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<div id="preamble" class="status">
<span style="color:#596a73; font-size:17px"><b>Marie-Hélène Burle</b></span><br><span style="color:#596a73; font-size:15px"><img src="./favicons/email.ico" alt="email" height="16" width="16"> <a href="mailto:[email protected]">[email protected]</a> <img src="./favicons/twitter.ico" alt="twitter" height="17" width="17"> <a href="https://twitter.com/MHBurle">@MHBurle</a> <img src="./favicons/gh.ico" alt="github" height="15" width="15"> <a href="https://github.com/prosoitos">prosoitos</a></span><br><span style="color:#596a73; font-size:16px">August 24, 2018</span>
</div>
<div id="content">
<h1 class="title">Functional programming in R (with <i>purrr</i>)</h1>
<div id="table-of-contents">
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org7cbb761">Introduction</a>
<ul>
<li><a href="#org356e41d">What is functional programming?</a></li>
<li><a href="#orgef931a6">Iterations</a></li>
<li><a href="#org90383c1">The purrr package</a>
<ul>
<li><a href="#orgaec6b4c">Goal</a></li>
<li><a href="#org0a2be65">Logistics</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#org1e3a71c">Let's dive in</a>
<ul>
<li><a href="#org6b2438d">Load packages</a></li>
<li><a href="#org7e97bfb">Create some fake banding data</a></li>
<li><a href="#org4867739">Map: apply functions to elements of a list</a>
<ul>
<li><a href="#orgc416f50">Usage</a></li>
<li><a href="#org2b45f8f">In our example</a></li>
<li><a href="#orgdb514c3">Stepping things up</a></li>
<li><a href="#orgdb14245">Formulas</a>
<ul>
<li><a href="#org848d02a">With one element</a></li>
<li><a href="#org8902327">With 2 elements</a></li>
<li><a href="#org5776459">Referring to elements</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#orgfac56a7"><code class="src src-R">map_if</code>/<code class="src src-R">modify_if</code> and <code class="src src-R">map_at</code>/<code class="src src-R">modify_at</code></a>
<ul>
<li><a href="#org50e21b0">Usage</a></li>
</ul>
</li>
<li><a href="#orgc8c62f8">Walk: apply side effects to elements of a list</a>
<ul>
<li><a href="#org10d0818">Usage</a></li>
<li><a href="#org72afb31">Apply to our example</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#org86cf23f">Summary of the map and walk functions family</a></li>
<li><a href="#org7d14c68">Conclusion</a></li>
</ul>
</div>
</div>
<div id="outline-container-org7cbb761" class="outline-2">
<h2 id="org7cbb761">Introduction</h2>
<div class="outline-text-2" id="text-org7cbb761">
</div>
<div id="outline-container-org356e41d" class="outline-3">
<h3 id="org356e41d">What is functional programming?</h3>
<div class="outline-text-3" id="text-org356e41d">
<p>
It is a programming paradigm based on the evaluation of functions. This is opposed to <i>imperative programming</i>. While some languages are based strictly on functional programming (e.g. Haskell), R allows both imperative code (e.g. loops) and functional code (e.g. many base functions, the <code class="src src-R"><span class="org-ess-function-call">apply</span><span class="org-ess-paren"><span class="org-rainbow-delimiters-depth-1">()</span></span></code> family, <code class="src src-R">purrr</code>).<br />
</p>
</div>
</div>
<div id="outline-container-orgef931a6" class="outline-3">
<h3 id="orgef931a6">Iterations</h3>
<div class="outline-text-3" id="text-orgef931a6">
<p>
Iterations are the repetition of a process (e.g. applying the same function to several variables, several datasets, or several files).<br />
</p>
<p>
The classic methods in R are:<br />
</p>
<ul class="org-ul">
<li>loops<br /></li>
<li><code class="src src-R"><span class="org-ess-function-call">apply</span><span class="org-ess-paren"><span class="org-rainbow-delimiters-depth-1">()</span></span></code> functions family<br /></li>
</ul>
</div>
</div>
<div id="outline-container-org90383c1" class="outline-3">
