing - fix CAPABILITIES pathing

2
sources
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@ -1 +1 @@
5a7506c8813432d1621c9725e86baf7a R-3.3.0.tar.gz f50a659738b73036e2f5635adbd229c5 R-3.3.1.tar.gz