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<!DOCTYPE html>
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<li><a href="./">Efficient R programming</a></li>
<li class="divider"></li>
<li class="chapter" data-level="1" data-path="index.html"><a href="index.html"><i class="fa fa-check"></i><b>1</b> Introduction (Place holder page for preface)</a><ul>
<li class="chapter" data-level="1.1" data-path="package-dependencies.html"><a href="package-dependencies.html"><i class="fa fa-check"></i><b>1.1</b> Package Dependencies</a></li>
</ul></li>
<li class="chapter" data-level="2" data-path="efficient-set-up.html"><a href="efficient-set-up.html"><i class="fa fa-check"></i><b>2</b> Efficient set-up</a><ul>
<li class="chapter" data-level="2.1" data-path="top-5-tips-for-an-efficient-r-set-up.html"><a href="top-5-tips-for-an-efficient-r-set-up.html"><i class="fa fa-check"></i><b>2.1</b> Top 5 tips for an efficient R set-up</a></li>
<li class="chapter" data-level="2.2" data-path="operating-system.html"><a href="operating-system.html"><i class="fa fa-check"></i><b>2.2</b> Operating system</a><ul>
<li class="chapter" data-level="2.2.1" data-path="operating-system.html"><a href="operating-system.html#operating-system-and-resource-monitoring"><i class="fa fa-check"></i><b>2.2.1</b> Operating system and resource monitoring</a></li>
</ul></li>
<li class="chapter" data-level="2.3" data-path="r-version.html"><a href="r-version.html"><i class="fa fa-check"></i><b>2.3</b> R version</a><ul>
<li class="chapter" data-level="2.3.1" data-path="r-version.html"><a href="r-version.html#installing-r"><i class="fa fa-check"></i><b>2.3.1</b> Installing R</a></li>
<li class="chapter" data-level="2.3.2" data-path="r-version.html"><a href="r-version.html#updating-r"><i class="fa fa-check"></i><b>2.3.2</b> Updating R</a></li>
<li class="chapter" data-level="2.3.3" data-path="r-version.html"><a href="r-version.html#installing-r-packages"><i class="fa fa-check"></i><b>2.3.3</b> Installing R packages</a></li>
<li class="chapter" data-level="2.3.4" data-path="r-version.html"><a href="r-version.html#deps"><i class="fa fa-check"></i><b>2.3.4</b> Installing R packages with dependencies</a></li>
<li class="chapter" data-level="2.3.5" data-path="r-version.html"><a href="r-version.html#updating-r-packages"><i class="fa fa-check"></i><b>2.3.5</b> Updating R packages</a></li>
</ul></li>
<li class="chapter" data-level="2.4" data-path="r-startup.html"><a href="r-startup.html"><i class="fa fa-check"></i><b>2.4</b> R startup</a><ul>
<li class="chapter" data-level="2.4.1" data-path="r-startup.html"><a href="r-startup.html#r-startup-arguments"><i class="fa fa-check"></i><b>2.4.1</b> R startup arguments</a></li>
<li class="chapter" data-level="2.4.2" data-path="r-startup.html"><a href="r-startup.html#an-overview-of-rs-startup-files"><i class="fa fa-check"></i><b>2.4.2</b> An overview of R’s startup files</a></li>
<li class="chapter" data-level="2.4.3" data-path="r-startup.html"><a href="r-startup.html#the-location-of-startup-files"><i class="fa fa-check"></i><b>2.4.3</b> The location of startup files</a></li>
<li class="chapter" data-level="2.4.4" data-path="r-startup.html"><a href="r-startup.html#rprofile"><i class="fa fa-check"></i><b>2.4.4</b> The <code>.Rprofile</code> file</a></li>
<li class="chapter" data-level="2.4.5" data-path="r-startup.html"><a href="r-startup.html#example-.rprofile-settings"><i class="fa fa-check"></i><b>2.4.5</b> Example <code>.Rprofile</code> settings</a></li>
<li class="chapter" data-level="2.4.6" data-path="r-startup.html"><a href="r-startup.html#renviron"><i class="fa fa-check"></i><b>2.4.6</b> The <code>.Renviron</code> file</a></li>
