4226 lines
235 KiB
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4226 lines
235 KiB
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<h1 class="settitle" align="center">R FAQ</h1>
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<h2>Frequently Asked Questions on R</h2>
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<h3 style="text-align: center;">Version 3.2.2015-12-04</h3>
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<h3 style="text-align: center;">Kurt Hornik</h3>
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<hr>
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<a name="SEC_Contents"></a>
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<h2 class="contents-heading">Table of Contents</h2>
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<div class="contents">
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<ul class="no-bullet">
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<li><a name="toc-Introduction-1" href="#Introduction">1 Introduction</a>
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<ul class="no-bullet">
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<li><a name="toc-Legalese-1" href="#Legalese">1.1 Legalese</a></li>
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<li><a name="toc-Obtaining-this-document-1" href="#Obtaining-this-document">1.2 Obtaining this document</a></li>
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<li><a name="toc-Citing-this-document-1" href="#Citing-this-document">1.3 Citing this document</a></li>
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<li><a name="toc-Notation-1" href="#Notation">1.4 Notation</a></li>
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<li><a name="toc-Feedback-1" href="#Feedback">1.5 Feedback</a></li>
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</ul></li>
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<li><a name="toc-R-Basics-1" href="#R-Basics">2 R Basics</a>
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<ul class="no-bullet">
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<li><a name="toc-What-is-R_003f-1" href="#What-is-R_003f">2.1 What is R?</a></li>
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<li><a name="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>
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<li><a name="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>
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<li><a name="toc-How-can-R-be-obtained_003f-1" href="#How-can-R-be-obtained_003f">2.4 How can R be obtained?</a></li>
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<li><a name="toc-How-can-R-be-installed_003f-1" href="#How-can-R-be-installed_003f">2.5 How can R be installed?</a>
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<ul class="no-bullet">
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<li><a name="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>
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<li><a name="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>
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<li><a name="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>
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</ul></li>
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<li><a name="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>
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<li><a name="toc-What-documentation-exists-for-R_003f-1" href="#What-documentation-exists-for-R_003f">2.7 What documentation exists for R?</a></li>
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<li><a name="toc-Citing-R-1" href="#Citing-R">2.8 Citing R</a></li>
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<li><a name="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>
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<li><a name="toc-What-is-CRAN_003f-1" href="#What-is-CRAN_003f">2.10 What is <acronym>CRAN</acronym>?</a></li>
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<li><a name="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>
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<li><a name="toc-Why-is-R-named-R_003f-1" href="#Why-is-R-named-R_003f">2.12 Why is R named R?</a></li>
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<li><a name="toc-What-is-the-R-Foundation_003f-1" href="#What-is-the-R-Foundation_003f">2.13 What is the R Foundation?</a></li>
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<li><a name="toc-What-is-R_002dForge_003f-1" href="#What-is-R_002dForge_003f">2.14 What is R-Forge?</a></li>
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</ul></li>
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<li><a name="toc-R-and-S-1" href="#R-and-S">3 R and S</a>
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<ul class="no-bullet">
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<li><a name="toc-What-is-S_003f-1" href="#What-is-S_003f">3.1 What is S?</a></li>
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<li><a name="toc-What-is-S_002dPLUS_003f-1" href="#What-is-S_002dPLUS_003f">3.2 What is <small>S-PLUS</small>?</a></li>
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<li><a name="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>
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<ul class="no-bullet">
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<li><a name="toc-Lexical-scoping-1" href="#Lexical-scoping">3.3.1 Lexical scoping</a></li>
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<li><a name="toc-Models-1" href="#Models">3.3.2 Models</a></li>
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<li><a name="toc-Others-1" href="#Others">3.3.3 Others</a></li>
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</ul></li>
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<li><a name="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>
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<li><a name="toc-What-is-R_002dplus_003f-1" href="#What-is-R_002dplus_003f">3.5 What is R-plus?</a></li>
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</ul></li>
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<li><a name="toc-R-Web-Interfaces-1" href="#R-Web-Interfaces">4 R Web Interfaces</a></li>
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<li><a name="toc-R-Add_002dOn-Packages-1" href="#R-Add_002dOn-Packages">5 R Add-On Packages</a>
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<ul class="no-bullet">
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<li><a name="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>
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<ul class="no-bullet">
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<li><a name="toc-Add_002don-packages-in-R-1" href="#Add_002don-packages-in-R">5.1.1 Add-on packages in R</a></li>
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<li><a name="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>
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<li><a name="toc-Add_002don-packages-from-Omegahat-1" href="#Add_002don-packages-from-Omegahat">5.1.3 Add-on packages from Omegahat</a></li>
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<li><a name="toc-Add_002don-packages-from-Bioconductor-1" href="#Add_002don-packages-from-Bioconductor">5.1.4 Add-on packages from Bioconductor</a></li>
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<li><a name="toc-Other-add_002don-packages-1" href="#Other-add_002don-packages">5.1.5 Other add-on packages</a></li>
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</ul></li>
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<li><a name="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>
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<li><a name="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>
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<li><a name="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>
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<li><a name="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>
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<li><a name="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>
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</ul></li>
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<li><a name="toc-R-and-Emacs-1" href="#R-and-Emacs">6 R and Emacs</a>
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<ul class="no-bullet">
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<li><a name="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>
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<li><a name="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>
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<li><a name="toc-Debugging-R-from-within-Emacs-1" href="#Debugging-R-from-within-Emacs">6.3 Debugging R from within Emacs</a></li>
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</ul></li>
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<li><a name="toc-R-Miscellanea-1" href="#R-Miscellanea">7 R Miscellanea</a>
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<ul class="no-bullet">
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<li><a name="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>
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<li><a name="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>
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<li><a name="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>
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<li><a name="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>
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<li><a name="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>
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<li><a name="toc-How-does-autoloading-work_003f-1" href="#How-does-autoloading-work_003f">7.6 How does autoloading work?</a></li>
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<li><a name="toc-How-should-I-set-options_003f-1" href="#How-should-I-set-options_003f">7.7 How should I set options?</a></li>
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<li><a name="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>
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<li><a name="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>
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<li><a name="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>
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<li><a name="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>
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<li><a name="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>
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<li><a name="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>
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<li><a name="toc-What-are-valid-names_003f-1" href="#What-are-valid-names_003f">7.14 What are valid names?</a></li>
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<li><a name="toc-Are-GAMs-implemented-in-R_003f-1" href="#Are-GAMs-implemented-in-R_003f">7.15 Are GAMs implemented in R?</a></li>
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<li><a name="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>
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<li><a name="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>
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<li><a name="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>
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<li><a name="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>
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<li><a name="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>
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<li><a name="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>
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<li><a name="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>
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<li><a name="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>
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<li><a name="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>
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<li><a name="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>
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<li><a name="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>
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<li><a name="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>
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<li><a name="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>
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<li><a name="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>
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<li><a name="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>
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<li><a name="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>
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<li><a name="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>
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<li><a name="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>
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<li><a name="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>
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<li><a name="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>
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<li><a name="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><a name="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><a name="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><a name="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><a name="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><a name="toc-Why-does-summary_0028_0029-report-strange-results-for-the-R_005e2-estimate-when-I-fit-a-linear-model-with-no-intercept_003f-1" href="#Why-does-summary_0028_0029-report-strange-results-for-the-R_005e2-estimate-when-I-fit-a-linear-model-with-no-intercept_003f">7.41 Why does summary() report strange results for the R^2 estimate when I fit a linear model with no intercept?</a></li>
|
|
<li><a name="toc-Why-is-R-apparently-not-releasing-memory_003f-1" href="#Why-is-R-apparently-not-releasing-memory_003f">7.42 Why is R apparently not releasing memory?</a></li>
|
|
<li><a name="toc-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>
|
|
</ul></li>
|
|
<li><a name="toc-R-Programming-1" href="#R-Programming">8 R Programming</a>
|
|
<ul class="no-bullet">
|
|
<li><a name="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><a name="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><a name="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><a name="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><a name="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><a name="toc-R-Bugs-1" href="#R-Bugs">9 R Bugs</a>
|
|
<ul class="no-bullet">
|
|
<li><a name="toc-What-is-a-bug_003f-1" href="#What-is-a-bug_003f">9.1 What is a bug?</a></li>
|
|
<li><a name="toc-How-to-report-a-bug-1" href="#How-to-report-a-bug">9.2 How to report a bug</a></li>
|
|
</ul></li>
|
|
<li><a name="toc-Acknowledgments-1" href="#Acknowledgments">10 Acknowledgments</a></li>
|
|
</ul>
|
|
</div>
|
|
|
|
|
|
<a name="Top"></a>
|
|
<div class="header">
|
|
<p>
|
|
Next: <a href="#Introduction" accesskey="n" rel="next">Introduction</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
|
|
</div>
|
|
<a name="R-FAQ"></a>
|
|
<h1 class="top">R FAQ</h1>
|
|
|
|
<table summary="" class="menu" border="0" cellspacing="0">
|
|
<tr><td align="left" valign="top">• <a href="#Introduction" accesskey="1">Introduction</a>:</td><td> </td><td align="left" valign="top">
|
|
</td></tr>
|
|
<tr><td align="left" valign="top">• <a href="#R-Basics" accesskey="2">R Basics</a>:</td><td> </td><td align="left" valign="top">
|
|
</td></tr>
|
|
<tr><td align="left" valign="top">• <a href="#R-and-S" accesskey="3">R and S</a>:</td><td> </td><td align="left" valign="top">
|
|
</td></tr>
|
|
<tr><td align="left" valign="top">• <a href="#R-Web-Interfaces" accesskey="4">R Web Interfaces</a>:</td><td> </td><td align="left" valign="top">
|
|
</td></tr>
|
|
<tr><td align="left" valign="top">• <a href="#R-Add_002dOn-Packages" accesskey="5">R Add-On Packages</a>:</td><td> </td><td align="left" valign="top">
|
|
</td></tr>
|
|
<tr><td align="left" valign="top">• <a href="#R-and-Emacs" accesskey="6">R and Emacs</a>:</td><td> </td><td align="left" valign="top">
|
|
</td></tr>
|
|
<tr><td align="left" valign="top">• <a href="#R-Miscellanea" accesskey="7">R Miscellanea</a>:</td><td> </td><td align="left" valign="top">
|
|
</td></tr>
|
|
<tr><td align="left" valign="top">• <a href="#R-Programming" accesskey="8">R Programming</a>:</td><td> </td><td align="left" valign="top">
|
|
</td></tr>
|
|
<tr><td align="left" valign="top">• <a href="#R-Bugs" accesskey="9">R Bugs</a>:</td><td> </td><td align="left" valign="top">
|
|
</td></tr>
|
|
<tr><td align="left" valign="top">• <a href="#Acknowledgments">Acknowledgments</a>:</td><td> </td><td align="left" valign="top">
|
|
</td></tr>
|
|
</table>
|
|
|
|
<hr>
|
|
<a name="Introduction"></a>
|
|
<div class="header">
|
|
<p>
|
|
Next: <a href="#R-Basics" accesskey="n" rel="next">R Basics</a>, Previous: <a href="#Top" accesskey="p" rel="prev">Top</a>, Up: <a href="#Top" accesskey="u" rel="up">Top</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
|
|
</div>
|
|
<a name="Introduction-1"></a>
|
|
<h2 class="chapter">1 Introduction</h2>
|
|
|
|
<p>This document contains answers to some of the most frequently asked
|
|
questions about R.
|
|
</p>
|
|
<table summary="" class="menu" border="0" cellspacing="0">
|
|
<tr><td align="left" valign="top">• <a href="#Legalese" accesskey="1">Legalese</a>:</td><td> </td><td align="left" valign="top">
|
|
</td></tr>
|
|
<tr><td align="left" valign="top">• <a href="#Obtaining-this-document" accesskey="2">Obtaining this document</a>:</td><td> </td><td align="left" valign="top">
|
|
</td></tr>
|
|
<tr><td align="left" valign="top">• <a href="#Citing-this-document" accesskey="3">Citing this document</a>:</td><td> </td><td align="left" valign="top">
|
|
</td></tr>
|
|
<tr><td align="left" valign="top">• <a href="#Notation" accesskey="4">Notation</a>:</td><td> </td><td align="left" valign="top">
|
|
</td></tr>
|
|
<tr><td align="left" valign="top">• <a href="#Feedback" accesskey="5">Feedback</a>:</td><td> </td><td align="left" valign="top">
|
|
</td></tr>
|
|
</table>
|
|
|
|
<hr>
|
|
<a name="Legalese"></a>
|
|
<div class="header">
|
|
<p>
|
|
Next: <a href="#Obtaining-this-document" accesskey="n" rel="next">Obtaining this document</a>, Previous: <a href="#Introduction" accesskey="p" rel="prev">Introduction</a>, Up: <a href="#Introduction" accesskey="u" rel="up">Introduction</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
|
|
</div>
|
|
<a name="Legalese-1"></a>
|
|
<h3 class="section">1.1 Legalese</h3>
|
|
|
|
<p>This document is copyright © 1998–2015 by Kurt
|
|
Hornik.
|
|
</p>
|
|
<p>This document is free software; you can redistribute it and/or modify it
|
|
under the terms of the <acronym>GNU</acronym> General Public License as published
|
|
by the Free Software Foundation; either version 2, or (at your option)
|
|
any later version.
|
|
</p>
|
|
<p>This document is distributed in the hope that it will be useful, but
|
|
WITHOUT ANY WARRANTY; without even the implied warranty of
|
|
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
|
|
<acronym>GNU</acronym> General Public License for more details.
|
|
</p>
|
|
<p>Copies of the <acronym>GNU</acronym> General Public License versions are
|
|
available at
|
|
</p>
|
|
<div class="display">
|
|
<pre class="display"><a href="https://www.R-project.org/Licenses/">https://www.R-project.org/Licenses/</a>
|
|
</pre></div>
|
|
|
|
|
|
<hr>
|
|
<a name="Obtaining-this-document"></a>
|
|
<div class="header">
|
|
<p>
|
|
Next: <a href="#Citing-this-document" accesskey="n" rel="next">Citing this document</a>, Previous: <a href="#Legalese" accesskey="p" rel="prev">Legalese</a>, Up: <a href="#Introduction" accesskey="u" rel="up">Introduction</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
|
|
</div>
|
|
<a name="Obtaining-this-document-1"></a>
|
|
<h3 class="section">1.2 Obtaining this document</h3>
|
|
|
|
<p>The latest version of this document is always available from
|
|
</p>
|
|
<div class="display">
|
|
<pre class="display"><a href="https://CRAN.R-project.org/doc/FAQ/">https://CRAN.R-project.org/doc/FAQ/</a>
|
|
</pre></div>
|
|
|
|
<p>From there, you can obtain versions converted to
|
|
<a href="https://CRAN.R-project.org/doc/FAQ/R-FAQ.txt">plain
|
|
<acronym>ASCII</acronym> text</a>,
|
|
<a href="https://CRAN.R-project.org/doc/FAQ/R-FAQ.info.gz"><acronym>GNU</acronym>
|
|
info</a>, <a href="https://CRAN.R-project.org/doc/FAQ/R-FAQ.html"><acronym>HTML</acronym></a>,
|
|
<a href="https://CRAN.R-project.org/doc/FAQ/R-FAQ.pdf">PDF</a>,
|
|
as well as the <a href="https://CRAN.R-project.org/doc/FAQ/R-FAQ.texi">Texinfo source</a> used for creating all these formats using the
|
|
<acronym>GNU</acronym> Texinfo system.
|
|
</p>
|
|
<p>You can also obtain the R <acronym>FAQ</acronym> from the <samp>doc/FAQ</samp>
|
|
subdirectory of a <acronym>CRAN</acronym> site (see <a href="#What-is-CRAN_003f">What is CRAN?</a>).
|
|
</p>
|
|
<hr>
|
|
<a name="Citing-this-document"></a>
|
|
<div class="header">
|
|
<p>
|
|
Next: <a href="#Notation" accesskey="n" rel="next">Notation</a>, Previous: <a href="#Obtaining-this-document" accesskey="p" rel="prev">Obtaining this document</a>, Up: <a href="#Introduction" accesskey="u" rel="up">Introduction</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
|
|
</div>
|
|
<a name="Citing-this-document-1"></a>
|
|
<h3 class="section">1.3 Citing this document</h3>
|
|
|
|
<p>In publications, please refer to this <acronym>FAQ</acronym> as Hornik
|
|
(2015), “The R <acronym>FAQ</acronym>”, and give the above,
|
|
<em>official</em> <acronym>URL</acronym>:
|
|
</p>
|
|
<div class="example">
|
|
<pre class="example">@Misc{,
|
|
author = {Kurt Hornik},
|
|
title = {{R} {FAQ}},
|
|
year = {2015},
|
|
url = {https://CRAN.R-project.org/doc/FAQ/R-FAQ.html}
|
|
}
|
|
</pre></div>
|
|
|
|
|
|
<hr>
|
|
<a name="Notation"></a>
|
|
<div class="header">
|
|
<p>
|
|
Next: <a href="#Feedback" accesskey="n" rel="next">Feedback</a>, Previous: <a href="#Citing-this-document" accesskey="p" rel="prev">Citing this document</a>, Up: <a href="#Introduction" accesskey="u" rel="up">Introduction</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
|
|
</div>
|
|
<a name="Notation-1"></a>
|
|
<h3 class="section">1.4 Notation</h3>
|
|
|
|
<p>Everything should be pretty standard. ‘<samp>R></samp>’ is used for the R
|
|
prompt, and a ‘<samp>$</samp>’ for the shell prompt (where applicable).
|
|
</p>
|
|
<hr>
|
|
<a name="Feedback"></a>
|
|
<div class="header">
|
|
<p>
|
|
Previous: <a href="#Notation" accesskey="p" rel="prev">Notation</a>, Up: <a href="#Introduction" accesskey="u" rel="up">Introduction</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
|
|
</div>
|
|
<a name="Feedback-1"></a>
|
|
<h3 class="section">1.5 Feedback</h3>
|
|
|
|
<p>Feedback via email to <a href="mailto:Kurt.Hornik@R-project.org">Kurt.Hornik@R-project.org</a> is of course
|
|
most welcome.
|
|
</p>
|
|
<p>In particular, note that I do not have access to Windows or Mac
|
|
systems. Features specific to the Windows and OS X ports of R are
|
|
described in the
|
|
<a href="https://CRAN.R-project.org/bin/windows/base/rw-FAQ.html">“R for
|
|
Windows <acronym>FAQ</acronym>”</a> and the
|
|
<a href="https://CRAN.R-project.org/bin/macosx/RMacOSX-FAQ.html">“R for Mac
|
|
OS X <acronym>FAQ</acronym>”</a>. If you have information on Mac or Windows
|
|
systems that you think should be added to this document, please let me
|
|
know.
|
|
</p>
|
|
|
|
<hr>
|
|
<a name="R-Basics"></a>
|
|
<div class="header">
|
|
<p>
|
|
Next: <a href="#R-and-S" accesskey="n" rel="next">R and S</a>, Previous: <a href="#Introduction" accesskey="p" rel="prev">Introduction</a>, Up: <a href="#Top" accesskey="u" rel="up">Top</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
|
|
</div>
|
|
<a name="R-Basics-1"></a>
|
|
<h2 class="chapter">2 R Basics</h2>
|
|
|
|
<table summary="" class="menu" border="0" cellspacing="0">
|
|
<tr><td align="left" valign="top">• <a href="#What-is-R_003f" accesskey="1">What is R?</a>:</td><td> </td><td align="left" valign="top">
|
|
</td></tr>
|
|
<tr><td align="left" valign="top">• <a href="#What-machines-does-R-run-on_003f" accesskey="2">What machines does R run on?</a>:</td><td> </td><td align="left" valign="top">
|
|
</td></tr>
|
|
<tr><td align="left" valign="top">• <a href="#What-is-the-current-version-of-R_003f" accesskey="3">What is the current version of R?</a>:</td><td> </td><td align="left" valign="top">
|
|
</td></tr>
|
|
<tr><td align="left" valign="top">• <a href="#How-can-R-be-obtained_003f" accesskey="4">How can R be obtained?</a>:</td><td> </td><td align="left" valign="top">
|
|
</td></tr>
|
|
<tr><td align="left" valign="top">• <a href="#How-can-R-be-installed_003f" accesskey="5">How can R be installed?</a>:</td><td> </td><td align="left" valign="top">
|
|
</td></tr>
|
|
<tr><td align="left" valign="top">• <a href="#Are-there-Unix_002dlike-binaries-for-R_003f" accesskey="6">Are there Unix-like binaries for R?</a>:</td><td> </td><td align="left" valign="top">
|
|
</td></tr>
|
|
<tr><td align="left" valign="top">• <a href="#What-documentation-exists-for-R_003f" accesskey="7">What documentation exists for R?</a>:</td><td> </td><td align="left" valign="top">
|
|
</td></tr>
|
|
<tr><td align="left" valign="top">• <a href="#Citing-R" accesskey="8">Citing R</a>:</td><td> </td><td align="left" valign="top">
|
|
</td></tr>
|
|
<tr><td align="left" valign="top">• <a href="#What-mailing-lists-exist-for-R_003f" accesskey="9">What mailing lists exist for R?</a>:</td><td> </td><td align="left" valign="top">
|
|
</td></tr>
|
|
<tr><td align="left" valign="top">• <a href="#What-is-CRAN_003f">What is CRAN?</a>:</td><td> </td><td align="left" valign="top">
|
|
</td></tr>
|
|
<tr><td align="left" valign="top">• <a href="#Can-I-use-R-for-commercial-purposes_003f">Can I use R for commercial purposes?</a>:</td><td> </td><td align="left" valign="top">
|
|
</td></tr>
|
|
<tr><td align="left" valign="top">• <a href="#Why-is-R-named-R_003f">Why is R named R?</a>:</td><td> </td><td align="left" valign="top">
|
|
</td></tr>
|
|
<tr><td align="left" valign="top">• <a href="#What-is-the-R-Foundation_003f">What is the R Foundation?</a>:</td><td> </td><td align="left" valign="top">
|
|
</td></tr>
|
|
<tr><td align="left" valign="top">• <a href="#What-is-R_002dForge_003f">What is R-Forge?</a>:</td><td> </td><td align="left" valign="top">
|
|
</td></tr>
|
|
</table>
|
|
|
|
<hr>
|
|
<a name="What-is-R_003f"></a>
|
|
<div class="header">
|
|
<p>
|
|
Next: <a href="#What-machines-does-R-run-on_003f" accesskey="n" rel="next">What machines does R run on?</a>, Previous: <a href="#R-Basics" accesskey="p" rel="prev">R Basics</a>, Up: <a href="#R-Basics" accesskey="u" rel="up">R Basics</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
|
|
</div>
|
|
<a name="What-is-R_003f-1"></a>
|
|
<h3 class="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 <a href="#What-is-S_003f">What is S?</a>) and Sussman’s
|
|
<a href="https://www.cs.indiana.edu/scheme-repository/home.html">Scheme</a>.
|
|
Whereas the resulting language is very similar in appearance to S, the
|
|
underlying implementation and semantics are derived from Scheme.
|
|
See <a href="#What-are-the-differences-between-R-and-S_003f">What are the differences between R and S?</a>, for further details.
