<li><aname="toc-R-Basics-1"href="#R-Basics">2 R Basics</a>
<ulclass="no-bullet">
<li><aname="toc-What-is-R_003f-1"href="#What-is-R_003f">2.1 What is R?</a></li>
<li><aname="toc-What-machines-does-R-run-on_003f-1"href="#What-machines-does-R-run-on_003f">2.2 What machines does R run on?</a></li>
<li><aname="toc-What-is-the-current-version-of-R_003f-1"href="#What-is-the-current-version-of-R_003f">2.3 What is the current version of R?</a></li>
<li><aname="toc-How-can-R-be-obtained_003f-1"href="#How-can-R-be-obtained_003f">2.4 How can R be obtained?</a></li>
<li><aname="toc-How-can-R-be-installed_003f-1"href="#How-can-R-be-installed_003f">2.5 How can R be installed?</a>
<ulclass="no-bullet">
<li><aname="toc-How-can-R-be-installed-_0028Unix_002dlike_0029-1"href="#How-can-R-be-installed-_0028Unix_002dlike_0029">2.5.1 How can R be installed (Unix-like)</a></li>
<li><aname="toc-How-can-R-be-installed-_0028Windows_0029-1"href="#How-can-R-be-installed-_0028Windows_0029">2.5.2 How can R be installed (Windows)</a></li>
<li><aname="toc-How-can-R-be-installed-_0028Mac_0029-1"href="#How-can-R-be-installed-_0028Mac_0029">2.5.3 How can R be installed (Mac)</a></li>
</ul></li>
<li><aname="toc-Are-there-Unix_002dlike-binaries-for-R_003f-1"href="#Are-there-Unix_002dlike-binaries-for-R_003f">2.6 Are there Unix-like binaries for R?</a></li>
<li><aname="toc-What-documentation-exists-for-R_003f-1"href="#What-documentation-exists-for-R_003f">2.7 What documentation exists for R?</a></li>
<li><aname="toc-What-mailing-lists-exist-for-R_003f-1"href="#What-mailing-lists-exist-for-R_003f">2.9 What mailing lists exist for R?</a></li>
<li><aname="toc-What-is-CRAN_003f-1"href="#What-is-CRAN_003f">2.10 What is <acronym>CRAN</acronym>?</a></li>
<li><aname="toc-Can-I-use-R-for-commercial-purposes_003f-1"href="#Can-I-use-R-for-commercial-purposes_003f">2.11 Can I use R for commercial purposes?</a></li>
<li><aname="toc-Why-is-R-named-R_003f-1"href="#Why-is-R-named-R_003f">2.12 Why is R named R?</a></li>
<li><aname="toc-What-is-the-R-Foundation_003f-1"href="#What-is-the-R-Foundation_003f">2.13 What is the R Foundation?</a></li>
<li><aname="toc-What-is-R_002dForge_003f-1"href="#What-is-R_002dForge_003f">2.14 What is R-Forge?</a></li>
</ul></li>
<li><aname="toc-R-and-S-1"href="#R-and-S">3 R and S</a>
<ulclass="no-bullet">
<li><aname="toc-What-is-S_003f-1"href="#What-is-S_003f">3.1 What is S?</a></li>
<li><aname="toc-What-is-S_002dPLUS_003f-1"href="#What-is-S_002dPLUS_003f">3.2 What is <small>S-PLUS</small>?</a></li>
<li><aname="toc-What-are-the-differences-between-R-and-S_003f-1"href="#What-are-the-differences-between-R-and-S_003f">3.3 What are the differences between R and S?</a>
<li><aname="toc-Is-there-anything-R-can-do-that-S_002dPLUS-cannot_003f-1"href="#Is-there-anything-R-can-do-that-S_002dPLUS-cannot_003f">3.4 Is there anything R can do that <small>S-PLUS</small> cannot?</a></li>
<li><aname="toc-What-is-R_002dplus_003f-1"href="#What-is-R_002dplus_003f">3.5 What is R-plus?</a></li>
</ul></li>
<li><aname="toc-R-Web-Interfaces-1"href="#R-Web-Interfaces">4 R Web Interfaces</a></li>
<li><aname="toc-R-Add_002dOn-Packages-1"href="#R-Add_002dOn-Packages">5 R Add-On Packages</a>
<ulclass="no-bullet">
<li><aname="toc-Which-add_002don-packages-exist-for-R_003f-1"href="#Which-add_002don-packages-exist-for-R_003f">5.1 Which add-on packages exist for R?</a>
<ulclass="no-bullet">
<li><aname="toc-Add_002don-packages-in-R-1"href="#Add_002don-packages-in-R">5.1.1 Add-on packages in R</a></li>
<li><aname="toc-Add_002don-packages-from-CRAN-1"href="#Add_002don-packages-from-CRAN">5.1.2 Add-on packages from <acronym>CRAN</acronym></a></li>
<li><aname="toc-Add_002don-packages-from-Omegahat-1"href="#Add_002don-packages-from-Omegahat">5.1.3 Add-on packages from Omegahat</a></li>
<li><aname="toc-Add_002don-packages-from-Bioconductor-1"href="#Add_002don-packages-from-Bioconductor">5.1.4 Add-on packages from Bioconductor</a></li>
<li><aname="toc-Other-add_002don-packages-1"href="#Other-add_002don-packages">5.1.5 Other add-on packages</a></li>
</ul></li>
<li><aname="toc-How-can-add_002don-packages-be-installed_003f-1"href="#How-can-add_002don-packages-be-installed_003f">5.2 How can add-on packages be installed?</a></li>
<li><aname="toc-How-can-add_002don-packages-be-used_003f-1"href="#How-can-add_002don-packages-be-used_003f">5.3 How can add-on packages be used?</a></li>
<li><aname="toc-How-can-add_002don-packages-be-removed_003f-1"href="#How-can-add_002don-packages-be-removed_003f">5.4 How can add-on packages be removed?</a></li>
<li><aname="toc-How-can-I-create-an-R-package_003f-1"href="#How-can-I-create-an-R-package_003f">5.5 How can I create an R package?</a></li>
<li><aname="toc-How-can-I-contribute-to-R_003f-1"href="#How-can-I-contribute-to-R_003f">5.6 How can I contribute to R?</a></li>
</ul></li>
<li><aname="toc-R-and-Emacs-1"href="#R-and-Emacs">6 R and Emacs</a>
<ulclass="no-bullet">
<li><aname="toc-Is-there-Emacs-support-for-R_003f-1"href="#Is-there-Emacs-support-for-R_003f">6.1 Is there Emacs support for R?</a></li>
<li><aname="toc-Should-I-run-R-from-within-Emacs_003f-1"href="#Should-I-run-R-from-within-Emacs_003f">6.2 Should I run R from within Emacs?</a></li>
<li><aname="toc-Debugging-R-from-within-Emacs-1"href="#Debugging-R-from-within-Emacs">6.3 Debugging R from within Emacs</a></li>
</ul></li>
<li><aname="toc-R-Miscellanea-1"href="#R-Miscellanea">7 R Miscellanea</a>
<ulclass="no-bullet">
<li><aname="toc-How-can-I-set-components-of-a-list-to-NULL_003f-1"href="#How-can-I-set-components-of-a-list-to-NULL_003f">7.1 How can I set components of a list to NULL?</a></li>
<li><aname="toc-How-can-I-save-my-workspace_003f-1"href="#How-can-I-save-my-workspace_003f">7.2 How can I save my workspace?</a></li>
<li><aname="toc-How-can-I-clean-up-my-workspace_003f-1"href="#How-can-I-clean-up-my-workspace_003f">7.3 How can I clean up my workspace?</a></li>
<li><aname="toc-How-can-I-get-eval_0028_0029-and-D_0028_0029-to-work_003f-1"href="#How-can-I-get-eval_0028_0029-and-D_0028_0029-to-work_003f">7.4 How can I get eval() and D() to work?</a></li>
<li><aname="toc-Why-do-my-matrices-lose-dimensions_003f-1"href="#Why-do-my-matrices-lose-dimensions_003f">7.5 Why do my matrices lose dimensions?</a></li>
<li><aname="toc-How-does-autoloading-work_003f-1"href="#How-does-autoloading-work_003f">7.6 How does autoloading work?</a></li>
<li><aname="toc-How-should-I-set-options_003f-1"href="#How-should-I-set-options_003f">7.7 How should I set options?</a></li>
<li><aname="toc-How-do-file-names-work-in-Windows_003f-1"href="#How-do-file-names-work-in-Windows_003f">7.8 How do file names work in Windows?</a></li>
<li><aname="toc-Why-does-plotting-give-a-color-allocation-error_003f-1"href="#Why-does-plotting-give-a-color-allocation-error_003f">7.9 Why does plotting give a color allocation error?</a></li>
<li><aname="toc-How-do-I-convert-factors-to-numeric_003f-1"href="#How-do-I-convert-factors-to-numeric_003f">7.10 How do I convert factors to numeric?</a></li>
<li><aname="toc-Are-Trellis-displays-implemented-in-R_003f-1"href="#Are-Trellis-displays-implemented-in-R_003f">7.11 Are Trellis displays implemented in R?</a></li>
<li><aname="toc-What-are-the-enclosing-and-parent-environments_003f-1"href="#What-are-the-enclosing-and-parent-environments_003f">7.12 What are the enclosing and parent environments?</a></li>
<li><aname="toc-How-can-I-substitute-into-a-plot-label_003f-1"href="#How-can-I-substitute-into-a-plot-label_003f">7.13 How can I substitute into a plot label?</a></li>
<li><aname="toc-What-are-valid-names_003f-1"href="#What-are-valid-names_003f">7.14 What are valid names?</a></li>
<li><aname="toc-Are-GAMs-implemented-in-R_003f-1"href="#Are-GAMs-implemented-in-R_003f">7.15 Are GAMs implemented in R?</a></li>
<li><aname="toc-Why-is-the-output-not-printed-when-I-source_0028_0029-a-file_003f-1"href="#Why-is-the-output-not-printed-when-I-source_0028_0029-a-file_003f">7.16 Why is the output not printed when I source() a file?</a></li>
<li><aname="toc-Why-does-outer_0028_0029-behave-strangely-with-my-function_003f-1"href="#Why-does-outer_0028_0029-behave-strangely-with-my-function_003f">7.17 Why does outer() behave strangely with my function?</a></li>
<li><aname="toc-Why-does-the-output-from-anova_0028_0029-depend-on-the-order-of-factors-in-the-model_003f-1"href="#Why-does-the-output-from-anova_0028_0029-depend-on-the-order-of-factors-in-the-model_003f">7.18 Why does the output from anova() depend on the order of factors in the model?</a></li>
<li><aname="toc-How-do-I-produce-PNG-graphics-in-batch-mode_003f-1"href="#How-do-I-produce-PNG-graphics-in-batch-mode_003f">7.19 How do I produce PNG graphics in batch mode?</a></li>
<li><aname="toc-How-can-I-get-command-line-editing-to-work_003f-1"href="#How-can-I-get-command-line-editing-to-work_003f">7.20 How can I get command line editing to work?</a></li>
<li><aname="toc-How-can-I-turn-a-string-into-a-variable_003f-1"href="#How-can-I-turn-a-string-into-a-variable_003f">7.21 How can I turn a string into a variable?</a></li>
<li><aname="toc-Why-do-lattice_002ftrellis-graphics-not-work_003f-1"href="#Why-do-lattice_002ftrellis-graphics-not-work_003f">7.22 Why do lattice/trellis graphics not work?</a></li>
<li><aname="toc-How-can-I-sort-the-rows-of-a-data-frame_003f-1"href="#How-can-I-sort-the-rows-of-a-data-frame_003f">7.23 How can I sort the rows of a data frame?</a></li>
<li><aname="toc-Why-does-the-help_002estart_0028_0029-search-engine-not-work_003f-1"href="#Why-does-the-help_002estart_0028_0029-search-engine-not-work_003f">7.24 Why does the help.start() search engine not work?</a></li>
<li><aname="toc-Why-did-my-_002eRprofile-stop-working-when-I-updated-R_003f-1"href="#Why-did-my-_002eRprofile-stop-working-when-I-updated-R_003f">7.25 Why did my .Rprofile stop working when I updated R?</a></li>
<li><aname="toc-Where-have-all-the-methods-gone_003f-1"href="#Where-have-all-the-methods-gone_003f">7.26 Where have all the methods gone?</a></li>
<li><aname="toc-How-can-I-create-rotated-axis-labels_003f-1"href="#How-can-I-create-rotated-axis-labels_003f">7.27 How can I create rotated axis labels?</a></li>
<li><aname="toc-Why-is-read_002etable_0028_0029-so-inefficient_003f-1"href="#Why-is-read_002etable_0028_0029-so-inefficient_003f">7.28 Why is read.table() so inefficient?</a></li>
<li><aname="toc-What-is-the-difference-between-package-and-library_003f-1"href="#What-is-the-difference-between-package-and-library_003f">7.29 What is the difference between package and library?</a></li>
<li><aname="toc-I-installed-a-package-but-the-functions-are-not-there-1"href="#I-installed-a-package-but-the-functions-are-not-there">7.30 I installed a package but the functions are not there</a></li>
<li><aname="toc-Why-doesn_0027t-R-think-these-numbers-are-equal_003f-1"href="#Why-doesn_0027t-R-think-these-numbers-are-equal_003f">7.31 Why doesn’t R think these numbers are equal?</a></li>
<li><aname="toc-How-can-I-capture-or-ignore-errors-in-a-long-simulation_003f-1"href="#How-can-I-capture-or-ignore-errors-in-a-long-simulation_003f">7.32 How can I capture or ignore errors in a long simulation?</a></li>
<li><aname="toc-Why-are-powers-of-negative-numbers-wrong_003f-1"href="#Why-are-powers-of-negative-numbers-wrong_003f">7.33 Why are powers of negative numbers wrong?</a></li>
<li><aname="toc-How-can-I-save-the-result-of-each-iteration-in-a-loop-into-a-separate-file_003f-1"href="#How-can-I-save-the-result-of-each-iteration-in-a-loop-into-a-separate-file_003f">7.34 How can I save the result of each iteration in a loop into a separate file?</a></li>
<li><aname="toc-Why-are-p_002dvalues-not-displayed-when-using-lmer_0028_0029_003f-1"href="#Why-are-p_002dvalues-not-displayed-when-using-lmer_0028_0029_003f">7.35 Why are <em>p</em>-values not displayed when using lmer()?</a></li>
<li><aname="toc-Why-are-there-unwanted-borders_002c-lines-or-grid_002dlike-artifacts-when-viewing-a-plot-saved-to-a-PS-or-PDF-file_003f"href="#Why-are-there-unwanted-borders">7.36 Why are there unwanted borders, lines or grid-like artifacts when viewing a plot saved to a PS or PDF file?</a></li>
<li><aname="toc-Why-does-backslash-behave-strangely-inside-strings_003f-1"href="#Why-does-backslash-behave-strangely-inside-strings_003f">7.37 Why does backslash behave strangely inside strings?</a></li>
<li><aname="toc-How-can-I-put-error-bars-or-confidence-bands-on-my-plot_003f-1"href="#How-can-I-put-error-bars-or-confidence-bands-on-my-plot_003f">7.38 How can I put error bars or confidence bands on my plot?</a></li>
<li><aname="toc-How-do-I-create-a-plot-with-two-y_002daxes_003f-1"href="#How-do-I-create-a-plot-with-two-y_002daxes_003f">7.39 How do I create a plot with two y-axes?</a></li>
<li><aname="toc-How-do-I-access-the-source-code-for-a-function_003f-1"href="#How-do-I-access-the-source-code-for-a-function_003f">7.40 How do I access the source code for a function?</a></li>
<li><aname="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><aname="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><aname="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><aname="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>
<li><aname="toc-R-Programming-1"href="#R-Programming">8 R Programming</a>
<ulclass="no-bullet">
<li><aname="toc-How-should-I-write-summary-methods_003f-1"href="#How-should-I-write-summary-methods_003f">8.1 How should I write summary methods?</a></li>
<li><aname="toc-How-can-I-debug-dynamically-loaded-code_003f-1"href="#How-can-I-debug-dynamically-loaded-code_003f">8.2 How can I debug dynamically loaded code?</a></li>
<li><aname="toc-How-can-I-inspect-R-objects-when-debugging_003f-1"href="#How-can-I-inspect-R-objects-when-debugging_003f">8.3 How can I inspect R objects when debugging?</a></li>
<li><aname="toc-How-can-I-change-compilation-flags_003f-1"href="#How-can-I-change-compilation-flags_003f">8.4 How can I change compilation flags?</a></li>
<li><aname="toc-How-can-I-debug-S4-methods_003f-1"href="#How-can-I-debug-S4-methods_003f">8.5 How can I debug S4 methods?</a></li>
</ul></li>
<li><aname="toc-R-Bugs-1"href="#R-Bugs">9 R Bugs</a>
<ulclass="no-bullet">
<li><aname="toc-What-is-a-bug_003f-1"href="#What-is-a-bug_003f">9.1 What is a bug?</a></li>
<li><aname="toc-How-to-report-a-bug-1"href="#How-to-report-a-bug">9.2 How to report a bug</a></li>
Next: <ahref="#Introduction"accesskey="n"rel="next">Introduction</a> [<ahref="#SEC_Contents"title="Table of contents"rel="contents">Contents</a>]</p>
<tr><tdalign="left"valign="top">•<ahref="#R-and-S"accesskey="3">R and S</a>:</td><td> </td><tdalign="left"valign="top">
</td></tr>
<tr><tdalign="left"valign="top">•<ahref="#R-Web-Interfaces"accesskey="4">R Web Interfaces</a>:</td><td> </td><tdalign="left"valign="top">
<tr><tdalign="left"valign="top">•<ahref="#Obtaining-this-document"accesskey="2">Obtaining this document</a>:</td><td> </td><tdalign="left"valign="top">
</td></tr>
<tr><tdalign="left"valign="top">•<ahref="#Citing-this-document"accesskey="3">Citing this document</a>:</td><td> </td><tdalign="left"valign="top">
<tr><tdalign="left"valign="top">•<ahref="#What-is-R_003f"accesskey="1">What is R?</a>:</td><td> </td><tdalign="left"valign="top">
</td></tr>
<tr><tdalign="left"valign="top">•<ahref="#What-machines-does-R-run-on_003f"accesskey="2">What machines does R run on?</a>:</td><td> </td><tdalign="left"valign="top">
</td></tr>
<tr><tdalign="left"valign="top">•<ahref="#What-is-the-current-version-of-R_003f"accesskey="3">What is the current version of R?</a>:</td><td> </td><tdalign="left"valign="top">
</td></tr>
<tr><tdalign="left"valign="top">•<ahref="#How-can-R-be-obtained_003f"accesskey="4">How can R be obtained?</a>:</td><td> </td><tdalign="left"valign="top">
</td></tr>
<tr><tdalign="left"valign="top">•<ahref="#How-can-R-be-installed_003f"accesskey="5">How can R be installed?</a>:</td><td> </td><tdalign="left"valign="top">
</td></tr>
<tr><tdalign="left"valign="top">•<ahref="#Are-there-Unix_002dlike-binaries-for-R_003f"accesskey="6">Are there Unix-like binaries for R?</a>:</td><td> </td><tdalign="left"valign="top">
</td></tr>
<tr><tdalign="left"valign="top">•<ahref="#What-documentation-exists-for-R_003f"accesskey="7">What documentation exists for R?</a>:</td><td> </td><tdalign="left"valign="top">
<tr><tdalign="left"valign="top">•<ahref="#What-mailing-lists-exist-for-R_003f"accesskey="9">What mailing lists exist for R?</a>:</td><td> </td><tdalign="left"valign="top">
</td></tr>
<tr><tdalign="left"valign="top">•<ahref="#What-is-CRAN_003f">What is CRAN?</a>:</td><td> </td><tdalign="left"valign="top">
</td></tr>
<tr><tdalign="left"valign="top">•<ahref="#Can-I-use-R-for-commercial-purposes_003f">Can I use R for commercial purposes?</a>:</td><td> </td><tdalign="left"valign="top">
</td></tr>
<tr><tdalign="left"valign="top">•<ahref="#Why-is-R-named-R_003f">Why is R named R?</a>:</td><td> </td><tdalign="left"valign="top">
</td></tr>
<tr><tdalign="left"valign="top">•<ahref="#What-is-the-R-Foundation_003f">What is the R Foundation?</a>:</td><td> </td><tdalign="left"valign="top">
</td></tr>
<tr><tdalign="left"valign="top">•<ahref="#What-is-R_002dForge_003f">What is R-Forge?</a>:</td><td> </td><tdalign="left"valign="top">
</td></tr>
</table>
<hr>
<aname="What-is-R_003f"></a>
<divclass="header">
<p>
Next: <ahref="#What-machines-does-R-run-on_003f"accesskey="n"rel="next">What machines does R run on?</a>, Previous: <ahref="#R-Basics"accesskey="p"rel="prev">R Basics</a>, Up: <ahref="#R-Basics"accesskey="u"rel="up">R Basics</a> [<ahref="#SEC_Contents"title="Table of contents"rel="contents">Contents</a>]</p>
</div>
<aname="What-is-R_003f-1"></a>
<h3class="section">2.1 What is R?</h3>
<p>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.
