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block009_dplyr-intro.html
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<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta charset="utf-8">
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
<meta name="generator" content="pandoc" />
<title>Introduction to dplyr</title>
<script src="libs/jquery-1.11.0/jquery.min.js"></script>
<meta name="viewport" content="width=device-width, initial-scale=1" />
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<h1 class="title">Introduction to dplyr</h1>
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<li><a href="#intro">Intro</a><ul>
<li><a href="#load-dplyr-and-gapminder">Load <code>dplyr</code> and <code>gapminder</code></a></li>
<li><a href="#load-the-gapminder-data">Load the Gapminder data</a></li>
</ul></li>
<li><a href="#meet-tbl_df-an-upgrade-to-data.frame">Meet <code>tbl_df</code>, an upgrade to <code>data.frame</code></a></li>
<li><a href="#think-before-you-create-excerpts-of-your-data">Think before you create excerpts of your data …</a></li>
<li><a href="#use-filter-to-subset-data-row-wise.">Use <code>filter()</code> to subset data row-wise.</a></li>
<li><a href="#meet-the-new-pipe-operator">Meet the new pipe operator</a></li>
<li><a href="#use-select-to-subset-the-data-on-variables-or-columns.">Use <code>select()</code> to subset the data on variables or columns.</a></li>
<li><a href="#revel-in-the-convenience">Revel in the convenience</a></li>
<li><a href="#pause-to-reflect">Pause to reflect</a></li>
<li><a href="#resources">Resources</a></li>
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<div id="intro" class="section level3">
<h3>Intro</h3>
<p><code>dplyr</code> is a new package for data manipulation. It is built to be fast, highly expressive, and open-minded about how your data is stored. It is developed by Hadley Wickham and Romain Francois.</p>
<p><code>dplyr</code>’s roots are in an earlier, still-very-useful package called <a href="http://plyr.had.co.nz"><code>plyr</code></a>, which implements the “split-apply-combine” strategy for data analysis. Where <code>plyr</code> covers a diverse set of inputs and outputs (e.g., arrays, data.frames, lists), <code>dplyr</code> has a laser-like focus on data.frames and related structures.</p>
<p>Have no idea what I’m talking about? Not sure if you care? If you use these base R functions: <code>subset()</code>, <code>apply()</code>, <code>[sl]apply()</code>, <code>tapply()</code>, <code>aggregate()</code>, <code>split()</code>, <code>do.call()</code>, then you should keep reading.</p>
<div id="load-dplyr-and-gapminder" class="section level4">
<h4>Load <code>dplyr</code> and <code>gapminder</code></h4>
<pre class="r"><code>## install if you do not already have
## from CRAN:
## install.packages("dplyr")
## from GitHub using devtools (which you also might need to install!):
## if (packageVersion("devtools") < 1.6) {
## install.packages("devtools")
## }
## devtools::install_github("hadley/lazyeval")
## devtools::install_github("hadley/dplyr")
suppressPackageStartupMessages(library(dplyr))
library(gapminder)</code></pre>
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<div id="load-the-gapminder-data" class="section level4">
<h4>Load the Gapminder data</h4>
<p>An excerpt of the Gapminder data which we work with alot.</p>
<pre class="r"><code>str(gapminder)</code></pre>
<pre><code>## 'data.frame': 1704 obs. of 6 variables:
## $ country : Factor w/ 142 levels "Afghanistan",..: 1 1 1 1 1 1 1 1 1 1 ...
## $ continent: Factor w/ 5 levels "Africa","Americas",..: 3 3 3 3 3 3 3 3 3 3 ...
## $ year : num 1952 1957 1962 1967 1972 ...
## $ lifeExp : num 28.8 30.3 32 34 36.1 ...
## $ pop : num 8425333 9240934 10267083 11537966 13079460 ...
## $ gdpPercap: num 779 821 853 836 740 ...</code></pre>
<pre class="r"><code>head(gapminder)</code></pre>
<pre><code>## country continent year lifeExp pop gdpPercap
## 1 Afghanistan Asia 1952 28.801 8425333 779.4453
## 2 Afghanistan Asia 1957 30.332 9240934 820.8530
## 3 Afghanistan Asia 1962 31.997 10267083 853.1007
## 4 Afghanistan Asia 1967 34.020 11537966 836.1971
## 5 Afghanistan Asia 1972 36.088 13079460 739.9811
## 6 Afghanistan Asia 1977 38.438 14880372 786.1134</code></pre>
</div>
</div>
<div id="meet-tbl_df-an-upgrade-to-data.frame" class="section level3">
<h3>Meet <code>tbl_df</code>, an upgrade to <code>data.frame</code></h3>
<pre class="r"><code>gtbl <- tbl_df(gapminder)
gtbl</code></pre>
<pre><code>## Source: local data frame [1,704 x 6]