</ul></li>
<li class="chapter" data-level="2.5" data-path="rstudio.html"><a href="rstudio.html"><i class="fa fa-check"></i><b>2.5</b> RStudio</a><ul>
<li class="chapter" data-level="2.5.1" data-path="rstudio.html"><a href="rstudio.html#install-rstudio"><i class="fa fa-check"></i><b>2.5.1</b> Installing and updating RStudio</a></li>
<li class="chapter" data-level="2.5.2" data-path="rstudio.html"><a href="rstudio.html#window-pane-layout"><i class="fa fa-check"></i><b>2.5.2</b> Window pane layout</a></li>
<li class="chapter" data-level="2.5.3" data-path="rstudio.html"><a href="rstudio.html#exercises-3"><i class="fa fa-check"></i><b>2.5.3</b> Exercises</a></li>
<li class="chapter" data-level="2.5.4" data-path="rstudio.html"><a href="rstudio.html#rstudio-options"><i class="fa fa-check"></i><b>2.5.4</b> RStudio options</a></li>
<li class="chapter" data-level="2.5.5" data-path="rstudio.html"><a href="rstudio.html#auto-completion"><i class="fa fa-check"></i><b>2.5.5</b> Auto-completion</a></li>
<li class="chapter" data-level="2.5.6" data-path="rstudio.html"><a href="rstudio.html#keyboard-shortcuts"><i class="fa fa-check"></i><b>2.5.6</b> Keyboard shortcuts</a></li>
<li class="chapter" data-level="2.5.7" data-path="rstudio.html"><a href="rstudio.html#object-display-and-output-table"><i class="fa fa-check"></i><b>2.5.7</b> Object display and output table</a></li>
<li class="chapter" data-level="2.5.8" data-path="rstudio.html"><a href="rstudio.html#project-management"><i class="fa fa-check"></i><b>2.5.8</b> Project management</a></li>
<li class="chapter" data-level="2.5.9" data-path="rstudio.html"><a href="rstudio.html#exercises-4"><i class="fa fa-check"></i><b>2.5.9</b> Exercises</a></li>
</ul></li>
<li class="chapter" data-level="2.6" data-path="blas-and-alternative-r-interpreters.html"><a href="blas-and-alternative-r-interpreters.html"><i class="fa fa-check"></i><b>2.6</b> BLAS and alternative R interpreters</a><ul>
<li class="chapter" data-level="2.6.1" data-path="blas-and-alternative-r-interpreters.html"><a href="blas-and-alternative-r-interpreters.html#testing-performance-gains-from-blas"><i class="fa fa-check"></i><b>2.6.1</b> Testing performance gains from BLAS</a></li>
<li class="chapter" data-level="2.6.2" data-path="blas-and-alternative-r-interpreters.html"><a href="blas-and-alternative-r-interpreters.html#revolution-r"><i class="fa fa-check"></i><b>2.6.2</b> Revolution R</a></li>
<li class="chapter" data-level="2.6.3" data-path="blas-and-alternative-r-interpreters.html"><a href="blas-and-alternative-r-interpreters.html#other-interpreters"><i class="fa fa-check"></i><b>2.6.3</b> Other interpreters</a></li>
<li class="chapter" data-level="2.6.4" data-path="blas-and-alternative-r-interpreters.html"><a href="blas-and-alternative-r-interpreters.html#useful-blasbenchmarking-resources"><i class="fa fa-check"></i><b>2.6.4</b> Useful BLAS/benchmarking resources</a></li>
<li class="chapter" data-level="2.6.5" data-path="blas-and-alternative-r-interpreters.html"><a href="blas-and-alternative-r-interpreters.html#exercises-5"><i class="fa fa-check"></i><b>2.6.5</b> Exercises</a></li>
</ul></li>
</ul></li>
<li class="chapter" data-level="3" data-path="programming.html"><a href="programming.html"><i class="fa fa-check"></i><b>3</b> Efficient programming</a><ul>
<li class="chapter" data-level="3.1" data-path="general-advice.html"><a href="general-advice.html"><i class="fa fa-check"></i><b>3.1</b> General advice</a><ul>
<li class="chapter" data-level="3.1.1" data-path="general-advice.html"><a href="general-advice.html#memory-allocation"><i class="fa fa-check"></i><b>3.1.1</b> Memory allocation</a></li>