|
|
</p>
|
|
<p>The core of R is an interpreted computer language which allows branching
|
|
and looping as well as modular programming using functions. Most of the
|
|
user-visible functions in R are written in R. It is possible for the
|
|
user to interface to procedures written in the C, C++, or FORTRAN
|
|
languages for efficiency. The R distribution contains functionality for
|
|
a large number of statistical procedures. Among these are: linear and
|
|
generalized linear models, nonlinear regression models, time series
|
|
analysis, classical parametric and nonparametric tests, clustering and
|
|
smoothing. There is also a large set of functions which provide a
|
|
flexible graphical environment for creating various kinds of data
|
|
presentations. Additional modules (“add-on packages”) are available
|
|
for a variety of specific purposes (see <a href="#R-Add_002dOn-Packages">R Add-On Packages</a>).
|
|
</p>
|
|
<p>R was initially written by <a href="mailto:Ross.Ihaka@R-project.org">Ross Ihaka</a>
|
|
and <a href="mailto:Robert.Gentleman@R-project.org">Robert Gentleman</a> at the
|
|
Department of Statistics of the University of Auckland in Auckland, New
|
|
Zealand. In addition, a large group of individuals has contributed to R
|
|
by sending code and bug reports.
|
|
</p>
|
|
<p>Since mid-1997 there has been a core group (the “R Core Team”) who can
|
|
modify the R source code archive. The group currently consists of Doug
|
|
Bates, John Chambers, Peter Dalgaard, Seth Falcon, Robert Gentleman,
|
|
Kurt Hornik, Stefano Iacus, Ross Ihaka, Friedrich Leisch, Uwe Ligges,
|
|
Thomas Lumley, Martin Maechler, Duncan Murdoch, Paul Murrell, Martyn
|
|
Plummer, Brian Ripley, Deepayan Sarkar, Duncan Temple Lang, Luke
|
|
Tierney, and Simon Urbanek.
|
|
</p>
|
|
<p>R has a home page at <a href="https://www.R-project.org/">https://www.R-project.org/</a>. It is
|
|
<a href="https://www.gnu.org/philosophy/free-sw.html">free software</a>
|
|
distributed under a <acronym>GNU</acronym>-style
|
|
<a href="https://www.gnu.org/copyleft/copyleft.html">copyleft</a>, and an
|
|
official part of the <a href="https://www.gnu.org/"><acronym>GNU</acronym></a> project
|
|
(“<acronym>GNU</acronym> S”).
|
|
</p>
|
|
<hr>
|
|
<a name="What-machines-does-R-run-on_003f"></a>
|
|
<div class="header">
|
|
<p>
|
|
Next: <a href="#What-is-the-current-version-of-R_003f" accesskey="n" rel="next">What is the current version of R?</a>, Previous: <a href="#What-is-R_003f" accesskey="p" rel="prev">What is R?</a>, Up: <a href="#R-Basics" accesskey="u" rel="up">R Basics</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
|
|
</div>
|
|
<a name="What-machines-does-R-run-on_003f-1"></a>
|
|
<h3 class="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., <a href="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
|
|
<acronym>CPU</acronym>s (e.g., <a href="https://buildd.debian.org/build.php?&pkg=r-base">https://buildd.debian.org/build.php?&pkg=r-base</a>),
|
|
i386-hurd-gnu, <var>cpu</var>-kfreebsd-gnu for i386 and amd64,
|
|
powerpc-apple-darwin, mips-sgi-irix,
|
|
i386-freebsd,
|
|
rs6000-ibm-aix, and sparc-sun-solaris.
|
|
</p>
|
|
|
|
<p>If you know about other platforms, please drop us a note.
|
|
</p>
|
|
<hr>
|
|
<a name="What-is-the-current-version-of-R_003f"></a>
|
|
<div class="header">
|
|
<p>
|
|
Next: <a href="#How-can-R-be-obtained_003f" accesskey="n" rel="next">How can R be obtained?</a>, Previous: <a href="#What-machines-does-R-run-on_003f" accesskey="p" rel="prev">What machines does R run on?</a>, Up: <a href="#R-Basics" accesskey="u" rel="up">R Basics</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
|
|
</div>
|
|
<a name="What-is-the-current-version-of-R_003f-1"></a>
|
|
<h3 class="section">2.3 What is the current version of R?</h3>
|
|
|
|
<p>The current released version is 3.2.3. Based on this
|
|
‘major.minor.patchlevel’ numbering scheme, there are two development
|
|
versions of R, a patched version of the current release (‘r-patched’)
|
|
and one working towards the next minor or eventually major (‘r-devel’)
|
|
releases of R, respectively. Version r-patched is for bug fixes mostly.
|
|
New features are typically introduced in r-devel.
|
|
</p>
|
|
<hr>
|
|
<a name="How-can-R-be-obtained_003f"></a>
|
|
<div class="header">
|
|
<p>
|
|
Next: <a href="#How-can-R-be-installed_003f" accesskey="n" rel="next">How can R be installed?</a>, Previous: <a href="#What-is-the-current-version-of-R_003f" accesskey="p" rel="prev">What is the current version of R?</a>, Up: <a href="#R-Basics" accesskey="u" rel="up">R Basics</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
|
|
</div>
|
|
<a name="How-can-R-be-obtained_003f-1"></a>
|
|
<h3 class="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 <a href="#What-is-CRAN_003f">What is CRAN?</a>).
|
|
</p>
|
|
<p>Sources are also available via <a href="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
|
|
versions of R can be found at
|
|
<a href="https://stat.ethz.ch/R/daily">https://stat.ethz.ch/R/daily</a>.
|
|
</p>
|
|
|
|
|
|
|
|
|
|
|
|
<hr>
|
|
<a name="How-can-R-be-installed_003f"></a>
|
|
<div class="header">
|
|
<p>
|
|
Next: <a href="#Are-there-Unix_002dlike-binaries-for-R_003f" accesskey="n" rel="next">Are there Unix-like binaries for R?</a>, Previous: <a href="#How-can-R-be-obtained_003f" accesskey="p" rel="prev">How can R be obtained?</a>, Up: <a href="#R-Basics" accesskey="u" rel="up">R Basics</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
|
|
</div>
|
|
<a name="How-can-R-be-installed_003f-1"></a>
|
|
<h3 class="section">2.5 How can R be installed?</h3>
|
|
|
|
<table summary="" class="menu" border="0" cellspacing="0">
|
|
<tr><td align="left" valign="top">• <a href="#How-can-R-be-installed-_0028Unix_002dlike_0029" accesskey="1">How can R be installed (Unix-like)</a>:</td><td> </td><td align="left" valign="top">
|
|
</td></tr>
|
|
<tr><td align="left" valign="top">• <a href="#How-can-R-be-installed-_0028Windows_0029" accesskey="2">How can R be installed (Windows)</a>:</td><td> </td><td align="left" valign="top">
|
|
</td></tr>
|
|
<tr><td align="left" valign="top">• <a href="#How-can-R-be-installed-_0028Mac_0029" accesskey="3">How can R be installed (Mac)</a>:</td><td> </td><td align="left" valign="top">
|
|
</td></tr>
|
|
</table>
|
|
|
|
<hr>
|
|
<a name="How-can-R-be-installed-_0028Unix_002dlike_0029"></a>
|
|
<div class="header">
|
|
<p>
|
|
Next: <a href="#How-can-R-be-installed-_0028Windows_0029" accesskey="n" rel="next">How can R be installed (Windows)</a>, Previous: <a href="#How-can-R-be-installed_003f" accesskey="p" rel="prev">How can R be installed?</a>, Up: <a href="#How-can-R-be-installed_003f" accesskey="u" rel="up">How can R be installed?</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
|
|
</div>
|
|
<a name="How-can-R-be-installed-_0028Unix_002dlike_0029-1"></a>
|
|
<h4 class="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 <a href="#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 <a href="#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 <a href="#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>
|
|
<div class="example">
|
|
<pre class="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>
|
|
<dl compact="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>${prefix}/lib/R</samp></dt>
|
|
<dd><p>all the rest (libraries, on-line help system, …). This is the “R
|
|
Home Directory” (<code>R_HOME</code>) of the installed system.
|
|
</p></dd>
|
|
</dl>
|
|
|
|
<p>In the above, <code>prefix</code> is determined during configuration
|
|
(typically <samp>/usr/local</samp>) and can be set by running
|
|
<code>configure</code> with the option
|
|
</p>
|
|
<div class="example">
|
|
<pre class="example">$ ./configure --prefix=/where/you/want/R/to/go
|
|
</pre></div>
|
|
|
|
<p>(E.g., the R executable will then be installed into
|
|
<samp>/where/you/want/R/to/go/bin</samp>.)
|
|
</p>
|
|
<p>To install DVI, info and PDF versions of the manuals, use <kbd>make
|
|
install-dvi</kbd>, <kbd>make install-info</kbd> and <kbd>make install-pdf</kbd>,
|
|
respectively.
|
|
</p>
|
|
<hr>
|
|
<a name="How-can-R-be-installed-_0028Windows_0029"></a>
|
|
<div class="header">
|
|
<p>
|
|
Next: <a href="#How-can-R-be-installed-_0028Mac_0029" accesskey="n" rel="next">How can R be installed (Mac)</a>, Previous: <a href="#How-can-R-be-installed-_0028Unix_002dlike_0029" accesskey="p" rel="prev">How can R be installed (Unix-like)</a>, Up: <a href="#How-can-R-be-installed_003f" accesskey="u" rel="up">How can R be installed?</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
|
|
</div>
|
|
<a name="How-can-R-be-installed-_0028Windows_0029-1"></a>
|
|
<h4 class="subsection">2.5.2 How can R be installed (Windows)</h4>
|
|
|
|
<p>The <samp>bin/windows</samp> directory of a <acronym>CRAN</acronym> site contains binaries for
|
|
a base distribution and add-on packages from <acronym>CRAN</acronym> to run on Windows
|
|
XP and later (including 64-bit versions of Windows) on ix86 and x86_64
|
|
chips. The Windows version of R was created by Robert Gentleman and
|
|
Guido Masarotto, and is now being developed and maintained by
|
|
<a href="mailto:murdoch@stats.uwo.ca">Duncan Murdoch</a> and
|
|
<a href="mailto:Brian.Ripley@R-project.org">Brian D. Ripley</a>.
|
|
</p>
|
|
<p>The same directory has links to snapshots of the r-patched and r-devel
|
|
versions of R.
|
|
</p>
|
|
<p>See the <a href="https://CRAN.R-project.org/bin/windows/base/rw-FAQ.html">“R for Windows <acronym>FAQ</acronym>”</a> for more details.
|
|
</p>
|
|
<hr>
|
|
<a name="How-can-R-be-installed-_0028Mac_0029"></a>
|
|
<div class="header">
|
|
<p>
|
|
Previous: <a href="#How-can-R-be-installed-_0028Windows_0029" accesskey="p" rel="prev">How can R be installed (Windows)</a>, Up: <a href="#How-can-R-be-installed_003f" accesskey="u" rel="up">How can R be installed?</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
|
|
</div>
|
|
<a name="How-can-R-be-installed-_0028Mac_0029-1"></a>
|
|
<h4 class="subsection">2.5.3 How can R be installed (Mac)</h4>
|
|
|
|
<p>The <samp>bin/macosx</samp> directory of a <acronym>CRAN</acronym> site contains a standard
|
|
Apple installer package to run on OS X 10.6 (‘Snow Leopard’) and later.
|
|
Once downloaded and executed, the installer will install the current
|
|
release of R and an R.app OS X <acronym>GUI</acronym>. This port of R for OS X
|
|
is maintained by <a href="mailto:Simon.Urbanek@R-project.org">Simon Urbanek</a>
|
|
(and previously by Stefano Iacus). The
|
|
<a href="https://CRAN.R-project.org/bin/macosx/RMacOSX-FAQ.html">“R for Mac
|
|
OS X <acronym>FAQ</acronym></a> has more details.
|
|
</p>
|
|
<p>Snapshots of the r-patched and r-devel versions of R are available as
|
|
Apple installer packages at <a href="https://r.research.att.com">https://r.research.att.com</a>.
|
|
</p>
|
|
<hr>
|
|
<a name="Are-there-Unix_002dlike-binaries-for-R_003f"></a>
|
|
<div class="header">
|
|
<p>
|
|
Next: <a href="#What-documentation-exists-for-R_003f" accesskey="n" rel="next">What documentation exists for R?</a>, Previous: <a href="#How-can-R-be-installed_003f" accesskey="p" rel="prev">How can R be installed?</a>, Up: <a href="#R-Basics" accesskey="u" rel="up">R Basics</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
|
|
</div>
|
|
<a name="Are-there-Unix_002dlike-binaries-for-R_003f-1"></a>
|
|
<h3 class="section">2.6 Are there Unix-like binaries for R?</h3>
|
|
|
|
|
|
<p>The <samp>bin/linux</samp> directory of a <acronym>CRAN</acronym> site contains the following
|
|
packages.
|
|
</p>
|
|
<blockquote>
|
|
<table summary="">
|
|
<thead><tr><th></th><th>CPU</th><th>Versions</th><th>Provider</th></tr></thead>
|
|
<tr><td>Debian</td><td>i386/amd64</td><td>squeeze/wheezy</td><td>Johannes Ranke</td></tr>
|
|
<tr><td></td><td>armel</td><td>wheezy</td><td>Johannes Ranke</td></tr>
|
|
<tr><td>Ubuntu</td><td>i386/amd64</td><td>lucid/precise/trusty</td><td>Michael Rutter</td></tr>
|
|
</table>
|
|
</blockquote>
|
|
|
|
<p>Debian packages, maintained by Dirk Eddelbuettel, have long been part of
|
|
the Debian distribution, and can be accessed through APT, the Debian
|
|
package maintenance tool. Use e.g. <code>apt-get install r-base
|
|
r-recommended</code> to install the R environment and recommended packages.
|
|
If you also want to build R packages from source, also run <code>apt-get
|
|
install r-base-dev</code> to obtain the additional tools required for this.
|
|
So-called “backports” of the current R packages for at least the
|
|
<em>stable</em> distribution of Debian are provided by Johannes Ranke, and
|
|
available from <acronym>CRAN</acronym>. See
|
|
<a href="https://CRAN.R-project.org/bin/linux/debian/index.html">https://CRAN.R-project.org/bin/linux/debian/index.html</a> for details on R
|
|
Debian packages and installing the backports, which should also be
|
|
suitable for other Debian derivatives. Native backports for Ubuntu are
|
|
provided by Michael Rutter.
|
|
</p>
|
|
<p>R binaries for Fedora, maintained by Tom “Spot” Callaway, are provided
|
|
as part of the Fedora distribution and can be accessed through
|
|
<code>yum</code>, the RPM installer/updater. Note that the “Software”
|
|
application (gnome-software), which is the default <acronym>GUI</acronym> for
|
|
software installation in Fedora 20, cannot be used to install R. It is
|
|
therefore recommended to use the yum command line tool.
|
|
The Fedora R RPM is a “meta-package” which installs all the user and
|
|
developer components of R (available separately as <code>R-core</code> and
|
|
<code>R-devel</code>), as well as <code>R-java</code>, which ensures that R is
|
|
configured for use with Java. The R RPM also installs the standalone R
|
|
math library (<code>libRmath</code> and <code>libRmath-devel</code>), although this
|
|
is not necessary to use R. When a new version of R is released, there
|
|
may be a delay of up to 2 weeks until the Fedora RPM becomes publicly
|
|
available, as it must pass through the statutory Fedora review process.
|
|
RPMs for a selection of R packages are also provided by Fedora. The
|
|
Extra Packages for Enterprise Linux (EPEL) project
|
|
(<a href="https://fedoraproject.org/wiki/EPEL">https://fedoraproject.org/wiki/EPEL</a>) provides ports of the Fedora
|
|
RPMs for RedHat Enterprise Linux and compatible distributions (e.g.,
|
|
Centos, Scientific Linux, Oracle Linux).
|
|
</p>
|
|
<p>See <a href="https://CRAN.R-project.org/bin/linux/suse/README.html">https://CRAN.R-project.org/bin/linux/suse/README.html</a> for
|
|
information about RPMs for openSUSE.
|
|
</p>
|
|
<p>No other binary distributions are currently publically available via
|
|
<acronym>CRAN</acronym>.
|
|
</p>
|
|
<hr>
|
|
<a name="What-documentation-exists-for-R_003f"></a>
|
|
<div class="header">
|
|
<p>
|
|
Next: <a href="#Citing-R" accesskey="n" rel="next">Citing R</a>, Previous: <a href="#Are-there-Unix_002dlike-binaries-for-R_003f" accesskey="p" rel="prev">Are there Unix-like binaries for R?</a>, Up: <a href="#R-Basics" accesskey="u" rel="up">R Basics</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
|
|
</div>
|
|
<a name="What-documentation-exists-for-R_003f-1"></a>
|
|
<h3 class="section">2.7 What documentation exists for R?</h3>
|
|
|
|
<p>Online documentation for most of the functions and variables in R
|
|
exists, and can be printed on-screen by typing <kbd>help(<var>name</var>)</kbd>
|
|
(or <kbd>?<var>name</var></kbd>) at the R prompt, where <var>name</var> is the name of
|
|
the topic help is sought for. (In the case of unary and binary
|
|
operators and control-flow special forms, the name may need to be be
|
|
quoted.)
|
|
</p>
|
|
<p>This documentation can also be made available as one reference manual
|
|
for on-line reading in <acronym>HTML</acronym> and PDF formats, and as hardcopy via
|
|
LaTeX, see <a href="#How-can-R-be-installed_003f">How can R be installed?</a>. An up-to-date <acronym>HTML</acronym>
|
|
version is always available for web browsing at
|
|
<a href="https://stat.ethz.ch/R-manual/">https://stat.ethz.ch/R-manual/</a>.
|
|
</p>
|
|
<p>Printed copies of the R reference manual for some version(s) are
|
|
available from Network Theory Ltd, at
|
|
<a href="http://www.network-theory.co.uk/R/base/">http://www.network-theory.co.uk/R/base/</a>. For each set of manuals
|
|
sold, the publisher donates USD 10 to the R Foundation (see <a href="#What-is-the-R-Foundation_003f">What is the R Foundation?</a>).
|
|
</p>
|
|
<p>The R distribution also comes with the following manuals.
|
|
</p>
|
|
<ul>
|
|
<li> “An Introduction to R” (<samp>R-intro</samp>)
|
|
includes information on data types, programming elements, statistical
|
|
modeling and graphics. This document is based on the “Notes on
|
|
<small>S-PLUS</small>” by Bill Venables and David Smith.
|
|
</li><li> “Writing R Extensions” (<samp>R-exts</samp>)
|
|
currently describes the process of creating R add-on packages, writing R
|
|
documentation, R’s system and foreign language interfaces, and the R
|
|
<acronym>API</acronym>.
|
|
</li><li> “R Data Import/Export” (<samp>R-data</samp>)
|
|
is a guide to importing and exporting data to and from R.
|
|
</li><li> “The R Language Definition” (<samp>R-lang</samp>),
|
|
a first version of the “Kernighan & Ritchie of R”, explains
|
|
evaluation, parsing, object oriented programming, computing on the
|
|
language, and so forth.
|
|
</li><li> “R Installation and Administration” (<samp>R-admin</samp>).
|
|
</li><li> “R Internals” (<samp>R-ints</samp>)
|
|
is a guide to R’s internal structures.
|
|
(Added in R 2.4.0.)
|
|
</li></ul>
|
|
|
|
<p>An annotated bibliography (BibTeX format) of R-related publications
|
|
can be found at
|
|
</p>
|
|
<div class="display">
|
|
<pre class="display"><a href="https://www.R-project.org/doc/bib/R.bib">https://www.R-project.org/doc/bib/R.bib</a>
|
|
</pre></div>
|
|
|
|
<p>Books on R by R Core Team members include
|
|
</p>
|
|
<blockquote>
|
|
<p>John M. Chambers (2008), “Software for Data Analysis: Programming with
|
|
R”. Springer, New York, ISBN 978-0-387-75935-7,
|
|
<a href="http://statweb.stanford.edu/~jmc4/Rbook/">http://statweb.stanford.edu/~jmc4/Rbook/</a>.
|
|
</p>
|
|
<p>Peter Dalgaard (2008), “Introductory Statistics with R”, 2nd edition.
|
|
Springer, ISBN 978-0-387-79053-4,
|
|
<a href="http://publicifsv.sund.ku.dk/~pd/ISwR.html">http://publicifsv.sund.ku.dk/~pd/ISwR.html</a>.
|
|
</p>
|
|
<p>Robert Gentleman (2008), “R Programming for Bioinformatics”. Chapman
|
|
& Hall/CRC, Boca Raton, FL, ISBN 978-1-420-06367-7,
|
|
<a href="https://www.bioconductor.org/pub/RBioinf/">https://www.bioconductor.org/pub/RBioinf/</a>.
|
|
</p>
|
|
<p>Stefano M. Iacus (2008), “Simulation and Inference for Stochastic
|
|
Differential Equations: With R Examples”. Springer, New York, ISBN
|
|
978-0-387-75838-1.
|
|
</p>
|
|
<p>Deepayan Sarkar (2007), “Lattice: Multivariate Data Visualization with
|
|
R”. Springer, New York, ISBN 978-0-387-75968-5.
|
|
</p>
|
|
<p>W. John Braun and Duncan J. Murdoch (2007), “A First Course in
|
|
Statistical Programming with R”. Cambridge University Press,
|
|
Cambridge, ISBN 978-0521872652.
|
|
</p>
|
|
<p>P. Murrell (2005), “R Graphics”, Chapman & Hall/CRC, ISBN:
|
|
1-584-88486-X,
|
|
<a href="https://www.stat.auckland.ac.nz/~paul/RGraphics/rgraphics.html">https://www.stat.auckland.ac.nz/~paul/RGraphics/rgraphics.html</a>.
|
|
</p>
|
|
<p>William N. Venables and Brian D. Ripley (2002), “Modern Applied
|
|
Statistics with S” (4th edition). Springer, ISBN 0-387-95457-0,
|
|
<a href="https://www.stats.ox.ac.uk/pub/MASS4/">https://www.stats.ox.ac.uk/pub/MASS4/</a>.
|
|
</p>
|
|
<p>Jose C. Pinheiro and Douglas M. Bates (2000), “Mixed-Effects Models in
|
|
S and S-Plus”. Springer, ISBN 0-387-98957-0.
|
|
</p></blockquote>
|
|
|
|
<p>Last, but not least, Ross’ and Robert’s experience in designing and
|
|
implementing R is described in Ihaka & Gentleman (1996), “R: A Language
|
|
for Data Analysis and Graphics”,
|
|
<a href="http://www.amstat.org/publications/jcgs/"><em>Journal of
|
|
Computational and Graphical Statistics</em></a>, <strong>5</strong>, 299–314.