<h3 id="org90383c1">The purrr package</h3>
<div class="outline-text-3" id="text-org90383c1">
<p>
One of the <code class="src src-R">tidyverse</code> core packages, <code class="src src-R">purrr</code> was written in 2015 by <a href="https://github.com/lionel-">Lionel Henry</a> (also the maintainer), <a href="http://hadley.nz/">Hadley Wickham</a>, and <a href="https://www.rstudio.com/">RStudio inc.</a> <br />
</p>
</div>
<div id="outline-container-orgaec6b4c" class="outline-4">
<h4 id="orgaec6b4c">Goal</h4>
<div class="outline-text-4" id="text-orgaec6b4c">
<p>
<code class="src src-R">Purrr</code> is a set of tools allowing consistent functional programming in R in a <code class="src src-R">tidyverse</code> style (using <code class="src src-R">magrittr</code> pipes and following the same naming conventions found in other <code class="src src-R">tidyverse</code> packages).<br />
</p>
<p>
As Hadley Wickham says, in many ways, <code class="src src-R">purrr</code> is the equivalent of the <code class="src src-R">dplyr</code>, but while <code class="src src-R">dplyr</code> focuses on data frames, <code class="src src-R">purrr</code> works on vectors: it works on the elements of atomic vectors, lists, and data frames. Since R's most basic data structure is the vector, this makes <code class="src src-R">purrr</code> extremely powerful and flexible.<br />
</p>
</div>
</div>
<div id="outline-container-org0a2be65" class="outline-4">
<h4 id="org0a2be65">Logistics</h4>
<div class="outline-text-4" id="text-org0a2be65">
<p>
Install it with:<br />
</p>
<div class="org-src-container">
<pre class="src src-R"><span class="org-ess-function-call">install.packages</span><span class="org-ess-paren"><span class="org-rainbow-delimiters-depth-1">(</span></span><span class="org-string">"tidyverse"</span><span class="org-ess-paren"><span class="org-rainbow-delimiters-depth-1">)</span></span>
<span class="org-comment-delimiter">## </span><span class="org-comment">or</span>
<span class="org-ess-function-call">install.packages</span><span class="org-ess-paren"><span class="org-rainbow-delimiters-depth-1">(</span></span><span class="org-string">"purrr"</span><span class="org-ess-paren"><span class="org-rainbow-delimiters-depth-1">)</span></span>
</pre>
</div>
<p>
Load it with:<br />
</p>
<div class="org-src-container">
<pre class="src src-R"><span class="org-ess-modifiers">library</span><span class="org-ess-paren"><span class="org-rainbow-delimiters-depth-1">(</span></span>tidyverse<span class="org-ess-paren"><span class="org-rainbow-delimiters-depth-1">)</span></span>
<span class="org-comment-delimiter">## </span><span class="org-comment">or</span>
<span class="org-ess-modifiers">library</span><span class="org-ess-paren"><span class="org-rainbow-delimiters-depth-1">(</span></span>purrr<span class="org-ess-paren"><span class="org-rainbow-delimiters-depth-1">)</span></span>
</pre>
</div>
<p>
As always, once the package is loaded, you can get information on the package with:<br />
</p>
<div class="org-src-container">
<pre class="src src-R">?purrr
</pre>
</div>
<p>
and on any of its functions with:<br />
</p>
<div class="org-src-container">
<pre class="src src-R">?function
<span class="org-comment-delimiter">## </span><span class="org-comment">e.g. for the map function</span>
?map
</pre>
</div>
</div>
</div>
</div>
</div>
<div id="outline-container-org1e3a71c" class="outline-2">
<h2 id="org1e3a71c">Let's dive in</h2>
<div class="outline-text-2" id="text-org1e3a71c">
</div>
<div id="outline-container-org6b2438d" class="outline-3">
<h3 id="org6b2438d">Load packages</h3>
<div class="outline-text-3" id="text-org6b2438d">
<p>
First, let's load the packages that we will use. It is always a good idea to write all the packages that you will be using at the top of the script. This will help others, using your script, to know what is required to run it.<br />