<li class="chapter" data-level="3.1.2" data-path="general-advice.html"><a href="general-advice.html#vectorised-code"><i class="fa fa-check"></i><b>3.1.2</b> Vectorised code</a></li>
<li class="chapter" data-level="" data-path="general-advice.html"><a href="general-advice.html#exercise-1"><i class="fa fa-check"></i>Exercise</a></li>
<li class="chapter" data-level="3.1.3" data-path="general-advice.html"><a href="general-advice.html#type-consistency"><i class="fa fa-check"></i><b>3.1.3</b> Type consistency</a></li>
<li class="chapter" data-level="3.1.4" data-path="general-advice.html"><a href="general-advice.html#invisible-returns"><i class="fa fa-check"></i><b>3.1.4</b> Invisible returns</a></li>
</ul></li>
<li class="chapter" data-level="3.2" data-path="factors.html"><a href="factors.html"><i class="fa fa-check"></i><b>3.2</b> Factors</a><ul>
<li class="chapter" data-level="3.2.1" data-path="factors.html"><a href="factors.html#example-months-of-the-year"><i class="fa fa-check"></i><b>3.2.1</b> Example: Months of the year</a></li>
<li class="chapter" data-level="3.2.2" data-path="factors.html"><a href="factors.html#example-graphics"><i class="fa fa-check"></i><b>3.2.2</b> Example: Graphics</a></li>
<li class="chapter" data-level="3.2.3" data-path="factors.html"><a href="factors.html#example-analysis-of-variance"><i class="fa fa-check"></i><b>3.2.3</b> Example: Analysis of variance</a></li>
<li class="chapter" data-level="3.2.4" data-path="factors.html"><a href="factors.html#example-data-input"><i class="fa fa-check"></i><b>3.2.4</b> Example: data input</a></li>
<li class="chapter" data-level="3.2.5" data-path="factors.html"><a href="factors.html#example-factors-are-not-character-vectors"><i class="fa fa-check"></i><b>3.2.5</b> Example: Factors are not character vectors</a></li>
</ul></li>
<li class="chapter" data-level="3.3" data-path="S3.html"><a href="S3.html"><i class="fa fa-check"></i><b>3.3</b> S3 objects</a></li>
<li class="chapter" data-level="3.4" data-path="caching-variables.html"><a href="caching-variables.html"><i class="fa fa-check"></i><b>3.4</b> Caching variables</a><ul>
<li class="chapter" data-level="3.4.1" data-path="caching-variables.html"><a href="caching-variables.html#function-closures"><i class="fa fa-check"></i><b>3.4.1</b> Function closures</a></li>
</ul></li>
<li class="chapter" data-level="3.5" data-path="the-byte-compiler.html"><a href="the-byte-compiler.html"><i class="fa fa-check"></i><b>3.5</b> The byte compiler</a><ul>
<li class="chapter" data-level="3.5.1" data-path="the-byte-compiler.html"><a href="the-byte-compiler.html#example-the-mean-function"><i class="fa fa-check"></i><b>3.5.1</b> Example: the mean function</a></li>
<li class="chapter" data-level="3.5.2" data-path="the-byte-compiler.html"><a href="the-byte-compiler.html#compiling-code"><i class="fa fa-check"></i><b>3.5.2</b> Compiling code</a></li>
</ul></li>
<li class="chapter" data-level="3.6" data-path="parallel-computing.html"><a href="parallel-computing.html"><i class="fa fa-check"></i><b>3.6</b> Parallel computing</a><ul>
<li class="chapter" data-level="3.6.1" data-path="parallel-computing.html"><a href="parallel-computing.html#parallel-versions-of-apply-functions"><i class="fa fa-check"></i><b>3.6.1</b> Parallel versions of apply functions</a></li>
<li class="chapter" data-level="3.6.2" data-path="parallel-computing.html"><a href="parallel-computing.html#example-snakes-and-ladders"><i class="fa fa-check"></i><b>3.6.2</b> Example: Snakes and Ladders</a></li>