|
|
</p>
|
|
<hr>
|
|
<a name="Citing-R"></a>
|
|
<div class="header">
|
|
<p>
|
|
Next: <a href="#What-mailing-lists-exist-for-R_003f" accesskey="n" rel="next">What mailing lists exist for R?</a>, Previous: <a href="#What-documentation-exists-for-R_003f" accesskey="p" rel="prev">What documentation exists for R?</a>, Up: <a href="#R-Basics" accesskey="u" rel="up">R Basics</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
|
|
</div>
|
|
<a name="Citing-R-1"></a>
|
|
<h3 class="section">2.8 Citing R</h3>
|
|
|
|
<p>To cite R in publications, use
|
|
</p>
|
|
<div class="example">
|
|
<pre class="example">@Manual{,
|
|
title = {R: A Language and Environment for Statistical
|
|
Computing},
|
|
author = {{R Core Team}},
|
|
organization = {R Foundation for Statistical Computing},
|
|
address = {Vienna, Austria},
|
|
year = 2015,
|
|
url = {https://www.R-project.org}
|
|
}
|
|
</pre></div>
|
|
|
|
<p>Citation strings (or BibTeX entries) for R and R packages can also be
|
|
obtained by <code>citation()</code>.
|
|
</p>
|
|
<hr>
|
|
<a name="What-mailing-lists-exist-for-R_003f"></a>
|
|
<div class="header">
|
|
<p>
|
|
Next: <a href="#What-is-CRAN_003f" accesskey="n" rel="next">What is CRAN?</a>, Previous: <a href="#Citing-R" accesskey="p" rel="prev">Citing R</a>, Up: <a href="#R-Basics" accesskey="u" rel="up">R Basics</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
|
|
</div>
|
|
<a name="What-mailing-lists-exist-for-R_003f-1"></a>
|
|
<h3 class="section">2.9 What mailing lists exist for R?</h3>
|
|
|
|
<p>Thanks to <a href="mailto:Martin.Maechler@R-project.org">Martin Maechler</a>, there
|
|
are several mailing lists devoted to R, including the following:
|
|
</p>
|
|
<dl compact="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 <a href="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
|
|
<a href="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 <a href="mailto:R-help-request@lists.R-project.org">R-help-request@lists.R-project.org</a>.
|
|
</p>
|
|
<p>Send email to <a href="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
|
|
<a href="#R-Bugs">R Bugs</a> for more details.
|
|
</p>
|
|
<p>See <a href="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 <a href="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
|
|
<a href="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
|
|
<a href="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 <a href="http://www.gmane.org/rss.php">http://www.gmane.org/rss.php</a> for
|
|
details on RSS feeds.
|
|
</p>
|
|
<hr>
|
|
<a name="What-is-CRAN_003f"></a>
|
|
<div class="header">
|
|
<p>
|
|
Next: <a href="#Can-I-use-R-for-commercial-purposes_003f" accesskey="n" rel="next">Can I use R for commercial purposes?</a>, Previous: <a href="#What-mailing-lists-exist-for-R_003f" accesskey="p" rel="prev">What mailing lists exist for R?</a>, Up: <a href="#R-Basics" accesskey="u" rel="up">R Basics</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
|
|
</div>
|
|
<a name="What-is-CRAN_003f-1"></a>
|
|
<h3 class="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
|
|
can be found at the <acronym>URL</acronym>
|
|
</p>
|
|
<blockquote>
|
|
<p><a href="https://CRAN.R-project.org/">https://CRAN.R-project.org/</a>
|
|
</p></blockquote>
|
|
|
|
<p>and is mirrored daily to many sites around the world.
|
|
See <a href="https://CRAN.R-project.org/mirrors.html">https://CRAN.R-project.org/mirrors.html</a> for a complete list of
|
|
mirrors. Please use the <acronym>CRAN</acronym> site closest to you to reduce network
|
|
load.
|
|
</p>
|
|
<p>From <acronym>CRAN</acronym>, you can obtain the latest official release of R, daily
|
|
snapshots of R (copies of the current source trees), as gzipped and
|
|
bzipped tar files, a wealth of additional contributed code, as well as
|
|
prebuilt binaries for various operating systems (Linux, Mac OS Classic,
|
|
OS X, and MS Windows). <acronym>CRAN</acronym> also provides access to
|
|
documentation on R, existing mailing lists and the R Bug Tracking
|
|
system.
|
|
</p>
|
|
<p>Please always use the <acronym>URL</acronym> of the master site when referring to
|
|
<acronym>CRAN</acronym>.
|
|
</p>
|
|
<hr>
|
|
<a name="Can-I-use-R-for-commercial-purposes_003f"></a>
|
|
<div class="header">
|
|
<p>
|
|
Next: <a href="#Why-is-R-named-R_003f" accesskey="n" rel="next">Why is R named R?</a>, Previous: <a href="#What-is-CRAN_003f" accesskey="p" rel="prev">What is CRAN?</a>, Up: <a href="#R-Basics" accesskey="u" rel="up">R Basics</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
|
|
</div>
|
|
<a name="Can-I-use-R-for-commercial-purposes_003f-1"></a>
|
|
<h3 class="section">2.11 Can I use R for commercial purposes?</h3>
|
|
|
|
<p>R is released under the
|
|
<a href="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
|
|
Fields of Endeavor”) of the
|
|
<a href="https://opensource.org/docs/definition.html">Open Source
|
|
Definition</a>:
|
|
</p>
|
|
<blockquote>
|
|
<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>
|
|
<a name="Why-is-R-named-R_003f"></a>
|
|
<div class="header">
|
|
<p>
|
|
Next: <a href="#What-is-the-R-Foundation_003f" accesskey="n" rel="next">What is the R Foundation?</a>, Previous: <a href="#Can-I-use-R-for-commercial-purposes_003f" accesskey="p" rel="prev">Can I use R for commercial purposes?</a>, Up: <a href="#R-Basics" accesskey="u" rel="up">R Basics</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
|
|
</div>
|
|
<a name="Why-is-R-named-R_003f-1"></a>
|
|
<h3 class="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 <a href="#What-is-S_003f">What is S?</a>).
|
|
</p>
|
|
|
|
<hr>
|
|
<a name="What-is-the-R-Foundation_003f"></a>
|
|
<div class="header">
|
|
<p>
|
|
Next: <a href="#What-is-R_002dForge_003f" accesskey="n" rel="next">What is R-Forge?</a>, Previous: <a href="#Why-is-R-named-R_003f" accesskey="p" rel="prev">Why is R named R?</a>, Up: <a href="#R-Basics" accesskey="u" rel="up">R Basics</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
|
|
</div>
|
|
<a name="What-is-the-R-Foundation_003f-1"></a>
|
|
<h3 class="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
|
|
<a href="https://www.R-project.org/foundation/">https://www.R-project.org/foundation/</a> for more information.
|
|
</p>
|
|
<hr>
|
|
<a name="What-is-R_002dForge_003f"></a>
|
|
<div class="header">
|
|
<p>
|
|
Previous: <a href="#What-is-the-R-Foundation_003f" accesskey="p" rel="prev">What is the R Foundation?</a>, Up: <a href="#R-Basics" accesskey="u" rel="up">R Basics</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
|
|
</div>
|
|
<a name="What-is-R_002dForge_003f-1"></a>
|
|
<h3 class="section">2.14 What is R-Forge?</h3>
|
|
|
|
<p>R-Forge (<a href="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 <a href="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”, <a href="https://journal.R-project.org/"><em>The R Journal</em></a>, <strong>1</strong>(1):9–14.
|
|
</p>
|
|
|
|
<hr>
|
|
<a name="R-and-S"></a>
|
|
<div class="header">
|
|
<p>
|
|
Next: <a href="#R-Web-Interfaces" accesskey="n" rel="next">R Web Interfaces</a>, Previous: <a href="#R-Basics" accesskey="p" rel="prev">R Basics</a>, Up: <a href="#Top" accesskey="u" rel="up">Top</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
|
|
</div>
|
|
<a name="R-and-S-1"></a>
|
|
<h2 class="chapter">3 R and S</h2>
|
|
|
|
<table summary="" class="menu" border="0" cellspacing="0">
|
|
<tr><td align="left" valign="top">• <a href="#What-is-S_003f" accesskey="1">What is S?</a>:</td><td> </td><td align="left" valign="top">
|
|
</td></tr>
|
|
<tr><td align="left" valign="top">• <a href="#What-is-S_002dPLUS_003f" accesskey="2">What is S-PLUS?</a>:</td><td> </td><td align="left" valign="top">
|
|
</td></tr>
|
|
<tr><td align="left" valign="top">• <a href="#What-are-the-differences-between-R-and-S_003f" accesskey="3">What are the differences between R and S?</a>:</td><td> </td><td align="left" valign="top">
|
|
</td></tr>
|
|
<tr><td align="left" valign="top">• <a href="#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><td align="left" valign="top">
|
|
</td></tr>
|
|
<tr><td align="left" valign="top">• <a href="#What-is-R_002dplus_003f" accesskey="5">What is R-plus?</a>:</td><td> </td><td align="left" valign="top">
|
|
</td></tr>
|
|
</table>
|
|
|
|
<hr>
|
|
<a name="What-is-S_003f"></a>
|
|
<div class="header">
|
|
<p>
|
|
Next: <a href="#What-is-S_002dPLUS_003f" accesskey="n" rel="next">What is S-PLUS?</a>, Previous: <a href="#R-and-S" accesskey="p" rel="prev">R and S</a>, Up: <a href="#R-and-S" accesskey="u" rel="up">R and S</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
|
|
</div>
|
|
<a name="What-is-S_003f-1"></a>
|
|
<h3 class="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,
|
|
ISBN 0-387-98503-4
|
|
(<a href="http://statweb.stanford.edu/~jmc4/Sbook/">http://statweb.stanford.edu/~jmc4/Sbook/</a>).
|
|
|
|
<p>This “<em>Green Book</em>” describes version 4 of S, a major revision of
|
|
S designed by John Chambers to improve its usefulness at every stage of
|
|
the programming process.
|
|
</p></li></ul>
|
|
|
|
<p>See <a href="http://statweb.stanford.edu/~jmc4/papers/96.7.ps">http://statweb.stanford.edu/~jmc4/papers/96.7.ps</a>
|
|
for further information on the “Evolution of the S Language”.
|
|
</p>
|
|
<p>There is a huge amount of user-contributed code for S, available at the
|
|
<a href="http://lib.stat.cmu.edu/S/">S Repository</a> at <acronym>CMU</acronym>.
|
|
</p>
|
|
|
|
<hr>
|
|
<a name="What-is-S_002dPLUS_003f"></a>
|
|
<div class="header">
|
|
<p>
|
|
Next: <a href="#What-are-the-differences-between-R-and-S_003f" accesskey="n" rel="next">What are the differences between R and S?</a>, Previous: <a href="#What-is-S_003f" accesskey="p" rel="prev">What is S?</a>, Up: <a href="#R-and-S" accesskey="u" rel="up">R and S</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
|
|
</div>
|
|
<a name="What-is-S_002dPLUS_003f-1"></a>
|
|
<h3 class="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
|
|
<a href="http://www.tibco.com/">TIBCO Software Inc</a> as ‘TIBCO Spotfire S+’.
|
|
See <a href="https://en.wikipedia.org/wiki/S-PLUS">https://en.wikipedia.org/wiki/S-PLUS</a> for more information.
|
|
</p>
|
|
<hr>
|
|
<a name="What-are-the-differences-between-R-and-S_003f"></a>
|
|
<div class="header">
|
|
<p>
|
|
Next: <a href="#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: <a href="#What-is-S_002dPLUS_003f" accesskey="p" rel="prev">What is S-PLUS?</a>, Up: <a href="#R-and-S" accesskey="u" rel="up">R and S</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
|
|
</div>
|
|
<a name="What-are-the-differences-between-R-and-S_003f-1"></a>
|
|
<h3 class="section">3.3 What are the differences between R and S?</h3>
|
|
|
|
<p>We can regard S as a language with three current implementations or
|
|
“engines”, the “old S engine” (S version 3; <small>S-PLUS</small> 3.x and 4.x),
|
|
the “new S engine” (S version 4; <small>S-PLUS</small> 5.x and above), and R.
|
|
Given this understanding, asking for “the differences between R and S”
|
|
really amounts to asking for the specifics of the R implementation of
|
|
the S language, i.e., the difference between the R and S <em>engines</em>.
|
|
</p>
|
|
<p>For the remainder of this section, “S” refers to the S engines and not
|
|
the S language.
|
|
</p>
|
|
<table summary="" class="menu" border="0" cellspacing="0">
|
|
<tr><td align="left" valign="top">• <a href="#Lexical-scoping" accesskey="1">Lexical scoping</a>:</td><td> </td><td align="left" valign="top">
|
|
</td></tr>
|
|
<tr><td align="left" valign="top">• <a href="#Models" accesskey="2">Models</a>:</td><td> </td><td align="left" valign="top">
|
|
</td></tr>
|
|
<tr><td align="left" valign="top">• <a href="#Others" accesskey="3">Others</a>:</td><td> </td><td align="left" valign="top">
|
|
</td></tr>
|
|
</table>
|
|
|
|
<hr>
|
|
<a name="Lexical-scoping"></a>
|
|
<div class="header">
|
|
<p>
|
|
Next: <a href="#Models" accesskey="n" rel="next">Models</a>, Previous: <a href="#What-are-the-differences-between-R-and-S_003f" accesskey="p" rel="prev">What are the differences between R and S?</a>, Up: <a href="#What-are-the-differences-between-R-and-S_003f" accesskey="u" rel="up">What are the differences between R and S?</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
|
|
</div>
|
|
<a name="Lexical-scoping-1"></a>
|
|
<h4 class="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>
|
|
<div class="example">
|
|
<pre class="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>
|
|
<div class="example">
|
|
<pre class="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>
|
|
<div class="example">
|
|
<pre class="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
|
|
following:
|
|
</p>
|
|
<div class="example">
|
|
<pre class="example">dorder <- function(n, r, pfun, dfun) {
|
|
f <- function(x) NULL
|
|
con <- round(exp(lgamma(n + 1) - lgamma(r) - lgamma(n - r + 1)))
|
|
PF <- call(substitute(pfun), as.name("x"))
|
|
DF <- call(substitute(dfun), as.name("x"))
|
|
f[[length(f)]] <-
|
|
call("*", con,
|
|
call("*", call("^", PF, r - 1),
|
|
call("*", call("^", call("-", 1, PF), n - r),
|
|
DF)))
|
|
f
|
|
}
|
|
</pre></div>
|
|
|
|
<p>Rather tricky, isn’t it? The code uses the fact that in S,
|
|
functions are just lists of special mode with the function body as the
|
|
last argument, and hence does not work in R (one could make the idea
|
|
work, though).
|
|
</p>
|
|
<p>A version which makes heavy use of <code>substitute()</code> and seems to work
|
|
under both S and R is
|
|
</p>
|
|
<div class="example">
|
|
<pre class="example">dorder <- function(n, r, pfun, dfun) {
|
|
con <- round(exp(lgamma(n + 1) - lgamma(r) - lgamma(n - r + 1)))
|
|
eval(substitute(function(x) K * PF(x)^a * (1 - PF(x))^b * DF(x),
|
|
list(PF = substitute(pfun), DF = substitute(dfun),
|
|
a = r - 1, b = n - r, K = con)))
|
|
}
|
|
</pre></div>
|
|
|
|
<p>(the <code>eval()</code> is not needed in S).
|
|
</p>
|
|
<p>However, in R there is a much easier solution:
|
|
</p>
|
|
<div class="example">
|
|
<pre class="example">dorder <- function(n, r, pfun, dfun) {
|
|
con <- round(exp(lgamma(n + 1) - lgamma(r) - lgamma(n - r + 1)))
|
|
function(x) {
|
|
con * pfun(x)^(r - 1) * (1 - pfun(x))^(n - r) * dfun(x)
|
|
}
|
|
}
|
|
</pre></div>
|
|
|
|
<p>This seems to be the “natural” implementation, and it works because
|
|
the free variables in the returned function can be looked up in the
|
|
defining environment (this is lexical scope).
|
|
</p>
|
|
<p>Note that what you really need is the function <em>closure</em>, i.e., the
|
|
body along with all variable bindings needed for evaluating it. Since
|
|
in the above version, the free variables in the value function are not
|
|
modified, you can actually use it in S as well if you abstract out the
|
|
closure operation into a function <code>MC()</code> (for “make closure”):
|
|
</p>
|
|
<div class="example">
|
|
<pre class="example">dorder <- function(n, r, pfun, dfun) {
|
|
con <- round(exp(lgamma(n + 1) - lgamma(r) - lgamma(n - r + 1)))
|
|
MC(function(x) {
|
|
con * pfun(x)^(r - 1) * (1 - pfun(x))^(n - r) * dfun(x)
|
|
},
|
|
list(con = con, pfun = pfun, dfun = dfun, r = r, n = n))
|
|
}
|
|
</pre></div>
|
|
|
|
<p>Given the appropriate definitions of the closure operator, this works in
|
|
both R and S, and is much “cleaner” than a substitute/eval solution
|
|
(or one which overrules the default scoping rules by using explicit
|
|
access to evaluation frames, as is of course possible in both R and S).
|
|
</p>
|
|
<p>For R, <code>MC()</code> simply is
|
|
</p>
|
|
<div class="example">
|
|
<pre class="example">MC <- function(f, env) f
|
|
</pre></div>
|
|
|
|
<p>(lexical scope!), a version for S is
|
|
</p>
|
|
<div class="example">
|
|
<pre class="example">MC <- function(f, env = NULL) {
|
|
env <- as.list(env)
|
|
if (mode(f) != "function")
|
|
stop(paste("not a function:", f))
|
|
if (length(env) > 0 && any(names(env) == ""))
|
|
stop(paste("not all arguments are named:", env))
|
|
fargs <- if(length(f) > 1) f[1:(length(f) - 1)] else NULL
|
|
fargs <- c(fargs, env)
|
|
if (any(duplicated(names(fargs))))
|
|
stop(paste("duplicated arguments:", paste(names(fargs)),
|
|
collapse = ", "))
|
|
fbody <- f[length(f)]
|
|
cf <- c(fargs, fbody)
|
|
mode(cf) <- "function"
|
|
return(cf)
|
|
}
|
|
</pre></div>
|
|
|
|
<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 <a href="#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”,
|
|
<a href="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
|
|
<a href="#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 <a href="#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>
|
|
<a name="Models"></a>
|
|
<div class="header">
|
|
<p>
|
|
Next: <a href="#Others" accesskey="n" rel="next">Others</a>, Previous: <a href="#Lexical-scoping" accesskey="p" rel="prev">Lexical scoping</a>, Up: <a href="#What-are-the-differences-between-R-and-S_003f" accesskey="u" rel="up">What are the differences between R and S?</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
|
|
</div>
|
|
<a name="Models-1"></a>
|
|
<h4 class="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>
|
|
<a name="Others"></a>
|
|
<div class="header">
|
|
<p>
|
|
Previous: <a href="#Models" accesskey="p" rel="prev">Models</a>, Up: <a href="#What-are-the-differences-between-R-and-S_003f" accesskey="u" rel="up">What are the differences between R and S?</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
|
|
</div>
|
|
<a name="Others-1"></a>
|
|
<h4 class="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
|
|
|
|
<div class="example">
|
|
<pre class="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
|
|
works.
|
|
</p>
|
|
<hr>
|
|
<a name="Is-there-anything-R-can-do-that-S_002dPLUS-cannot_003f"></a>
|
|
<div class="header">
|
|
<p>
|
|
Next: <a href="#What-is-R_002dplus_003f" accesskey="n" rel="next">What is R-plus?</a>, Previous: <a href="#What-are-the-differences-between-R-and-S_003f" accesskey="p" rel="prev">What are the differences between R and S?</a>, Up: <a href="#R-and-S" accesskey="u" rel="up">R and S</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
|
|
</div>
|
|
<a name="Is-there-anything-R-can-do-that-S_002dPLUS-cannot_003f-1"></a>
|
|
<h3 class="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”, <a href="http://www.amstat.org/publications/jcgs/"><em>Journal of Computational and Graphical Statistics</em></a>, <strong>9</strong>,
|
|
582–599.
|
|
</p>
|
|
<hr>
|
|
<a name="What-is-R_002dplus_003f"></a>
|
|
<div class="header">
|
|
<p>
|
|
Previous: <a href="#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: <a href="#R-and-S" accesskey="u" rel="up">R and S</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
|
|
</div>
|
|
<a name="What-is-R_002dplus_003f-1"></a>
|
|
<h3 class="section">3.5 What is R-plus?</h3>
|
|
|
|
<p>For a very long time, there was no such thing.
|
|
</p>
|
|
<p><a href="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><a href="http://www.revolution-computing.com/">Revolution Analytics</a> has
|
|
released
|
|
<a href="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
|
|
environments.
|
|
</p>
|
|
|
|
<p>See also
|
|
<a href="https://en.wikipedia.org/wiki/R_programming_language#Commercialized_versions_of_R">https://en.wikipedia.org/wiki/R_programming_language#Commercialized_versions_of_R</a>
|
|
for pointers to commercialized versions of R.
|
|
</p>
|
|
<hr>
|
|
<a name="R-Web-Interfaces"></a>
|
|
<div class="header">
|
|
<p>
|
|
Next: <a href="#R-Add_002dOn-Packages" accesskey="n" rel="next">R Add-On Packages</a>, Previous: <a href="#R-and-S" accesskey="p" rel="prev">R and S</a>, Up: <a href="#Top" accesskey="u" rel="up">Top</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
|
|
</div>
|
|
<a name="R-Web-Interfaces-1"></a>
|
|
<h2 class="chapter">4 R Web Interfaces</h2>
|
|
|
|
<p><strong>Rweb</strong> is developed and maintained by
|
|
<a href="mailto:jeff@math.montana.edu">Jeff Banfield</a>. The
|
|
<a href="http://www.math.montana.edu/Rweb/">Rweb Home Page</a> provides access
|
|
to all three versions of Rweb—a simple text entry form that returns
|
|
output and graphs, a more sophisticated JavaScript version that provides
|
|
a multiple window environment, and a set of point and click modules that
|
|
are useful for introductory statistics courses and require no knowledge
|
|
of the R language. All of the Rweb versions can analyze Web accessible
|
|
datasets if a <acronym>URL</acronym> is provided.
|
|
</p>
|
|
<p>The paper “Rweb: Web-based Statistical Analysis”, providing a detailed
|
|
explanation of the different versions of Rweb and an overview of how
|
|
Rweb works, was published in the Journal of Statistical Software
|
|
(<a href="http://www.jstatsoft.org/v04/i01/">http://www.jstatsoft.org/v04/i01/</a>).
|
|
</p>
|
|
<p><a href="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 <a href="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 <a href="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
|
|
collection of links available from
|
|
<a href="http://biostat.mc.vanderbilt.edu/twiki/bin/view/Main/StatCompCourse">http://biostat.mc.vanderbilt.edu/twiki/bin/view/Main/StatCompCourse</a>.
|
|
</p>
|
|
<p><a href="http://www.warwick.ac.uk/go/dfirth">David Firth</a> has written
|
|
<a href="https://CRAN.R-project.org/package=CGIwithR"><strong>CGIwithR</strong></a>, an R add-on package available from <acronym>CRAN</acronym>. It
|
|
provides some simple extensions to R to facilitate running R scripts
|
|
through the CGI interface to a web server, and allows submission of data
|
|
using both GET and POST methods. It is easily installed using Apache
|
|
under Linux and in principle should run on any platform that supports R
|
|
and a web server provided that the installer has the necessary security
|
|
permissions. David’s paper “CGIwithR: Facilities for Processing Web
|
|
Forms Using R” was published in the Journal of Statistical Software
|
|
(<a href="http://www.jstatsoft.org/v08/i10/">http://www.jstatsoft.org/v08/i10/</a>). The package is now
|
|
maintained by <a href="mailto:duncan@wald.ucdavis.edu">Duncan Temple Lang</a> and
|
|
has a web page at <a href="http://www.omegahat.org/CGIwithR/">http://www.omegahat.org/CGIwithR/</a>.