</p>
<div class="org-src-container">
<pre class="src src-R"><span class="org-ess-modifiers">library</span><span class="org-ess-paren"><span class="org-rainbow-delimiters-depth-1">(</span></span>tidyverse<span class="org-ess-paren"><span class="org-rainbow-delimiters-depth-1">)</span></span> <span class="org-comment-delimiter"># </span><span class="org-comment">we will use purrr and other core packages</span>
<span class="org-ess-modifiers">library</span><span class="org-ess-paren"><span class="org-rainbow-delimiters-depth-1">(</span></span>magrittr<span class="org-ess-paren"><span class="org-rainbow-delimiters-depth-1">)</span></span> <span class="org-comment-delimiter"># </span><span class="org-comment">we will use several types of pipes</span>
</pre>
</div>
</div>
</div>
<div id="outline-container-org7e97bfb" class="outline-3">
<h3 id="org7e97bfb">Create some fake banding data</h3>
<div class="outline-text-3" id="text-org7e97bfb">
<p>
Let's create some imaginary bird banding data:<br />
</p>
<div class="org-src-container">
<pre class="src src-R">banding <span class="org-ess-assignment"><-</span> <span class="org-ess-function-call">tibble</span><span class="org-ess-paren"><span class="org-rainbow-delimiters-depth-1">(</span></span>
bird <span class="org-ess-operator">=</span> <span class="org-ess-function-call">paste0</span><span class="org-ess-paren"><span class="org-rainbow-delimiters-depth-2">(</span></span><span class="org-string">"bird"</span>, <span class="org-ess-numbers">1</span>:<span class="org-ess-numbers">50</span><span class="org-ess-paren"><span class="org-rainbow-delimiters-depth-2">)</span></span>,
sex <span class="org-ess-operator">=</span> <span class="org-ess-function-call">sample</span><span class="org-ess-paren"><span class="org-rainbow-delimiters-depth-2">(</span></span><span class="org-ess-function-call">c</span><span class="org-ess-paren"><span class="org-rainbow-delimiters-depth-3">(</span></span><span class="org-string">"F"</span>, <span class="org-string">"M"</span><span class="org-ess-paren"><span class="org-rainbow-delimiters-depth-3">)</span></span>, <span class="org-ess-numbers">50</span>, replace <span class="org-ess-operator">=</span> <span class="org-ess-f-t">T</span><span class="org-ess-paren"><span class="org-rainbow-delimiters-depth-2">)</span></span>,
population <span class="org-ess-operator">=</span> <span class="org-ess-function-call">sample</span><span class="org-ess-paren"><span class="org-rainbow-delimiters-depth-2">(</span></span>LETTERS<span class="org-ess-paren"><span class="org-rainbow-delimiters-depth-3">[</span></span><span class="org-ess-numbers">1</span>:<span class="org-ess-numbers">3</span><span class="org-ess-paren"><span class="org-rainbow-delimiters-depth-3">]</span></span>, <span class="org-ess-numbers">50</span>, replace <span class="org-ess-operator">=</span> <span class="org-ess-f-t">T</span><span class="org-ess-paren"><span class="org-rainbow-delimiters-depth-2">)</span></span>,
mass <span class="org-ess-operator">=</span> <span class="org-ess-function-call">rnorm</span><span class="org-ess-paren"><span class="org-rainbow-delimiters-depth-2">(</span></span><span class="org-ess-numbers">50</span>, <span class="org-ess-numbers">43</span>, <span class="org-ess-numbers">4</span><span class="org-ess-paren"><span class="org-rainbow-delimiters-depth-2">)</span></span> <span class="org-ess-XopX">%>%</span> <span class="org-ess-function-call">round</span><span class="org-ess-paren"><span class="org-rainbow-delimiters-depth-2">(</span></span><span class="org-ess-numbers">1</span><span class="org-ess-paren"><span class="org-rainbow-delimiters-depth-2">)</span></span>,