<li class="chapter" data-level="3.6.3" data-path="parallel-computing.html"><a href="parallel-computing.html#exit-functions-with-care"><i class="fa fa-check"></i><b>3.6.3</b> Exit functions with care</a></li>
<li class="chapter" data-level="3.6.4" data-path="parallel-computing.html"><a href="parallel-computing.html#process-forking"><i class="fa fa-check"></i><b>3.6.4</b> Process forking</a></li>
</ul></li>
</ul></li>
<li class="chapter" data-level="4" data-path="efficient-workflow.html"><a href="efficient-workflow.html"><i class="fa fa-check"></i><b>4</b> Efficient workflow</a><ul>
<li class="chapter" data-level="4.1" data-path="project-planning.html"><a href="project-planning.html"><i class="fa fa-check"></i><b>4.1</b> Project planning</a><ul>
<li class="chapter" data-level="4.1.1" data-path="project-planning.html"><a href="project-planning.html#chunking-your-work"><i class="fa fa-check"></i><b>4.1.1</b> ‘Chunking’ your work</a></li>
<li class="chapter" data-level="4.1.2" data-path="project-planning.html"><a href="project-planning.html#smart"><i class="fa fa-check"></i><b>4.1.2</b> Making your workflow SMART</a></li>
<li class="chapter" data-level="4.1.3" data-path="project-planning.html"><a href="project-planning.html#r-packages-for-planning"><i class="fa fa-check"></i><b>4.1.3</b> R packages for planning</a></li>
<li class="chapter" data-level="4.1.4" data-path="project-planning.html"><a href="project-planning.html#exercises-9"><i class="fa fa-check"></i><b>4.1.4</b> Exercises</a></li>
</ul></li>
<li class="chapter" data-level="4.2" data-path="pkgs.html"><a href="pkgs.html"><i class="fa fa-check"></i><b>4.2</b> Package selection</a></li>
<li class="chapter" data-level="4.3" data-path="importing-data.html"><a href="importing-data.html"><i class="fa fa-check"></i><b>4.3</b> Importing data</a><ul>
<li class="chapter" data-level="4.3.1" data-path="importing-data.html"><a href="importing-data.html#fread"><i class="fa fa-check"></i><b>4.3.1</b> Fast data reading</a></li>
<li class="chapter" data-level="4.3.2" data-path="importing-data.html"><a href="importing-data.html#preprocessing-outside-r"><i class="fa fa-check"></i><b>4.3.2</b> Preprocessing outside R</a></li>
<li class="chapter" data-level="4.3.3" data-path="importing-data.html"><a href="importing-data.html#working-with-databases"><i class="fa fa-check"></i><b>4.3.3</b> Working with databases</a></li>
</ul></li>
<li class="chapter" data-level="4.4" data-path="tidying-data-with-tidyr.html"><a href="tidying-data-with-tidyr.html"><i class="fa fa-check"></i><b>4.4</b> Tidying data with tidyr</a></li>
<li class="chapter" data-level="4.5" data-path="dplyr.html"><a href="dplyr.html"><i class="fa fa-check"></i><b>4.5</b> Data processing with dplyr</a><ul>
<li class="chapter" data-level="4.5.1" data-path="dplyr.html"><a href="dplyr.html#renaming-columns"><i class="fa fa-check"></i><b>4.5.1</b> Renaming columns</a></li>
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<li class="chapter" data-level="4.6" data-path="data-processing-with-data-table.html"><a href="data-processing-with-data-table.html"><i class="fa fa-check"></i><b>4.6</b> Data processing with data.table</a></li>
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<li class="chapter" data-level="4.7.1" data-path="publication.html"><a href="publication.html#dynamic-documents-with-knitr"><i class="fa fa-check"></i><b>4.7.1</b> Dynamic documents with knitr</a></li>
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<li class="chapter" data-level="5" data-path="efficient-data-carpentry.html"><a href="efficient-data-carpentry.html"><i class="fa fa-check"></i><b>5</b> Efficient data carpentry</a></li>