</p>
<p>The design of R has been heavily influenced by two existing languages:
Becker, Chambers & Wilks’ S (see <ahref="#What-is-S_003f">What is S?</a>) and Sussman’s
<ahref="https://www.gnu.org/copyleft/copyleft.html">copyleft</a>, and an
official part of the <ahref="https://www.gnu.org/"><acronym>GNU</acronym></a> project
(“<acronym>GNU</acronym> S”).
</p>
<hr>
<aname="What-machines-does-R-run-on_003f"></a>
<divclass="header">
<p>
Next: <ahref="#What-is-the-current-version-of-R_003f"accesskey="n"rel="next">What is the current version of R?</a>, Previous: <ahref="#What-is-R_003f"accesskey="p"rel="prev">What is R?</a>, Up: <ahref="#R-Basics"accesskey="u"rel="up">R Basics</a> [<ahref="#SEC_Contents"title="Table of contents"rel="contents">Contents</a>]</p>
</div>
<aname="What-machines-does-R-run-on_003f-1"></a>
<h3class="section">2.2 What machines does R run on?</h3>
<p>R is being developed for the Unix-like, Windows and Mac families of
operating systems. Support for Mac OS Classic ended with R 1.7.1.
</p>
<p>The current version of R will configure and build under a number of
common Unix-like (e.g., <ahref="https://en.wikipedia.org/wiki/Unix-like">https://en.wikipedia.org/wiki/Unix-like</a>)
platforms including <var>cpu</var>-linux-gnu for the i386, amd64, alpha,
arm/armel, hppa, ia64, m68k, mips/mipsel, powerpc, s390 and sparc
Next: <ahref="#How-can-R-be-obtained_003f"accesskey="n"rel="next">How can R be obtained?</a>, Previous: <ahref="#What-machines-does-R-run-on_003f"accesskey="p"rel="prev">What machines does R run on?</a>, Up: <ahref="#R-Basics"accesskey="u"rel="up">R Basics</a> [<ahref="#SEC_Contents"title="Table of contents"rel="contents">Contents</a>]</p>
Next: <ahref="#How-can-R-be-installed_003f"accesskey="n"rel="next">How can R be installed?</a>, Previous: <ahref="#What-is-the-current-version-of-R_003f"accesskey="p"rel="prev">What is the current version of R?</a>, Up: <ahref="#R-Basics"accesskey="u"rel="up">R Basics</a> [<ahref="#SEC_Contents"title="Table of contents"rel="contents">Contents</a>]</p>
</div>
<aname="How-can-R-be-obtained_003f-1"></a>
<h3class="section">2.4 How can R be obtained?</h3>
<p>Sources, binaries and documentation for R can be obtained via <acronym>CRAN</acronym>,
the “Comprehensive R Archive Network” (see <ahref="#What-is-CRAN_003f">What is CRAN?</a>).
</p>
<p>Sources are also available via <ahref="https://svn.R-project.org/R/">https://svn.R-project.org/R/</a>, the
R Subversion repository, but currently not via anonymous rsync (nor
CVS).
</p>
<p>Tarballs with daily snapshots of the r-devel and r-patched development
Next: <ahref="#Are-there-Unix_002dlike-binaries-for-R_003f"accesskey="n"rel="next">Are there Unix-like binaries for R?</a>, Previous: <ahref="#How-can-R-be-obtained_003f"accesskey="p"rel="prev">How can R be obtained?</a>, Up: <ahref="#R-Basics"accesskey="u"rel="up">R Basics</a> [<ahref="#SEC_Contents"title="Table of contents"rel="contents">Contents</a>]</p>
</div>
<aname="How-can-R-be-installed_003f-1"></a>
<h3class="section">2.5 How can R be installed?</h3>
<tr><tdalign="left"valign="top">•<ahref="#How-can-R-be-installed-_0028Unix_002dlike_0029"accesskey="1">How can R be installed (Unix-like)</a>:</td><td> </td><tdalign="left"valign="top">
</td></tr>
<tr><tdalign="left"valign="top">•<ahref="#How-can-R-be-installed-_0028Windows_0029"accesskey="2">How can R be installed (Windows)</a>:</td><td> </td><tdalign="left"valign="top">
</td></tr>
<tr><tdalign="left"valign="top">•<ahref="#How-can-R-be-installed-_0028Mac_0029"accesskey="3">How can R be installed (Mac)</a>:</td><td> </td><tdalign="left"valign="top">
Next: <ahref="#How-can-R-be-installed-_0028Windows_0029"accesskey="n"rel="next">How can R be installed (Windows)</a>, Previous: <ahref="#How-can-R-be-installed_003f"accesskey="p"rel="prev">How can R be installed?</a>, Up: <ahref="#How-can-R-be-installed_003f"accesskey="u"rel="up">How can R be installed?</a> [<ahref="#SEC_Contents"title="Table of contents"rel="contents">Contents</a>]</p>
<h4class="subsection">2.5.1 How can R be installed (Unix-like)</h4>
<p>If R is already installed, it can be started by typing <kbd>R</kbd> at the
shell prompt (of course, provided that the executable is in your path).
</p>
<p>If binaries are available for your platform (see <ahref="#Are-there-Unix_002dlike-binaries-for-R_003f">Are there Unix-like binaries for R?</a>), you can use these, following the
instructions that come with them.
</p>
<p>Otherwise, you can compile and install R yourself, which can be done
very easily under a number of common Unix-like platforms (see <ahref="#What-machines-does-R-run-on_003f">What machines does R run on?</a>). The file <samp>INSTALL</samp> that comes with the
R distribution contains a brief introduction, and the “R Installation
and Administration” guide (see <ahref="#What-documentation-exists-for-R_003f">What documentation exists for R?</a>)
has full details.
</p>
<p>Note that you need a FORTRAN compiler or perhaps <code>f2c</code> in
addition to a C compiler to build R.
</p>
<p>In the simplest case, untar the R source code, change to the directory
thus created, and issue the following commands (at the shell prompt):
</p>
<divclass="example">
<preclass="example">$ ./configure
$ make
</pre></div>
<p>If these commands execute successfully, the R binary and a shell script
front-end called <samp>R</samp> are created and copied to the <samp>bin</samp>
directory. You can copy the script to a place where users can invoke
it, for example to <samp>/usr/local/bin</samp>. In addition, plain text help
pages as well as <acronym>HTML</acronym> and LaTeX versions of the documentation are
built.
</p>
<p>Use <kbd>make dvi</kbd> to create DVI versions of the R manuals, such as
<samp>refman.dvi</samp> (an R object reference index) and <samp>R-exts.dvi</samp>,
the “R Extension Writers Guide”, in the <samp>doc/manual</samp>
subdirectory. These files can be previewed and printed using standard
programs such as <code>xdvi</code> and <code>dvips</code>. You can also use
<kbd>make pdf</kbd> to build PDF (Portable Document Format) version of the
manuals, and view these using e.g. Acrobat. Manuals written in the
<acronym>GNU</acronym> Texinfo system can also be converted to info files
suitable for reading online with Emacs or stand-alone <acronym>GNU</acronym>
Info; use <kbd>make info</kbd> to create these versions (note that this
requires Makeinfo version 4.5).
</p>
<p>Finally, use <kbd>make check</kbd> to find out whether your R system works
correctly.
</p>
<p>You can also perform a “system-wide” installation using <kbd>make
install</kbd>. By default, this will install to the following directories:
</p>
<dlcompact="compact">
<dt><samp>${prefix}/bin</samp></dt>
<dd><p>the front-end shell script
</p></dd>
<dt><samp>${prefix}/man/man1</samp></dt>
<dd><p>the man page
</p></dd>
<dt><samp>${prefix}/lib/R</samp></dt>
<dd><p>all the rest (libraries, on-line help system, …). This is the “R
Home Directory” (<code>R_HOME</code>) of the installed system.
</p></dd>
</dl>
<p>In the above, <code>prefix</code> is determined during configuration
(typically <samp>/usr/local</samp>) and can be set by running
Next: <ahref="#How-can-R-be-installed-_0028Mac_0029"accesskey="n"rel="next">How can R be installed (Mac)</a>, Previous: <ahref="#How-can-R-be-installed-_0028Unix_002dlike_0029"accesskey="p"rel="prev">How can R be installed (Unix-like)</a>, Up: <ahref="#How-can-R-be-installed_003f"accesskey="u"rel="up">How can R be installed?</a> [<ahref="#SEC_Contents"title="Table of contents"rel="contents">Contents</a>]</p>
Previous: <ahref="#How-can-R-be-installed-_0028Windows_0029"accesskey="p"rel="prev">How can R be installed (Windows)</a>, Up: <ahref="#How-can-R-be-installed_003f"accesskey="u"rel="up">How can R be installed?</a> [<ahref="#SEC_Contents"title="Table of contents"rel="contents">Contents</a>]</p>
Next: <ahref="#What-documentation-exists-for-R_003f"accesskey="n"rel="next">What documentation exists for R?</a>, Previous: <ahref="#How-can-R-be-installed_003f"accesskey="p"rel="prev">How can R be installed?</a>, Up: <ahref="#R-Basics"accesskey="u"rel="up">R Basics</a> [<ahref="#SEC_Contents"title="Table of contents"rel="contents">Contents</a>]</p>
<h3class="section">2.9 What mailing lists exist for R?</h3>
<p>Thanks to <ahref="mailto:Martin.Maechler@R-project.org">Martin Maechler</a>, there
are several mailing lists devoted to R, including the following:
</p>
<dlcompact="compact">
<dt><code>R-announce</code></dt>
<dd><p>A moderated list for major announcements about the development of R and
the availability of new code.
</p></dd>
<dt><code>R-packages</code></dt>
<dd><p>A moderated list for announcements on the availability of new or
enhanced contributed packages.
</p></dd>
<dt><code>R-help</code></dt>
<dd><p>The ‘main’ R mailing list, for discussion about problems and solutions
using R, announcements (not covered by ‘R-announce’ and ‘R-packages’)
about the development of R and the availability of new code.
</p></dd>
<dt><code>R-devel</code></dt>
<dd><p>This list is for questions and discussion about code development in R.
</p></dd>
<dt><code>R-package-devel</code></dt>
<dd><p>A list which which provides a forum for learning about the R package
development process.
</p></dd>
</dl>
<p>Please read the <ahref="https://www.R-project.org/posting-guide.html">posting guide</a><em>before</em> sending anything to any mailing list.
</p>
<p>Note in particular that R-help is intended to be comprehensible to
people who want to use R to solve problems but who are not necessarily
interested in or knowledgeable about programming. Questions likely to
prompt discussion unintelligible to non-programmers (e.g., questions
involving C or C++) should go to R-devel.
</p>
<p>Convenient access to information on these lists, subscription, and
archives is provided by the web interface at
<ahref="https://stat.ethz.ch/mailman/listinfo/">https://stat.ethz.ch/mailman/listinfo/</a>. One can also subscribe
(or unsubscribe) via email, e.g. to R-help by sending ‘<samp>subscribe</samp>’
(or ‘<samp>unsubscribe</samp>’) in the <em>body</em> of the message (not in the
subject!) to <ahref="mailto:R-help-request@lists.R-project.org">R-help-request@lists.R-project.org</a>.
</p>
<p>Send email to <ahref="mailto:R-help@lists.R-project.org">R-help@lists.R-project.org</a> to send a message to
everyone on the R-help mailing list. Subscription and posting to the
other lists is done analogously, with ‘<samp>R-help</samp>’ replaced by
‘<samp>R-announce</samp>’, ‘<samp>R-packages</samp>’, and ‘<samp>R-devel</samp>’, respectively.
Note that the R-announce and R-packages lists are gatewayed into R-help.
Hence, you should subscribe to either of them only in case you are not
subscribed to R-help.
</p>
<p>It is recommended that you send mail to R-help rather than only to the R
Core developers (who are also subscribed to the list, of course). This
may save them precious time they can use for constantly improving R, and
will typically also result in much quicker feedback for yourself.
</p>
<p>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
<ahref="#R-Bugs">R Bugs</a> for more details.
</p>
<p>See <ahref="https://www.R-project.org/mail.html">https://www.R-project.org/mail.html</a> for more information on
the R mailing lists.
</p>
<p>The R Core Team can be reached at <ahref="mailto:R-core@lists.R-project.org">R-core@lists.R-project.org</a>
for comments and reports.