tarsus <span class="org-ess-operator">=</span> <span class="org-ess-function-call">rnorm</span><span class="org-ess-paren"><span class="org-rainbow-delimiters-depth-2">(</span></span><span class="org-ess-numbers">50</span>, <span class="org-ess-numbers">27</span>, <span class="org-ess-numbers">1</span><span class="org-ess-paren"><span class="org-rainbow-delimiters-depth-2">)</span></span> <span class="org-ess-XopX">%>%</span> <span class="org-ess-function-call">round</span><span class="org-ess-paren"><span class="org-rainbow-delimiters-depth-2">(</span></span><span class="org-ess-numbers">1</span><span class="org-ess-paren"><span class="org-rainbow-delimiters-depth-2">)</span></span>,
wing <span class="org-ess-operator">=</span> <span class="org-ess-function-call">rnorm</span><span class="org-ess-paren"><span class="org-rainbow-delimiters-depth-2">(</span></span><span class="org-ess-numbers">50</span>, <span class="org-ess-numbers">112</span>, <span class="org-ess-numbers">3</span><span class="org-ess-paren"><span class="org-rainbow-delimiters-depth-2">)</span></span> <span class="org-ess-XopX">%>%</span> <span class="org-ess-function-call">round</span><span class="org-ess-paren"><span class="org-rainbow-delimiters-depth-2">(</span></span><span class="org-ess-numbers">0</span><span class="org-ess-paren"><span class="org-rainbow-delimiters-depth-2">)</span></span>
<span class="org-ess-paren"><span class="org-rainbow-delimiters-depth-1">)</span></span>
banding
</pre>
</div>
</div>
</div>
<div id="outline-container-org4867739" class="outline-3">
<h3 id="org4867739">Map: apply functions to elements of a list</h3>
<div class="outline-text-3" id="text-org4867739">
<p>
Imagine that you want to calculate the mean for each of the morphometric measurements (mass, tarsus, and wing).<br />
</p>
<div class="VERBATIM">
<p>
How would you usually do this?<br />
Spend 5 minutes writing code you would usually use.<br />
</p>
</div>
<p>
To apply functions to elements of a list, you can use <code class="src src-R">map</code>, one of the key function of the <code class="src src-R">purrr</code> package.<br />
</p>
</div>
<div id="outline-container-orgc416f50" class="outline-4">
<h4 id="orgc416f50">Usage</h4>
<div class="outline-text-4" id="text-orgc416f50">
<div class="org-src-container">
<pre class="src src-R"><span class="org-ess-function-call">map</span><span class="org-ess-paren"><span class="org-rainbow-delimiters-depth-1">(</span></span>.x, .f, ...<span class="org-ess-paren"><span class="org-rainbow-delimiters-depth-1">)</span></span>
</pre>
</div>
<pre class="example">
.x a list or atomic vector
.f a function, formula, or atomic vector
... additional arguments passed to .f
</pre>
<p>
For every element of <code class="src src-R">.x</code>, apply <code class="src src-R">.f</code>.<br />
</p>
<p>
What we have, in the simplest case, is:<br />
</p>
<div class="org-src-container">
<pre class="src src-R"><span class="org-ess-function-call">map</span><span class="org-ess-paren"><span class="org-rainbow-delimiters-depth-1">(</span></span>list, function<span class="org-ess-paren"><span class="org-rainbow-delimiters-depth-1">)</span></span>
</pre>
</div>
</div>
</div>
<div id="outline-container-org2b45f8f" class="outline-4">
<h4 id="org2b45f8f">In our example</h4>
<div class="outline-text-4" id="text-org2b45f8f">
<div class="VERBATIM">
<p>
How could we use <code class="src src-R"><span class="org-ess-function-call">map</span><span class="org-ess-paren"><span class="org-rainbow-delimiters-depth-1">()</span></span></code> to calculate the means of all 3 measurement types?<br />
</p>
</div>
<div class="RED">
<p>
A data frame is a list! It is a list of vectors.<br />
</p>
<p>
Without running it in your computer, try to guess what the result of the following will be:<br />
</p>
<div class="org-src-container">
<pre class="src src-R"><span class="org-ess-function-call">length</span><span class="org-ess-paren"><span class="org-rainbow-delimiters-depth-1">(</span></span>banding<span class="org-ess-paren"><span class="org-rainbow-delimiters-depth-1">)</span></span>