<li class="chapter" data-level="6" data-path="efficient-visualisation.html"><a href="efficient-visualisation.html"><i class="fa fa-check"></i><b>6</b> Efficient visualisation</a><ul>
<li class="chapter" data-level="6.1" data-path="rough-outline.html"><a href="rough-outline.html"><i class="fa fa-check"></i><b>6.1</b> Rough outline</a></li>
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<li class="chapter" data-level="7" data-path="efficient-performance.html"><a href="efficient-performance.html"><i class="fa fa-check"></i><b>7</b> Efficient performance</a><ul>
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<li><a href="efficient-base-r.html#the-if-vs-ifelse-functions">The <code>if</code> vs <code>ifelse</code> functions</a></li>
<li class="chapter" data-level="" data-path="efficient-base-r.html"><a href="efficient-base-r.html#sorting-and-ordering"><i class="fa fa-check"></i>Sorting and ordering</a></li>
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<li><a href="efficient-base-r.html#which-indices-are-true">Which indices are <code>TRUE</code> </a></li>
<li class="chapter" data-level="" data-path="efficient-base-r.html"><a href="efficient-base-r.html#converting-factors-to-numerics"><i class="fa fa-check"></i>Converting factors to numerics</a></li>
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<li class="chapter" data-level="7.1.1" data-path="efficient-base-r.html"><a href="efficient-base-r.html#is.na-and-anyna"><i class="fa fa-check"></i><b>7.1.1</b> <code>is.na</code> and <code class="unnumbered">anyNA</code></a></li>
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<li class="chapter" data-level="7.3.1" data-path="rcpp.html"><a href="rcpp.html#pre-requisites"><i class="fa fa-check"></i><b>7.3.1</b> Pre-requisites</a></li>
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<li class="chapter" data-level="7.3.7" data-path="rcpp.html"><a href="rcpp.html#sugar"><i class="fa fa-check"></i><b>7.3.7</b> C++ with sugar on top</a></li>
<li class="chapter" data-level="7.3.8" data-path="rcpp.html"><a href="rcpp.html#rcpp-resources"><i class="fa fa-check"></i><b>7.3.8</b> Rcpp resources</a></li>
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<li class="chapter" data-level="8" data-path="efficient-hardware.html"><a href="efficient-hardware.html"><i class="fa fa-check"></i><b>8</b> Efficient hardware</a><ul>
<li class="chapter" data-level="8.1" data-path="background-what-is-a-byte.html"><a href="background-what-is-a-byte.html"><i class="fa fa-check"></i><b>8.1</b> Background: what is a byte?</a></li>
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<li class="chapter" data-level="8.3" data-path="hard-drives-hdd-vs-ssd.html"><a href="hard-drives-hdd-vs-ssd.html"><i class="fa fa-check"></i><b>8.3</b> Hard drives: HDD vs SSD</a></li>
<li class="chapter" data-level="8.4" data-path="operating-systems-32-bit-or-64-bit.html"><a href="operating-systems-32-bit-or-64-bit.html"><i class="fa fa-check"></i><b>8.4</b> Operating systems: 32-bit or 64-bit</a></li>
<li class="chapter" data-level="8.5" data-path="central-processing-unit-cpu.html"><a href="central-processing-unit-cpu.html"><i class="fa fa-check"></i><b>8.5</b> Central processing unit (CPU)</a></li>
<li class="chapter" data-level="8.6" data-path="cloud-computing.html"><a href="cloud-computing.html"><i class="fa fa-check"></i><b>8.6</b> Cloud computing</a><ul>
<li class="chapter" data-level="8.6.1" data-path="cloud-computing.html"><a href="cloud-computing.html#amazon-ec2"><i class="fa fa-check"></i><b>8.6.1</b> Amazon EC2</a></li>