</p>
<p>Many of the R project’s mailing lists are also available via
<ahref="http://gmane.org">Gmane</a>, from which they can be read with a web
browser, using an NNTP news reader, or via RSS feeds. See
<ahref="http://dir.gmane.org/index.php?prefix=gmane.comp.lang.r.">http://dir.gmane.org/index.php?prefix=gmane.comp.lang.r.</a> for
the available mailing lists, and <ahref="http://www.gmane.org/rss.php">http://www.gmane.org/rss.php</a> for
details on RSS feeds.
</p>
<hr>
<aname="What-is-CRAN_003f"></a>
<divclass="header">
<p>
Next: <ahref="#Can-I-use-R-for-commercial-purposes_003f"accesskey="n"rel="next">Can I use R for commercial purposes?</a>, Previous: <ahref="#What-mailing-lists-exist-for-R_003f"accesskey="p"rel="prev">What mailing lists exist for R?</a>, Up: <ahref="#R-Basics"accesskey="u"rel="up">R Basics</a> [<ahref="#SEC_Contents"title="Table of contents"rel="contents">Contents</a>]</p>
</div>
<aname="What-is-CRAN_003f-1"></a>
<h3class="section">2.10 What is <acronym>CRAN</acronym>?</h3>
<p>The “Comprehensive R Archive Network” (<acronym>CRAN</acronym>) is a collection of
sites which carry identical material, consisting of the R
distribution(s), the contributed extensions, documentation for R, and
binaries.
</p>
<p>The <acronym>CRAN</acronym> master site at WU (Wirtschaftsuniversität Wien) in Austria
Next: <ahref="#Why-is-R-named-R_003f"accesskey="n"rel="next">Why is R named R?</a>, Previous: <ahref="#What-is-CRAN_003f"accesskey="p"rel="prev">What is CRAN?</a>, Up: <ahref="#R-Basics"accesskey="u"rel="up">R Basics</a> [<ahref="#SEC_Contents"title="Table of contents"rel="contents">Contents</a>]</p>
<h3class="section">2.11 Can I use R for commercial purposes?</h3>
<p>R is released under the
<ahref="https://www.gnu.org/licenses/old-licenses/gpl-2.0.html"><acronym>GNU</acronym> General Public License (<acronym>GPL</acronym>), version 2</a>. If
you have any questions regarding the legality of using R in any
particular situation you should bring it up with your legal counsel. We
are in no position to offer legal advice.
</p>
<p>It is the opinion of the R Core Team that one can use R for commercial
purposes (e.g., in business or in consulting). The <acronym>GPL</acronym>, like
all Open Source licenses, permits all and any use of the package. It
only restricts distribution of R or of other programs containing code
from R. This is made clear in clause 6 (“No Discrimination Against
<p>The license must not restrict anyone from making use of the program in a
specific field of endeavor. For example, it may not restrict the
program from being used in a business, or from being used for genetic
research.
</p></blockquote>
<p>It is also explicitly stated in clause 0 of the GPL, which says in part
</p>
<blockquote>
<p>Activities other than copying, distribution and modification are not
covered by this License; they are outside its scope. The act of running
the Program is not restricted, and the output from the Program is
covered only if its contents constitute a work based on the Program.
</p></blockquote>
<p>Most add-on packages, including all recommended ones, also explicitly
allow commercial use in this way. A few packages are restricted to
“non-commercial use”; you should contact the author to clarify whether
these may be used or seek the advice of your legal counsel.
</p>
<p>None of the discussion in this section constitutes legal advice. The R
Core Team does not provide legal advice under any circumstances.
</p>
<hr>
<aname="Why-is-R-named-R_003f"></a>
<divclass="header">
<p>
Next: <ahref="#What-is-the-R-Foundation_003f"accesskey="n"rel="next">What is the R Foundation?</a>, Previous: <ahref="#Can-I-use-R-for-commercial-purposes_003f"accesskey="p"rel="prev">Can I use R for commercial purposes?</a>, Up: <ahref="#R-Basics"accesskey="u"rel="up">R Basics</a> [<ahref="#SEC_Contents"title="Table of contents"rel="contents">Contents</a>]</p>
</div>
<aname="Why-is-R-named-R_003f-1"></a>
<h3class="section">2.12 Why is R named R?</h3>
<p>The name is partly based on the (first) names of the first two R authors
(Robert Gentleman and Ross Ihaka), and partly a play on the name of the
Bell Labs language ‘S’ (see <ahref="#What-is-S_003f">What is S?</a>).
</p>
<hr>
<aname="What-is-the-R-Foundation_003f"></a>
<divclass="header">
<p>
Next: <ahref="#What-is-R_002dForge_003f"accesskey="n"rel="next">What is R-Forge?</a>, Previous: <ahref="#Why-is-R-named-R_003f"accesskey="p"rel="prev">Why is R named R?</a>, Up: <ahref="#R-Basics"accesskey="u"rel="up">R Basics</a> [<ahref="#SEC_Contents"title="Table of contents"rel="contents">Contents</a>]</p>
</div>
<aname="What-is-the-R-Foundation_003f-1"></a>
<h3class="section">2.13 What is the R Foundation?</h3>
<p>The R Foundation is a not for profit organization working in the public
interest. It was founded by the members of the R Core Team in order to
provide support for the R project and other innovations in statistical
computing, provide a reference point for individuals, institutions or
commercial enterprises that want to support or interact with the R
development community, and to hold and administer the copyright of R
software and documentation. See
<ahref="https://www.R-project.org/foundation/">https://www.R-project.org/foundation/</a> for more information.
</p>
<hr>
<aname="What-is-R_002dForge_003f"></a>
<divclass="header">
<p>
Previous: <ahref="#What-is-the-R-Foundation_003f"accesskey="p"rel="prev">What is the R Foundation?</a>, Up: <ahref="#R-Basics"accesskey="u"rel="up">R Basics</a> [<ahref="#SEC_Contents"title="Table of contents"rel="contents">Contents</a>]</p>
</div>
<aname="What-is-R_002dForge_003f-1"></a>
<h3class="section">2.14 What is R-Forge?</h3>
<p>R-Forge (<ahref="https://R-Forge.R-project.org/">https://R-Forge.R-project.org/</a>) offers a central platform
for the development of R packages, R-related software and further
projects. It is based on <ahref="https://en.wikipedia.org/wiki/GForge">GForge</a> offering
easy access to the best in SVN, daily built and checked packages,
mailing lists, bug tracking, message boards/forums, site hosting,
permanent file archival, full backups, and total web-based
administration. For more information, see the R-Forge web page and
Stefan Theußl and Achim Zeileis (2009), “Collaborative software
development using R-Forge”, <ahref="https://journal.R-project.org/"><em>The R Journal</em></a>, <strong>1</strong>(1):9–14.
</p>
<hr>
<aname="R-and-S"></a>
<divclass="header">
<p>
Next: <ahref="#R-Web-Interfaces"accesskey="n"rel="next">R Web Interfaces</a>, Previous: <ahref="#R-Basics"accesskey="p"rel="prev">R Basics</a>, Up: <ahref="#Top"accesskey="u"rel="up">Top</a> [<ahref="#SEC_Contents"title="Table of contents"rel="contents">Contents</a>]</p>
<tr><tdalign="left"valign="top">•<ahref="#What-is-S_003f"accesskey="1">What is S?</a>:</td><td> </td><tdalign="left"valign="top">
</td></tr>
<tr><tdalign="left"valign="top">•<ahref="#What-is-S_002dPLUS_003f"accesskey="2">What is S-PLUS?</a>:</td><td> </td><tdalign="left"valign="top">
</td></tr>
<tr><tdalign="left"valign="top">•<ahref="#What-are-the-differences-between-R-and-S_003f"accesskey="3">What are the differences between R and S?</a>:</td><td> </td><tdalign="left"valign="top">
</td></tr>
<tr><tdalign="left"valign="top">•<ahref="#Is-there-anything-R-can-do-that-S_002dPLUS-cannot_003f"accesskey="4">Is there anything R can do that S-PLUS cannot?</a>:</td><td> </td><tdalign="left"valign="top">
</td></tr>
<tr><tdalign="left"valign="top">•<ahref="#What-is-R_002dplus_003f"accesskey="5">What is R-plus?</a>:</td><td> </td><tdalign="left"valign="top">
</td></tr>
</table>
<hr>
<aname="What-is-S_003f"></a>
<divclass="header">
<p>
Next: <ahref="#What-is-S_002dPLUS_003f"accesskey="n"rel="next">What is S-PLUS?</a>, Previous: <ahref="#R-and-S"accesskey="p"rel="prev">R and S</a>, Up: <ahref="#R-and-S"accesskey="u"rel="up">R and S</a> [<ahref="#SEC_Contents"title="Table of contents"rel="contents">Contents</a>]</p>
</div>
<aname="What-is-S_003f-1"></a>
<h3class="section">3.1 What is S?</h3>
<p>S is a very high level language and an environment for data analysis and
graphics. In 1998, the Association for Computing Machinery
(<acronym>ACM</acronym>) presented its Software System Award to John M. Chambers,
the principal designer of S, for
</p>
<blockquote>
<p>the S system, which has forever altered the way people analyze,
visualize, and manipulate data …
</p>
<p>S is an elegant, widely accepted, and enduring software system, with
conceptual integrity, thanks to the insight, taste, and effort of John
Chambers.
</p></blockquote>
<p>The evolution of the S language is characterized by four books by John
Chambers and coauthors, which are also the primary references for S.
</p>
<ul>
<li> Richard A. Becker and John M. Chambers (1984), “S. An Interactive
Environment for Data Analysis and Graphics,” Monterey: Wadsworth and
Brooks/Cole.
<p>This is also referred to as the “<em>Brown Book</em>”, and of historical
interest only.
</p>
</li><li> Richard A. Becker, John M. Chambers and Allan R. Wilks (1988), “The New
S Language,” London: Chapman & Hall.
<p>This book is often called the “<em>Blue Book</em>”, and introduced what
is now known as S version 2.
</p>
</li><li> John M. Chambers and Trevor J. Hastie (1992), “Statistical Models in
S,” London: Chapman & Hall.
<p>This is also called the “<em>White Book</em>”, and introduced S version
3, which added structures to facilitate statistical modeling in S.
</p>
</li><li> John M. Chambers (1998), “Programming with Data,” New York: Springer,
Next: <ahref="#What-are-the-differences-between-R-and-S_003f"accesskey="n"rel="next">What are the differences between R and S?</a>, Previous: <ahref="#What-is-S_003f"accesskey="p"rel="prev">What is S?</a>, Up: <ahref="#R-and-S"accesskey="u"rel="up">R and S</a> [<ahref="#SEC_Contents"title="Table of contents"rel="contents">Contents</a>]</p>
</div>
<aname="What-is-S_002dPLUS_003f-1"></a>
<h3class="section">3.2 What is <small>S-PLUS</small>?</h3>
<p><small>S-PLUS</small> is a value-added version of S currently sold by
<ahref="http://www.tibco.com/">TIBCO Software Inc</a> as ‘TIBCO Spotfire S+’.
See <ahref="https://en.wikipedia.org/wiki/S-PLUS">https://en.wikipedia.org/wiki/S-PLUS</a> for more information.
Next: <ahref="#Is-there-anything-R-can-do-that-S_002dPLUS-cannot_003f"accesskey="n"rel="next">Is there anything R can do that S-PLUS cannot?</a>, Previous: <ahref="#What-is-S_002dPLUS_003f"accesskey="p"rel="prev">What is S-PLUS?</a>, Up: <ahref="#R-and-S"accesskey="u"rel="up">R and S</a> [<ahref="#SEC_Contents"title="Table of contents"rel="contents">Contents</a>]</p>
Next: <ahref="#Models"accesskey="n"rel="next">Models</a>, Previous: <ahref="#What-are-the-differences-between-R-and-S_003f"accesskey="p"rel="prev">What are the differences between R and S?</a>, Up: <ahref="#What-are-the-differences-between-R-and-S_003f"accesskey="u"rel="up">What are the differences between R and S?</a> [<ahref="#SEC_Contents"title="Table of contents"rel="contents">Contents</a>]</p>
</div>
<aname="Lexical-scoping-1"></a>
<h4class="subsection">3.3.1 Lexical scoping</h4>
<p>Contrary to other implementations of the S language, R has adopted an
evaluation model in which nested function definitions are lexically
scoped. This is analogous to the evaluation model in Scheme.
</p>
<p>This difference becomes manifest when <em>free</em> 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). In S, the
values of free variables are determined by a set of global variables
(similar to C, there is only local and global scope). In R, they are
determined by the environment in which the function was created.
</p>
<p>Consider the following function:
</p>
<divclass="example">
<preclass="example">cube <- function(n) {
sq <- function() n * n
n * sq()
}
</pre></div>
<p>Under S, <code>sq()</code> does not “know” about the variable <code>n</code>
unless it is defined globally:
</p>
<divclass="example">
<preclass="example">S> cube(2)
Error in sq(): Object "n" not found
Dumped
S> n <- 3
S> cube(2)
[1] 18
</pre></div>
<p>In R, the “environment” created when <code>cube()</code> was invoked is
also looked in:
</p>
<divclass="example">
<preclass="example">R> cube(2)
[1] 8
</pre></div>
<p>As a more “interesting” real-world problem, suppose you want to write
a function which returns the density function of the <em>r</em>-th order
statistic from a sample of size <em>n</em> 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.)
</p>
<p>The <small>S-PLUS</small> documentation for <code>call()</code> basically suggests the
<p>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.
</p>
<p>Nested lexically scoped functions allow using function closures and
maintaining local state. A simple example (taken from Abelson and
Sussman) is obtained by typing <kbd>demo("scoping")</kbd> at the R prompt.
Further information is provided in the standard R reference “R: A
Language for Data Analysis and Graphics” (see <ahref="#What-documentation-exists-for-R_003f">What documentation exists for R?</a>) and in Robert Gentleman and Ross Ihaka (2000), “Lexical
Scope and Statistical Computing”,
<ahref="http://www.amstat.org/publications/jcgs/"><em>Journal of
Computational and Graphical Statistics</em></a>, <strong>9</strong>, 491–508.
</p>
<p>Nested lexically scoped functions also imply a further major difference.
Whereas S stores all objects as separate files in a directory somewhere
(usually <samp>.Data</samp> under the current directory), R does not. All
objects in R are stored internally. When R is started up it grabs a
piece of memory and uses it to store the objects. R performs its own
memory management of this piece of memory, growing and shrinking its
size as needed. Having everything in memory is necessary because it is
not really possible to externally maintain all relevant “environments”
of symbol/value pairs. This difference also seems to make R
<em>faster</em> than S.
</p>
<p>The down side is that if R crashes you will lose all the work for the
current session. Saving and restoring the memory “images” (the
functions and data stored in R’s internal memory at any time) can be a
bit slow, especially if they are big. In S this does not happen,
because everything is saved in disk files and if you crash nothing is
likely to happen to them. (In fact, one might conjecture that the S
developers felt that the price of changing their approach to persistent
storage just to accommodate lexical scope was far too expensive.)
Hence, when doing important work, you might consider saving often (see
<ahref="#How-can-I-save-my-workspace_003f">How can I save my workspace?</a>) to safeguard against possible
crashes. Other possibilities are logging your sessions, or have your R
commands stored in text files which can be read in using
<code>source()</code>.
</p>
<blockquote>
<p><b>Note:</b> If you run R from within Emacs (see <ahref="#R-and-Emacs">R and Emacs</a>), you can save the
contents of the interaction buffer to a file and conveniently manipulate
it using <code>ess-transcript-mode</code>, as well as save source copies of
all functions and data used.
</p></blockquote>
<hr>
<aname="Models"></a>
<divclass="header">
<p>
Next: <ahref="#Others"accesskey="n"rel="next">Others</a>, Previous: <ahref="#Lexical-scoping"accesskey="p"rel="prev">Lexical scoping</a>, Up: <ahref="#What-are-the-differences-between-R-and-S_003f"accesskey="u"rel="up">What are the differences between R and S?</a> [<ahref="#SEC_Contents"title="Table of contents"rel="contents">Contents</a>]</p>
</div>
<aname="Models-1"></a>
<h4class="subsection">3.3.2 Models</h4>
<p>There are some differences in the modeling code, such as
</p>
<ul>
<li> Whereas in S, you would use <code>lm(y ~ x^3)</code> to regress <code>y</code> on
<code>x^3</code>, in R, you have to insulate powers of numeric vectors (using
<code>I()</code>), i.e., you have to use <code>lm(y ~ I(x^3))</code>.
</li><li> The glm family objects are implemented differently in R and S. The same
functionality is available but the components have different names.
</li><li> Option <code>na.action</code> is set to <code>"na.omit"</code> by default in R,
but not set in S.
</li><li> Terms objects are stored differently. In S a terms object is an
expression with attributes, in R it is a formula with attributes. The
attributes have the same names but are mostly stored differently.
</li><li> Finally, in R <code>y ~ x + 0</code> is an alternative to <code>y ~ x - 1</code> for
specifying a model with no intercept. Models with no parameters at all
can be specified by <code>y ~ 0</code>.