|
|
</p>
|
|
|
|
<p>Jeff Horner is working on the R/Apache Integration Project which embeds
|
|
the R interpreter inside Apache 2 (and beyond). A tutorial and
|
|
presentation are available from the project web page at
|
|
<a href="http://biostat.mc.vanderbilt.edu/twiki/bin/view/Main/RApacheProject">http://biostat.mc.vanderbilt.edu/twiki/bin/view/Main/RApacheProject</a>.
|
|
</p>
|
|
<p><a href="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.
|
|
<a href="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. <a href="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><a href="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><a href="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 <a href="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 <a href="https://CRAN.R-project.org/package=brew"><strong>brew</strong></a> package with
|
|
<a href="http://rapache.net/">Rapache</a> with the advantage of cross-platform
|
|
support and easy installation.
|
|
</p>
|
|
<p>The <a href="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, <a href="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), <a href="https://rstudio.org/">Rstudio</a> (R code designing and testing, file management), CKEditor
|
|
(<acronym>HTML</acronym> Layer design), and PHP.
|
|
</p>
|
|
|
|
|
|
<hr>
|
|
<a name="R-Add_002dOn-Packages"></a>
|
|
<div class="header">
|
|
<p>
|
|
Next: <a href="#R-and-Emacs" accesskey="n" rel="next">R and Emacs</a>, Previous: <a href="#R-Web-Interfaces" accesskey="p" rel="prev">R Web Interfaces</a>, Up: <a href="#Top" accesskey="u" rel="up">Top</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
|
|
</div>
|
|
<a name="R-Add_002dOn-Packages-1"></a>
|
|
<h2 class="chapter">5 R Add-On Packages</h2>
|
|
|
|
<table summary="" class="menu" border="0" cellspacing="0">
|
|
<tr><td align="left" valign="top">• <a href="#Which-add_002don-packages-exist-for-R_003f" accesskey="1">Which add-on packages exist for R?</a>:</td><td> </td><td align="left" valign="top">
|
|
</td></tr>
|
|
<tr><td align="left" valign="top">• <a href="#How-can-add_002don-packages-be-installed_003f" accesskey="2">How can add-on packages be installed?</a>:</td><td> </td><td align="left" valign="top">
|
|
</td></tr>
|
|
<tr><td align="left" valign="top">• <a href="#How-can-add_002don-packages-be-used_003f" accesskey="3">How can add-on packages be used?</a>:</td><td> </td><td align="left" valign="top">
|
|
</td></tr>
|
|
<tr><td align="left" valign="top">• <a href="#How-can-add_002don-packages-be-removed_003f" accesskey="4">How can add-on packages be removed?</a>:</td><td> </td><td align="left" valign="top">
|
|
</td></tr>
|
|
<tr><td align="left" valign="top">• <a href="#How-can-I-create-an-R-package_003f" accesskey="5">How can I create an R package?</a>:</td><td> </td><td align="left" valign="top">
|
|
</td></tr>
|
|
<tr><td align="left" valign="top">• <a href="#How-can-I-contribute-to-R_003f" accesskey="6">How can I contribute to R?</a>:</td><td> </td><td align="left" valign="top">
|
|
</td></tr>
|
|
</table>
|
|
|
|
<hr>
|
|
<a name="Which-add_002don-packages-exist-for-R_003f"></a>
|
|
<div class="header">
|
|
<p>
|
|
Next: <a href="#How-can-add_002don-packages-be-installed_003f" accesskey="n" rel="next">How can add-on packages be installed?</a>, Previous: <a href="#R-Add_002dOn-Packages" accesskey="p" rel="prev">R Add-On Packages</a>, Up: <a href="#R-Add_002dOn-Packages" accesskey="u" rel="up">R Add-On Packages</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
|
|
</div>
|
|
<a name="Which-add_002don-packages-exist-for-R_003f-1"></a>
|
|
<h3 class="section">5.1 Which add-on packages exist for R?</h3>
|
|
|
|
<table summary="" class="menu" border="0" cellspacing="0">
|
|
<tr><td align="left" valign="top">• <a href="#Add_002don-packages-in-R" accesskey="1">Add-on packages in R</a>:</td><td> </td><td align="left" valign="top">
|
|
</td></tr>
|
|
<tr><td align="left" valign="top">• <a href="#Add_002don-packages-from-CRAN" accesskey="2">Add-on packages from CRAN</a>:</td><td> </td><td align="left" valign="top">
|
|
</td></tr>
|
|
<tr><td align="left" valign="top">• <a href="#Add_002don-packages-from-Omegahat" accesskey="3">Add-on packages from Omegahat</a>:</td><td> </td><td align="left" valign="top">
|
|
</td></tr>
|
|
<tr><td align="left" valign="top">• <a href="#Add_002don-packages-from-Bioconductor" accesskey="4">Add-on packages from Bioconductor</a>:</td><td> </td><td align="left" valign="top">
|
|
</td></tr>
|
|
<tr><td align="left" valign="top">• <a href="#Other-add_002don-packages" accesskey="5">Other add-on packages</a>:</td><td> </td><td align="left" valign="top">
|
|
</td></tr>
|
|
</table>
|
|
|
|
<hr>
|
|
<a name="Add_002don-packages-in-R"></a>
|
|
<div class="header">
|
|
<p>
|
|
Next: <a href="#Add_002don-packages-from-CRAN" accesskey="n" rel="next">Add-on packages from CRAN</a>, Previous: <a href="#Which-add_002don-packages-exist-for-R_003f" accesskey="p" rel="prev">Which add-on packages exist for R?</a>, Up: <a href="#Which-add_002don-packages-exist-for-R_003f" accesskey="u" rel="up">Which add-on packages exist for R?</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
|
|
</div>
|
|
<a name="Add_002don-packages-in-R-1"></a>
|
|
<h4 class="subsection">5.1.1 Add-on packages in R</h4>
|
|
|
|
<p>The R distribution comes with the following packages:
|
|
</p>
|
|
<dl compact="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 <a href="https://CRAN.R-project.org/package=MASS"><strong>MASS</strong></a>, and package <strong>mle</strong> moved to
|
|
<strong>stats4</strong>.
|
|
</p>
|
|
<hr>
|
|
<a name="Add_002don-packages-from-CRAN"></a>
|
|
<div class="header">
|
|
<p>
|
|
Next: <a href="#Add_002don-packages-from-Omegahat" accesskey="n" rel="next">Add-on packages from Omegahat</a>, Previous: <a href="#Add_002don-packages-in-R" accesskey="p" rel="prev">Add-on packages in R</a>, Up: <a href="#Which-add_002don-packages-exist-for-R_003f" accesskey="u" rel="up">Which add-on packages exist for R?</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
|
|
</div>
|
|
<a name="Add_002don-packages-from-CRAN-1"></a>
|
|
<h4 class="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>
|
|
<dl compact="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 <a href="https://CRAN.R-project.org/web/packages/"><acronym>CRAN</acronym>
|
|
contributed packages page</a> for more information.
|
|
</p>
|
|
<p>Many of these packages are categorized into
|
|
<a href="https://CRAN.R-project.org/web/views/"><acronym>CRAN</acronym> Task Views</a>, allowing
|
|
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
|
|
<a href="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>
|
|
<a name="Add_002don-packages-from-Omegahat"></a>
|
|
<div class="header">
|
|
<p>
|
|
Next: <a href="#Add_002don-packages-from-Bioconductor" accesskey="n" rel="next">Add-on packages from Bioconductor</a>, Previous: <a href="#Add_002don-packages-from-CRAN" accesskey="p" rel="prev">Add-on packages from CRAN</a>, Up: <a href="#Which-add_002don-packages-exist-for-R_003f" accesskey="u" rel="up">Which add-on packages exist for R?</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
|
|
</div>
|
|
<a name="Add_002don-packages-from-Omegahat-1"></a>
|
|
<h4 class="subsection">5.1.3 Add-on packages from Omegahat</h4>
|
|
|
|
<p>The <a href="http://www.omegahat.org/">Omega Project for Statistical
|
|
Computing</a> provides a variety of open-source software for statistical
|
|
applications, with special emphasis on web-based software, Java, the
|
|
Java virtual machine, and distributed computing. A <acronym>CRAN</acronym> style
|
|
R package repository is available via <a href="http://www.omegahat.org/R/">http://www.omegahat.org/R/</a>.
|
|
See <a href="http://www.omegahat.org/">http://www.omegahat.org/</a> for information on most R packages
|
|
available from the Omega project.
|
|
</p>
|
|
<hr>
|
|
<a name="Add_002don-packages-from-Bioconductor"></a>
|
|
<div class="header">
|
|
<p>
|
|
Next: <a href="#Other-add_002don-packages" accesskey="n" rel="next">Other add-on packages</a>, Previous: <a href="#Add_002don-packages-from-Omegahat" accesskey="p" rel="prev">Add-on packages from Omegahat</a>, Up: <a href="#Which-add_002don-packages-exist-for-R_003f" accesskey="u" rel="up">Which add-on packages exist for R?</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
|
|
</div>
|
|
<a name="Add_002don-packages-from-Bioconductor-1"></a>
|
|
<h4 class="subsection">5.1.4 Add-on packages from Bioconductor</h4>
|
|
|
|
<p><a href="https://www.bioconductor.org/">Bioconductor</a> is an open source and
|
|
open development software project for the analysis and comprehension of
|
|
genomic data. Most Bioconductor components are distributed as R add-on
|
|
packages. Initially most of the
|
|
<a href="https://bioconductor.org/packages/release/BiocViews.html#___Software">Bioconductor software packages</a>
|
|
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
|
|
<a href="https://www.bioconductor.org/download/">https://www.bioconductor.org/download/</a> for available packages and a
|
|
complete taxonomy via BioC Views.
|
|
</p>
|
|
<hr>
|
|
<a name="Other-add_002don-packages"></a>
|
|
<div class="header">
|
|
<p>
|
|
Previous: <a href="#Add_002don-packages-from-Bioconductor" accesskey="p" rel="prev">Add-on packages from Bioconductor</a>, Up: <a href="#Which-add_002don-packages-exist-for-R_003f" accesskey="u" rel="up">Which add-on packages exist for R?</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
|
|
</div>
|
|
<a name="Other-add_002don-packages-1"></a>
|
|
<h4 class="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 <a href="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
|
|
obtained from the mailing list archive.
|
|
</p>
|
|
<hr>
|
|
<a name="How-can-add_002don-packages-be-installed_003f"></a>
|
|
<div class="header">
|
|
<p>
|
|
Next: <a href="#How-can-add_002don-packages-be-used_003f" accesskey="n" rel="next">How can add-on packages be used?</a>, Previous: <a href="#Which-add_002don-packages-exist-for-R_003f" accesskey="p" rel="prev">Which add-on packages exist for R?</a>, Up: <a href="#R-Add_002dOn-Packages" accesskey="u" rel="up">R Add-On Packages</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
|
|
</div>
|
|
<a name="How-can-add_002don-packages-be-installed_003f-1"></a>
|
|
<h3 class="section">5.2 How can add-on packages be installed?</h3>
|
|
|
|
<p>(Unix-like only.) The add-on packages on <acronym>CRAN</acronym> come as gzipped tar
|
|
files named <code><var>pkg</var>_<var>version</var>.tar.gz</code>, which may in fact be
|
|
“bundles” containing more than one package. Let <var>path</var> be the
|
|
path to such a package file. Provided that <code>tar</code> and
|
|
<code>gzip</code> are available on your system, type
|
|
</p>
|
|
<div class="example">
|
|
<pre class="example">$ R CMD INSTALL <var>path</var>/<var>pkg</var>_<var>version</var>.tar.gz
|
|
</pre></div>
|
|
|
|
<p>at the shell prompt to install to the library tree rooted at the first
|
|
directory in your library search path (see the help page for
|
|
<code>.libPaths()</code> for details on how the search path is determined).
|
|
</p>
|
|
<p>To install to another tree (e.g., your private one), use
|
|
</p>
|
|
<div class="example">
|
|
<pre class="example">$ R CMD INSTALL -l <var>lib</var> <var>path</var>/<var>pkg</var>_<var>version</var>.tar.gz
|
|
</pre></div>
|
|
|
|
<p>where <var>lib</var> gives the path to the library tree to install to.
|
|
</p>
|
|
<p>Even more conveniently, you can install and automatically update
|
|
packages from within R if you have access to repositories such as
|
|
<acronym>CRAN</acronym>. See the help page for <code>available.packages()</code> for more
|
|
information.
|
|
</p>
|
|
|
|
|
|
|
|
|
|
|
|
<hr>
|
|
<a name="How-can-add_002don-packages-be-used_003f"></a>
|
|
<div class="header">
|
|
<p>
|
|
Next: <a href="#How-can-add_002don-packages-be-removed_003f" accesskey="n" rel="next">How can add-on packages be removed?</a>, Previous: <a href="#How-can-add_002don-packages-be-installed_003f" accesskey="p" rel="prev">How can add-on packages be installed?</a>, Up: <a href="#R-Add_002dOn-Packages" accesskey="u" rel="up">R Add-On Packages</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
|
|
</div>
|
|
<a name="How-can-add_002don-packages-be-used_003f-1"></a>
|
|
<h3 class="section">5.3 How can add-on packages be used?</h3>
|
|
|
|
<p>To find out which additional packages are available on your system, type
|
|
</p>
|
|
<div class="example">
|
|
<pre class="example">library()
|
|
</pre></div>
|
|
|
|
<p>at the R prompt.
|
|
</p>
|
|
<p>This produces something like
|
|
</p>
|
|
<blockquote>
|
|
<table summary="" class="cartouche" border="1"><tr><td>
|
|
<div class="smallexample">
|
|
<pre class="smallexample">Packages in `/home/me/lib/R':
|
|
|
|
mystuff My own R functions, nicely packaged but not documented
|
|
|
|
Packages in `/usr/local/lib/R/library':
|
|
|
|
KernSmooth Functions for kernel smoothing for Wand & Jones (1995)
|
|
MASS Main Package of Venables and Ripley's MASS
|
|
Matrix Sparse and Dense Matrix Classes and Methods
|
|
base The R Base package
|
|
boot Bootstrap R (S-Plus) Functions (Canty)
|
|
class Functions for Classification
|
|
cluster Functions for clustering (by Rousseeuw et al.)
|
|
codetools Code Analysis Tools for R
|
|
datasets The R Datasets Package
|
|
foreign Read Data Stored by Minitab, S, SAS, SPSS, Stata, Systat,
|
|
dBase, ...
|
|
grDevices The R Graphics Devices and Support for Colours and Fonts
|
|
graphics The R Graphics Package
|
|
grid The Grid Graphics Package
|
|
lattice Lattice Graphics
|
|
methods Formal Methods and Classes
|
|
mgcv GAMs with GCV/AIC/REML smoothness estimation and GAMMs
|
|
by PQL
|
|
nlme Linear and Nonlinear Mixed Effects Models
|
|
nnet Feed-forward Neural Networks and Multinomial Log-Linear
|
|
Models
|
|
rpart Recursive Partitioning
|
|
spatial Functions for Kriging and Point Pattern Analysis
|
|
splines Regression Spline Functions and Classes
|
|
stats The R Stats Package
|
|
stats4 Statistical functions using S4 Classes
|
|
survival Survival analysis, including penalised likelihood
|
|
tcltk Tcl/Tk Interface
|
|
tools Tools for Package Development
|
|
utils The R Utils Package
|
|
</pre></div>
|
|
</td></tr></table>
|
|
</blockquote>
|
|
|
|
<p>You can “load” the installed package <var>pkg</var> by
|
|
</p>
|
|
<div class="example">
|
|
<pre class="example">library(<var>pkg</var>)
|
|
</pre></div>
|
|
|
|
<p>You can then find out which functions it provides by typing one of
|
|
</p>
|
|
<div class="example">
|
|
<pre class="example">library(help = <var>pkg</var>)
|
|
help(package = <var>pkg</var>)
|
|
</pre></div>
|
|
|
|
<p>You can unload the loaded package <var>pkg</var> by
|
|
</p>
|
|
<div class="example">
|
|
<pre class="example">detach("package:<var>pkg</var>", unload = TRUE)
|
|
</pre></div>
|
|
|
|
<p>(where <code>unload = TRUE</code> is needed only for packages with a
|
|
namespace, see <code>?unload</code>).
|
|
</p>
|
|
<hr>
|
|
<a name="How-can-add_002don-packages-be-removed_003f"></a>
|
|
<div class="header">
|
|
<p>
|
|
Next: <a href="#How-can-I-create-an-R-package_003f" accesskey="n" rel="next">How can I create an R package?</a>, Previous: <a href="#How-can-add_002don-packages-be-used_003f" accesskey="p" rel="prev">How can add-on packages be used?</a>, Up: <a href="#R-Add_002dOn-Packages" accesskey="u" rel="up">R Add-On Packages</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
|
|
</div>
|
|
<a name="How-can-add_002don-packages-be-removed_003f-1"></a>
|
|
<h3 class="section">5.4 How can add-on packages be removed?</h3>
|
|
|
|
<p>Use
|
|
</p>
|
|
<div class="example">
|
|
<pre class="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>
|
|
<div class="example">
|
|
<pre class="example">$ R CMD REMOVE -l <var>lib</var> <var>pkg_1</var> … <var>pkg_n</var>
|
|
</pre></div>
|
|
|
|
<hr>
|
|
<a name="How-can-I-create-an-R-package_003f"></a>
|
|
<div class="header">
|
|
<p>
|
|
Next: <a href="#How-can-I-contribute-to-R_003f" accesskey="n" rel="next">How can I contribute to R?</a>, Previous: <a href="#How-can-add_002don-packages-be-removed_003f" accesskey="p" rel="prev">How can add-on packages be removed?</a>, Up: <a href="#R-Add_002dOn-Packages" accesskey="u" rel="up">R Add-On Packages</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
|
|
</div>
|
|
<a name="How-can-I-create-an-R-package_003f-1"></a>
|
|
<h3 class="section">5.5 How can I create an R package?</h3>
|
|
|
|
<p>A package consists of a subdirectory containing a file
|
|
<samp>DESCRIPTION</samp> and the subdirectories <samp>R</samp>, <samp>data</samp>,
|
|
<samp>demo</samp>, <samp>exec</samp>, <samp>inst</samp>, <samp>man</samp>, <samp>po</samp>,
|
|
<samp>src</samp>, and <samp>tests</samp> (some of which can be missing). The
|
|
package subdirectory may also contain files <samp>INDEX</samp>,
|
|
<samp>NAMESPACE</samp>, <samp>configure</samp>, <samp>cleanup</samp>, <samp>LICENSE</samp>,
|
|
<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 <a href="#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 <a href="#What-is-CRAN_003f">What is CRAN?</a>, for information on uploading a package to <acronym>CRAN</acronym>.
|
|
</p>
|
|
<hr>
|
|
<a name="How-can-I-contribute-to-R_003f"></a>
|
|
<div class="header">
|
|
<p>
|
|
Previous: <a href="#How-can-I-create-an-R-package_003f" accesskey="p" rel="prev">How can I create an R package?</a>, Up: <a href="#R-Add_002dOn-Packages" accesskey="u" rel="up">R Add-On Packages</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
|
|
</div>
|
|
<a name="How-can-I-contribute-to-R_003f-1"></a>
|
|
<h3 class="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 <a href="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.
|
|
</p>
|
|
<hr>
|
|
<a name="R-and-Emacs"></a>
|
|
<div class="header">
|
|
<p>
|
|
Next: <a href="#R-Miscellanea" accesskey="n" rel="next">R Miscellanea</a>, Previous: <a href="#R-Add_002dOn-Packages" accesskey="p" rel="prev">R Add-On Packages</a>, Up: <a href="#Top" accesskey="u" rel="up">Top</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
|
|
</div>
|
|
<a name="R-and-Emacs-1"></a>
|
|
<h2 class="chapter">6 R and Emacs</h2>
|
|
|
|
<table summary="" class="menu" border="0" cellspacing="0">
|
|
<tr><td align="left" valign="top">• <a href="#Is-there-Emacs-support-for-R_003f" accesskey="1">Is there Emacs support for R?</a>:</td><td> </td><td align="left" valign="top">
|
|
</td></tr>
|
|
<tr><td align="left" valign="top">• <a href="#Should-I-run-R-from-within-Emacs_003f" accesskey="2">Should I run R from within Emacs?</a>:</td><td> </td><td align="left" valign="top">
|
|
</td></tr>
|
|
<tr><td align="left" valign="top">• <a href="#Debugging-R-from-within-Emacs" accesskey="3">Debugging R from within Emacs</a>:</td><td> </td><td align="left" valign="top">
|
|
</td></tr>
|
|
</table>
|
|
|
|
<hr>
|
|
<a name="Is-there-Emacs-support-for-R_003f"></a>
|
|
<div class="header">
|
|
<p>
|
|
Next: <a href="#Should-I-run-R-from-within-Emacs_003f" accesskey="n" rel="next">Should I run R from within Emacs?</a>, Previous: <a href="#R-and-Emacs" accesskey="p" rel="prev">R and Emacs</a>, Up: <a href="#R-and-Emacs" accesskey="u" rel="up">R and Emacs</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
|
|
</div>
|
|
<a name="Is-there-Emacs-support-for-R_003f-1"></a>
|
|
<h3 class="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>
|
|
3.x/4.x/5.x/6.x/7.x), LispStat dialects (XLispStat, ViSta), SAS, Stata,
|
|
and BUGS.
|
|
</p>
|
|
<p><acronym>ESS</acronym> grew out of the need for bug fixes and extensions to
|
|
S-mode 4.8 (which was a <acronym>GNU</acronym> Emacs interface to S/<small>S-PLUS</small>
|
|
version 3 only). The current set of developers desired support for
|
|
XEmacs, R, S4, and MS Windows. In addition, with new modes being
|
|
developed for R, Stata, and SAS, it was felt that a unifying interface
|
|
and framework for the user interface would benefit both the user and the
|
|
developer, by helping both groups conform to standard Emacs usage. The
|
|
end result is an increase in efficiency for statistical programming and
|
|
data analysis, over the usual tools.
|
|
</p>
|
|
<p>R support contains code for editing R source code (syntactic indentation
|
|
and highlighting of source code, partial evaluations of code, loading
|
|
and error-checking of code, and source code revision maintenance) and
|
|
documentation (syntactic indentation and highlighting of source code,
|
|
sending examples to running <acronym>ESS</acronym> process, and previewing),
|
|
interacting with an inferior R process from within Emacs (command-line
|
|
editing, searchable command history, command-line completion of R object
|
|
and file names, quick access to object and search lists, transcript
|
|
recording, and an interface to the help system), and transcript
|
|
manipulation (recording and saving transcript files, manipulating and
|
|
editing saved transcripts, and re-evaluating commands from transcript
|
|
files).