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<li class="chapter" data-level="9.1.1" data-path="coding-style.html"><a href="coding-style.html#reformatting-code-with-rstudio"><i class="fa fa-check"></i><b>9.1.1</b> Reformatting code with RStudio</a></li>
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<li class="chapter" data-level="10.7.1" data-path="look-at-the-source-code.html"><a href="look-at-the-source-code.html#r-journal-and-journal-of-statistical-software"><i class="fa fa-check"></i><b>10.7.1</b> R-journal and Journal of Statistical Software</a></li>
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<li><a href="http://www.mas.ncl.ac.uk/~ncsg3/">Colin Gillespie</a>, Robin Lovelace</li>
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<i class="fa fa-circle-o-notch fa-spin"></i><a href="./">Efficient R programming</a>
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<div id="central-processing-unit-cpu" class="section level2">
<h2><span class="header-section-number">8.5</span> Central processing unit (CPU)</h2>
<p>The central processing unit (CPU), or the processor, is the brains of a computer. The CPU is responsible for performing numerical calculations. The faster the processor, the faster R will run. The clock speed (or clock rate, measured in hertz) is frequency with which the CPU executes instructions. The faster the clock speed, the more instructions a CPU can execute in a section. CPU clock speed for a single CPU has been fairly static in the last couple of years, hovering around 3.4GHz (see figure <a href="central-processing-unit-cpu.html#fig:3-3">8.3</a>).</p>
<div class="figure"><span id="fig:3-3"></span>
<img src="_main_files/figure-html/3-3-1.png" alt="CPU clock speed. The data for this figure was collected from web-forum and wikipedia. It is intended to indicate general trends in CPU speed." width="576" />
<p class="caption">
Figure 8.3: CPU clock speed. The data for this figure was collected from web-forum and wikipedia. It is intended to indicate general trends in CPU speed.
</p>
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<p>Unfortunately we can’t simply use clock speeds to compare CPUs, since the internal architecture of a CPU plays a crucial role in determining the CPU performance. The R package <strong>benchmarkme</strong> provides functions for benchmarking your system and contains data from previous benchmarks. Figure <a href="central-processing-unit-cpu.html#fig:3-4">8.4</a> shows the relative performance for over <span class="math inline">\(150\)</span> CPUs.</p>
<div class="figure"><span id="fig:3-4"></span>
<img src="_main_files/figure-html/3-4-1.png" alt="CPU benchmarks from the R package, **benchmarkme**. Each point represents an individual CPU result." width="576" />
<p class="caption">
Figure 8.4: CPU benchmarks from the R package, <strong>benchmarkme</strong>. Each point represents an individual CPU result.
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<p>Running the benchmarks and comparing your CPU to others is straightforward. First load the package</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">library</span>(<span class="st">"benchmarkme"</span>)</code></pre></div>
<p>Then run the benchmarks and plot via</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">res =<span class="st"> </span><span class="kw">benchmark_std</span>()
<span class="kw">plot</span>(res)
<span class="co"># Upload your benchmarks for future users</span>
<span class="kw">upload_results</span>(res) </code></pre></div>
<p>You get the model specifications of the top CPUs using <code>get_datatable(res)</code>.</p>
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