</li></ul>
<hr>
<aname="Others"></a>
<divclass="header">
<p>
Previous: <ahref="#Models"accesskey="p"rel="prev">Models</a>, Up: <ahref="#What-are-the-differences-between-R-and-S_003f"accesskey="u"rel="up">What are the differences between R and S?</a> [<ahref="#SEC_Contents"title="Table of contents"rel="contents">Contents</a>]</p>
</div>
<aname="Others-1"></a>
<h4class="subsection">3.3.3 Others</h4>
<p>Apart from lexical scoping and its implications, R follows the S
language definition in the Blue and White Books as much as possible, and
hence really is an “implementation” of S. There are some intentional
differences where the behavior of S is considered “not clean”. In
general, the rationale is that R should help you detect programming
errors, while at the same time being as compatible as possible with S.
</p>
<p>Some known differences are the following.
</p>
<ul>
<li> In R, if <code>x</code> is a list, then <code>x[i] <- NULL</code> and <code>x[[i]]
<- NULL</code> remove the specified elements from <code>x</code>. The first of
these is incompatible with S, where it is a no-op. (Note that you can
set elements to <code>NULL</code> using <code>x[i] <- list(NULL)</code>.)
</li><li> In S, the functions named <code>.First</code> and <code>.Last</code> in the
<samp>.Data</samp> directory can be used for customizing, as they are executed
at the very beginning and end of a session, respectively.
<p>In R, the startup mechanism is as follows. Unless <samp>--no-environ</samp>
was given on the command line, R searches for site and user files to
process for setting environment variables. Then, R searches for a
site-wide startup profile unless the command line option
<samp>--no-site-file</samp> was given. This code is loaded in package
<strong>base</strong>. Then, unless <samp>--no-init-file</samp> was given, R
searches for a user profile file, and sources it into the user
workspace. It then loads a saved image of the user workspace from
<samp>.RData</samp> in case there is one (unless <samp>--no-restore-data</samp> or
<samp>--no-restore</samp> were specified). Next, a function <code>.First()</code>
is run if found on the search path. Finally, function <code>.First.sys</code>
in the <strong>base</strong> package is run. When terminating an R session, by
default a function <code>.Last</code> is run if found on the search path,
followed by <code>.Last.sys</code>. If needed, the functions <code>.First()</code>
and <code>.Last()</code> should be defined in the appropriate startup
profiles. See the help pages for <code>.First</code> and <code>.Last</code> for
more details.
</p>
</li><li> In R, <code>T</code> and <code>F</code> are just variables being set to <code>TRUE</code>
and <code>FALSE</code>, 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 <code>"T"</code> or <code>"F"</code>.) Hence, when writing code
you should always use <code>TRUE</code> and <code>FALSE</code>.
</li><li> In R, <code>dyn.load()</code> can only load <em>shared objects</em>, as created
for example by <kbd>R CMD SHLIB</kbd>.
</li><li> In R, <code>attach()</code> currently only works for lists and data frames,
but not for directories. (In fact, <code>attach()</code> also works for R
data files created with <code>save()</code>, which is analogous to attaching
directories in S.) Also, you cannot attach at position 1.
</li><li> Categories do not exist in R, and never will as they are deprecated now
in S. Use factors instead.
</li><li> In R, <code>For()</code> loops are not necessary and hence not supported.
</li><li> In R, <code>assign()</code> uses the argument <samp>envir=</samp> rather than
<samp>where=</samp> as in S.
</li><li> The random number generators are different, and the seeds have different
length.
</li><li> R passes integer objects to C as <code>int *</code> rather than <code>long *</code>
as in S.
</li><li> R has no single precision storage mode. However, as of version 0.65.1,
there is a single precision interface to C/FORTRAN subroutines.
</li><li> By default, <code>ls()</code> returns the names of the objects in the current
(under R) and global (under S) environment, respectively. For example,
given
<divclass="example">
<preclass="example">x <- 1; fun <- function() {y <- 1; ls()}
</pre></div>
<p>then <code>fun()</code> returns <code>"y"</code> in R and <code>"x"</code> (together with
the rest of the global environment) in S.
</p>
</li><li> R allows for zero-extent matrices (and arrays, i.e., some elements of
the <code>dim</code> 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 <code>x</code> is a matrix, <code>x[, FALSE]</code>
is not <code>NULL</code> but a “matrix” with 0 columns. Hence, such objects
need to be tested for by checking whether their <code>length()</code> is zero
(which works in both R and S), and not using <code>is.null()</code>.
</li><li> Named vectors are considered vectors in R but not in S (e.g.,
<code>is.vector(c(a = 1:3))</code> returns <code>FALSE</code> in S and <code>TRUE</code>
in R).
</li><li> Data frames are not considered as matrices in R (i.e., if <code>DF</code> is a
data frame, then <code>is.matrix(DF)</code> returns <code>FALSE</code> in R and
<code>TRUE</code> in S).
</li><li> R by default uses treatment contrasts in the unordered case, whereas S
uses the Helmert ones. This is a deliberate difference reflecting the
opinion that treatment contrasts are more natural.
</li><li> In R, the argument of a replacement function which corresponds to the
right hand side must be named ‘<samp>value</samp>’. E.g., <code>f(a) <- b</code> is
evaluated as <code>a <- "f<-"(a, value = b)</code>. S always takes the last
argument, irrespective of its name.
</li><li> In S, <code>substitute()</code> 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.
</li><li> In S, the index variable in a <code>for()</code> loop is local to the inside
of the loop. In R it is local to the environment where the <code>for()</code>
statement is executed.
</li><li> In S, <code>tapply(simplify=TRUE)</code> returns a vector where R returns a
one-dimensional array (which can have named dimnames).
</li><li> In S(-<small>PLUS</small>) the C locale is used, whereas in R the current
operating system locale is used for determining which characters are
alphanumeric and how they are sorted. This affects the set of valid
names for R objects (for example accented chars may be allowed in R) and
ordering in sorts and comparisons (such as whether <code>"aA"<"Bb"</code> is
true or false). From version 1.2.0 the locale can be (re-)set in R by
the <code>Sys.setlocale()</code> function.
</li><li> In S, <code>missing(<var>arg</var>)</code> remains <code>TRUE</code> if <var>arg</var> is
subsequently modified; in R it doesn’t.
</li><li> From R version 1.3.0, <code>data.frame</code> strips <code>I()</code> when creating
(column) names.
</li><li> In R, the string <code>"NA"</code> is not treated as a missing value in a
character variable. Use <code>as.character(NA)</code> to create a missing
character value.
</li><li> R disallows repeated formal arguments in function calls.
</li><li> In S, <code>dump()</code>, <code>dput()</code> and <code>deparse()</code> are essentially
different interfaces to the same code. In R from version 2.0.0, this is
only true if the same <code>control</code> argument is used, but by default it
is not. By default <code>dump()</code> tries to write code that will evaluate
to reproduce the object, whereas <code>dput()</code> and <code>deparse()</code>
default to options for producing deparsed code that is readable.
</li><li> In R, indexing a vector, matrix, array or data frame with <code>[</code> using
a character vector index looks only for exact matches (whereas <code>[[</code>
and <code>$</code> allow partial matches). In S, <code>[</code> allows partial
matches.
</li><li> S has a two-argument version of <code>atan</code> and no <code>atan2</code>. A call
in S such as <code>atan(x1, x2)</code> is equivalent to R’s <code>atan2(x1,
x2)</code>. However, beware of named arguments since S’s <code>atan(x = a, y
= b)</code> is equivalent to R’s <code>atan2(y = a, x = b)</code> with the meanings
of <code>x</code> and <code>y</code> interchanged. (R used to have undocumented
support for a two-argument <code>atan</code> with positional arguments, but
this has been withdrawn to avoid further confusion.)
</li><li> Numeric constants with no fractional and exponent (i.e., only integer)
part are taken as integer in <small>S-PLUS</small> 6.x or later, but as double in R.
</li></ul>
<p>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
Next: <ahref="#What-is-R_002dplus_003f"accesskey="n"rel="next">What is R-plus?</a>, Previous: <ahref="#What-are-the-differences-between-R-and-S_003f"accesskey="p"rel="prev">What are the differences between R and S?</a>, Up: <ahref="#R-and-S"accesskey="u"rel="up">R and S</a> [<ahref="#SEC_Contents"title="Table of contents"rel="contents">Contents</a>]</p>
<h3class="section">3.4 Is there anything R can do that <small>S-PLUS</small> cannot?</h3>
<p>Since almost anything you can do in R has source code that you could
port to <small>S-PLUS</small> with little effort there will never be much you can do
in R that you couldn’t do in <small>S-PLUS</small> if you wanted to. (Note that
using lexical scoping may simplify matters considerably, though.)
</p>
<p>R offers several graphics features that <small>S-PLUS</small> does not, such as finer
handling of line types, more convenient color handling (via palettes),
gamma correction for color, and, most importantly, mathematical
annotation in plot texts, via input expressions reminiscent of TeX
constructs. See the help page for <code>plotmath</code>, which features an
impressive on-line example. More details can be found in Paul Murrell
and Ross Ihaka (2000), “An Approach to Providing Mathematical
Annotation in Plots”, <ahref="http://www.amstat.org/publications/jcgs/"><em>Journal of Computational and Graphical Statistics</em></a>, <strong>9</strong>,
582–599.
</p>
<hr>
<aname="What-is-R_002dplus_003f"></a>
<divclass="header">
<p>
Previous: <ahref="#Is-there-anything-R-can-do-that-S_002dPLUS-cannot_003f"accesskey="p"rel="prev">Is there anything R can do that S-PLUS cannot?</a>, Up: <ahref="#R-and-S"accesskey="u"rel="up">R and S</a> [<ahref="#SEC_Contents"title="Table of contents"rel="contents">Contents</a>]</p>
</div>
<aname="What-is-R_002dplus_003f-1"></a>
<h3class="section">3.5 What is R-plus?</h3>
<p>For a very long time, there was no such thing.
</p>
<p><ahref="http://www.xlsolutions-corp.com/">XLSolutions Corporation</a> is
currently beta testing a commercially supported version of R named R+
(read R plus).
</p>
<p><ahref="http://www.revolution-computing.com/">Revolution Analytics</a> has
released
<ahref="http://www.revolution-computing.com/products/revolution-r.php">REvolution R</a>, an enterprise-class statistical analysis system based on
R, suitable for deployment in professional, commercial and regulated
<p><ahref="mailto:ulfi@cs.tu-berlin.de">Ulf Bartel</a> has developed
<strong>R-Online</strong>, a simple on-line programming environment for R which
intends to make the first steps in statistical programming with R
(especially with time series) as easy as possible. There is no need for
a local installation since the only requirement for the user is a
JavaScript capable browser. See <ahref="http://www.osvisions.com/r_online/">http://www.osvisions.com/r_online/</a>
for more information.
</p>
<p><strong>Rcgi</strong> is a CGI WWW interface to R by <ahref="mailto:mjr@dsl.pipex.com">MJ Ray</a>. It had the ability to use “embedded code”: you could mix
user input and code, allowing the <acronym>HTML</acronym> author to do anything from
load in data sets to enter most of the commands for users without
writing CGI scripts. Graphical output was possible in PostScript or GIF
formats and the executed code was presented to the user for revision.
However, it is not clear if the project is still active.
</p>
<p>There are many additional examples of web interfaces to R which
basically allow to submit R code to a remote server, see for example the
<p><ahref="https://www.rforge.net/Rserve/">Rserve</a> is a project
actively developed by Simon Urbanek. It implements a TCP/IP server which
allows other programs to use facilities of R. Clients are available from
the web site for Java and C++ (and could be written for other languages
that support TCP/IP sockets).
</p>
<p>Two projects use PHP to provide a web interface to R.
<ahref="http://steve-chen.net/R_PHP/">R_PHP_Online</a> by Steve Chen (though
it is unclear if this project is still active) is somewhat similar to
the above Rcgi and Rweb. <ahref="http://dssm.unipa.it/R-php/?cmd=home">R-php</a> is actively developed by Alfredo Pontillo and Angelo Mineo and
provides both a web interface to R and a set of pre-specified analyses
that need no R code input.
</p>
<p><ahref="https://www.bioconductor.org/">webbioc</a> is “an integrated web
interface for doing microarray analysis using several of the
Bioconductor packages” and is designed to be installed at local sites
as a shared computing resource.
</p>
<p><ahref="http://sysbio.mrc-bsu.cam.ac.uk/Rwui">Rwui</a> is a web application to
create user-friendly web interfaces for R scripts. All code for the web
interface is created automatically. There is no need for the user to do
any extra scripting or learn any new scripting techniques.
</p>
<p>The <ahref="https://CRAN.R-project.org/package=R.rsp"><strong>R.rsp</strong></a> package by Henrik Bengtsson introduces “R Server
Pages”. Analogous to Java Server Pages, an R server page is typically
<acronym>HTML</acronym> with embedded R code that gets evaluated when the page is
requested. The package includes an internal cross-platform
<acronym>HTTP</acronym> server implemented in Tcl, so provides a good framework
for including web-based user interfaces in packages. The approach is
similar to the use of the <ahref="https://CRAN.R-project.org/package=brew"><strong>brew</strong></a> package with
<ahref="http://rapache.net/">Rapache</a> with the advantage of cross-platform
support and easy installation.
</p>
<p>The <ahref="https://CRAN.R-project.org/package=Rook"><strong>Rook</strong></a> package by Jeffrey Horner provides a web server
interface borrowing heavily from Ruby’s Rack project.
</p>
<p>Finally, <ahref="http://code.google.com/p/concerto-platform/">Concerto</a> is
a user friendly open-source Web Interface to R developed at the
Psychometrics Centre of Cambridge University. It was designed as an
online platform to design and run Computerized Adaptive Tests, but can
be also used as a general-purpose R Web Interface. It allows R users
with no programming or web designing background to quickly develop
flexible and powerful online applications, websites, and psychometrics
tests. To maximize its reliability, security, and performance, Concerto
relies on the popular and reliable open-source elements such as MySQL
server (exchange and storage of the data), <ahref="https://rstudio.org/">Rstudio</a> (R code designing and testing, file management), CKEditor
(<acronym>HTML</acronym> Layer design), and PHP.
</p>
<hr>
<aname="R-Add_002dOn-Packages"></a>
<divclass="header">
<p>
Next: <ahref="#R-and-Emacs"accesskey="n"rel="next">R and Emacs</a>, Previous: <ahref="#R-Web-Interfaces"accesskey="p"rel="prev">R Web Interfaces</a>, Up: <ahref="#Top"accesskey="u"rel="up">Top</a> [<ahref="#SEC_Contents"title="Table of contents"rel="contents">Contents</a>]</p>
<tr><tdalign="left"valign="top">•<ahref="#Which-add_002don-packages-exist-for-R_003f"accesskey="1">Which add-on packages exist for R?</a>:</td><td> </td><tdalign="left"valign="top">
</td></tr>
<tr><tdalign="left"valign="top">•<ahref="#How-can-add_002don-packages-be-installed_003f"accesskey="2">How can add-on packages be installed?</a>:</td><td> </td><tdalign="left"valign="top">
</td></tr>
<tr><tdalign="left"valign="top">•<ahref="#How-can-add_002don-packages-be-used_003f"accesskey="3">How can add-on packages be used?</a>:</td><td> </td><tdalign="left"valign="top">
</td></tr>
<tr><tdalign="left"valign="top">•<ahref="#How-can-add_002don-packages-be-removed_003f"accesskey="4">How can add-on packages be removed?</a>:</td><td> </td><tdalign="left"valign="top">
</td></tr>
<tr><tdalign="left"valign="top">•<ahref="#How-can-I-create-an-R-package_003f"accesskey="5">How can I create an R package?</a>:</td><td> </td><tdalign="left"valign="top">
</td></tr>
<tr><tdalign="left"valign="top">•<ahref="#How-can-I-contribute-to-R_003f"accesskey="6">How can I contribute to R?</a>:</td><td> </td><tdalign="left"valign="top">
<tr><tdalign="left"valign="top">•<ahref="#Add_002don-packages-in-R"accesskey="1">Add-on packages in R</a>:</td><td> </td><tdalign="left"valign="top">
</td></tr>
<tr><tdalign="left"valign="top">•<ahref="#Add_002don-packages-from-CRAN"accesskey="2">Add-on packages from CRAN</a>:</td><td> </td><tdalign="left"valign="top">
</td></tr>
<tr><tdalign="left"valign="top">•<ahref="#Add_002don-packages-from-Omegahat"accesskey="3">Add-on packages from Omegahat</a>:</td><td> </td><tdalign="left"valign="top">
</td></tr>
<tr><tdalign="left"valign="top">•<ahref="#Add_002don-packages-from-Bioconductor"accesskey="4">Add-on packages from Bioconductor</a>:</td><td> </td><tdalign="left"valign="top">
Next: <ahref="#Add_002don-packages-from-CRAN"accesskey="n"rel="next">Add-on packages from CRAN</a>, Previous: <ahref="#Which-add_002don-packages-exist-for-R_003f"accesskey="p"rel="prev">Which add-on packages exist for R?</a>, Up: <ahref="#Which-add_002don-packages-exist-for-R_003f"accesskey="u"rel="up">Which add-on packages exist for R?</a> [<ahref="#SEC_Contents"title="Table of contents"rel="contents">Contents</a>]</p>
</div>
<aname="Add_002don-packages-in-R-1"></a>
<h4class="subsection">5.1.1 Add-on packages in R</h4>
<p>The R distribution comes with the following packages:
</p>
<dlcompact="compact">
<dt><strong>base</strong></dt>
<dd><p>Base R functions (and datasets before R 2.0.0).