|
|
</p>
|
|
<p>The latest stable version of <acronym>ESS</acronym> is available via <acronym>CRAN</acronym> or
|
|
the <a href="http://ESS.R-project.org/">ESS web page</a>. The <acronym>HTML</acronym> version
|
|
of the documentation can be found at <a href="https://stat.ethz.ch/ESS/">https://stat.ethz.ch/ESS/</a>.
|
|
</p>
|
|
<p><acronym>ESS</acronym> comes with detailed installation instructions.
|
|
</p>
|
|
<p>For help with <acronym>ESS</acronym>, send email to
|
|
<a href="mailto:ESS-help@stat.math.ethz.ch">ESS-help@stat.math.ethz.ch</a>.
|
|
</p>
|
|
<p>Please send bug reports and suggestions on <acronym>ESS</acronym> to
|
|
<a href="mailto:ESS-bugs@stat.math.ethz.ch">ESS-bugs@stat.math.ethz.ch</a>. The easiest way to do this from is
|
|
within Emacs by typing <kbd>M-x ess-submit-bug-report</kbd> or using the
|
|
[ESS] or [iESS] pulldown menus.
|
|
</p>
|
|
<hr>
|
|
<a name="Should-I-run-R-from-within-Emacs_003f"></a>
|
|
<div class="header">
|
|
<p>
|
|
Next: <a href="#Debugging-R-from-within-Emacs" accesskey="n" rel="next">Debugging R from within Emacs</a>, Previous: <a href="#Is-there-Emacs-support-for-R_003f" accesskey="p" rel="prev">Is there Emacs support for R?</a>, Up: <a href="#R-and-Emacs" accesskey="u" rel="up">R and Emacs</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
|
|
</div>
|
|
<a name="Should-I-run-R-from-within-Emacs_003f-1"></a>
|
|
<h3 class="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>
|
|
<a name="Debugging-R-from-within-Emacs"></a>
|
|
<div class="header">
|
|
<p>
|
|
Previous: <a href="#Should-I-run-R-from-within-Emacs_003f" accesskey="p" rel="prev">Should I run R from within Emacs?</a>, Up: <a href="#R-and-Emacs" accesskey="u" rel="up">R and Emacs</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
|
|
</div>
|
|
<a name="Debugging-R-from-within-Emacs-1"></a>
|
|
<h3 class="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 <span class="key">RET</span> - d
|
|
<span class="key">SPC</span> g d b <span class="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>
|
|
<div class="example">
|
|
<pre class="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>
|
|
<a name="R-Miscellanea"></a>
|
|
<div class="header">
|
|
<p>
|
|
Next: <a href="#R-Programming" accesskey="n" rel="next">R Programming</a>, Previous: <a href="#R-and-Emacs" accesskey="p" rel="prev">R and Emacs</a>, Up: <a href="#Top" accesskey="u" rel="up">Top</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
|
|
</div>
|
|
<a name="R-Miscellanea-1"></a>
|
|
<h2 class="chapter">7 R Miscellanea</h2>
|
|
|
|
<table summary="" class="menu" border="0" cellspacing="0">
|
|
<tr><td align="left" valign="top">• <a href="#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><td align="left" valign="top">
|
|
</td></tr>
|
|
<tr><td align="left" valign="top">• <a href="#How-can-I-save-my-workspace_003f" accesskey="2">How can I save my workspace?</a>:</td><td> </td><td align="left" valign="top">
|
|
</td></tr>
|
|
<tr><td align="left" valign="top">• <a href="#How-can-I-clean-up-my-workspace_003f" accesskey="3">How can I clean up my workspace?</a>:</td><td> </td><td align="left" valign="top">
|
|
</td></tr>
|
|
<tr><td align="left" valign="top">• <a href="#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><td align="left" valign="top">
|
|
</td></tr>
|
|
<tr><td align="left" valign="top">• <a href="#Why-do-my-matrices-lose-dimensions_003f" accesskey="5">Why do my matrices lose dimensions?</a>:</td><td> </td><td align="left" valign="top">
|
|
</td></tr>
|
|
<tr><td align="left" valign="top">• <a href="#How-does-autoloading-work_003f" accesskey="6">How does autoloading work?</a>:</td><td> </td><td align="left" valign="top">
|
|
</td></tr>
|
|
<tr><td align="left" valign="top">• <a href="#How-should-I-set-options_003f" accesskey="7">How should I set options?</a>:</td><td> </td><td align="left" valign="top">
|
|
</td></tr>
|
|
<tr><td align="left" valign="top">• <a href="#How-do-file-names-work-in-Windows_003f" accesskey="8">How do file names work in Windows?</a>:</td><td> </td><td align="left" valign="top">
|
|
</td></tr>
|
|
<tr><td align="left" valign="top">• <a href="#Why-does-plotting-give-a-color-allocation-error_003f" accesskey="9">Why does plotting give a color allocation error?</a>:</td><td> </td><td align="left" valign="top">
|
|
</td></tr>
|
|
<tr><td align="left" valign="top">• <a href="#How-do-I-convert-factors-to-numeric_003f">How do I convert factors to numeric?</a>:</td><td> </td><td align="left" valign="top">
|
|
</td></tr>
|
|
<tr><td align="left" valign="top">• <a href="#Are-Trellis-displays-implemented-in-R_003f">Are Trellis displays implemented in R?</a>:</td><td> </td><td align="left" valign="top">
|
|
</td></tr>
|
|
<tr><td align="left" valign="top">• <a href="#What-are-the-enclosing-and-parent-environments_003f">What are the enclosing and parent environments?</a>:</td><td> </td><td align="left" valign="top">
|
|
</td></tr>
|
|
<tr><td align="left" valign="top">• <a href="#How-can-I-substitute-into-a-plot-label_003f">How can I substitute into a plot label?</a>:</td><td> </td><td align="left" valign="top">
|
|
</td></tr>
|
|
<tr><td align="left" valign="top">• <a href="#What-are-valid-names_003f">What are valid names?</a>:</td><td> </td><td align="left" valign="top">
|
|
</td></tr>
|
|
<tr><td align="left" valign="top">• <a href="#Are-GAMs-implemented-in-R_003f">Are GAMs implemented in R?</a>:</td><td> </td><td align="left" valign="top">
|
|
</td></tr>
|
|
<tr><td align="left" valign="top">• <a href="#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><td align="left" valign="top">
|
|
</td></tr>
|
|
<tr><td align="left" valign="top">• <a href="#Why-does-outer_0028_0029-behave-strangely-with-my-function_003f">Why does outer() behave strangely with my function?</a>:</td><td> </td><td align="left" valign="top">
|
|
</td></tr>
|
|
<tr><td align="left" valign="top">• <a href="#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><td align="left" valign="top">
|
|
</td></tr>
|
|
<tr><td align="left" valign="top">• <a href="#How-do-I-produce-PNG-graphics-in-batch-mode_003f">How do I produce PNG graphics in batch mode?</a>:</td><td> </td><td align="left" valign="top">
|
|
</td></tr>
|
|
<tr><td align="left" valign="top">• <a href="#How-can-I-get-command-line-editing-to-work_003f">How can I get command line editing to work?</a>:</td><td> </td><td align="left" valign="top">
|
|
</td></tr>
|
|
<tr><td align="left" valign="top">• <a href="#How-can-I-turn-a-string-into-a-variable_003f">How can I turn a string into a variable?</a>:</td><td> </td><td align="left" valign="top">
|
|
</td></tr>
|
|
<tr><td align="left" valign="top">• <a href="#Why-do-lattice_002ftrellis-graphics-not-work_003f">Why do lattice/trellis graphics not work?</a>:</td><td> </td><td align="left" valign="top">
|
|
</td></tr>
|
|
<tr><td align="left" valign="top">• <a href="#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><td align="left" valign="top">
|
|
</td></tr>
|
|
<tr><td align="left" valign="top">• <a href="#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><td align="left" valign="top">
|
|
</td></tr>
|
|
<tr><td align="left" valign="top">• <a href="#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><td align="left" valign="top">
|
|
</td></tr>
|
|
<tr><td align="left" valign="top">• <a href="#Where-have-all-the-methods-gone_003f">Where have all the methods gone?</a>:</td><td> </td><td align="left" valign="top">
|
|
</td></tr>
|
|
<tr><td align="left" valign="top">• <a href="#How-can-I-create-rotated-axis-labels_003f">How can I create rotated axis labels?</a>:</td><td> </td><td align="left" valign="top">
|
|
</td></tr>
|
|
<tr><td align="left" valign="top">• <a href="#Why-is-read_002etable_0028_0029-so-inefficient_003f">Why is read.table() so inefficient?</a>:</td><td> </td><td align="left" valign="top">
|
|
</td></tr>
|
|
<tr><td align="left" valign="top">• <a href="#What-is-the-difference-between-package-and-library_003f">What is the difference between package and library?</a>:</td><td> </td><td align="left" valign="top">
|
|
</td></tr>
|
|
<tr><td align="left" valign="top">• <a href="#I-installed-a-package-but-the-functions-are-not-there">I installed a package but the functions are not there</a>:</td><td> </td><td align="left" valign="top">
|
|
</td></tr>
|
|
<tr><td align="left" valign="top">• <a href="#Why-doesn_0027t-R-think-these-numbers-are-equal_003f">Why doesn't R think these numbers are equal?</a>:</td><td> </td><td align="left" valign="top">
|
|
</td></tr>
|
|
<tr><td align="left" valign="top">• <a href="#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><td align="left" valign="top">
|
|
</td></tr>
|
|
<tr><td align="left" valign="top">• <a href="#Why-are-powers-of-negative-numbers-wrong_003f">Why are powers of negative numbers wrong?</a>:</td><td> </td><td align="left" valign="top">
|
|
</td></tr>
|
|
<tr><td align="left" valign="top">• <a href="#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><td align="left" valign="top">
|
|
</td></tr>
|
|
<tr><td align="left" valign="top">• <a href="#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><td align="left" valign="top">
|
|
</td></tr>
|
|
<tr><td align="left" valign="top">• <a href="#Why-are-there-unwanted-borders">Why are there unwanted borders</a>:</td><td> </td><td align="left" valign="top">
|
|
</td></tr>
|
|
<tr><td align="left" valign="top">• <a href="#Why-does-backslash-behave-strangely-inside-strings_003f">Why does backslash behave strangely inside strings?</a>:</td><td> </td><td align="left" valign="top">
|
|
</td></tr>
|
|
<tr><td align="left" valign="top">• <a href="#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><td align="left" valign="top">
|
|
</td></tr>
|
|
<tr><td align="left" valign="top">• <a href="#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><td align="left" valign="top">
|
|
</td></tr>
|
|
<tr><td align="left" valign="top">• <a href="#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><td align="left" valign="top">
|
|
</td></tr>
|
|
<tr><td align="left" valign="top">• <a href="#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><td align="left" valign="top">
|
|
</td></tr>
|
|
<tr><td align="left" valign="top">• <a href="#Why-is-R-apparently-not-releasing-memory_003f">Why is R apparently not releasing memory?</a>:</td><td> </td><td align="left" valign="top">
|
|
</td></tr>
|
|
<tr><td align="left" valign="top">• <a href="#How-can-I-enable-secure-https-downloads-in-R_003f">How can I enable secure https downloads in R?</a>:</td><td> </td><td align="left" valign="top">
|
|
</td></tr>
|
|
</table>
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
<hr>
|
|
<a name="How-can-I-set-components-of-a-list-to-NULL_003f"></a>
|
|
<div class="header">
|
|
<p>
|
|
Next: <a href="#How-can-I-save-my-workspace_003f" accesskey="n" rel="next">How can I save my workspace?</a>, Previous: <a href="#R-Miscellanea" accesskey="p" rel="prev">R Miscellanea</a>, Up: <a href="#R-Miscellanea" accesskey="u" rel="up">R Miscellanea</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
|
|
</div>
|
|
<a name="How-can-I-set-components-of-a-list-to-NULL_003f-1"></a>
|
|
<h3 class="section">7.1 How can I set components of a list to NULL?</h3>
|
|
|
|
<p>You can use
|
|
</p>
|
|
<div class="example">
|
|
<pre class="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>
|
|
<a name="How-can-I-save-my-workspace_003f"></a>
|
|
<div class="header">
|
|
<p>
|
|
Next: <a href="#How-can-I-clean-up-my-workspace_003f" accesskey="n" rel="next">How can I clean up my workspace?</a>, Previous: <a href="#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: <a href="#R-Miscellanea" accesskey="u" rel="up">R Miscellanea</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
|
|
</div>
|
|
<a name="How-can-I-save-my-workspace_003f-1"></a>
|
|
<h3 class="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
|
|
can save the image under a different name.
|
|
</p>
|
|
<hr>
|
|
<a name="How-can-I-clean-up-my-workspace_003f"></a>
|
|
<div class="header">
|
|
<p>
|
|
Next: <a href="#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: <a href="#How-can-I-save-my-workspace_003f" accesskey="p" rel="prev">How can I save my workspace?</a>, Up: <a href="#R-Miscellanea" accesskey="u" rel="up">R Miscellanea</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
|
|
</div>
|
|
<a name="How-can-I-clean-up-my-workspace_003f-1"></a>
|
|
<h3 class="section">7.3 How can I clean up my workspace?</h3>
|
|
|
|
<p>To remove all objects in the currently active environment (typically
|
|
<code>.GlobalEnv</code>), you can do
|
|
</p>
|
|
<div class="example">
|
|
<pre class="example">rm(list = ls(all = TRUE))
|
|
</pre></div>
|
|
|
|
<p>(Without <samp>all = TRUE</samp>, only the objects with names not starting
|
|
with a ‘<samp>.</samp>’ are removed.)
|
|
</p>
|
|
<hr>
|
|
<a name="How-can-I-get-eval_0028_0029-and-D_0028_0029-to-work_003f"></a>
|
|
<div class="header">
|
|
<p>
|
|
Next: <a href="#Why-do-my-matrices-lose-dimensions_003f" accesskey="n" rel="next">Why do my matrices lose dimensions?</a>, Previous: <a href="#How-can-I-clean-up-my-workspace_003f" accesskey="p" rel="prev">How can I clean up my workspace?</a>, Up: <a href="#R-Miscellanea" accesskey="u" rel="up">R Miscellanea</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
|
|
</div>
|
|
<a name="How-can-I-get-eval_0028_0029-and-D_0028_0029-to-work_003f-1"></a>
|
|
<h3 class="section">7.4 How can I get eval() and D() to work?</h3>
|
|
|
|
<p>Strange things will happen if you use <code>eval(print(x), envir = e)</code>
|
|
or <code>D(x^2, "x")</code>. The first one will either tell you that
|
|
"<code>x</code>" is not found, or print the value of the wrong <code>x</code>.
|
|
The other one will likely return zero if <code>x</code> exists, and an error
|
|
otherwise.
|
|
</p>
|
|
<p>This is because in both cases, the first argument is evaluated in the
|
|
calling environment first. The result (which should be an object of
|
|
mode <code>"expression"</code> or <code>"call"</code>) is then evaluated or
|
|
differentiated. What you (most likely) really want is obtained by
|
|
“quoting” the first argument upon surrounding it with
|
|
<code>expression()</code>. For example,
|
|
</p>
|
|
<div class="example">
|
|
<pre class="example">R> D(expression(x^2), "x")
|
|
2 * x
|
|
</pre></div>
|
|
|
|
<p>Although this behavior may initially seem to be rather strange, it is
|
|
perfectly logical. The “intuitive” behavior could easily be
|
|
implemented, but problems would arise whenever the expression is
|
|
contained in a variable, passed as a parameter, or is the result of a
|
|
function call. Consider for instance the semantics in cases like
|
|
</p>
|
|
<div class="example">
|
|
<pre class="example">D2 <- function(e, n) D(D(e, n), n)
|
|
</pre></div>
|
|
|
|
<p>or
|
|
</p>
|
|
<div class="example">
|
|
<pre class="example">g <- function(y) eval(substitute(y), sys.frame(sys.parent(n = 2)))
|
|
g(a * b)
|
|
</pre></div>
|
|
|
|
<p>See the help page for <code>deriv()</code> for more examples.
|
|
</p>
|
|
<hr>
|
|
<a name="Why-do-my-matrices-lose-dimensions_003f"></a>
|
|
<div class="header">
|
|
<p>
|
|
Next: <a href="#How-does-autoloading-work_003f" accesskey="n" rel="next">How does autoloading work?</a>, Previous: <a href="#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: <a href="#R-Miscellanea" accesskey="u" rel="up">R Miscellanea</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
|
|
</div>
|
|
<a name="Why-do-my-matrices-lose-dimensions_003f-1"></a>
|
|
<h3 class="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>
|
|
<div class="example">
|
|
<pre class="example">rowmatrix <- mat[2, , drop = FALSE] # <span class="roman">creates a row matrix</span>
|
|
colmatrix <- mat[, 2, drop = FALSE] # <span class="roman">creates a column matrix</span>
|
|
a <- b[1, 1, 1, drop = FALSE] # <span class="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>
|
|
<div class="example">
|
|
<pre class="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>
|
|
<div class="example">
|
|
<pre class="example">somerows <- mat[index, , drop = FALSE]
|
|
</pre></div>
|
|
|
|
<hr>
|
|
<a name="How-does-autoloading-work_003f"></a>
|
|
<div class="header">
|
|
<p>
|
|
Next: <a href="#How-should-I-set-options_003f" accesskey="n" rel="next">How should I set options?</a>, Previous: <a href="#Why-do-my-matrices-lose-dimensions_003f" accesskey="p" rel="prev">Why do my matrices lose dimensions?</a>, Up: <a href="#R-Miscellanea" accesskey="u" rel="up">R Miscellanea</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
|
|
</div>
|
|
<a name="How-does-autoloading-work_003f-1"></a>
|
|
<h3 class="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>
|
|
<a name="How-should-I-set-options_003f"></a>
|
|
<div class="header">
|
|
<p>
|
|
Next: <a href="#How-do-file-names-work-in-Windows_003f" accesskey="n" rel="next">How do file names work in Windows?</a>, Previous: <a href="#How-does-autoloading-work_003f" accesskey="p" rel="prev">How does autoloading work?</a>, Up: <a href="#R-Miscellanea" accesskey="u" rel="up">R Miscellanea</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
|
|
</div>
|
|
<a name="How-should-I-set-options_003f-1"></a>
|
|
<h3 class="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”
|
|
variable.
|
|
</p>
|
|
<p>For example, given
|
|
</p>
|
|
<div class="example">
|
|
<pre class="example">test1 <- function(x = pi, dig = 3) {
|
|
oo <- options(digits = dig); on.exit(options(oo));
|
|
cat(.Options$digits, x, "\n")
|
|
}
|
|
test2 <- function(x = pi, dig = 3) {
|
|
.Options$digits <- dig
|
|
cat(.Options$digits, x, "\n")
|
|
}
|
|
</pre></div>
|
|
|
|
<p>we obtain:
|
|
</p>
|
|
<div class="example">
|
|
<pre class="example">R> test1()
|
|
3 3.14
|
|
R> test2()
|
|
3 3.141593
|
|
</pre></div>
|
|
|
|
<p>What is really used is the <em>global</em> value of <code>.Options</code>, and
|
|
using <kbd>options(OPT = VAL)</kbd> correctly updates it. Local copies of
|
|
<code>.Options</code>, either in <code>.GlobalEnv</code> or in a function
|
|
environment (frame), are just silently disregarded.
|
|
</p>
|
|
<hr>
|
|
<a name="How-do-file-names-work-in-Windows_003f"></a>
|
|
<div class="header">
|
|
<p>
|
|
Next: <a href="#Why-does-plotting-give-a-color-allocation-error_003f" accesskey="n" rel="next">Why does plotting give a color allocation error?</a>, Previous: <a href="#How-should-I-set-options_003f" accesskey="p" rel="prev">How should I set options?</a>, Up: <a href="#R-Miscellanea" accesskey="u" rel="up">R Miscellanea</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
|
|
</div>
|
|
<a name="How-do-file-names-work-in-Windows_003f-1"></a>
|
|
<h3 class="section">7.8 How do file names work in Windows?</h3>
|
|
|
|
<p>As R uses C-style string handling, ‘<samp>\</samp>’ is treated as an escape
|
|
character, so that for example one can enter a newline as ‘<samp>\n</samp>’.
|
|
When you really need a ‘<samp>\</samp>’, you have to escape it with another
|
|
‘<samp>\</samp>’.
|
|
</p>
|
|
<p>Thus, in filenames use something like <code>"c:\\data\\money.dat"</code>. You
|
|
can also replace ‘<samp>\</samp>’ by ‘<samp>/</samp>’ (<code>"c:/data/money.dat"</code>).
|
|
</p>
|
|
<hr>
|
|
<a name="Why-does-plotting-give-a-color-allocation-error_003f"></a>
|
|
<div class="header">
|
|
<p>
|
|
Next: <a href="#How-do-I-convert-factors-to-numeric_003f" accesskey="n" rel="next">How do I convert factors to numeric?</a>, Previous: <a href="#How-do-file-names-work-in-Windows_003f" accesskey="p" rel="prev">How do file names work in Windows?</a>, Up: <a href="#R-Miscellanea" accesskey="u" rel="up">R Miscellanea</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
|
|
</div>
|
|
<a name="Why-does-plotting-give-a-color-allocation-error_003f-1"></a>
|
|
<h3 class="section">7.9 Why does plotting give a color allocation error?</h3>
|
|
|
|
<p>On an X11 device, plotting sometimes, e.g., when running
|
|
<code>demo("image")</code>, results in “Error: color allocation error”.
|
|
This is an X problem, and only indirectly related to R. It occurs when
|
|
applications started prior to R have used all the available colors.
|
|
(How many colors are available depends on the X configuration; sometimes
|
|
only 256 colors can be used.)
|
|
</p>
|
|
<p>One application which is notorious for “eating” colors is Netscape.
|
|
If the problem occurs when Netscape is running, try (re)starting it with
|
|
either the <samp>-no-install</samp> (to use the default colormap) or the
|
|
<samp>-install</samp> (to install a private colormap) option.
|
|
</p>
|
|
<p>You could also set the <code>colortype</code> of <code>X11()</code> to
|
|
<code>"pseudo.cube"</code> rather than the default <code>"pseudo"</code>. See the
|
|
help page for <code>X11()</code> for more information.
|
|
</p>
|
|
|
|
|
|
|
|
<hr>
|
|
<a name="How-do-I-convert-factors-to-numeric_003f"></a>
|
|
<div class="header">
|
|
<p>
|
|
Next: <a href="#Are-Trellis-displays-implemented-in-R_003f" accesskey="n" rel="next">Are Trellis displays implemented in R?</a>, Previous: <a href="#Why-does-plotting-give-a-color-allocation-error_003f" accesskey="p" rel="prev">Why does plotting give a color allocation error?</a>, Up: <a href="#R-Miscellanea" accesskey="u" rel="up">R Miscellanea</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
|
|
</div>
|
|
<a name="How-do-I-convert-factors-to-numeric_003f-1"></a>
|
|
<h3 class="section">7.10 How do I convert factors to numeric?</h3>
|
|
|
|
<p>It may happen that when reading numeric data into R (usually, when
|
|
reading in a file), they come in as factors. If <code>f</code> is such a
|
|
factor object, you can use
|
|
</p>
|
|
<div class="example">
|
|
<pre class="example">as.numeric(as.character(f))
|
|
</pre></div>
|
|
|
|
<p>to get the numbers back. More efficient, but harder to remember, is
|
|
</p>
|
|
<div class="example">
|
|
<pre class="example">as.numeric(levels(f))[as.integer(f)]
|
|
</pre></div>
|
|
|
|
<p>In any case, do not call <code>as.numeric()</code> or their likes directly for
|
|
the task at hand (as <code>as.numeric()</code> or <code>unclass()</code> give the
|
|
internal codes).