</pre>
</div>
<p>
Now, run it. What do you get? Why?<br />
</p>
</div>
<p>
So, back to our example, we do have a list: a list of vectors. That's what our banding data frame is! So no problem about applying <code class="src src-R"><span class="org-ess-function-call">map</span><span class="org-ess-paren"><span class="org-rainbow-delimiters-depth-1">()</span></span></code> to it.<br />
</p>
<div class="accordion">
<p>
Answer<br />
</p>
</div>
<div class="panel">
<div class="org-src-container">
<pre class="src src-R"><span class="org-ess-function-call">map</span><span class="org-ess-paren"><span class="org-rainbow-delimiters-depth-1">(</span></span>banding<span class="org-ess-paren"><span class="org-rainbow-delimiters-depth-2">[</span></span><span class="org-ess-numbers">4</span>:<span class="org-ess-numbers">6</span><span class="org-ess-paren"><span class="org-rainbow-delimiters-depth-2">]</span></span>, mean<span class="org-ess-paren"><span class="org-rainbow-delimiters-depth-1">)</span></span>
</pre>
</div>
<p>
or using a pipe<br />
</p>
<div class="org-src-container">
<pre class="src src-R">banding<span class="org-ess-paren"><span class="org-rainbow-delimiters-depth-1">[</span></span><span class="org-ess-numbers">4</span>:<span class="org-ess-numbers">6</span><span class="org-ess-paren"><span class="org-rainbow-delimiters-depth-1">]</span></span> <span class="org-ess-XopX">%>%</span> <span class="org-ess-function-call">map</span><span class="org-ess-paren"><span class="org-rainbow-delimiters-depth-1">(</span></span>mean<span class="org-ess-paren"><span class="org-rainbow-delimiters-depth-1">)</span></span>
</pre>
</div>
</div>
<p>
However, the output of <code class="src src-R"><span class="org-ess-function-call">map</span><span class="org-ess-paren"><span class="org-rainbow-delimiters-depth-1">()</span></span></code> is always a list. And a list as output is not really convenient here. There are other map functions which have vector or data frame outputs. To get a numeric vector as the output, we use <code class="src src-R"><span class="org-ess-function-call">map_dbl</span><span class="org-ess-paren"><span class="org-rainbow-delimiters-depth-1">()</span></span></code>:<br />
</p>
<div class="accordion">
<p>
Answer<br />
</p>
</div>
<div class="panel">
<div class="org-src-container">
<pre class="src src-R"><span class="org-ess-function-call">map_dbl</span><span class="org-ess-paren"><span class="org-rainbow-delimiters-depth-1">(</span></span>banding<span class="org-ess-paren"><span class="org-rainbow-delimiters-depth-2">[</span></span><span class="org-ess-numbers">4</span>:<span class="org-ess-numbers">6</span><span class="org-ess-paren"><span class="org-rainbow-delimiters-depth-2">]</span></span>, mean<span class="org-ess-paren"><span class="org-rainbow-delimiters-depth-1">)</span></span>
</pre>
</div>
<p>
or<br />
</p>
<div class="org-src-container">
<pre class="src src-R">banding<span class="org-ess-paren"><span class="org-rainbow-delimiters-depth-1">[</span></span><span class="org-ess-numbers">4</span>:<span class="org-ess-numbers">6</span><span class="org-ess-paren"><span class="org-rainbow-delimiters-depth-1">]</span></span> <span class="org-ess-XopX">%>%</span> <span class="org-ess-function-call">map_dbl</span><span class="org-ess-paren"><span class="org-rainbow-delimiters-depth-1">(</span></span>mean<span class="org-ess-paren"><span class="org-rainbow-delimiters-depth-1">)</span></span>
</pre>
</div>
</div>
<p>
Similarly, you can calculate the variance, the sum, look for the largest value, or apply any other function to our data.<br />
</p>
<div class="VERBATIM">
<p>
Spend 2 min writing codes for these.<br />
</p>
</div>
<div class="accordion">
<p>
Answer<br />
</p>
</div>
<div class="panel">