</p></dd>
<dt><strong>compiler</strong></dt>
<dd><p>R byte code compiler (added in R 2.13.0).
</p></dd>
<dt><strong>datasets</strong></dt>
<dd><p>Base R datasets (added in R 2.0.0).
</p></dd>
<dt><strong>grDevices</strong></dt>
<dd><p>Graphics devices for base and grid graphics (added in R 2.0.0).
</p></dd>
<dt><strong>graphics</strong></dt>
<dd><p>R functions for base graphics.
</p></dd>
<dt><strong>grid</strong></dt>
<dd><p>A rewrite of the graphics layout capabilities, plus some support for
interaction.
</p></dd>
<dt><strong>methods</strong></dt>
<dd><p>Formally defined methods and classes for R objects, plus other
programming tools, as described in the Green Book.
</p></dd>
<dt><strong>parallel</strong></dt>
<dd><p>Support for parallel computation, including by forking and by sockets,
and random-number generation (added in R 2.14.0).
</p></dd>
<dt><strong>splines</strong></dt>
<dd><p>Regression spline functions and classes.
</p></dd>
<dt><strong>stats</strong></dt>
<dd><p>R statistical functions.
</p></dd>
<dt><strong>stats4</strong></dt>
<dd><p>Statistical functions using S4 classes.
</p></dd>
<dt><strong>tcltk</strong></dt>
<dd><p>Interface and language bindings to Tcl/Tk <acronym>GUI</acronym> elements.
</p></dd>
<dt><strong>tools</strong></dt>
<dd><p>Tools for package development and administration.
</p></dd>
<dt><strong>utils</strong></dt>
<dd><p>R utility functions.
</p></dd>
</dl>
<p>These “base packages” were substantially reorganized in R 1.9.0. The
former <strong>base</strong> was split into the four packages <strong>base</strong>,
<strong>graphics</strong>, <strong>stats</strong>, and <strong>utils</strong>. Packages <strong>ctest</strong>,
<strong>eda</strong>, <strong>modreg</strong>, <strong>mva</strong>, <strong>nls</strong>, <strong>stepfun</strong> and
<strong>ts</strong> were merged into <strong>stats</strong>, package <strong>lqs</strong> returned to the
recommended package <ahref="https://CRAN.R-project.org/package=MASS"><strong>MASS</strong></a>, and package <strong>mle</strong> moved to
<strong>stats4</strong>.
</p>
<hr>
<aname="Add_002don-packages-from-CRAN"></a>
<divclass="header">
<p>
Next: <ahref="#Add_002don-packages-from-Omegahat"accesskey="n"rel="next">Add-on packages from Omegahat</a>, Previous: <ahref="#Add_002don-packages-in-R"accesskey="p"rel="prev">Add-on packages in R</a>, Up: <ahref="#Which-add_002don-packages-exist-for-R_003f"accesskey="u"rel="up">Which add-on packages exist for R?</a> [<ahref="#SEC_Contents"title="Table of contents"rel="contents">Contents</a>]</p>
</div>
<aname="Add_002don-packages-from-CRAN-1"></a>
<h4class="subsection">5.1.2 Add-on packages from <acronym>CRAN</acronym></h4>
<p>The <acronym>CRAN</acronym><samp>src/contrib</samp> area contains a wealth of add-on
packages, including the following <em>recommended</em> packages which are
to be included in all binary distributions of R.
</p>
<dlcompact="compact">
<dt><strong>KernSmooth</strong></dt>
<dd><p>Functions for kernel smoothing (and density estimation) corresponding to
the book “Kernel Smoothing” by M. P. Wand and M. C. Jones, 1995.
</p></dd>
<dt><strong>MASS</strong></dt>
<dd><p>Functions and datasets from the main package of Venables and Ripley,
“Modern Applied Statistics with S”.
(Contained in the <samp>VR</samp> bundle for R versions prior to 2.10.0.)
</p></dd>
<dt><strong>Matrix</strong></dt>
<dd><p>A Matrix package.
(Recommended for R 2.9.0 or later.)
</p></dd>
<dt><strong>boot</strong></dt>
<dd><p>Functions and datasets for bootstrapping from the book “Bootstrap
Methods and Their Applications” by A. C. Davison and D. V. Hinkley,
1997, Cambridge University Press.
</p></dd>
<dt><strong>class</strong></dt>
<dd><p>Functions for classification (<em>k</em>-nearest neighbor and LVQ).
(Contained in the <samp>VR</samp> bundle for R versions prior to 2.10.0.)
</p></dd>
<dt><strong>cluster</strong></dt>
<dd><p>Functions for cluster analysis.
</p></dd>
<dt><strong>codetools</strong></dt>
<dd><p>Code analysis tools.
(Recommended for R 2.5.0 or later.)
</p></dd>
<dt><strong>foreign</strong></dt>
<dd><p>Functions for reading and writing data stored by statistical software
like Minitab, S, SAS, SPSS, Stata, Systat, etc.
</p></dd>
<dt><strong>lattice</strong></dt>
<dd><p>Lattice graphics, an implementation of Trellis Graphics functions.
</p></dd>
<dt><strong>mgcv</strong></dt>
<dd><p>Routines for GAMs and other generalized ridge regression problems with
multiple smoothing parameter selection by GCV or UBRE.
</p></dd>
<dt><strong>nlme</strong></dt>
<dd><p>Fit and compare Gaussian linear and nonlinear mixed-effects models.
</p></dd>
<dt><strong>nnet</strong></dt>
<dd><p>Software for single hidden layer perceptrons (“feed-forward neural
networks”), and for multinomial log-linear models.
(Contained in the <samp>VR</samp> bundle for R versions prior to 2.10.0.)
</p></dd>
<dt><strong>rpart</strong></dt>
<dd><p>Recursive PARTitioning and regression trees.
</p></dd>
<dt><strong>spatial</strong></dt>
<dd><p>Functions for kriging and point pattern analysis from “Modern Applied
Statistics with S” by W. Venables and B. Ripley.
(Contained in the <samp>VR</samp> bundle for R versions prior to 2.10.0.)
</p></dd>
<dt><strong>survival</strong></dt>
<dd><p>Functions for survival analysis, including penalized likelihood.
</p></dd>
</dl>
<p>See the <ahref="https://CRAN.R-project.org/web/packages/"><acronym>CRAN</acronym>
contributed packages page</a> for more information.
to browse packages by topic and providing tools to automatically install
all packages for special areas of interest.
</p>
<p>Some <acronym>CRAN</acronym> packages that do not build out of the box on Windows,
require additional software, or are shipping third party libraries for
Windows cannot be made available on <acronym>CRAN</acronym> in form of a Windows binary
packages. Nevertheless, some of these packages are available at the
“<acronym>CRAN</acronym> extras” repository at
<ahref="https://www.stats.ox.ac.uk/pub/RWin/">https://www.stats.ox.ac.uk/pub/RWin/</a> kindly provided by Brian
D. Ripley. Note that this repository is a default repository for recent
versions of R for Windows.
</p>
<hr>
<aname="Add_002don-packages-from-Omegahat"></a>
<divclass="header">
<p>
Next: <ahref="#Add_002don-packages-from-Bioconductor"accesskey="n"rel="next">Add-on packages from Bioconductor</a>, Previous: <ahref="#Add_002don-packages-from-CRAN"accesskey="p"rel="prev">Add-on packages from CRAN</a>, Up: <ahref="#Which-add_002don-packages-exist-for-R_003f"accesskey="u"rel="up">Which add-on packages exist for R?</a> [<ahref="#SEC_Contents"title="Table of contents"rel="contents">Contents</a>]</p>
</div>
<aname="Add_002don-packages-from-Omegahat-1"></a>
<h4class="subsection">5.1.3 Add-on packages from Omegahat</h4>
focused primarily on DNA microarray data analysis. As the
project has matured, the functional scope of the software packages
broadened to include the analysis of all types of genomic data, such as
SAGE, sequence, or SNP data. In addition, there are metadata
(annotation, CDF and probe) and experiment data packages. See
<ahref="https://www.bioconductor.org/download/">https://www.bioconductor.org/download/</a> for available packages and a
complete taxonomy via BioC Views.
</p>
<hr>
<aname="Other-add_002don-packages"></a>
<divclass="header">
<p>
Previous: <ahref="#Add_002don-packages-from-Bioconductor"accesskey="p"rel="prev">Add-on packages from Bioconductor</a>, Up: <ahref="#Which-add_002don-packages-exist-for-R_003f"accesskey="u"rel="up">Which add-on packages exist for R?</a> [<ahref="#SEC_Contents"title="Table of contents"rel="contents">Contents</a>]</p>
</div>
<aname="Other-add_002don-packages-1"></a>
<h4class="subsection">5.1.5 Other add-on packages</h4>
<p>Many more packages are available from places other than the three
default repositories discussed above (<acronym>CRAN</acronym>, Bioconductor and
Omegahat). In particular, R-Forge provides a <acronym>CRAN</acronym> style repository
at <ahref="https://R-Forge.R-project.org/">https://R-Forge.R-project.org/</a>.
</p>
<p>More code has been posted to the R-help mailing list, and can be
Next: <ahref="#How-can-add_002don-packages-be-removed_003f"accesskey="n"rel="next">How can add-on packages be removed?</a>, Previous: <ahref="#How-can-add_002don-packages-be-installed_003f"accesskey="p"rel="prev">How can add-on packages be installed?</a>, Up: <ahref="#R-Add_002dOn-Packages"accesskey="u"rel="up">R Add-On Packages</a> [<ahref="#SEC_Contents"title="Table of contents"rel="contents">Contents</a>]</p>
Next: <ahref="#How-can-I-create-an-R-package_003f"accesskey="n"rel="next">How can I create an R package?</a>, Previous: <ahref="#How-can-add_002don-packages-be-used_003f"accesskey="p"rel="prev">How can add-on packages be used?</a>, Up: <ahref="#R-Add_002dOn-Packages"accesskey="u"rel="up">R Add-On Packages</a> [<ahref="#SEC_Contents"title="Table of contents"rel="contents">Contents</a>]</p>
<h3class="section">5.4 How can add-on packages be removed?</h3>
<p>Use
</p>
<divclass="example">
<preclass="example">$ R CMD REMOVE <var>pkg_1</var>…<var>pkg_n</var>
</pre></div>
<p>to remove the packages <var>pkg_1</var>, …, <var>pkg_n</var> from the
library tree rooted at the first directory given in <code>R_LIBS</code> if this
is set and non-null, and from the default library otherwise. (Versions
of R prior to 1.3.0 removed from the default library by default.)
</p>
<p>To remove from library <var>lib</var>, do
</p>
<divclass="example">
<preclass="example">$ R CMD REMOVE -l <var>lib</var><var>pkg_1</var>…<var>pkg_n</var>
</pre></div>
<hr>
<aname="How-can-I-create-an-R-package_003f"></a>
<divclass="header">
<p>
Next: <ahref="#How-can-I-contribute-to-R_003f"accesskey="n"rel="next">How can I contribute to R?</a>, Previous: <ahref="#How-can-add_002don-packages-be-removed_003f"accesskey="p"rel="prev">How can add-on packages be removed?</a>, Up: <ahref="#R-Add_002dOn-Packages"accesskey="u"rel="up">R Add-On Packages</a> [<ahref="#SEC_Contents"title="Table of contents"rel="contents">Contents</a>]</p>
<samp>LICENCE</samp>, <samp>COPYING</samp> and <samp>NEWS</samp>.
</p>
<p>See section “Creating R packages” in <cite>Writing R Extensions</cite>, for
details. This manual is included in the R distribution, see <ahref="#What-documentation-exists-for-R_003f">What documentation exists for R?</a>, and gives information on package
structure, the configure and cleanup mechanisms, and on automated
package checking and building.
</p>
<p>R version 1.3.0 has added the function <code>package.skeleton()</code> which
will set up directories, save data and code, and create skeleton help
files for a set of R functions and datasets.
</p>
<p>See <ahref="#What-is-CRAN_003f">What is CRAN?</a>, for information on uploading a package to <acronym>CRAN</acronym>.
</p>
<hr>
<aname="How-can-I-contribute-to-R_003f"></a>
<divclass="header">
<p>
Previous: <ahref="#How-can-I-create-an-R-package_003f"accesskey="p"rel="prev">How can I create an R package?</a>, Up: <ahref="#R-Add_002dOn-Packages"accesskey="u"rel="up">R Add-On Packages</a> [<ahref="#SEC_Contents"title="Table of contents"rel="contents">Contents</a>]</p>
</div>
<aname="How-can-I-contribute-to-R_003f-1"></a>
<h3class="section">5.6 How can I contribute to R?</h3>
<p>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.
</p>
<p>The <ahref="https://developer.R-project.org/">R Developer Page</a> acts as an
intermediate repository for more or less finalized ideas and plans for
the R statistical system. It contains (pointers to) TODO lists, RFCs,
various other writeups, ideas lists, and SVN miscellanea.
<tr><tdalign="left"valign="top">•<ahref="#Is-there-Emacs-support-for-R_003f"accesskey="1">Is there Emacs support for R?</a>:</td><td> </td><tdalign="left"valign="top">
</td></tr>
<tr><tdalign="left"valign="top">•<ahref="#Should-I-run-R-from-within-Emacs_003f"accesskey="2">Should I run R from within Emacs?</a>:</td><td> </td><tdalign="left"valign="top">
</td></tr>
<tr><tdalign="left"valign="top">•<ahref="#Debugging-R-from-within-Emacs"accesskey="3">Debugging R from within Emacs</a>:</td><td> </td><tdalign="left"valign="top">
</td></tr>
</table>
<hr>
<aname="Is-there-Emacs-support-for-R_003f"></a>
<divclass="header">
<p>
Next: <ahref="#Should-I-run-R-from-within-Emacs_003f"accesskey="n"rel="next">Should I run R from within Emacs?</a>, Previous: <ahref="#R-and-Emacs"accesskey="p"rel="prev">R and Emacs</a>, Up: <ahref="#R-and-Emacs"accesskey="u"rel="up">R and Emacs</a> [<ahref="#SEC_Contents"title="Table of contents"rel="contents">Contents</a>]</p>
</div>
<aname="Is-there-Emacs-support-for-R_003f-1"></a>
<h3class="section">6.1 Is there Emacs support for R?</h3>
<p>There is an Emacs package called <acronym>ESS</acronym> (“Emacs Speaks
Statistics”) which provides a standard interface between statistical
programs and statistical processes. It is intended to provide
assistance for interactive statistical programming and data analysis.
Languages supported include: S dialects (R, S 3/4, and <small>S-PLUS</small>
Next: <ahref="#Debugging-R-from-within-Emacs"accesskey="n"rel="next">Debugging R from within Emacs</a>, Previous: <ahref="#Is-there-Emacs-support-for-R_003f"accesskey="p"rel="prev">Is there Emacs support for R?</a>, Up: <ahref="#R-and-Emacs"accesskey="u"rel="up">R and Emacs</a> [<ahref="#SEC_Contents"title="Table of contents"rel="contents">Contents</a>]</p>
<h3class="section">6.2 Should I run R from within Emacs?</h3>
<p>Yes, <em>definitely</em>. 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.
</p>
<p>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.
</p>
<p>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.
</p>
<p>To specify command line arguments for the inferior R process, use
<kbd>C-u M-x R</kbd> for starting R.
</p>
<hr>
<aname="Debugging-R-from-within-Emacs"></a>
<divclass="header">
<p>
Previous: <ahref="#Should-I-run-R-from-within-Emacs_003f"accesskey="p"rel="prev">Should I run R from within Emacs?</a>, Up: <ahref="#R-and-Emacs"accesskey="u"rel="up">R and Emacs</a> [<ahref="#SEC_Contents"title="Table of contents"rel="contents">Contents</a>]</p>
</div>
<aname="Debugging-R-from-within-Emacs-1"></a>
<h3class="section">6.3 Debugging R from within Emacs</h3>
<p>To debug R “from within Emacs”, there are several possibilities. To
use the Emacs GUD (Grand Unified Debugger) library with the recommended
debugger GDB, type <kbd>M-x gdb</kbd> and give the path to the R
<em>binary</em> as argument. At the <code>gdb</code> prompt, set
<code>R_HOME</code> and other environment variables as needed (using e.g.