|
|
</p>
|
|
<hr>
|
|
<a name="Are-Trellis-displays-implemented-in-R_003f"></a>
|
|
<div class="header">
|
|
<p>
|
|
Next: <a href="#What-are-the-enclosing-and-parent-environments_003f" accesskey="n" rel="next">What are the enclosing and parent environments?</a>, Previous: <a href="#How-do-I-convert-factors-to-numeric_003f" accesskey="p" rel="prev">How do I convert factors to numeric?</a>, Up: <a href="#R-Miscellanea" accesskey="u" rel="up">R Miscellanea</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
|
|
</div>
|
|
<a name="Are-Trellis-displays-implemented-in-R_003f-1"></a>
|
|
<h3 class="section">7.11 Are Trellis displays implemented in R?</h3>
|
|
|
|
<p>The recommended package <a href="https://CRAN.R-project.org/package=lattice"><strong>lattice</strong></a> (which is based on base
|
|
package <strong>grid</strong>) provides graphical functionality that is compatible
|
|
with most Trellis commands.
|
|
</p>
|
|
<p>You could also look at <code>coplot()</code> and <code>dotchart()</code> which might
|
|
do at least some of what you want. Note also that the R version of
|
|
<code>pairs()</code> is fairly general and provides most of the functionality
|
|
of <code>splom()</code>, and that R’s default plot method has an argument
|
|
<code>asp</code> allowing to specify (and fix against device resizing) the
|
|
aspect ratio of the plot.
|
|
</p>
|
|
<p>(Because the word “Trellis” has been claimed as a trademark we do not
|
|
use it in R. The name “lattice” has been chosen for the R
|
|
equivalent.)
|
|
</p>
|
|
<hr>
|
|
<a name="What-are-the-enclosing-and-parent-environments_003f"></a>
|
|
<div class="header">
|
|
<p>
|
|
Next: <a href="#How-can-I-substitute-into-a-plot-label_003f" accesskey="n" rel="next">How can I substitute into a plot label?</a>, Previous: <a href="#Are-Trellis-displays-implemented-in-R_003f" accesskey="p" rel="prev">Are Trellis displays implemented in R?</a>, Up: <a href="#R-Miscellanea" accesskey="u" rel="up">R Miscellanea</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
|
|
</div>
|
|
<a name="What-are-the-enclosing-and-parent-environments_003f-1"></a>
|
|
<h3 class="section">7.12 What are the enclosing and parent environments?</h3>
|
|
|
|
<p>Inside a function you may want to access variables in two additional
|
|
environments: the one that the function was defined in (“enclosing”),
|
|
and the one it was invoked in (“parent”).
|
|
</p>
|
|
<p>If you create a function at the command line or load it in a package its
|
|
enclosing environment is the global workspace. If you define a function
|
|
<code>f()</code> inside another function <code>g()</code> its enclosing environment
|
|
is the environment inside <code>g()</code>. The enclosing environment for a
|
|
function is fixed when the function is created. You can find out the
|
|
enclosing environment for a function <code>f()</code> using
|
|
<code>environment(f)</code>.
|
|
</p>
|
|
<p>The “parent” environment, on the other hand, is defined when you
|
|
invoke a function. If you invoke <code>lm()</code> at the command line its
|
|
parent environment is the global workspace, if you invoke it inside a
|
|
function <code>f()</code> then its parent environment is the environment
|
|
inside <code>f()</code>. You can find out the parent environment for an
|
|
invocation of a function by using <code>parent.frame()</code> or
|
|
<code>sys.frame(sys.parent())</code>.
|
|
</p>
|
|
<p>So for most user-visible functions the enclosing environment will be the
|
|
global workspace, since that is where most functions are defined. The
|
|
parent environment will be wherever the function happens to be called
|
|
from. If a function <code>f()</code> is defined inside another function
|
|
<code>g()</code> it will probably be used inside <code>g()</code> as well, so its
|
|
parent environment and enclosing environment will probably be the same.
|
|
</p>
|
|
<p>Parent environments are important because things like model formulas
|
|
need to be evaluated in the environment the function was called from,
|
|
since that’s where all the variables will be available. This relies on
|
|
the parent environment being potentially different with each invocation.
|
|
</p>
|
|
<p>Enclosing environments are important because a function can use
|
|
variables in the enclosing environment to share information with other
|
|
functions or with other invocations of itself (see the section on
|
|
lexical scoping). This relies on the enclosing environment being the
|
|
same each time the function is invoked. (In C this would be done with
|
|
static variables.)
|
|
</p>
|
|
<p>Scoping <em>is</em> hard. Looking at examples helps. It is particularly
|
|
instructive to look at examples that work differently in R and S and try
|
|
to see why they differ. One way to describe the scoping differences
|
|
between R and S is to say that in S the enclosing environment is
|
|
<em>always</em> the global workspace, but in R the enclosing environment
|
|
is wherever the function was created.
|
|
</p>
|
|
<hr>
|
|
<a name="How-can-I-substitute-into-a-plot-label_003f"></a>
|
|
<div class="header">
|
|
<p>
|
|
Next: <a href="#What-are-valid-names_003f" accesskey="n" rel="next">What are valid names?</a>, Previous: <a href="#What-are-the-enclosing-and-parent-environments_003f" accesskey="p" rel="prev">What are the enclosing and parent environments?</a>, Up: <a href="#R-Miscellanea" accesskey="u" rel="up">R Miscellanea</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
|
|
</div>
|
|
<a name="How-can-I-substitute-into-a-plot-label_003f-1"></a>
|
|
<h3 class="section">7.13 How can I substitute into a plot label?</h3>
|
|
|
|
<p>Often, it is desired to use the value of an R object in a plot label,
|
|
e.g., a title. This is easily accomplished using <code>paste()</code> if the
|
|
label is a simple character string, but not always obvious in case the
|
|
label is an expression (for refined mathematical annotation). In such a
|
|
case, either use <code>parse()</code> on your pasted character string or use
|
|
<code>substitute()</code> on an expression. For example, if <code>ahat</code> is an
|
|
estimator of your parameter <em>a</em> of interest, use
|
|
</p>
|
|
<div class="example">
|
|
<pre class="example">title(substitute(hat(a) == ahat, list(ahat = ahat)))
|
|
</pre></div>
|
|
|
|
<p>(note that it is ‘<samp>==</samp>’ and not ‘<samp>=</samp>’). Sometimes <code>bquote()</code>
|
|
gives a more compact form, e.g.,
|
|
</p>
|
|
<div class="example">
|
|
<pre class="example">title(bquote(hat(a) = .(ahat)))
|
|
</pre></div>
|
|
|
|
<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>
|
|
<a name="What-are-valid-names_003f"></a>
|
|
<div class="header">
|
|
<p>
|
|
Next: <a href="#Are-GAMs-implemented-in-R_003f" accesskey="n" rel="next">Are GAMs implemented in R?</a>, Previous: <a href="#How-can-I-substitute-into-a-plot-label_003f" accesskey="p" rel="prev">How can I substitute into a plot label?</a>, Up: <a href="#R-Miscellanea" accesskey="u" rel="up">R Miscellanea</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
|
|
</div>
|
|
<a name="What-are-valid-names_003f-1"></a>
|
|
<h3 class="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>
|
|
<a name="Are-GAMs-implemented-in-R_003f"></a>
|
|
<div class="header">
|
|
<p>
|
|
Next: <a href="#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: <a href="#What-are-valid-names_003f" accesskey="p" rel="prev">What are valid names?</a>, Up: <a href="#R-Miscellanea" accesskey="u" rel="up">R Miscellanea</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
|
|
</div>
|
|
<a name="Are-GAMs-implemented-in-R_003f-1"></a>
|
|
<h3 class="section">7.15 Are GAMs implemented in R?</h3>
|
|
|
|
<p>Package <a href="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 <a href="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 <a href="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 <a href="https://CRAN.R-project.org/package=mda"><strong>mda</strong></a>.
|
|
</p>
|
|
<hr>
|
|
<a name="Why-is-the-output-not-printed-when-I-source_0028_0029-a-file_003f"></a>
|
|
<div class="header">
|
|
<p>
|
|
Next: <a href="#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: <a href="#Are-GAMs-implemented-in-R_003f" accesskey="p" rel="prev">Are GAMs implemented in R?</a>, Up: <a href="#R-Miscellanea" accesskey="u" rel="up">R Miscellanea</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
|
|
</div>
|
|
<a name="Why-is-the-output-not-printed-when-I-source_0028_0029-a-file_003f-1"></a>
|
|
<h3 class="section">7.16 Why is the output not printed when I source() a file?</h3>
|
|
|
|
<p>Most R commands do not generate any output. The command
|
|
</p>
|
|
<div class="example">
|
|
<pre class="example">1+1
|
|
</pre></div>
|
|
|
|
<p>computes the value 2 and returns it; the command
|
|
</p>
|
|
<div class="example">
|
|
<pre class="example">summary(glm(y~x+z, family=binomial))
|
|
</pre></div>
|
|
|
|
<p>fits a logistic regression model, computes some summary information and
|
|
returns an object of class <code>"summary.glm"</code> (see <a href="#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
|
|
specifically print it.
|
|
</p>
|
|
<p>To print the value use
|
|
</p>
|
|
<div class="example">
|
|
<pre class="example">print(1+1)
|
|
</pre></div>
|
|
|
|
<p>or
|
|
</p>
|
|
<div class="example">
|
|
<pre class="example">print(summary(glm(y~x+z, family=binomial)))
|
|
</pre></div>
|
|
|
|
<p>instead, or use <code>source(<var>file</var>, echo=TRUE)</code>.
|
|
</p>
|
|
<hr>
|
|
<a name="Why-does-outer_0028_0029-behave-strangely-with-my-function_003f"></a>
|
|
<div class="header">
|
|
<p>
|
|
Next: <a href="#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: <a href="#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: <a href="#R-Miscellanea" accesskey="u" rel="up">R Miscellanea</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
|
|
</div>
|
|
<a name="Why-does-outer_0028_0029-behave-strangely-with-my-function_003f-1"></a>
|
|
<h3 class="section">7.17 Why does outer() behave strangely with my function?</h3>
|
|
|
|
<p>As the help for <code>outer()</code> indicates, it does not work on arbitrary
|
|
functions the way the <code>apply()</code> family does. It requires functions
|
|
that are vectorized to work elementwise on arrays. As you can see by
|
|
looking at the code, <code>outer(x, y, FUN)</code> creates two large vectors
|
|
containing every possible combination of elements of <code>x</code> and
|
|
<code>y</code> and then passes this to <code>FUN</code> all at once. Your function
|
|
probably cannot handle two large vectors as parameters.
|
|
</p>
|
|
<p>If you have a function that cannot handle two vectors but can handle two
|
|
scalars, then you can still use <code>outer()</code> but you will need to wrap
|
|
your function up first, to simulate vectorized behavior. Suppose your
|
|
function is
|
|
</p>
|
|
<div class="example">
|
|
<pre class="example">foo <- function(x, y, happy) {
|
|
stopifnot(length(x) == 1, length(y) == 1) # scalars only!
|
|
(x + y) * happy
|
|
}
|
|
</pre></div>
|
|
|
|
<p>If you define the general function
|
|
</p>
|
|
<div class="example">
|
|
<pre class="example">wrapper <- function(x, y, my.fun, ...) {
|
|
sapply(seq_along(x), FUN = function(i) my.fun(x[i], y[i], ...))
|
|
}
|
|
</pre></div>
|
|
|
|
<p>then you can use <code>outer()</code> by writing, e.g.,
|
|
</p>
|
|
<div class="example">
|
|
<pre class="example">outer(1:4, 1:2, FUN = wrapper, my.fun = foo, happy = 10)
|
|
</pre></div>
|
|
|
|
<p>Scalar functions can also be vectorized using <code>Vectorize()</code>.
|
|
</p>
|
|
<hr>
|
|
<a name="Why-does-the-output-from-anova_0028_0029-depend-on-the-order-of-factors-in-the-model_003f"></a>
|
|
<div class="header">
|
|
<p>
|
|
Next: <a href="#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: <a href="#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: <a href="#R-Miscellanea" accesskey="u" rel="up">R Miscellanea</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
|
|
</div>
|
|
<a name="Why-does-the-output-from-anova_0028_0029-depend-on-the-order-of-factors-in-the-model_003f-1"></a>
|
|
<h3 class="section">7.18 Why does the output from anova() depend on the order of factors in the model?</h3>
|
|
|
|
<p>In a model such as <code>~A+B+A:B</code>, R will report the difference in sums
|
|
of squares between the models <code>~1</code>, <code>~A</code>, <code>~A+B</code> and
|
|
<code>~A+B+A:B</code>. If the model were <code>~B+A+A:B</code>, R would report
|
|
differences between <code>~1</code>, <code>~B</code>, <code>~A+B</code>, and
|
|
<code>~A+B+A:B</code> . In the first case the sum of squares for <code>A</code> is
|
|
comparing <code>~1</code> and <code>~A</code>, in the second case it is comparing
|
|
<code>~B</code> and <code>~B+A</code>. In a non-orthogonal design (i.e., most
|
|
unbalanced designs) these comparisons are (conceptually and numerically)
|
|
different.
|
|
</p>
|
|
<p>Some packages report instead the sums of squares based on comparing the
|
|
full model to the models with each factor removed one at a time (the
|
|
famous ‘Type III sums of squares’ from SAS, for example). These do not
|
|
depend on the order of factors in the model. The question of which set
|
|
of sums of squares is the Right Thing provokes low-level holy wars on
|
|
R-help from time to time.
|
|
</p>
|
|
<p>There is no need to be agitated about the particular sums of squares
|
|
that R reports. You can compute your favorite sums of squares quite
|
|
easily. Any two models can be compared with <code>anova(<var>model1</var>,
|
|
<var>model2</var>)</code>, and <code>drop1(<var>model1</var>)</code> will show the sums of
|
|
squares resulting from dropping single terms.
|
|
</p>
|
|
<hr>
|
|
<a name="How-do-I-produce-PNG-graphics-in-batch-mode_003f"></a>
|
|
<div class="header">
|
|
<p>
|
|
Next: <a href="#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: <a href="#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: <a href="#R-Miscellanea" accesskey="u" rel="up">R Miscellanea</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
|
|
</div>
|
|
<a name="How-do-I-produce-PNG-graphics-in-batch-mode_003f-1"></a>
|
|
<h3 class="section">7.19 How do I produce PNG graphics in batch mode?</h3>
|
|
|
|
<p>Under a Unix-like, if your installation supports the
|
|
<code>type="cairo"</code> option to the <code>png()</code> device there should be no
|
|
problems, and the default settings should just work. This option is not
|
|
available for versions of R prior to 2.7.0, or without support for
|
|
cairo. From R 2.7.0 <code>png()</code> by default uses the Quartz device
|
|
on OS X, and that too works in batch mode.
|
|
</p>
|
|
<p>Earlier versions of the <code>png()</code> device used the X11 driver, which
|
|
is a problem in batch mode or for remote operation. If you have
|
|
Ghostscript you can use <code>bitmap()</code>, which produces a PostScript or
|
|
PDF file then converts it to any bitmap format supported by Ghostscript.
|
|
On some installations this produces ugly output, on others it is
|
|
perfectly satisfactory. Many systems now come with Xvfb from
|
|
<a href="http://www.x.org/">X.Org</a> (possibly as an optional
|
|
install), which is an X11 server that does not require a screen; and
|
|
there is the <a href="https://CRAN.R-project.org/package=GDD"><strong>GDD</strong></a> package from <acronym>CRAN</acronym>, which produces PNG,
|
|
JPEG and GIF bitmaps without X11.
|
|
</p>
|
|
<hr>
|
|
<a name="How-can-I-get-command-line-editing-to-work_003f"></a>
|
|
<div class="header">
|
|
<p>
|
|
Next: <a href="#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: <a href="#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: <a href="#R-Miscellanea" accesskey="u" rel="up">R Miscellanea</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
|
|
</div>
|
|
<a name="How-can-I-get-command-line-editing-to-work_003f-1"></a>
|
|
<h3 class="section">7.20 How can I get command line editing to work?</h3>
|
|
|
|
<p>The Unix-like command-line interface to R can only provide the inbuilt
|
|
command line editor which allows recall, editing and re-submission of
|
|
prior commands provided that the <acronym>GNU</acronym> readline library is
|
|
available at the time R is configured for compilation. Note that the
|
|
‘development’ version of readline including the appropriate headers is
|
|
needed: users of Linux binary distributions will need to install
|
|
packages such as <code>libreadline-dev</code> (Debian) or
|
|
<code>readline-devel</code> (Red Hat).
|
|
</p>
|
|
<hr>
|
|
<a name="How-can-I-turn-a-string-into-a-variable_003f"></a>
|
|
<div class="header">
|
|
<p>
|
|
Next: <a href="#Why-do-lattice_002ftrellis-graphics-not-work_003f" accesskey="n" rel="next">Why do lattice/trellis graphics not work?</a>, Previous: <a href="#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: <a href="#R-Miscellanea" accesskey="u" rel="up">R Miscellanea</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
|
|
</div>
|
|
<a name="How-can-I-turn-a-string-into-a-variable_003f-1"></a>
|
|
<h3 class="section">7.21 How can I turn a string into a variable?</h3>
|
|
|
|
<p>If you have
|
|
</p>
|
|
<div class="example">
|
|
<pre class="example">varname <- c("a", "b", "d")
|
|
</pre></div>
|
|
|
|
<p>you can do
|
|
</p>
|
|
<div class="example">
|
|
<pre class="example">get(varname[1]) + 2
|
|
</pre></div>
|
|
|
|
<p>for
|
|
</p>
|
|
<div class="example">
|
|
<pre class="example">a + 2
|
|
</pre></div>
|
|
|
|
<p>or
|
|
</p>
|
|
<div class="example">
|
|
<pre class="example">assign(varname[1], 2 + 2)
|
|
</pre></div>
|
|
|
|
<p>for
|
|
</p>
|
|
<div class="example">
|
|
<pre class="example">a <- 2 + 2
|
|
</pre></div>
|
|
|
|
<p>or
|
|
</p>
|
|
<div class="example">
|
|
<pre class="example">eval(substitute(lm(y ~ x + variable),
|
|
list(variable = as.name(varname[1]))))
|
|
</pre></div>
|
|
|
|
<p>for
|
|
</p>
|
|
<div class="example">
|
|
<pre class="example">lm(y ~ x + a)
|
|
</pre></div>
|
|
|
|
<p>At least in the first two cases it is often easier to just use a list,
|
|
and then you can easily index it by name
|
|
</p>
|
|
<div class="example">
|
|
<pre class="example">vars <- list(a = 1:10, b = rnorm(100), d = LETTERS)
|
|
vars[["a"]]
|
|
</pre></div>
|
|
|
|
<p>without any of this messing about.
|
|
</p>
|
|
<hr>
|
|
<a name="Why-do-lattice_002ftrellis-graphics-not-work_003f"></a>
|
|
<div class="header">
|
|
<p>
|
|
Next: <a href="#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: <a href="#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: <a href="#R-Miscellanea" accesskey="u" rel="up">R Miscellanea</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
|
|
</div>
|
|
<a name="Why-do-lattice_002ftrellis-graphics-not-work_003f-1"></a>
|
|
<h3 class="section">7.22 Why do lattice/trellis graphics not work?</h3>
|
|
|
|
<p>The most likely reason is that you forgot to tell R to display the
|
|
graph. Lattice functions such as <code>xyplot()</code> create a graph object,
|
|
but do not display it (the same is true of <a href="https://CRAN.R-project.org/package=ggplot2"><strong>ggplot2</strong></a> graphics,
|
|
and Trellis graphics in <small>S-PLUS</small>). The <code>print()</code> method for the
|
|
graph object produces the actual display. When you use these functions
|
|
interactively at the command line, the result is automatically printed,
|
|
but in <code>source()</code> or inside your own functions you will need an
|
|
explicit <code>print()</code> statement.
|
|
</p>
|
|
<hr>
|
|
<a name="How-can-I-sort-the-rows-of-a-data-frame_003f"></a>
|
|
<div class="header">
|
|
<p>
|
|
Next: <a href="#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: <a href="#Why-do-lattice_002ftrellis-graphics-not-work_003f" accesskey="p" rel="prev">Why do lattice/trellis graphics not work?</a>, Up: <a href="#R-Miscellanea" accesskey="u" rel="up">R Miscellanea</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
|
|
</div>
|
|
<a name="How-can-I-sort-the-rows-of-a-data-frame_003f-1"></a>
|
|
<h3 class="section">7.23 How can I sort the rows of a data frame?</h3>
|
|
|
|
<p>To sort the rows within a data frame, with respect to the values in one
|
|
or more of the columns, simply use <code>order()</code> (e.g.,
|
|
<code>DF[order(DF$a, DF[["b"]]), ]</code> to sort the data frame <code>DF</code> on
|
|
columns named <code>a</code> and <code>b</code>).
|
|
</p>
|
|
<hr>
|
|
<a name="Why-does-the-help_002estart_0028_0029-search-engine-not-work_003f"></a>
|
|
<div class="header">
|
|
<p>
|
|
Next: <a href="#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: <a href="#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: <a href="#R-Miscellanea" accesskey="u" rel="up">R Miscellanea</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
|
|
</div>
|
|
<a name="Why-does-the-help_002estart_0028_0029-search-engine-not-work_003f-1"></a>
|
|
<h3 class="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 <a href="#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>
|
|
search page.
|
|
</p>
|
|
<hr>
|
|
<a name="Why-did-my-_002eRprofile-stop-working-when-I-updated-R_003f"></a>
|
|
<div class="header">
|
|
<p>
|
|
Next: <a href="#Where-have-all-the-methods-gone_003f" accesskey="n" rel="next">Where have all the methods gone?</a>, Previous: <a href="#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: <a href="#R-Miscellanea" accesskey="u" rel="up">R Miscellanea</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
|
|
</div>
|
|
<a name="Why-did-my-_002eRprofile-stop-working-when-I-updated-R_003f-1"></a>
|
|
<h3 class="section">7.25 Why did my .Rprofile stop working when I updated R?</h3>
|
|
|
|
<p>Did you read the <samp>NEWS</samp> file? For functions that are not in the
|
|
<strong>base</strong> package you need to specify the correct package namespace,
|
|
since the code will be run <em>before</em> the packages are loaded. E.g.,
|
|
</p>
|
|
<div class="example">
|
|
<pre class="example">ps.options(horizontal = FALSE)
|
|
help.start()
|
|
</pre></div>
|
|
|
|
<p>needs to be
|
|
</p>
|
|
<div class="example">
|
|
<pre class="example">grDevices::ps.options(horizontal = FALSE)
|
|
utils::help.start()
|
|
</pre></div>
|
|
|
|
<p>(<code>graphics::ps.options(horizontal = FALSE)</code> in R 1.9.x).