<kbd>set env R_HOME /path/to/R/</kbd>, but see also below), and start the
binary with the desired arguments (e.g., <kbd>run --quiet</kbd>).
</p>
<p>If you have <acronym>ESS</acronym>, you can do <kbd>C-u M-x R <spanclass="key">RET</span> - d
<spanclass="key">SPC</span> g d b <spanclass="key">RET</span></kbd> to start an inferior R process with arguments
<samp>-d gdb</samp>.
</p>
<p>A third option is to start an inferior R process via <acronym>ESS</acronym>
(<kbd>M-x R</kbd>) and then start GUD (<kbd>M-x gdb</kbd>) giving the R binary
(using its full path name) as the program to debug. Use the program
<code>ps</code> to find the process number of the currently running R
process then use the <code>attach</code> command in gdb to attach it to that
process. One advantage of this method is that you have separate
<code>*R*</code> and <code>*gud-gdb*</code> windows. Within the <code>*R*</code> window
you have all the <acronym>ESS</acronym> facilities, such as object-name
completion, that we know and love.
</p>
<p>When using GUD mode for debugging from within Emacs, you may find it
most convenient to use the directory with your code in it as the current
working directory and then make a symbolic link from that directory to
the R binary. That way <samp>.gdbinit</samp> 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:
</p>
<divclass="example">
<preclass="example">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
</pre></div>
<hr>
<aname="R-Miscellanea"></a>
<divclass="header">
<p>
Next: <ahref="#R-Programming"accesskey="n"rel="next">R Programming</a>, Previous: <ahref="#R-and-Emacs"accesskey="p"rel="prev">R and Emacs</a>, Up: <ahref="#Top"accesskey="u"rel="up">Top</a> [<ahref="#SEC_Contents"title="Table of contents"rel="contents">Contents</a>]</p>
<tr><tdalign="left"valign="top">•<ahref="#How-can-I-set-components-of-a-list-to-NULL_003f"accesskey="1">How can I set components of a list to NULL?</a>:</td><td> </td><tdalign="left"valign="top">
</td></tr>
<tr><tdalign="left"valign="top">•<ahref="#How-can-I-save-my-workspace_003f"accesskey="2">How can I save my workspace?</a>:</td><td> </td><tdalign="left"valign="top">
</td></tr>
<tr><tdalign="left"valign="top">•<ahref="#How-can-I-clean-up-my-workspace_003f"accesskey="3">How can I clean up my workspace?</a>:</td><td> </td><tdalign="left"valign="top">
</td></tr>
<tr><tdalign="left"valign="top">•<ahref="#How-can-I-get-eval_0028_0029-and-D_0028_0029-to-work_003f"accesskey="4">How can I get eval() and D() to work?</a>:</td><td> </td><tdalign="left"valign="top">
</td></tr>
<tr><tdalign="left"valign="top">•<ahref="#Why-do-my-matrices-lose-dimensions_003f"accesskey="5">Why do my matrices lose dimensions?</a>:</td><td> </td><tdalign="left"valign="top">
</td></tr>
<tr><tdalign="left"valign="top">•<ahref="#How-does-autoloading-work_003f"accesskey="6">How does autoloading work?</a>:</td><td> </td><tdalign="left"valign="top">
</td></tr>
<tr><tdalign="left"valign="top">•<ahref="#How-should-I-set-options_003f"accesskey="7">How should I set options?</a>:</td><td> </td><tdalign="left"valign="top">
</td></tr>
<tr><tdalign="left"valign="top">•<ahref="#How-do-file-names-work-in-Windows_003f"accesskey="8">How do file names work in Windows?</a>:</td><td> </td><tdalign="left"valign="top">
</td></tr>
<tr><tdalign="left"valign="top">•<ahref="#Why-does-plotting-give-a-color-allocation-error_003f"accesskey="9">Why does plotting give a color allocation error?</a>:</td><td> </td><tdalign="left"valign="top">
</td></tr>
<tr><tdalign="left"valign="top">•<ahref="#How-do-I-convert-factors-to-numeric_003f">How do I convert factors to numeric?</a>:</td><td> </td><tdalign="left"valign="top">
</td></tr>
<tr><tdalign="left"valign="top">•<ahref="#Are-Trellis-displays-implemented-in-R_003f">Are Trellis displays implemented in R?</a>:</td><td> </td><tdalign="left"valign="top">
</td></tr>
<tr><tdalign="left"valign="top">•<ahref="#What-are-the-enclosing-and-parent-environments_003f">What are the enclosing and parent environments?</a>:</td><td> </td><tdalign="left"valign="top">
</td></tr>
<tr><tdalign="left"valign="top">•<ahref="#How-can-I-substitute-into-a-plot-label_003f">How can I substitute into a plot label?</a>:</td><td> </td><tdalign="left"valign="top">
</td></tr>
<tr><tdalign="left"valign="top">•<ahref="#What-are-valid-names_003f">What are valid names?</a>:</td><td> </td><tdalign="left"valign="top">
</td></tr>
<tr><tdalign="left"valign="top">•<ahref="#Are-GAMs-implemented-in-R_003f">Are GAMs implemented in R?</a>:</td><td> </td><tdalign="left"valign="top">
</td></tr>
<tr><tdalign="left"valign="top">•<ahref="#Why-is-the-output-not-printed-when-I-source_0028_0029-a-file_003f">Why is the output not printed when I source() a file?</a>:</td><td> </td><tdalign="left"valign="top">
</td></tr>
<tr><tdalign="left"valign="top">•<ahref="#Why-does-outer_0028_0029-behave-strangely-with-my-function_003f">Why does outer() behave strangely with my function?</a>:</td><td> </td><tdalign="left"valign="top">
</td></tr>
<tr><tdalign="left"valign="top">•<ahref="#Why-does-the-output-from-anova_0028_0029-depend-on-the-order-of-factors-in-the-model_003f">Why does the output from anova() depend on the order of factors in the model?</a>:</td><td> </td><tdalign="left"valign="top">
</td></tr>
<tr><tdalign="left"valign="top">•<ahref="#How-do-I-produce-PNG-graphics-in-batch-mode_003f">How do I produce PNG graphics in batch mode?</a>:</td><td> </td><tdalign="left"valign="top">
</td></tr>
<tr><tdalign="left"valign="top">•<ahref="#How-can-I-get-command-line-editing-to-work_003f">How can I get command line editing to work?</a>:</td><td> </td><tdalign="left"valign="top">
</td></tr>
<tr><tdalign="left"valign="top">•<ahref="#How-can-I-turn-a-string-into-a-variable_003f">How can I turn a string into a variable?</a>:</td><td> </td><tdalign="left"valign="top">
</td></tr>
<tr><tdalign="left"valign="top">•<ahref="#Why-do-lattice_002ftrellis-graphics-not-work_003f">Why do lattice/trellis graphics not work?</a>:</td><td> </td><tdalign="left"valign="top">
</td></tr>
<tr><tdalign="left"valign="top">•<ahref="#How-can-I-sort-the-rows-of-a-data-frame_003f">How can I sort the rows of a data frame?</a>:</td><td> </td><tdalign="left"valign="top">
</td></tr>
<tr><tdalign="left"valign="top">•<ahref="#Why-does-the-help_002estart_0028_0029-search-engine-not-work_003f">Why does the help.start() search engine not work?</a>:</td><td> </td><tdalign="left"valign="top">
</td></tr>
<tr><tdalign="left"valign="top">•<ahref="#Why-did-my-_002eRprofile-stop-working-when-I-updated-R_003f">Why did my .Rprofile stop working when I updated R?</a>:</td><td> </td><tdalign="left"valign="top">
</td></tr>
<tr><tdalign="left"valign="top">•<ahref="#Where-have-all-the-methods-gone_003f">Where have all the methods gone?</a>:</td><td> </td><tdalign="left"valign="top">
</td></tr>
<tr><tdalign="left"valign="top">•<ahref="#How-can-I-create-rotated-axis-labels_003f">How can I create rotated axis labels?</a>:</td><td> </td><tdalign="left"valign="top">
</td></tr>
<tr><tdalign="left"valign="top">•<ahref="#Why-is-read_002etable_0028_0029-so-inefficient_003f">Why is read.table() so inefficient?</a>:</td><td> </td><tdalign="left"valign="top">
</td></tr>
<tr><tdalign="left"valign="top">•<ahref="#What-is-the-difference-between-package-and-library_003f">What is the difference between package and library?</a>:</td><td> </td><tdalign="left"valign="top">
</td></tr>
<tr><tdalign="left"valign="top">•<ahref="#I-installed-a-package-but-the-functions-are-not-there">I installed a package but the functions are not there</a>:</td><td> </td><tdalign="left"valign="top">
</td></tr>
<tr><tdalign="left"valign="top">•<ahref="#Why-doesn_0027t-R-think-these-numbers-are-equal_003f">Why doesn't R think these numbers are equal?</a>:</td><td> </td><tdalign="left"valign="top">
</td></tr>
<tr><tdalign="left"valign="top">•<ahref="#How-can-I-capture-or-ignore-errors-in-a-long-simulation_003f">How can I capture or ignore errors in a long simulation?</a>:</td><td> </td><tdalign="left"valign="top">
</td></tr>
<tr><tdalign="left"valign="top">•<ahref="#Why-are-powers-of-negative-numbers-wrong_003f">Why are powers of negative numbers wrong?</a>:</td><td> </td><tdalign="left"valign="top">
</td></tr>
<tr><tdalign="left"valign="top">•<ahref="#How-can-I-save-the-result-of-each-iteration-in-a-loop-into-a-separate-file_003f">How can I save the result of each iteration in a loop into a separate file?</a>:</td><td> </td><tdalign="left"valign="top">
</td></tr>
<tr><tdalign="left"valign="top">•<ahref="#Why-are-p_002dvalues-not-displayed-when-using-lmer_0028_0029_003f">Why are p-values not displayed when using lmer()?</a>:</td><td> </td><tdalign="left"valign="top">
</td></tr>
<tr><tdalign="left"valign="top">•<ahref="#Why-are-there-unwanted-borders">Why are there unwanted borders</a>:</td><td> </td><tdalign="left"valign="top">
</td></tr>
<tr><tdalign="left"valign="top">•<ahref="#Why-does-backslash-behave-strangely-inside-strings_003f">Why does backslash behave strangely inside strings?</a>:</td><td> </td><tdalign="left"valign="top">
</td></tr>
<tr><tdalign="left"valign="top">•<ahref="#How-can-I-put-error-bars-or-confidence-bands-on-my-plot_003f">How can I put error bars or confidence bands on my plot?</a>:</td><td> </td><tdalign="left"valign="top">
</td></tr>
<tr><tdalign="left"valign="top">•<ahref="#How-do-I-create-a-plot-with-two-y_002daxes_003f">How do I create a plot with two y-axes?</a>:</td><td> </td><tdalign="left"valign="top">
</td></tr>
<tr><tdalign="left"valign="top">•<ahref="#How-do-I-access-the-source-code-for-a-function_003f">How do I access the source code for a function?</a>:</td><td> </td><tdalign="left"valign="top">
</td></tr>
<tr><tdalign="left"valign="top">•<ahref="#Why-does-summary_0028_0029-report-strange-results-for-the-R_005e2-estimate-when-I-fit-a-linear-model-with-no-intercept_003f">Why does summary() report strange results for the R^2 estimate when I fit a linear model with no intercept?</a>:</td><td> </td><tdalign="left"valign="top">
</td></tr>
<tr><tdalign="left"valign="top">•<ahref="#Why-is-R-apparently-not-releasing-memory_003f">Why is R apparently not releasing memory?</a>:</td><td> </td><tdalign="left"valign="top">
</td></tr>
<tr><tdalign="left"valign="top">•<ahref="#How-can-I-enable-secure-https-downloads-in-R_003f">How can I enable secure https downloads in R?</a>:</td><td> </td><tdalign="left"valign="top">
<tr><tdalign="left"valign="top">•<ahref="#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> </td><tdalign="left"valign="top">
Next: <ahref="#How-can-I-save-my-workspace_003f"accesskey="n"rel="next">How can I save my workspace?</a>, Previous: <ahref="#R-Miscellanea"accesskey="p"rel="prev">R Miscellanea</a>, Up: <ahref="#R-Miscellanea"accesskey="u"rel="up">R Miscellanea</a> [<ahref="#SEC_Contents"title="Table of contents"rel="contents">Contents</a>]</p>
<h3class="section">7.1 How can I set components of a list to NULL?</h3>
<p>You can use
</p>
<divclass="example">
<preclass="example">x[i] <- list(NULL)
</pre></div>
<p>to set component <code>i</code> of the list <code>x</code> to <code>NULL</code>, similarly
for named components. Do not set <code>x[i]</code> or <code>x[[i]]</code> to
<code>NULL</code>, because this will remove the corresponding component from
the list.
</p>
<p>For dropping the row names of a matrix <code>x</code>, it may be easier to use
<code>rownames(x) <- NULL</code>, similarly for column names.
</p>
<hr>
<aname="How-can-I-save-my-workspace_003f"></a>
<divclass="header">
<p>
Next: <ahref="#How-can-I-clean-up-my-workspace_003f"accesskey="n"rel="next">How can I clean up my workspace?</a>, Previous: <ahref="#How-can-I-set-components-of-a-list-to-NULL_003f"accesskey="p"rel="prev">How can I set components of a list to NULL?</a>, Up: <ahref="#R-Miscellanea"accesskey="u"rel="up">R Miscellanea</a> [<ahref="#SEC_Contents"title="Table of contents"rel="contents">Contents</a>]</p>
</div>
<aname="How-can-I-save-my-workspace_003f-1"></a>
<h3class="section">7.2 How can I save my workspace?</h3>
<p><code>save.image()</code> saves the objects in the user’s <code>.GlobalEnv</code> to
the file <samp>.RData</samp> in the R startup directory. (This is also what
happens after <kbd>q("yes")</kbd>.) Using <code>save.image(<var>file</var>)</code> one
Next: <ahref="#How-can-I-get-eval_0028_0029-and-D_0028_0029-to-work_003f"accesskey="n"rel="next">How can I get eval() and D() to work?</a>, Previous: <ahref="#How-can-I-save-my-workspace_003f"accesskey="p"rel="prev">How can I save my workspace?</a>, Up: <ahref="#R-Miscellanea"accesskey="u"rel="up">R Miscellanea</a> [<ahref="#SEC_Contents"title="Table of contents"rel="contents">Contents</a>]</p>
Next: <ahref="#Why-do-my-matrices-lose-dimensions_003f"accesskey="n"rel="next">Why do my matrices lose dimensions?</a>, Previous: <ahref="#How-can-I-clean-up-my-workspace_003f"accesskey="p"rel="prev">How can I clean up my workspace?</a>, Up: <ahref="#R-Miscellanea"accesskey="u"rel="up">R Miscellanea</a> [<ahref="#SEC_Contents"title="Table of contents"rel="contents">Contents</a>]</p>
Next: <ahref="#How-does-autoloading-work_003f"accesskey="n"rel="next">How does autoloading work?</a>, Previous: <ahref="#How-can-I-get-eval_0028_0029-and-D_0028_0029-to-work_003f"accesskey="p"rel="prev">How can I get eval() and D() to work?</a>, Up: <ahref="#R-Miscellanea"accesskey="u"rel="up">R Miscellanea</a> [<ahref="#SEC_Contents"title="Table of contents"rel="contents">Contents</a>]</p>
<h3class="section">7.5 Why do my matrices lose dimensions?</h3>
<p>When a matrix with a single row or column is created by a subscripting
operation, e.g., <code>row <- mat[2, ]</code>, 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<!-- /@w --> is created by subscripting it will be coerced into a 2 x 3 x 4<!-- /@w -->
array, losing the unnecessary dimension. After much discussion this has
been determined to be a <em>feature</em>.
</p>
<p>To prevent this happening, add the option <samp>drop = FALSE</samp> to the
subscripting. For example,
</p>
<divclass="example">
<preclass="example">rowmatrix <- mat[2, , drop = FALSE] # <spanclass="roman">creates a row matrix</span>
colmatrix <- mat[, 2, drop = FALSE] # <spanclass="roman">creates a column matrix</span>
a <- b[1, 1, 1, drop = FALSE] # <spanclass="roman">creates a 1 x 1 x 1 array</span>
</pre></div>
<p>The <samp>drop = FALSE</samp> option should be used defensively when
programming. For example, the statement
</p>
<divclass="example">
<preclass="example">somerows <- mat[index, ]
</pre></div>
<p>will return a vector rather than a matrix if <code>index</code> happens to
have length 1, causing errors later in the code. It should probably be
rewritten as
</p>
<divclass="example">
<preclass="example">somerows <- mat[index, , drop = FALSE]
</pre></div>
<hr>
<aname="How-does-autoloading-work_003f"></a>
<divclass="header">
<p>
Next: <ahref="#How-should-I-set-options_003f"accesskey="n"rel="next">How should I set options?</a>, Previous: <ahref="#Why-do-my-matrices-lose-dimensions_003f"accesskey="p"rel="prev">Why do my matrices lose dimensions?</a>, Up: <ahref="#R-Miscellanea"accesskey="u"rel="up">R Miscellanea</a> [<ahref="#SEC_Contents"title="Table of contents"rel="contents">Contents</a>]</p>
</div>
<aname="How-does-autoloading-work_003f-1"></a>
<h3class="section">7.6 How does autoloading work?</h3>
<p>R has a special environment called <code>.AutoloadEnv</code>. Using
<kbd>autoload(<var>name</var>, <var>pkg</var>)</kbd>, where <var>name</var> and
<var>pkg</var> are strings giving the names of an object and the package
containing it, stores some information in this environment. When R
tries to evaluate <var>name</var>, it loads the corresponding package
<var>pkg</var> and reevaluates <var>name</var> in the new package’s
environment.
</p>
<p>Using this mechanism makes R behave as if the package was loaded, but
does not occupy memory (yet).
</p>
<p>See the help page for <code>autoload()</code> for a very nice example.
</p>
<hr>
<aname="How-should-I-set-options_003f"></a>
<divclass="header">
<p>
Next: <ahref="#How-do-file-names-work-in-Windows_003f"accesskey="n"rel="next">How do file names work in Windows?</a>, Previous: <ahref="#How-does-autoloading-work_003f"accesskey="p"rel="prev">How does autoloading work?</a>, Up: <ahref="#R-Miscellanea"accesskey="u"rel="up">R Miscellanea</a> [<ahref="#SEC_Contents"title="Table of contents"rel="contents">Contents</a>]</p>
</div>
<aname="How-should-I-set-options_003f-1"></a>
<h3class="section">7.7 How should I set options?</h3>
<p>The function <code>options()</code> allows setting and examining a variety of
global “options” which affect the way in which R computes and displays
its results. The variable <code>.Options</code> 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”
Next: <ahref="#Why-does-plotting-give-a-color-allocation-error_003f"accesskey="n"rel="next">Why does plotting give a color allocation error?</a>, Previous: <ahref="#How-should-I-set-options_003f"accesskey="p"rel="prev">How should I set options?</a>, Up: <ahref="#R-Miscellanea"accesskey="u"rel="up">R Miscellanea</a> [<ahref="#SEC_Contents"title="Table of contents"rel="contents">Contents</a>]</p>
Next: <ahref="#How-do-I-convert-factors-to-numeric_003f"accesskey="n"rel="next">How do I convert factors to numeric?</a>, Previous: <ahref="#How-do-file-names-work-in-Windows_003f"accesskey="p"rel="prev">How do file names work in Windows?</a>, Up: <ahref="#R-Miscellanea"accesskey="u"rel="up">R Miscellanea</a> [<ahref="#SEC_Contents"title="Table of contents"rel="contents">Contents</a>]</p>
Next: <ahref="#Are-Trellis-displays-implemented-in-R_003f"accesskey="n"rel="next">Are Trellis displays implemented in R?</a>, Previous: <ahref="#Why-does-plotting-give-a-color-allocation-error_003f"accesskey="p"rel="prev">Why does plotting give a color allocation error?</a>, Up: <ahref="#R-Miscellanea"accesskey="u"rel="up">R Miscellanea</a> [<ahref="#SEC_Contents"title="Table of contents"rel="contents">Contents</a>]</p>
Next: <ahref="#What-are-the-enclosing-and-parent-environments_003f"accesskey="n"rel="next">What are the enclosing and parent environments?</a>, Previous: <ahref="#How-do-I-convert-factors-to-numeric_003f"accesskey="p"rel="prev">How do I convert factors to numeric?</a>, Up: <ahref="#R-Miscellanea"accesskey="u"rel="up">R Miscellanea</a> [<ahref="#SEC_Contents"title="Table of contents"rel="contents">Contents</a>]</p>
Next: <ahref="#How-can-I-substitute-into-a-plot-label_003f"accesskey="n"rel="next">How can I substitute into a plot label?</a>, Previous: <ahref="#Are-Trellis-displays-implemented-in-R_003f"accesskey="p"rel="prev">Are Trellis displays implemented in R?</a>, Up: <ahref="#R-Miscellanea"accesskey="u"rel="up">R Miscellanea</a> [<ahref="#SEC_Contents"title="Table of contents"rel="contents">Contents</a>]</p>
Next: <ahref="#What-are-valid-names_003f"accesskey="n"rel="next">What are valid names?</a>, Previous: <ahref="#What-are-the-enclosing-and-parent-environments_003f"accesskey="p"rel="prev">What are the enclosing and parent environments?</a>, Up: <ahref="#R-Miscellanea"accesskey="u"rel="up">R Miscellanea</a> [<ahref="#SEC_Contents"title="Table of contents"rel="contents">Contents</a>]</p>
<p>where subexpressions enclosed in ‘<samp>.()</samp>’ are replaced by their
values.
</p>
<p>There are more examples in the mailing list archives.
</p>
<hr>
<aname="What-are-valid-names_003f"></a>
<divclass="header">
<p>
Next: <ahref="#Are-GAMs-implemented-in-R_003f"accesskey="n"rel="next">Are GAMs implemented in R?</a>, Previous: <ahref="#How-can-I-substitute-into-a-plot-label_003f"accesskey="p"rel="prev">How can I substitute into a plot label?</a>, Up: <ahref="#R-Miscellanea"accesskey="u"rel="up">R Miscellanea</a> [<ahref="#SEC_Contents"title="Table of contents"rel="contents">Contents</a>]</p>
</div>
<aname="What-are-valid-names_003f-1"></a>
<h3class="section">7.14 What are valid names?</h3>
<p>When creating data frames using <code>data.frame()</code> or
<code>read.table()</code>, R by default ensures that the variable names are
syntactically valid. (The argument <samp>check.names</samp> to these
functions controls whether variable names are checked and adjusted by
<code>make.names()</code> if needed.)
</p>
<p>To understand what names are “valid”, one needs to take into account
that the term “name” is used in several different (but related) ways
in the language:
</p>
<ol>
<li> A <em>syntactic name</em> is a string the parser interprets as this type
of expression. It consists of letters, numbers, and the dot and (for
versions of R at least 1.9.0) underscore characters, and starts with
either a letter or a dot not followed by a number. Reserved words are
not syntactic names.
</li><li> An <em>object name</em> is a string associated with an object that is
assigned in an expression either by having the object name on the left
of an assignment operation or as an argument to the <code>assign()</code>
function. It is usually a syntactic name as well, but can be any
non-empty string if it is quoted (and it is always quoted in the call to
<code>assign()</code>).
</li><li> An <em>argument name</em> is what appears to the left of the equals sign
when supplying an argument in a function call (for example,
<code>f(trim=.5)</code>). Argument names are also usually syntactic names,
but again can be anything if they are quoted.
</li><li> An <em>element name</em> is a string that identifies a piece of an object
(a component of a list, for example.) When it is used on the right of
the ‘<samp>$</samp>’ operator, it must be a syntactic name, or quoted.
Otherwise, element names can be any strings. (When an object is used as
a database, as in a call to <code>eval()</code> or <code>attach()</code>, the
element names become object names.)
</li><li> Finally, a <em>file name</em> is a string identifying a file in the
operating system for reading, writing, etc. It really has nothing much
to do with names in the language, but it is traditional to call these
strings file “names”.
</li></ol>
<hr>
<aname="Are-GAMs-implemented-in-R_003f"></a>
<divclass="header">
<p>
Next: <ahref="#Why-is-the-output-not-printed-when-I-source_0028_0029-a-file_003f"accesskey="n"rel="next">Why is the output not printed when I source() a file?</a>, Previous: <ahref="#What-are-valid-names_003f"accesskey="p"rel="prev">What are valid names?</a>, Up: <ahref="#R-Miscellanea"accesskey="u"rel="up">R Miscellanea</a> [<ahref="#SEC_Contents"title="Table of contents"rel="contents">Contents</a>]</p>
</div>
<aname="Are-GAMs-implemented-in-R_003f-1"></a>
<h3class="section">7.15 Are GAMs implemented in R?</h3>
<p>Package <ahref="https://CRAN.R-project.org/package=gam"><strong>gam</strong></a> from <acronym>CRAN</acronym> implements all the Generalized
Additive Models (GAM) functionality as described in the GAM chapter of
the White Book. In particular, it implements backfitting with both
local regression and smoothing splines, and is extendable. There is a
<code>gam()</code> function for GAMs in package <ahref="https://CRAN.R-project.org/package=mgcv"><strong>mgcv</strong></a>, but it is not
an exact clone of what is described in the White Book (no <code>lo()</code>
for example). Package <ahref="https://CRAN.R-project.org/package=gss"><strong>gss</strong></a> can fit spline-based GAMs too. And
if you can accept regression splines you can use <code>glm()</code>. For
Gaussian GAMs you can use <code>bruto()</code> from package <ahref="https://CRAN.R-project.org/package=mda"><strong>mda</strong></a>.
Next: <ahref="#Why-does-outer_0028_0029-behave-strangely-with-my-function_003f"accesskey="n"rel="next">Why does outer() behave strangely with my function?</a>, Previous: <ahref="#Are-GAMs-implemented-in-R_003f"accesskey="p"rel="prev">Are GAMs implemented in R?</a>, Up: <ahref="#R-Miscellanea"accesskey="u"rel="up">R Miscellanea</a> [<ahref="#SEC_Contents"title="Table of contents"rel="contents">Contents</a>]</p>
<p>fits a logistic regression model, computes some summary information and
returns an object of class <code>"summary.glm"</code> (see <ahref="#How-should-I-write-summary-methods_003f">How should I write summary methods?</a>).
</p>
<p>If you type ‘<samp>1+1</samp>’ or ‘<samp>summary(glm(y~x+z, family=binomial))</samp>’ at
the command line the returned value is automatically printed (unless it
is <code>invisible()</code>), but in other circumstances, such as in a
<code>source()</code>d file or inside a function it isn’t printed unless you
Next: <ahref="#Why-does-the-output-from-anova_0028_0029-depend-on-the-order-of-factors-in-the-model_003f"accesskey="n"rel="next">Why does the output from anova() depend on the order of factors in the model?</a>, Previous: <ahref="#Why-is-the-output-not-printed-when-I-source_0028_0029-a-file_003f"accesskey="p"rel="prev">Why is the output not printed when I source() a file?</a>, Up: <ahref="#R-Miscellanea"accesskey="u"rel="up">R Miscellanea</a> [<ahref="#SEC_Contents"title="Table of contents"rel="contents">Contents</a>]</p>
Next: <ahref="#How-do-I-produce-PNG-graphics-in-batch-mode_003f"accesskey="n"rel="next">How do I produce PNG graphics in batch mode?</a>, Previous: <ahref="#Why-does-outer_0028_0029-behave-strangely-with-my-function_003f"accesskey="p"rel="prev">Why does outer() behave strangely with my function?</a>, Up: <ahref="#R-Miscellanea"accesskey="u"rel="up">R Miscellanea</a> [<ahref="#SEC_Contents"title="Table of contents"rel="contents">Contents</a>]</p>
Next: <ahref="#How-can-I-get-command-line-editing-to-work_003f"accesskey="n"rel="next">How can I get command line editing to work?</a>, Previous: <ahref="#Why-does-the-output-from-anova_0028_0029-depend-on-the-order-of-factors-in-the-model_003f"accesskey="p"rel="prev">Why does the output from anova() depend on the order of factors in the model?</a>, Up: <ahref="#R-Miscellanea"accesskey="u"rel="up">R Miscellanea</a> [<ahref="#SEC_Contents"title="Table of contents"rel="contents">Contents</a>]</p>
Next: <ahref="#How-can-I-turn-a-string-into-a-variable_003f"accesskey="n"rel="next">How can I turn a string into a variable?</a>, Previous: <ahref="#How-do-I-produce-PNG-graphics-in-batch-mode_003f"accesskey="p"rel="prev">How do I produce PNG graphics in batch mode?</a>, Up: <ahref="#R-Miscellanea"accesskey="u"rel="up">R Miscellanea</a> [<ahref="#SEC_Contents"title="Table of contents"rel="contents">Contents</a>]</p>
Next: <ahref="#Why-do-lattice_002ftrellis-graphics-not-work_003f"accesskey="n"rel="next">Why do lattice/trellis graphics not work?</a>, Previous: <ahref="#How-can-I-get-command-line-editing-to-work_003f"accesskey="p"rel="prev">How can I get command line editing to work?</a>, Up: <ahref="#R-Miscellanea"accesskey="u"rel="up">R Miscellanea</a> [<ahref="#SEC_Contents"title="Table of contents"rel="contents">Contents</a>]</p>
Next: <ahref="#How-can-I-sort-the-rows-of-a-data-frame_003f"accesskey="n"rel="next">How can I sort the rows of a data frame?</a>, Previous: <ahref="#How-can-I-turn-a-string-into-a-variable_003f"accesskey="p"rel="prev">How can I turn a string into a variable?</a>, Up: <ahref="#R-Miscellanea"accesskey="u"rel="up">R Miscellanea</a> [<ahref="#SEC_Contents"title="Table of contents"rel="contents">Contents</a>]</p>
Next: <ahref="#Why-does-the-help_002estart_0028_0029-search-engine-not-work_003f"accesskey="n"rel="next">Why does the help.start() search engine not work?</a>, Previous: <ahref="#Why-do-lattice_002ftrellis-graphics-not-work_003f"accesskey="p"rel="prev">Why do lattice/trellis graphics not work?</a>, Up: <ahref="#R-Miscellanea"accesskey="u"rel="up">R Miscellanea</a> [<ahref="#SEC_Contents"title="Table of contents"rel="contents">Contents</a>]</p>
Next: <ahref="#Why-did-my-_002eRprofile-stop-working-when-I-updated-R_003f"accesskey="n"rel="next">Why did my .Rprofile stop working when I updated R?</a>, Previous: <ahref="#How-can-I-sort-the-rows-of-a-data-frame_003f"accesskey="p"rel="prev">How can I sort the rows of a data frame?</a>, Up: <ahref="#R-Miscellanea"accesskey="u"rel="up">R Miscellanea</a> [<ahref="#SEC_Contents"title="Table of contents"rel="contents">Contents</a>]</p>
<h3class="section">7.24 Why does the help.start() search engine not work?</h3>
<p>The browser-based search engine in <code>help.start()</code> utilizes a Java
applet. In order for this to function properly, a compatible version of
Java must installed on your system and linked to your browser, and both
Java <em>and</em> JavaScript need to be enabled in your browser.
</p>
<p>There have been a number of compatibility issues with versions of Java
and of browsers.
For further details please consult section “Enabling search in HTML
help” in <cite>R Installation and Administration</cite>. This manual is
included in the R distribution, see <ahref="#What-documentation-exists-for-R_003f">What documentation exists for R?</a>, and its <acronym>HTML</acronym> version is linked from the <acronym>HTML</acronym>
Next: <ahref="#Where-have-all-the-methods-gone_003f"accesskey="n"rel="next">Where have all the methods gone?</a>, Previous: <ahref="#Why-does-the-help_002estart_0028_0029-search-engine-not-work_003f"accesskey="p"rel="prev">Why does the help.start() search engine not work?</a>, Up: <ahref="#R-Miscellanea"accesskey="u"rel="up">R Miscellanea</a> [<ahref="#SEC_Contents"title="Table of contents"rel="contents">Contents</a>]</p>
Next: <ahref="#How-can-I-create-rotated-axis-labels_003f"accesskey="n"rel="next">How can I create rotated axis labels?</a>, Previous: <ahref="#Why-did-my-_002eRprofile-stop-working-when-I-updated-R_003f"accesskey="p"rel="prev">Why did my .Rprofile stop working when I updated R?</a>, Up: <ahref="#R-Miscellanea"accesskey="u"rel="up">R Miscellanea</a> [<ahref="#SEC_Contents"title="Table of contents"rel="contents">Contents</a>]</p>
Next: <ahref="#Why-is-read_002etable_0028_0029-so-inefficient_003f"accesskey="n"rel="next">Why is read.table() so inefficient?</a>, Previous: <ahref="#Where-have-all-the-methods-gone_003f"accesskey="p"rel="prev">Where have all the methods gone?</a>, Up: <ahref="#R-Miscellanea"accesskey="u"rel="up">R Miscellanea</a> [<ahref="#SEC_Contents"title="Table of contents"rel="contents">Contents</a>]</p>
Next: <ahref="#What-is-the-difference-between-package-and-library_003f"accesskey="n"rel="next">What is the difference between package and library?</a>, Previous: <ahref="#How-can-I-create-rotated-axis-labels_003f"accesskey="p"rel="prev">How can I create rotated axis labels?</a>, Up: <ahref="#R-Miscellanea"accesskey="u"rel="up">R Miscellanea</a> [<ahref="#SEC_Contents"title="Table of contents"rel="contents">Contents</a>]</p>
Next: <ahref="#I-installed-a-package-but-the-functions-are-not-there"accesskey="n"rel="next">I installed a package but the functions are not there</a>, Previous: <ahref="#Why-is-read_002etable_0028_0029-so-inefficient_003f"accesskey="p"rel="prev">Why is read.table() so inefficient?</a>, Up: <ahref="#R-Miscellanea"accesskey="u"rel="up">R Miscellanea</a> [<ahref="#SEC_Contents"title="Table of contents"rel="contents">Contents</a>]</p>
Next: <ahref="#Why-doesn_0027t-R-think-these-numbers-are-equal_003f"accesskey="n"rel="next">Why doesn't R think these numbers are equal?</a>, Previous: <ahref="#What-is-the-difference-between-package-and-library_003f"accesskey="p"rel="prev">What is the difference between package and library?</a>, Up: <ahref="#R-Miscellanea"accesskey="u"rel="up">R Miscellanea</a> [<ahref="#SEC_Contents"title="Table of contents"rel="contents">Contents</a>]</p>
<h3class="section">7.30 I installed a package but the functions are not there</h3>
<p>To actually <em>use</em> the package, it needs to be <em>loaded</em> using
<code>library()</code>.