|
|
</p>
|
|
<hr>
|
|
<a name="Where-have-all-the-methods-gone_003f"></a>
|
|
<div class="header">
|
|
<p>
|
|
Next: <a href="#How-can-I-create-rotated-axis-labels_003f" accesskey="n" rel="next">How can I create rotated axis labels?</a>, Previous: <a href="#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: <a href="#R-Miscellanea" accesskey="u" rel="up">R Miscellanea</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
|
|
</div>
|
|
<a name="Where-have-all-the-methods-gone_003f-1"></a>
|
|
<h3 class="section">7.26 Where have all the methods gone?</h3>
|
|
|
|
<p>Many functions, particularly S3 methods, are now hidden in namespaces.
|
|
This has the advantage that they cannot be called inadvertently with
|
|
arguments of the wrong class, but it makes them harder to view.
|
|
</p>
|
|
<p>To see the code for an S3 method (e.g., <code>[.terms</code>) use
|
|
</p>
|
|
<div class="example">
|
|
<pre class="example">getS3method("[", "terms")
|
|
</pre></div>
|
|
|
|
<p>To see the code for an unexported function <code>foo()</code> in the namespace
|
|
of package <code>"bar"</code> use <code>bar:::foo</code>. Don’t use these
|
|
constructions to call unexported functions in your own code—they are
|
|
probably unexported for a reason and may change without warning.
|
|
</p>
|
|
<hr>
|
|
<a name="How-can-I-create-rotated-axis-labels_003f"></a>
|
|
<div class="header">
|
|
<p>
|
|
Next: <a href="#Why-is-read_002etable_0028_0029-so-inefficient_003f" accesskey="n" rel="next">Why is read.table() so inefficient?</a>, Previous: <a href="#Where-have-all-the-methods-gone_003f" accesskey="p" rel="prev">Where have all the methods gone?</a>, Up: <a href="#R-Miscellanea" accesskey="u" rel="up">R Miscellanea</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
|
|
</div>
|
|
<a name="How-can-I-create-rotated-axis-labels_003f-1"></a>
|
|
<h3 class="section">7.27 How can I create rotated axis labels?</h3>
|
|
|
|
<p>To rotate axis labels (using base graphics), you need to use
|
|
<code>text()</code>, rather than <code>mtext()</code>, as the latter does not
|
|
support <code>par("srt")</code>.
|
|
</p>
|
|
<div class="example">
|
|
<pre class="example">## <span class="roman">Increase bottom margin to make room for rotated labels</span>
|
|
par(mar = c(7, 4, 4, 2) + 0.1)
|
|
## <span class="roman">Create plot with no x axis and no x axis label</span>
|
|
plot(1 : 8, xaxt = "n", xlab = "")
|
|
## <span class="roman">Set up x axis with tick marks alone</span>
|
|
axis(1, labels = FALSE)
|
|
## <span class="roman">Create some text labels</span>
|
|
labels <- paste("Label", 1:8, sep = " ")
|
|
## <span class="roman">Plot x axis labels at default tick marks</span>
|
|
text(1:8, par("usr")[3] - 0.25, srt = 45, adj = 1,
|
|
labels = labels, xpd = TRUE)
|
|
## <span class="roman">Plot x axis label at line 6 (of 7)</span>
|
|
mtext(1, text = "X Axis Label", line = 6)
|
|
</pre></div>
|
|
|
|
<p>When plotting the x axis labels, we use <code>srt = 45</code> for text
|
|
rotation angle, <code>adj = 1</code> to place the right end of text at the
|
|
tick marks, and <code>xpd = TRUE</code> to allow for text outside the plot
|
|
region. You can adjust the value of the <code>0.25</code> offset as required
|
|
to move the axis labels up or down relative to the x axis. See
|
|
<code>?par</code> for more information.
|
|
</p>
|
|
<p>Also see Figure 1 and associated code in Paul Murrell (2003),
|
|
“Integrating grid Graphics Output with Base Graphics Output”,
|
|
<em>R News</em>, <strong>3/2</strong>, 7–12.
|
|
</p>
|
|
<hr>
|
|
<a name="Why-is-read_002etable_0028_0029-so-inefficient_003f"></a>
|
|
<div class="header">
|
|
<p>
|
|
Next: <a href="#What-is-the-difference-between-package-and-library_003f" accesskey="n" rel="next">What is the difference between package and library?</a>, Previous: <a href="#How-can-I-create-rotated-axis-labels_003f" accesskey="p" rel="prev">How can I create rotated axis labels?</a>, Up: <a href="#R-Miscellanea" accesskey="u" rel="up">R Miscellanea</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
|
|
</div>
|
|
<a name="Why-is-read_002etable_0028_0029-so-inefficient_003f-1"></a>
|
|
<h3 class="section">7.28 Why is read.table() so inefficient?</h3>
|
|
|
|
<p>By default, <code>read.table()</code> needs to read in everything as character
|
|
data, and then try to figure out which variables to convert to numerics
|
|
or factors. For a large data set, this takes considerable amounts of
|
|
time and memory. Performance can substantially be improved by using the
|
|
<code>colClasses</code> argument to specify the classes to be assumed for the
|
|
columns of the table.
|
|
</p>
|
|
<hr>
|
|
<a name="What-is-the-difference-between-package-and-library_003f"></a>
|
|
<div class="header">
|
|
<p>
|
|
Next: <a href="#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: <a href="#Why-is-read_002etable_0028_0029-so-inefficient_003f" accesskey="p" rel="prev">Why is read.table() so inefficient?</a>, Up: <a href="#R-Miscellanea" accesskey="u" rel="up">R Miscellanea</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
|
|
</div>
|
|
<a name="What-is-the-difference-between-package-and-library_003f-1"></a>
|
|
<h3 class="section">7.29 What is the difference between package and library?</h3>
|
|
|
|
<p>A <em>package</em> is a standardized collection of material extending R,
|
|
e.g. providing code, data, or documentation. A <em>library</em> is a
|
|
place (directory) where R knows to find packages it can use (i.e., which
|
|
were <em>installed</em>). R is told to use a package (to “load” it and
|
|
add it to the search path) via calls to the function <code>library</code>.
|
|
I.e., <code>library()</code> is employed to load a package from libraries
|
|
containing packages.
|
|
</p>
|
|
<p>See <a href="#R-Add_002dOn-Packages">R Add-On Packages</a>, for more details. See also Uwe Ligges (2003),
|
|
“R Help Desk: Package Management”, <em>R News</em>, <strong>3/3</strong>,
|
|
37–39.
|
|
</p>
|
|
<hr>
|
|
<a name="I-installed-a-package-but-the-functions-are-not-there"></a>
|
|
<div class="header">
|
|
<p>
|
|
Next: <a href="#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: <a href="#What-is-the-difference-between-package-and-library_003f" accesskey="p" rel="prev">What is the difference between package and library?</a>, Up: <a href="#R-Miscellanea" accesskey="u" rel="up">R Miscellanea</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
|
|
</div>
|
|
<a name="I-installed-a-package-but-the-functions-are-not-there-1"></a>
|
|
<h3 class="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 <a href="#R-Add_002dOn-Packages">R Add-On Packages</a> and <a href="#What-is-the-difference-between-package-and-library_003f">What is the difference between package and library?</a> for more information.
|
|
</p>
|
|
<hr>
|
|
<a name="Why-doesn_0027t-R-think-these-numbers-are-equal_003f"></a>
|
|
<div class="header">
|
|
<p>
|
|
Next: <a href="#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: <a href="#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: <a href="#R-Miscellanea" accesskey="u" rel="up">R Miscellanea</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
|
|
</div>
|
|
<a name="Why-doesn_0027t-R-think-these-numbers-are-equal_003f-1"></a>
|
|
<h3 class="section">7.31 Why doesn’t R think these numbers are equal?</h3>
|
|
|
|
<p>The only numbers that can be represented exactly in R’s numeric type
|
|
are integers and fractions whose denominator is a power of 2. Other
|
|
numbers have to be rounded to (typically) 53 binary digits accuracy. As a
|
|
result, two floating point numbers will not reliably be equal unless they
|
|
have been computed by the same algorithm, and not always even then. For
|
|
example
|
|
</p>
|
|
<div class="example">
|
|
<pre class="example">R> a <- sqrt(2)
|
|
R> a * a == 2
|
|
[1] FALSE
|
|
R> a * a - 2
|
|
[1] 4.440892e-16
|
|
</pre></div>
|
|
|
|
<p>The function <code>all.equal()</code> compares two objects using a numeric
|
|
tolerance of <code>.Machine$double.eps ^ 0.5</code>. If you want much greater
|
|
accuracy than this you will need to consider error propagation
|
|
carefully.
|
|
</p>
|
|
<p>For more information, see e.g. David Goldberg (1991), “What Every
|
|
Computer Scientist Should Know About Floating-Point Arithmetic”,
|
|
<em>ACM Computing Surveys</em>, <strong>23/1</strong>, 5–48, also available via
|
|
<a href="http://www.validlab.com/goldberg/paper.pdf">http://www.validlab.com/goldberg/paper.pdf</a>.
|
|
</p>
|
|
<p>To quote from “The Elements of Programming Style” by Kernighan and
|
|
Plauger:
|
|
</p>
|
|
<blockquote>
|
|
<p><em>10.0 times 0.1 is hardly ever 1.0</em>.
|
|
</p></blockquote>
|
|
|
|
|
|
<hr>
|
|
<a name="How-can-I-capture-or-ignore-errors-in-a-long-simulation_003f"></a>
|
|
<div class="header">
|
|
<p>
|
|
Next: <a href="#Why-are-powers-of-negative-numbers-wrong_003f" accesskey="n" rel="next">Why are powers of negative numbers wrong?</a>, Previous: <a href="#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: <a href="#R-Miscellanea" accesskey="u" rel="up">R Miscellanea</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
|
|
</div>
|
|
<a name="How-can-I-capture-or-ignore-errors-in-a-long-simulation_003f-1"></a>
|
|
<h3 class="section">7.32 How can I capture or ignore errors in a long simulation?</h3>
|
|
|
|
<p>Use <code>try()</code>, which returns an object of class <code>"try-error"</code>
|
|
instead of an error, or preferably <code>tryCatch()</code>, where the return
|
|
value can be configured more flexibly. For example
|
|
</p>
|
|
<div class="example">
|
|
<pre class="example">beta[i,] <- tryCatch(coef(lm(formula, data)),
|
|
error = function(e) rep(NaN, 4))
|
|
</pre></div>
|
|
|
|
<p>would return the coefficients if the <code>lm()</code> call succeeded and
|
|
would return <code>c(NaN, NaN, NaN, NaN)</code> if it failed (presumably there
|
|
are supposed to be 4 coefficients in this example).
|
|
</p>
|
|
<hr>
|
|
<a name="Why-are-powers-of-negative-numbers-wrong_003f"></a>
|
|
<div class="header">
|
|
<p>
|
|
Next: <a href="#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: <a href="#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: <a href="#R-Miscellanea" accesskey="u" rel="up">R Miscellanea</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
|
|
</div>
|
|
<a name="Why-are-powers-of-negative-numbers-wrong_003f-1"></a>
|
|
<h3 class="section">7.33 Why are powers of negative numbers wrong?</h3>
|
|
|
|
<p>You are probably seeing something like
|
|
</p>
|
|
<div class="example">
|
|
<pre class="example">R> -2^2
|
|
[1] -4
|
|
</pre></div>
|
|
|
|
<p>and misunderstanding the precedence rules for expressions in R.
|
|
Write
|
|
</p>
|
|
<div class="example">
|
|
<pre class="example">R> (-2)^2
|
|
[1] 4
|
|
</pre></div>
|
|
|
|
<p>to get the square of <em>-2</em>.
|
|
</p>
|
|
<p>The precedence rules are documented in <code>?Syntax</code>, and to see how R
|
|
interprets an expression you can look at the parse tree
|
|
</p>
|
|
<div class="example">
|
|
<pre class="example">R> as.list(quote(-2^2))
|
|
[[1]]
|
|
`-`
|
|
|
|
[[2]]
|
|
2^2
|
|
</pre></div>
|
|
|
|
<hr>
|
|
<a name="How-can-I-save-the-result-of-each-iteration-in-a-loop-into-a-separate-file_003f"></a>
|
|
<div class="header">
|
|
<p>
|
|
Next: <a href="#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: <a href="#Why-are-powers-of-negative-numbers-wrong_003f" accesskey="p" rel="prev">Why are powers of negative numbers wrong?</a>, Up: <a href="#R-Miscellanea" accesskey="u" rel="up">R Miscellanea</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
|
|
</div>
|
|
<a name="How-can-I-save-the-result-of-each-iteration-in-a-loop-into-a-separate-file_003f-1"></a>
|
|
<h3 class="section">7.34 How can I save the result of each iteration in a loop into a separate file?</h3>
|
|
|
|
<p>One way is to use <code>paste()</code> (or <code>sprintf()</code>) to concatenate a
|
|
stem filename and the iteration number while <code>file.path()</code>
|
|
constructs the path. For example, to save results into files
|
|
<samp>result1.rda</samp>, …, <samp>result100.rda</samp> in the subdirectory
|
|
<samp>Results</samp> of the current working directory, one can use
|
|
</p>
|
|
<div class="example">
|
|
<pre class="example">for(i in 1:100) {
|
|
## Calculations constructing "some_object" ...
|
|
fp <- file.path("Results", paste("result", i, ".rda", sep = ""))
|
|
save(list = "some_object", file = fp)
|
|
}
|
|
</pre></div>
|
|
|
|
<hr>
|
|
<a name="Why-are-p_002dvalues-not-displayed-when-using-lmer_0028_0029_003f"></a>
|
|
<div class="header">
|
|
<p>
|
|
Next: <a href="#Why-are-there-unwanted-borders" accesskey="n" rel="next">Why are there unwanted borders</a>, Previous: <a href="#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: <a href="#R-Miscellanea" accesskey="u" rel="up">R Miscellanea</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
|
|
</div>
|
|
<a name="Why-are-p_002dvalues-not-displayed-when-using-lmer_0028_0029_003f-1"></a>
|
|
<h3 class="section">7.35 Why are <em>p</em>-values not displayed when using lmer()?</h3>
|
|
|
|
<p>Doug Bates has kindly provided an extensive response in a post to the
|
|
r-help list, which can be reviewed at
|
|
<a href="https://stat.ethz.ch/pipermail/r-help/2006-May/094765.html">https://stat.ethz.ch/pipermail/r-help/2006-May/094765.html</a>.
|
|
</p>
|
|
<hr>
|
|
<a name="Why-are-there-unwanted-borders"></a>
|
|
<div class="header">
|
|
<p>
|
|
Next: <a href="#Why-does-backslash-behave-strangely-inside-strings_003f" accesskey="n" rel="next">Why does backslash behave strangely inside strings?</a>, Previous: <a href="#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: <a href="#R-Miscellanea" accesskey="u" rel="up">R Miscellanea</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
|
|
</div>
|
|
<a name="Why-are-there-unwanted-borders_002c-lines-or-grid_002dlike-artifacts-when-viewing-a-plot-saved-to-a-PS-or-PDF-file_003f"></a>
|
|
<h3 class="section">7.36 Why are there unwanted borders, lines or grid-like artifacts when viewing a plot saved to a PS or PDF file?</h3>
|
|
|
|
<p>This can occur when using functions such as <code>polygon()</code>,
|
|
<code>filled.contour()</code>, <code>image()</code> or other functions which may
|
|
call these internally. In the case of <code>polygon()</code>, you may observe
|
|
unwanted borders between the polygons even when setting the
|
|
<code>border</code> argument to <code>NA</code> or <code>"transparent"</code>.
|
|
</p>
|
|
<p>The source of the problem is the PS/PDF viewer when the plot is
|
|
anti-aliased. The details for the solution will be different depending
|
|
upon the viewer used, the operating system and may change over time.
|
|
For some common viewers, consider the following:
|
|
</p>
|
|
<dl compact="compact">
|
|
<dt>Acrobat Reader (cross platform)
|
|
<a name="index-Acrobat-Reader-_0028cross-platform_0029"></a>
|
|
</dt>
|
|
<dd><p>There are options in Preferences to enable/disable text smoothing, image
|
|
smoothing and line art smoothing.
|
|
Disable line art smoothing.
|
|
</p></dd>
|
|
<dt>Preview (OS X)
|
|
<a name="index-Preview-_0028OS-X_0029"></a>
|
|
</dt>
|
|
<dd><p>There is an option in Preferences to enable/disable anti-aliasing of
|
|
text and line art.
|
|
Disable this option.
|
|
</p></dd>
|
|
<dt>GSview (cross platform)
|
|
<a name="index-GSview-_0028cross-platform_0029"></a>
|
|
</dt>
|
|
<dd><p>There are settings for Text Alpha and Graphics Alpha.
|
|
Change Graphics Alpha from 4 bits to 1 bit to disable graphic
|
|
anti-aliasing.
|
|
</p></dd>
|
|
<dt>gv (Unix-like X)
|
|
<a name="index-gv-_0028Unix_002dlike-X_0029"></a>
|
|
</dt>
|
|
<dd><p>There is an option to enable/disable anti-aliasing.
|
|
Disable this option.
|
|
</p></dd>
|
|
<dt>Evince (Linux/GNOME)
|
|
<a name="index-Evince-_0028Linux_002fGNOME_0029"></a>
|
|
</dt>
|
|
<dd><p>There is not an option to disable anti-aliasing in this viewer.
|
|
</p></dd>
|
|
<dt>Okular (Linux/KDE)
|
|
<a name="index-Okular-_0028Linux_002fKDE_0029"></a>
|
|
</dt>
|
|
<dd><p>There is not an option in the GUI to enable/disable anti-aliasing.
|
|
From a console command line, use:
|
|
</p><div class="smallexample">
|
|
<pre class="smallexample">$ kwriteconfig --file okularpartrc --group 'Dlg Performance' \
|
|
--key GraphicsAntialias Disabled
|
|
</pre></div>
|
|
<p>Then restart Okular. Change the final word to ‘<samp>Enabled</samp>’ to restore
|
|
the original setting.
|
|
</p></dd>
|
|
</dl>
|
|
|
|
<hr>
|
|
<a name="Why-does-backslash-behave-strangely-inside-strings_003f"></a>
|
|
<div class="header">
|
|
<p>
|
|
Next: <a href="#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: <a href="#Why-are-there-unwanted-borders" accesskey="p" rel="prev">Why are there unwanted borders</a>, Up: <a href="#R-Miscellanea" accesskey="u" rel="up">R Miscellanea</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
|
|
</div>
|
|
<a name="Why-does-backslash-behave-strangely-inside-strings_003f-1"></a>
|
|
<h3 class="section">7.37 Why does backslash behave strangely inside strings?</h3>
|
|
|
|
<p>This question most often comes up in relation to file names (see
|
|
<a href="#How-do-file-names-work-in-Windows_003f">How do file names work in Windows?</a>) but it also happens that
|
|
people complain that they cannot seem to put a single ‘<samp>\</samp>’ character
|
|
into a text string unless it happens to be followed by certain other
|
|
characters.
|
|
</p>
|
|
<p>To understand this, you have to distinguish between character strings
|
|
and <em>representations</em> of character strings. Mostly, the
|
|
representation in R is just the string with a single or double quote at
|
|
either end, but there are strings that cannot be represented that way,
|
|
e.g., strings that themselves contain the quote character. So
|
|
</p>
|
|
<div class="example">
|
|
<pre class="example">> str <- "This \"text\" is quoted"
|
|
> str
|
|
[1] "This \"text\" is quoted"
|
|
> cat(str, "\n")
|
|
This "text" is quoted
|
|
</pre></div>
|
|
|
|
<p>The <em>escape sequences</em> ‘<samp>\"</samp>’ and ‘<samp>\n</samp>’ represent a double
|
|
quote and the newline character respectively. Printing text strings,
|
|
using <code>print()</code> or by typing the name at the prompt will use the
|
|
escape sequences too, but the <code>cat()</code> function will display the
|
|
string as-is. Notice that ‘<samp>"\n"</samp>’ is a one-character string, not
|
|
two; the backslash is not actually in the string, it is just generated
|
|
in the printed representation.
|
|
</p>
|
|
<div class="example">
|
|
<pre class="example">> nchar("\n")
|
|
[1] 1
|
|
> substring("\n", 1, 1)
|
|
[1] "\n"
|
|
</pre></div>
|
|
|
|
<p>So how do you put a backslash in a string? For this, you have to
|
|
escape the escape character. I.e., you have to double the backslash.
|
|
as in
|
|
</p>
|
|
<div class="example">
|
|
<pre class="example">> cat("\\n", "\n")
|
|
\n
|
|
</pre></div>
|
|
|
|
<p>Some functions, particularly those involving regular expression
|
|
matching, themselves use metacharacters, which may need to be escaped by
|
|
the backslash mechanism. In those cases you may need a <em>quadruple</em>
|
|
backslash to represent a single literal one.
|
|
</p>
|
|
<p>In versions of R up to 2.4.1 an unknown escape sequence like ‘<samp>\p</samp>’
|
|
was quietly interpreted as just ‘<samp>p</samp>’. Current versions of R emit a
|
|
warning.
|
|
</p>
|
|
<hr>
|
|
<a name="How-can-I-put-error-bars-or-confidence-bands-on-my-plot_003f"></a>
|
|
<div class="header">
|
|
<p>
|
|
Next: <a href="#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: <a href="#Why-does-backslash-behave-strangely-inside-strings_003f" accesskey="p" rel="prev">Why does backslash behave strangely inside strings?</a>, Up: <a href="#R-Miscellanea" accesskey="u" rel="up">R Miscellanea</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
|
|
</div>
|
|
<a name="How-can-I-put-error-bars-or-confidence-bands-on-my-plot_003f-1"></a>
|
|
<h3 class="section">7.38 How can I put error bars or confidence bands on my plot?</h3>
|
|
|
|
<p>Some functions will display a particular kind of plot with error bars,
|
|
such as the <code>bar.err()</code> function in the <a href="https://CRAN.R-project.org/package=agricolae"><strong>agricolae</strong></a>
|
|
package, the <code>plotCI()</code> function in the <a href="https://CRAN.R-project.org/package=gplots"><strong>gplots</strong></a> package,
|
|
the <code>plotCI()</code> and <code>brkdn.plot()</code> functions in the
|
|
<a href="https://CRAN.R-project.org/package=plotrix"><strong>plotrix</strong></a> package and the <code>error.bars()</code>,
|
|
<code>error.crosses()</code> and <code>error.bars.by()</code> functions in the
|
|
<a href="https://CRAN.R-project.org/package=psych"><strong>psych</strong></a> package. Within these types of functions, some will
|
|
accept the measures of dispersion (e.g., <code>plotCI</code>), some will
|
|
calculate the dispersion measures from the raw values (<code>bar.err</code>,
|
|
<code>brkdn.plot</code>), and some will do both (<code>error.bars</code>). Still
|
|
other functions will just display error bars, like the dispersion
|
|
function in the <a href="https://CRAN.R-project.org/package=plotrix"><strong>plotrix</strong></a> package. Most of the above functions
|
|
use the <code>arrows()</code> function in the base <strong>graphics</strong> package to
|
|
draw the error bars.