</p>
<p>See <ahref="#R-Add_002dOn-Packages">R Add-On Packages</a> and <ahref="#What-is-the-difference-between-package-and-library_003f">What is the difference between package and library?</a> for more information.
Next: <ahref="#How-can-I-capture-or-ignore-errors-in-a-long-simulation_003f"accesskey="n"rel="next">How can I capture or ignore errors in a long simulation?</a>, Previous: <ahref="#I-installed-a-package-but-the-functions-are-not-there"accesskey="p"rel="prev">I installed a package but the functions are not there</a>, Up: <ahref="#R-Miscellanea"accesskey="u"rel="up">R Miscellanea</a> [<ahref="#SEC_Contents"title="Table of contents"rel="contents">Contents</a>]</p>
Next: <ahref="#Why-are-powers-of-negative-numbers-wrong_003f"accesskey="n"rel="next">Why are powers of negative numbers wrong?</a>, Previous: <ahref="#Why-doesn_0027t-R-think-these-numbers-are-equal_003f"accesskey="p"rel="prev">Why doesn't R think these numbers are equal?</a>, Up: <ahref="#R-Miscellanea"accesskey="u"rel="up">R Miscellanea</a> [<ahref="#SEC_Contents"title="Table of contents"rel="contents">Contents</a>]</p>
Next: <ahref="#How-can-I-save-the-result-of-each-iteration-in-a-loop-into-a-separate-file_003f"accesskey="n"rel="next">How can I save the result of each iteration in a loop into a separate file?</a>, Previous: <ahref="#How-can-I-capture-or-ignore-errors-in-a-long-simulation_003f"accesskey="p"rel="prev">How can I capture or ignore errors in a long simulation?</a>, Up: <ahref="#R-Miscellanea"accesskey="u"rel="up">R Miscellanea</a> [<ahref="#SEC_Contents"title="Table of contents"rel="contents">Contents</a>]</p>
Next: <ahref="#Why-are-p_002dvalues-not-displayed-when-using-lmer_0028_0029_003f"accesskey="n"rel="next">Why are p-values not displayed when using lmer()?</a>, Previous: <ahref="#Why-are-powers-of-negative-numbers-wrong_003f"accesskey="p"rel="prev">Why are powers of negative numbers wrong?</a>, Up: <ahref="#R-Miscellanea"accesskey="u"rel="up">R Miscellanea</a> [<ahref="#SEC_Contents"title="Table of contents"rel="contents">Contents</a>]</p>
Next: <ahref="#Why-are-there-unwanted-borders"accesskey="n"rel="next">Why are there unwanted borders</a>, Previous: <ahref="#How-can-I-save-the-result-of-each-iteration-in-a-loop-into-a-separate-file_003f"accesskey="p"rel="prev">How can I save the result of each iteration in a loop into a separate file?</a>, Up: <ahref="#R-Miscellanea"accesskey="u"rel="up">R Miscellanea</a> [<ahref="#SEC_Contents"title="Table of contents"rel="contents">Contents</a>]</p>
Next: <ahref="#Why-does-backslash-behave-strangely-inside-strings_003f"accesskey="n"rel="next">Why does backslash behave strangely inside strings?</a>, Previous: <ahref="#Why-are-p_002dvalues-not-displayed-when-using-lmer_0028_0029_003f"accesskey="p"rel="prev">Why are p-values not displayed when using lmer()?</a>, Up: <ahref="#R-Miscellanea"accesskey="u"rel="up">R Miscellanea</a> [<ahref="#SEC_Contents"title="Table of contents"rel="contents">Contents</a>]</p>
Next: <ahref="#How-can-I-put-error-bars-or-confidence-bands-on-my-plot_003f"accesskey="n"rel="next">How can I put error bars or confidence bands on my plot?</a>, Previous: <ahref="#Why-are-there-unwanted-borders"accesskey="p"rel="prev">Why are there unwanted borders</a>, Up: <ahref="#R-Miscellanea"accesskey="u"rel="up">R Miscellanea</a> [<ahref="#SEC_Contents"title="Table of contents"rel="contents">Contents</a>]</p>
Next: <ahref="#How-do-I-create-a-plot-with-two-y_002daxes_003f"accesskey="n"rel="next">How do I create a plot with two y-axes?</a>, Previous: <ahref="#Why-does-backslash-behave-strangely-inside-strings_003f"accesskey="p"rel="prev">Why does backslash behave strangely inside strings?</a>, Up: <ahref="#R-Miscellanea"accesskey="u"rel="up">R Miscellanea</a> [<ahref="#SEC_Contents"title="Table of contents"rel="contents">Contents</a>]</p>
Next: <ahref="#How-do-I-access-the-source-code-for-a-function_003f"accesskey="n"rel="next">How do I access the source code for a function?</a>, Previous: <ahref="#How-can-I-put-error-bars-or-confidence-bands-on-my-plot_003f"accesskey="p"rel="prev">How can I put error bars or confidence bands on my plot?</a>, Up: <ahref="#R-Miscellanea"accesskey="u"rel="up">R Miscellanea</a> [<ahref="#SEC_Contents"title="Table of contents"rel="contents">Contents</a>]</p>
Next: <ahref="#Why-does-summary_0028_0029-report-strange-results-for-the-R_005e2-estimate-when-I-fit-a-linear-model-with-no-intercept_003f"accesskey="n"rel="next">Why does summary() report strange results for the R^2 estimate when I fit a linear model with no intercept?</a>, Previous: <ahref="#How-do-I-create-a-plot-with-two-y_002daxes_003f"accesskey="p"rel="prev">How do I create a plot with two y-axes?</a>, Up: <ahref="#R-Miscellanea"accesskey="u"rel="up">R Miscellanea</a> [<ahref="#SEC_Contents"title="Table of contents"rel="contents">Contents</a>]</p>
Next: <ahref="#Why-is-R-apparently-not-releasing-memory_003f"accesskey="n"rel="next">Why is R apparently not releasing memory?</a>, Previous: <ahref="#How-do-I-access-the-source-code-for-a-function_003f"accesskey="p"rel="prev">How do I access the source code for a function?</a>, Up: <ahref="#R-Miscellanea"accesskey="u"rel="up">R Miscellanea</a> [<ahref="#SEC_Contents"title="Table of contents"rel="contents">Contents</a>]</p>
Next: <ahref="#How-can-I-enable-secure-https-downloads-in-R_003f"accesskey="n"rel="next">How can I enable secure https downloads in R?</a>, Previous: <ahref="#Why-does-summary_0028_0029-report-strange-results-for-the-R_005e2-estimate-when-I-fit-a-linear-model-with-no-intercept_003f"accesskey="p"rel="prev">Why does summary() report strange results for the R^2 estimate when I fit a linear model with no intercept?</a>, Up: <ahref="#R-Miscellanea"accesskey="u"rel="up">R Miscellanea</a> [<ahref="#SEC_Contents"title="Table of contents"rel="contents">Contents</a>]</p>
Next: <ahref="#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: <ahref="#Why-is-R-apparently-not-releasing-memory_003f"accesskey="p"rel="prev">Why is R apparently not releasing memory?</a>, Up: <ahref="#R-Miscellanea"accesskey="u"rel="up">R Miscellanea</a> [<ahref="#SEC_Contents"title="Table of contents"rel="contents">Contents</a>]</p>
Previous: <ahref="#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: <ahref="#R-Miscellanea"accesskey="u"rel="up">R Miscellanea</a> [<ahref="#SEC_Contents"title="Table of contents"rel="contents">Contents</a>]</p>
<tr><tdalign="left"valign="top">•<ahref="#How-should-I-write-summary-methods_003f"accesskey="1">How should I write summary methods?</a>:</td><td> </td><tdalign="left"valign="top">
</td></tr>
<tr><tdalign="left"valign="top">•<ahref="#How-can-I-debug-dynamically-loaded-code_003f"accesskey="2">How can I debug dynamically loaded code?</a>:</td><td> </td><tdalign="left"valign="top">
</td></tr>
<tr><tdalign="left"valign="top">•<ahref="#How-can-I-inspect-R-objects-when-debugging_003f"accesskey="3">How can I inspect R objects when debugging?</a>:</td><td> </td><tdalign="left"valign="top">
</td></tr>
<tr><tdalign="left"valign="top">•<ahref="#How-can-I-change-compilation-flags_003f"accesskey="4">How can I change compilation flags?</a>:</td><td> </td><tdalign="left"valign="top">
</td></tr>
<tr><tdalign="left"valign="top">•<ahref="#How-can-I-debug-S4-methods_003f"accesskey="5">How can I debug S4 methods?</a>:</td><td> </td><tdalign="left"valign="top">
Next: <ahref="#How-can-I-inspect-R-objects-when-debugging_003f"accesskey="n"rel="next">How can I inspect R objects when debugging?</a>, Previous: <ahref="#How-should-I-write-summary-methods_003f"accesskey="p"rel="prev">How should I write summary methods?</a>, Up: <ahref="#R-Programming"accesskey="u"rel="up">R Programming</a> [<ahref="#SEC_Contents"title="Table of contents"rel="contents">Contents</a>]</p>
Next: <ahref="#How-can-I-change-compilation-flags_003f"accesskey="n"rel="next">How can I change compilation flags?</a>, Previous: <ahref="#How-can-I-debug-dynamically-loaded-code_003f"accesskey="p"rel="prev">How can I debug dynamically loaded code?</a>, Up: <ahref="#R-Programming"accesskey="u"rel="up">R Programming</a> [<ahref="#SEC_Contents"title="Table of contents"rel="contents">Contents</a>]</p>
Next: <ahref="#How-can-I-debug-S4-methods_003f"accesskey="n"rel="next">How can I debug S4 methods?</a>, Previous: <ahref="#How-can-I-inspect-R-objects-when-debugging_003f"accesskey="p"rel="prev">How can I inspect R objects when debugging?</a>, Up: <ahref="#R-Programming"accesskey="u"rel="up">R Programming</a> [<ahref="#SEC_Contents"title="Table of contents"rel="contents">Contents</a>]</p>
<h3class="section">8.4 How can I change compilation flags?</h3>
<p>Suppose you have C code file for dynloading into R, but you want to use
<code>R CMD SHLIB</code> with compilation flags other than the default ones
(which were determined when R was built).
</p>
<p>Starting with R 2.1.0, users can provide personal Makevars configuration
files in <samp>$<code>HOME</code>/.R</samp> to override the default flags.
See section “Add-on packages” in <cite>R Installation and
Administration</cite>.
</p>
<p>For earlier versions of R, you could change the file
<samp><var>R_HOME</var>/etc/Makeconf</samp> to reflect your preferences, or (at
least for systems using <acronym>GNU</acronym> Make) override them by the
environment variable <code>MAKEFLAGS</code>.
See section “Creating shared objects” in <cite>Writing R Extensions</cite>.
</p>
<hr>
<aname="How-can-I-debug-S4-methods_003f"></a>
<divclass="header">
<p>
Previous: <ahref="#How-can-I-change-compilation-flags_003f"accesskey="p"rel="prev">How can I change compilation flags?</a>, Up: <ahref="#R-Programming"accesskey="u"rel="up">R Programming</a> [<ahref="#SEC_Contents"title="Table of contents"rel="contents">Contents</a>]</p>
</div>
<aname="How-can-I-debug-S4-methods_003f-1"></a>
<h3class="section">8.5 How can I debug S4 methods?</h3>
<p>Use the <code>trace()</code> function with argument <code>signature=</code> to add
calls to the browser or any other code to the method that will be
dispatched for the corresponding signature. See <code>?trace</code> for
details.
</p>
<hr>
<aname="R-Bugs"></a>
<divclass="header">
<p>
Next: <ahref="#Acknowledgments"accesskey="n"rel="next">Acknowledgments</a>, Previous: <ahref="#R-Programming"accesskey="p"rel="prev">R Programming</a>, Up: <ahref="#Top"accesskey="u"rel="up">Top</a> [<ahref="#SEC_Contents"title="Table of contents"rel="contents">Contents</a>]</p>
<tr><tdalign="left"valign="top">•<ahref="#What-is-a-bug_003f"accesskey="1">What is a bug?</a>:</td><td> </td><tdalign="left"valign="top">
</td></tr>
<tr><tdalign="left"valign="top">•<ahref="#How-to-report-a-bug"accesskey="2">How to report a bug</a>:</td><td> </td><tdalign="left"valign="top">
</td></tr>
</table>
<hr>
<aname="What-is-a-bug_003f"></a>
<divclass="header">
<p>
Next: <ahref="#How-to-report-a-bug"accesskey="n"rel="next">How to report a bug</a>, Previous: <ahref="#R-Bugs"accesskey="p"rel="prev">R Bugs</a>, Up: <ahref="#R-Bugs"accesskey="u"rel="up">R Bugs</a> [<ahref="#SEC_Contents"title="Table of contents"rel="contents">Contents</a>]</p>
</div>
<aname="What-is-a-bug_003f-1"></a>
<h3class="section">9.1 What is a bug?</h3>
<p>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
<code>.C()</code>, <code>.Fortran()</code>, <code>.External()</code> or <code>.Call()</code> (or
<code>.Internal()</code>) yourself (or in a function you wrote), you can
always crash R by using wrong argument types (modes). This is not a
bug.
</p>
<p>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 <em>know</em> 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.
</p>
<p>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. For example, people sometimes
think there is a bug in R’s mathematics because they don’t understand
how finite-precision arithmetic works. Rather than jumping to
conclusions, show the problem to someone who knows for certain.
Unexpected results of comparison of decimal numbers, for example
<code>0.28 * 100 != 28</code> or <code>0.1 + 0.2 != 0.3</code>, are not a bug.
See <ahref="#Why-doesn_0027t-R-think-these-numbers-are-equal_003f">Why doesn't R think these numbers are equal?</a>, for more details.
</p>
<p>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.
</p>
<p>If the online argument list of a function disagrees with the manual, one
of them must be wrong, so report the bug.
</p>
<hr>
<aname="How-to-report-a-bug"></a>
<divclass="header">
<p>
Previous: <ahref="#What-is-a-bug_003f"accesskey="p"rel="prev">What is a bug?</a>, Up: <ahref="#R-Bugs"accesskey="u"rel="up">R Bugs</a> [<ahref="#SEC_Contents"title="Table of contents"rel="contents">Contents</a>]</p>
</div>
<aname="How-to-report-a-bug-1"></a>
<h3class="section">9.2 How to report a bug</h3>
<p>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 <kbd>version</kbd> in
R to print this.
</p>
<p>The most important principle in reporting a bug is to report
<em>facts</em>, 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.
</p>
<p>For example, suppose that on a data set which you know to be quite large
the command
</p>
<divclass="example">
<preclass="example">R> data.frame(x, y, z, monday, tuesday)
</pre></div>
<p>never returns. Do not report that <code>data.frame()</code> 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
<code>data.frame()</code> 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.
</p>
<p>Or perhaps the command fails because the last command you used was a
method for <code>"["()</code> that had a bug causing R’s internal data
structures to be corrupted and making the <code>data.frame()</code> command
fail from then on. This is why others need to know what other commands
you have typed (or read from your startup file).
</p>
<p>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
(e.g., <ahref="https://en.wikipedia.org/wiki/Reproducibility">https://en.wikipedia.org/wiki/Reproducibility</a>) the problem,
preferably the simplest one you have found.
</p>
<p>Invoking R with the <samp>--vanilla</samp> option may help in isolating a
bug. This ensures that the site profile and saved data files are not
read.
</p>
<p>Before you actually submit a bug report, you should check whether the
bug has already been reported and/or fixed. First, try the “Show open