|
|
</p>
|
|
<p>The above functions all use the base graphics system. The grid and
|
|
lattice graphics systems also have specific functions for displaying
|
|
error bars, e.g., the <code>grid.arrow()</code> function in the <strong>grid</strong>
|
|
package, and the <code>geom_errorbar()</code>, <code>geom_errorbarh()</code>,
|
|
<code>geom_pointrange()</code>, <code>geom_linerange()</code>,
|
|
<code>geom_crossbar()</code> and <code>geom_ribbon()</code> functions in the
|
|
<a href="https://CRAN.R-project.org/package=ggplot2"><strong>ggplot2</strong></a> package. In the lattice system, error bars can be
|
|
displayed with <code>Dotplot()</code> or <code>xYplot()</code> in the
|
|
<a href="https://CRAN.R-project.org/package=Hmisc"><strong>Hmisc</strong></a> package and <code>segplot()</code> in the
|
|
<a href="https://CRAN.R-project.org/package=latticeExtra"><strong>latticeExtra</strong></a> package.
|
|
</p>
|
|
<hr>
|
|
<a name="How-do-I-create-a-plot-with-two-y_002daxes_003f"></a>
|
|
<div class="header">
|
|
<p>
|
|
Next: <a href="#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: <a href="#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: <a href="#R-Miscellanea" accesskey="u" rel="up">R Miscellanea</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
|
|
</div>
|
|
<a name="How-do-I-create-a-plot-with-two-y_002daxes_003f-1"></a>
|
|
<h3 class="section">7.39 How do I create a plot with two y-axes?</h3>
|
|
|
|
<p>Creating a graph with two y-axes, i.e., with two sorts of data that are
|
|
scaled to the same vertical size and showing separate vertical axes on
|
|
the left and right sides of the plot that reflect the original scales of
|
|
the data, is possible in R but is not recommended. The basic approach
|
|
for constructing such graphs is to use <code>par(new=TRUE)</code> (see
|
|
<code>?par</code>); functions <code>twoord.plot()</code> (in the <a href="https://CRAN.R-project.org/package=plotrix"><strong>plotrix</strong></a>
|
|
package) and <code>doubleYScale()</code> (in the <a href="https://CRAN.R-project.org/package=latticeExtra"><strong>latticeExtra</strong></a>
|
|
package) automate the process somewhat.
|
|
</p>
|
|
<hr>
|
|
<a name="How-do-I-access-the-source-code-for-a-function_003f"></a>
|
|
<div class="header">
|
|
<p>
|
|
Next: <a href="#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: <a href="#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: <a href="#R-Miscellanea" accesskey="u" rel="up">R Miscellanea</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
|
|
</div>
|
|
<a name="How-do-I-access-the-source-code-for-a-function_003f-1"></a>
|
|
<h3 class="section">7.40 How do I access the source code for a function?</h3>
|
|
|
|
<p>In most cases, typing the name of the function will print its source
|
|
code. However, code is sometimes hidden in a namespace, or compiled. For
|
|
a complete overview on how to access source code, see Uwe Ligges (2006),
|
|
“Help Desk: Accessing the sources”, <em>R News</em>, <strong>6/4</strong>,
|
|
43–45 (<a href="https://CRAN.R-project.org/doc/Rnews/Rnews_2006-4.pdf">https://CRAN.R-project.org/doc/Rnews/Rnews_2006-4.pdf</a>).
|
|
</p>
|
|
<hr>
|
|
<a name="Why-does-summary_0028_0029-report-strange-results-for-the-R_005e2-estimate-when-I-fit-a-linear-model-with-no-intercept_003f"></a>
|
|
<div class="header">
|
|
<p>
|
|
Next: <a href="#Why-is-R-apparently-not-releasing-memory_003f" accesskey="n" rel="next">Why is R apparently not releasing memory?</a>, Previous: <a href="#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: <a href="#R-Miscellanea" accesskey="u" rel="up">R Miscellanea</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
|
|
</div>
|
|
<a name="Why-does-summary_0028_0029-report-strange-results-for-the-R_005e2-estimate-when-I-fit-a-linear-model-with-no-intercept_003f-1"></a>
|
|
<h3 class="section">7.41 Why does summary() report strange results for the R^2 estimate when I fit a linear model with no intercept?</h3>
|
|
|
|
<p>As described in <code>?summary.lm</code>, when the intercept is zero (e.g.,
|
|
from <code>y ~ x - 1</code> or <code>y ~ x + 0</code>), <code>summary.lm()</code> uses the
|
|
formula
|
|
R^2 = 1 - Sum(R[i]^2) / Sum((y[i])^2)
|
|
which is different from the usual
|
|
R^2 = 1 - Sum(R[i]^2) / Sum((y[i] - mean(y))^2).
|
|
There are several reasons for this:
|
|
</p><ul>
|
|
<li> Otherwise the <em>R^2</em> could be negative (because the model with zero
|
|
intercept can fit <em>worse</em> than the constant-mean model it is
|
|
implicitly compared to).
|
|
</li><li> If you set the slope to zero in the model with a line through the
|
|
origin you get fitted values y*=0
|
|
</li><li> The model with constant, non-zero mean is not nested in the model
|
|
with a line through the origin.
|
|
</li></ul>
|
|
|
|
<p>All these come down to saying that if you know <em>a priori</em> that
|
|
<em>E[Y]=0</em> when <em>x=0</em> then the ‘null’ model that you should
|
|
compare to the fitted line, the model where <em>x</em> doesn’t explain any
|
|
of the variance, is the model where <em>E[Y]=0</em> everywhere. (If you
|
|
don’t know a priori that <em>E[Y]=0</em> when <em>x=0</em>, then you
|
|
probably shouldn’t be fitting a line through the origin.)
|
|
</p>
|
|
<hr>
|
|
<a name="Why-is-R-apparently-not-releasing-memory_003f"></a>
|
|
<div class="header">
|
|
<p>
|
|
Next: <a href="#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: <a href="#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: <a href="#R-Miscellanea" accesskey="u" rel="up">R Miscellanea</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
|
|
</div>
|
|
<a name="Why-is-R-apparently-not-releasing-memory_003f-1"></a>
|
|
<h3 class="section">7.42 Why is R apparently not releasing memory?</h3>
|
|
|
|
<p>This question is often asked in different flavors along the lines of
|
|
“I have removed objects in R and run <code>gc()</code> and yet
|
|
<code>ps</code>/<code>top</code> still shows the R process using a lot of
|
|
memory”, often on Linux machines.
|
|
</p>
|
|
<p>This is an artifact of the way the operating system (OS) allocates
|
|
memory. In general it is common that the OS is not capable of
|
|
releasing all unused memory. In extreme cases it is possible that even
|
|
if R frees almost all its memory, the OS can not release any of it due
|
|
to its design and thus tools such as <code>ps</code> or <code>top</code> will
|
|
report substantial amount of resident RAM used by the R process even
|
|
though R has released all that memory. In general such tools do
|
|
<em>not</em> report the actual memory usage of the process but rather
|
|
what the OS is reserving for that process.
|
|
</p>
|
|
<p>The short answer is that this is a limitation of the memory allocator
|
|
in the operating system and there is nothing R can do about it. That
|
|
space is simply kept by the OS in the hope that R will ask for it
|
|
later. The following paragraph gives more in-depth answer with
|
|
technical details on how this happens.
|
|
</p>
|
|
<p>Most systems use two separate ways to allocate memory. For allocation
|
|
of large chunks they will use <code>mmap</code> to map memory into the
|
|
process address space. Such chunks can be released immediately when
|
|
they are completely free, because they can reside anywhere in the
|
|
virtual memory. However, this is a relatively expensive operation and
|
|
many OSes have a limit on the number of such allocated chunks, so this
|
|
is only used for allocating large memory regions. For smaller
|
|
allocations the system can expand the data segment of the process
|
|
(historically using the <code>brk</code> system call), but this whole area
|
|
is always contiguous. The OS can only move the end of this space, it
|
|
cannot create any “holes”. Since this operation is fairly cheap, it
|
|
is used for allocations of small pieces of memory. However, the
|
|
side-effect is that even if there is just one byte that is in use
|
|
at the end of the data segment, the OS cannot release any memory
|
|
at all, because it cannot change the address of that byte. This is
|
|
actually more common than it may seem, because allocating a lot of
|
|
intermediate objects, then allocating a result object and removing all
|
|
intermediate objects is a very common practice. Since the result is
|
|
allocated at the end it will prevent the OS from releasing any memory
|
|
used by the intermediate objects. In practice, this is not necessarily
|
|
a problem, because modern operating systems can page out unused
|
|
portions of the virtual memory so it does not necessarily reduce the
|
|
amount of real memory available for other applications. Typically,
|
|
small objects such as strings or pairlists will be affected by this
|
|
behavior, whereas large objects such as long vectors will be allocated
|
|
using <code>mmap</code> and thus not affected. On Linux (and possibly other
|
|
Unix-like systems) it is possible to use the <code>mallinfo</code> system call
|
|
(also see the <a href="https://rforge.net/mallinfo">mallinfo</a> package) to
|
|
query the allocator about the layout of the allocations, including the
|
|
actually used memory as well as unused memory that cannot be released.
|
|
</p>
|
|
<hr>
|
|
<a name="How-can-I-enable-secure-https-downloads-in-R_003f"></a>
|
|
<div class="header">
|
|
<p>
|
|
Previous: <a href="#Why-is-R-apparently-not-releasing-memory_003f" accesskey="p" rel="prev">Why is R apparently not releasing memory?</a>, Up: <a href="#R-Miscellanea" accesskey="u" rel="up">R Miscellanea</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
|
|
</div>
|
|
<a name="How-can-I-enable-secure-https-downloads-in-R_003f-1"></a>
|
|
<h3 class="section">7.43 How can I enable secure https downloads in R?</h3>
|
|
|
|
|
|
<p>When R transfers files over <acronym>HTTP</acronym> (e.g., using the
|
|
<code>install.packages()</code> or <code>download.file()</code> function), a
|
|
download method is chosen based on the <samp>download.file.method</samp>
|
|
option. There are several methods available and the default behavior if
|
|
no option is explicitly specified is to use R’s internal <acronym>HTTP</acronym>
|
|
implementation. In most circumstances this internal method will not
|
|
support <acronym>HTTPS</acronym> URLs so you will need to override the default:
|
|
this is done automatically for such URLs as from R 3.2.2.
|
|
</p>
|
|
<p>R versions 3.2.0 and greater include two download methods
|
|
(<code>"libcurl"</code> and <code>"wininet"</code>) that both support
|
|
<acronym>HTTPS</acronym> connections: we recommend that you use these methods.
|
|
The requisite code to add to <samp>.Rprofile</samp> or <samp>Rprofile.site</samp> is:
|
|
</p>
|
|
<div class="example">
|
|
<pre class="example">options(download.file.method = "wininet", url.method = "wininet") <span class="roman">(Windows)</span>
|
|
options(download.file.method = "libcurl", url.method = "libcurl") <span class="roman">(Linux and OS X)</span>
|
|
</pre></div>
|
|
|
|
<p>(Method <code>"wininet"</code> is the default on Windows as from R 3.2.2.)
|
|
</p>
|
|
<p>Note that the <code>"libcurl"</code> method may or may not have been compiled
|
|
in. In the case that it was not, i.e.. <code>capabilities("libcurl") ==
|
|
FALSE</code>, we recommend method <code>"wget"</code> on Linux and <code>"curl"</code> on
|
|
OS X. It is possible that system versions of <code>"libcurl"</code>,
|
|
<code>wget</code> or <code>curl</code> may have been compiled without
|
|
<acronym>HTTPS</acronym> support, but this is unlikely. As from R 3.3.0
|
|
<code>"libcurl"</code> with <acronym>HTTPS</acronym> support is required except on
|
|
Windows.
|
|
</p>
|
|
|
|
<hr>
|
|
<a name="R-Programming"></a>
|
|
<div class="header">
|
|
<p>
|
|
Next: <a href="#R-Bugs" accesskey="n" rel="next">R Bugs</a>, Previous: <a href="#R-Miscellanea" accesskey="p" rel="prev">R Miscellanea</a>, Up: <a href="#Top" accesskey="u" rel="up">Top</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
|
|
</div>
|
|
<a name="R-Programming-1"></a>
|
|
<h2 class="chapter">8 R Programming</h2>
|
|
|
|
<table summary="" class="menu" border="0" cellspacing="0">
|
|
<tr><td align="left" valign="top">• <a href="#How-should-I-write-summary-methods_003f" accesskey="1">How should I write summary methods?</a>:</td><td> </td><td align="left" valign="top">
|
|
</td></tr>
|
|
<tr><td align="left" valign="top">• <a href="#How-can-I-debug-dynamically-loaded-code_003f" accesskey="2">How can I debug dynamically loaded code?</a>:</td><td> </td><td align="left" valign="top">
|
|
</td></tr>
|
|
<tr><td align="left" valign="top">• <a href="#How-can-I-inspect-R-objects-when-debugging_003f" accesskey="3">How can I inspect R objects when debugging?</a>:</td><td> </td><td align="left" valign="top">
|
|
</td></tr>
|
|
<tr><td align="left" valign="top">• <a href="#How-can-I-change-compilation-flags_003f" accesskey="4">How can I change compilation flags?</a>:</td><td> </td><td align="left" valign="top">
|
|
</td></tr>
|
|
<tr><td align="left" valign="top">• <a href="#How-can-I-debug-S4-methods_003f" accesskey="5">How can I debug S4 methods?</a>:</td><td> </td><td align="left" valign="top">
|
|
</td></tr>
|
|
</table>
|
|
|
|
<hr>
|
|
<a name="How-should-I-write-summary-methods_003f"></a>
|
|
<div class="header">
|
|
<p>
|
|
Next: <a href="#How-can-I-debug-dynamically-loaded-code_003f" accesskey="n" rel="next">How can I debug dynamically loaded code?</a>, Previous: <a href="#R-Programming" accesskey="p" rel="prev">R Programming</a>, Up: <a href="#R-Programming" accesskey="u" rel="up">R Programming</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
|
|
</div>
|
|
<a name="How-should-I-write-summary-methods_003f-1"></a>
|
|
<h3 class="section">8.1 How should I write summary methods?</h3>
|
|
|
|
<p>Suppose you want to provide a summary method for class <code>"foo"</code>.
|
|
Then <code>summary.foo()</code> should not print anything, but return an
|
|
object of class <code>"summary.foo"</code>, <em>and</em> you should write a
|
|
method <code>print.summary.foo()</code> which nicely prints the summary
|
|
information and invisibly returns its object. This approach is
|
|
preferred over having <code>summary.foo()</code> print summary information and
|
|
return something useful, as sometimes you need to grab something
|
|
computed by <code>summary()</code> inside a function or similar. In such
|
|
cases you don’t want anything printed.
|
|
</p>
|
|
<hr>
|
|
<a name="How-can-I-debug-dynamically-loaded-code_003f"></a>
|
|
<div class="header">
|
|
<p>
|
|
Next: <a href="#How-can-I-inspect-R-objects-when-debugging_003f" accesskey="n" rel="next">How can I inspect R objects when debugging?</a>, Previous: <a href="#How-should-I-write-summary-methods_003f" accesskey="p" rel="prev">How should I write summary methods?</a>, Up: <a href="#R-Programming" accesskey="u" rel="up">R Programming</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
|
|
</div>
|
|
<a name="How-can-I-debug-dynamically-loaded-code_003f-1"></a>
|
|
<h3 class="section">8.2 How can I debug dynamically loaded code?</h3>
|
|
|
|
<p>Roughly speaking, you need to start R inside the debugger, load the
|
|
code, send an interrupt, and then set the required breakpoints.
|
|
</p>
|
|
<p>See section “Finding entry points in dynamically loaded code” in
|
|
<cite>Writing R Extensions</cite>. This manual is included in the R
|
|
distribution, see <a href="#What-documentation-exists-for-R_003f">What documentation exists for R?</a>.
|
|
</p>
|
|
<hr>
|
|
<a name="How-can-I-inspect-R-objects-when-debugging_003f"></a>
|
|
<div class="header">
|
|
<p>
|
|
Next: <a href="#How-can-I-change-compilation-flags_003f" accesskey="n" rel="next">How can I change compilation flags?</a>, Previous: <a href="#How-can-I-debug-dynamically-loaded-code_003f" accesskey="p" rel="prev">How can I debug dynamically loaded code?</a>, Up: <a href="#R-Programming" accesskey="u" rel="up">R Programming</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
|
|
</div>
|
|
<a name="How-can-I-inspect-R-objects-when-debugging_003f-1"></a>
|
|
<h3 class="section">8.3 How can I inspect R objects when debugging?</h3>
|
|
|
|
<p>The most convenient way is to call <code>R_PV</code> from the symbolic
|
|
debugger.
|
|
</p>
|
|
<p>See section “Inspecting R objects when debugging” in <cite>Writing R
|
|
Extensions</cite>.
|
|
</p>
|
|
<hr>
|
|
<a name="How-can-I-change-compilation-flags_003f"></a>
|
|
<div class="header">
|
|
<p>
|
|
Next: <a href="#How-can-I-debug-S4-methods_003f" accesskey="n" rel="next">How can I debug S4 methods?</a>, Previous: <a href="#How-can-I-inspect-R-objects-when-debugging_003f" accesskey="p" rel="prev">How can I inspect R objects when debugging?</a>, Up: <a href="#R-Programming" accesskey="u" rel="up">R Programming</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
|
|
</div>
|
|
<a name="How-can-I-change-compilation-flags_003f-1"></a>
|
|
<h3 class="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>
|
|
<a name="How-can-I-debug-S4-methods_003f"></a>
|
|
<div class="header">
|
|
<p>
|
|
Previous: <a href="#How-can-I-change-compilation-flags_003f" accesskey="p" rel="prev">How can I change compilation flags?</a>, Up: <a href="#R-Programming" accesskey="u" rel="up">R Programming</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
|
|
</div>
|
|
<a name="How-can-I-debug-S4-methods_003f-1"></a>
|
|
<h3 class="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>
|
|
<a name="R-Bugs"></a>
|
|
<div class="header">
|
|
<p>
|
|
Next: <a href="#Acknowledgments" accesskey="n" rel="next">Acknowledgments</a>, Previous: <a href="#R-Programming" accesskey="p" rel="prev">R Programming</a>, Up: <a href="#Top" accesskey="u" rel="up">Top</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
|
|
</div>
|
|
<a name="R-Bugs-1"></a>
|
|
<h2 class="chapter">9 R Bugs</h2>
|
|
|
|
<table summary="" class="menu" border="0" cellspacing="0">
|
|
<tr><td align="left" valign="top">• <a href="#What-is-a-bug_003f" accesskey="1">What is a bug?</a>:</td><td> </td><td align="left" valign="top">
|
|
</td></tr>
|
|
<tr><td align="left" valign="top">• <a href="#How-to-report-a-bug" accesskey="2">How to report a bug</a>:</td><td> </td><td align="left" valign="top">
|
|
</td></tr>
|
|
</table>
|
|
|
|
<hr>
|
|
<a name="What-is-a-bug_003f"></a>
|
|
<div class="header">
|
|
<p>
|
|
Next: <a href="#How-to-report-a-bug" accesskey="n" rel="next">How to report a bug</a>, Previous: <a href="#R-Bugs" accesskey="p" rel="prev">R Bugs</a>, Up: <a href="#R-Bugs" accesskey="u" rel="up">R Bugs</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
|
|
</div>
|
|
<a name="What-is-a-bug_003f-1"></a>
|
|
<h3 class="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 <a href="#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
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|
documentation is seriously inadequate, so you don’t need to report this.
|
|
</p>
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|
<p>If the online argument list of a function disagrees with the manual, one
|
|
of them must be wrong, so report the bug.
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|
</p>
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<hr>
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<a name="How-to-report-a-bug"></a>
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|
<div class="header">
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<p>
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|
Previous: <a href="#What-is-a-bug_003f" accesskey="p" rel="prev">What is a bug?</a>, Up: <a href="#R-Bugs" accesskey="u" rel="up">R Bugs</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
|
|
</div>
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|
<a name="How-to-report-a-bug-1"></a>
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|
<h3 class="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>
|
|
<div class="example">
|
|
<pre class="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., <a href="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
|
|
bugs new-to-old” or the search facility on
|
|
<a href="https://bugs.R-project.org/">https://bugs.R-project.org/</a>. Second, consult
|
|
<a href="https://svn.R-project.org/R/trunk/doc/NEWS.Rd">https://svn.R-project.org/R/trunk/doc/NEWS.Rd</a>, which
|
|
records changes that will appear in the <em>next</em> release of R,
|
|
including bug fixes that do not appear on the Bug Tracker.
|
|
Third, if possible try the current r-patched or r-devel version of R.
|
|
If a bug has already been reported or fixed, please do not submit
|
|
further bug reports on it. Finally, check carefully whether the bug is
|
|
with R, or a contributed package. Bug reports on contributed packages
|
|
should be sent first to the package maintainer, and only submitted to
|
|
the R-bugs repository by package maintainers, mentioning the package in
|
|
the subject line.
|
|
</p>
|
|
<p>A bug report can be generated using the function <code>bug.report()</code>.
|
|
For reports on R this will open the Web page at
|
|
<a href="https://bugs.R-project.org/">https://bugs.R-project.org/</a>: for a contributed package it will open
|
|
the package’s bug tracker Web page or help you compose an email to the
|
|
maintainer.
|
|
</p>
|
|
<p>There is a section of the bug repository for suggestions for
|
|
enhancements for R labelled ‘<samp>wishlist</samp>’. Suggestions can be
|
|
submitted in the same ways as bugs, but please ensure that the subject
|
|
line makes clear that this is for the wishlist and not a bug report, for
|
|
example by starting with ‘<samp>Wishlist:</samp>’.
|
|
</p>
|
|
<p>Comments on and suggestions for the Windows port of R should be sent to
|
|
<a href="mailto:R-windows@R-project.org">R-windows@R-project.org</a>.
|
|
</p>
|
|
<p>Corrections to and comments on message translations should be sent to the
|
|
last translator (listed at the top of the appropriate ‘<samp>.po</samp>’ file)
|
|
or to the translation team as listed at
|
|
<a href="https://developer.R-project.org/TranslationTeams.html">https://developer.R-project.org/TranslationTeams.html</a>.
|
|
</p>
|
|
<hr>
|
|
<a name="Acknowledgments"></a>
|
|
<div class="header">
|
|
<p>
|
|
Previous: <a href="#R-Bugs" accesskey="p" rel="prev">R Bugs</a>, Up: <a href="#Top" accesskey="u" rel="up">Top</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
|
|
</div>
|
|
<a name="Acknowledgments-1"></a>
|
|
<h2 class="chapter">10 Acknowledgments</h2>
|
|
|
|
<p>Of course, many many thanks to Robert and Ross for the R system, and to
|
|
the package writers and porters for adding to it.
|
|
</p>
|
|
<p>Special thanks go to Doug Bates, Peter Dalgaard, Paul Gilbert, Stefano
|
|
Iacus, Fritz Leisch, Jim Lindsey, Thomas Lumley, Martin Maechler, Brian
|
|
D. Ripley, Anthony Rossini, and Andreas Weingessel for their comments
|
|
which helped me improve this <acronym>FAQ</acronym>.
|
|
</p>
|
|
<p>More to come soon …
|
|
</p>
|
|
<hr>
|
|
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</body>
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</html>
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