##
## country continent year lifeExp pop gdpPercap
## (fctr) (fctr) (dbl) (dbl) (dbl) (dbl)
## 1 Afghanistan Asia 1952 28.801 8425333 779.4453
## 2 Afghanistan Asia 1957 30.332 9240934 820.8530
## 3 Afghanistan Asia 1962 31.997 10267083 853.1007
## 4 Afghanistan Asia 1967 34.020 11537966 836.1971
## 5 Afghanistan Asia 1972 36.088 13079460 739.9811
## 6 Afghanistan Asia 1977 38.438 14880372 786.1134
## 7 Afghanistan Asia 1982 39.854 12881816 978.0114
## 8 Afghanistan Asia 1987 40.822 13867957 852.3959
## 9 Afghanistan Asia 1992 41.674 16317921 649.3414
## 10 Afghanistan Asia 1997 41.763 22227415 635.3414
## .. ... ... ... ... ... ...</code></pre>
<pre class="r"><code>glimpse(gtbl)</code></pre>
<pre><code>## Observations: 1,704
## Variables: 6
## $ country (fctr) Afghanistan, Afghanistan, Afghanistan, Afghanistan,...
## $ continent (fctr) Asia, Asia, Asia, Asia, Asia, Asia, Asia, Asia, Asi...
## $ year (dbl) 1952, 1957, 1962, 1967, 1972, 1977, 1982, 1987, 1992...
## $ lifeExp (dbl) 28.801, 30.332, 31.997, 34.020, 36.088, 38.438, 39.8...
## $ pop (dbl) 8425333, 9240934, 10267083, 11537966, 13079460, 1488...
## $ gdpPercap (dbl) 779.4453, 820.8530, 853.1007, 836.1971, 739.9811, 78...</code></pre>
<p>A <code>tbl_df</code> is basically an improved data.frame, for which <code>dplyr</code> provides nice methods for high-level inspection. Specifically, these methods do something sensible for datasets with many observations and/or variables. You do <strong>NOT</strong> need to turn your data.frames into <code>tbl_df</code>s to use <code>dplyr</code>. I do so here for demonstration purposes only.</p>
</div>
<div id="think-before-you-create-excerpts-of-your-data" class="section level3">
<h3>Think before you create excerpts of your data …</h3>
<p>If you feel the urge to store a little snippet of your data:</p>
<pre class="r"><code>(snippet <- subset(gapminder, country == "Canada"))</code></pre>
<pre><code>## country continent year lifeExp pop gdpPercap
## 241 Canada Americas 1952 68.750 14785584 11367.16
## 242 Canada Americas 1957 69.960 17010154 12489.95
## 243 Canada Americas 1962 71.300 18985849 13462.49
## 244 Canada Americas 1967 72.130 20819767 16076.59
## 245 Canada Americas 1972 72.880 22284500 18970.57
## 246 Canada Americas 1977 74.210 23796400 22090.88
## 247 Canada Americas 1982 75.760 25201900 22898.79
## 248 Canada Americas 1987 76.860 26549700 26626.52
## 249 Canada Americas 1992 77.950 28523502 26342.88
## 250 Canada Americas 1997 78.610 30305843 28954.93
## 251 Canada Americas 2002 79.770 31902268 33328.97
## 252 Canada Americas 2007 80.653 33390141 36319.24</code></pre>
<p>Stop and ask yourself …</p>
<blockquote>
<p>Do I want to create mini datasets for each level of some factor (or unique combination of several factors) … in order to compute or graph something?</p>
</blockquote>
<p>If YES, <strong>use proper data aggregation techniques</strong> or facetting in <code>ggplot2</code> plots or conditioning in <code>lattice</code> – <strong>don’t subset the data</strong>. Or, more realistic, only subset the data as a temporary measure while you develop your elegant code for computing on or visualizing these data subsets.</p>
<p>If NO, then maybe you really do need to store a copy of a subset of the data. But seriously consider whether you can achieve your goals by simply using the <code>subset =</code> argument of, e.g., the <code>lm()</code> function, to limit computation to your excerpt of choice. Lots of functions offer a <code>subset =</code> argument!</p>
<p>Copies and excerpts of your data clutter your workspace, invite mistakes, and sow general confusion. Avoid whenever possible.</p>
<p>Reality can also lie somewhere in between. You will find the workflows presented below can help you accomplish your goals with minimal creation of temporary, intermediate objects.</p>
</div>
<div id="use-filter-to-subset-data-row-wise." class="section level3">
<h3>Use <code>filter()</code> to subset data row-wise.</h3>
<p><code>filter()</code> takes logical expressions and returns the rows for which all are <code>TRUE</code>.</p>
<pre class="r"><code>filter(gtbl, lifeExp < 29)</code></pre>
<pre><code>## Source: local data frame [2 x 6]
##
## country continent year lifeExp pop gdpPercap
## (fctr) (fctr) (dbl) (dbl) (dbl) (dbl)
## 1 Afghanistan Asia 1952 28.801 8425333 779.4453
## 2 Rwanda Africa 1992 23.599 7290203 737.0686</code></pre>
<pre class="r"><code>filter(gtbl, country == "Rwanda")</code></pre>
<pre><code>## Source: local data frame [12 x 6]
##
## country continent year lifeExp pop gdpPercap
## (fctr) (fctr) (dbl) (dbl) (dbl) (dbl)
## 1 Rwanda Africa 1952 40.000 2534927 493.3239
## 2 Rwanda Africa 1957 41.500 2822082 540.2894
## 3 Rwanda Africa 1962 43.000 3051242 597.4731
## 4 Rwanda Africa 1967 44.100 3451079 510.9637
## 5 Rwanda Africa 1972 44.600 3992121 590.5807
## 6 Rwanda Africa 1977 45.000 4657072 670.0806
## 7 Rwanda Africa 1982 46.218 5507565 881.5706
## 8 Rwanda Africa 1987 44.020 6349365 847.9912
## 9 Rwanda Africa 1992 23.599 7290203 737.0686
## 10 Rwanda Africa 1997 36.087 7212583 589.9445
## 11 Rwanda Africa 2002 43.413 7852401 785.6538
## 12 Rwanda Africa 2007 46.242 8860588 863.0885</code></pre>
<pre class="r"><code>filter(gtbl, country %in% c("Rwanda", "Afghanistan"))</code></pre>
<pre><code>## Source: local data frame [24 x 6]
##
## country continent year lifeExp pop gdpPercap
## (fctr) (fctr) (dbl) (dbl) (dbl) (dbl)
## 1 Afghanistan Asia 1952 28.801 8425333 779.4453
## 2 Afghanistan Asia 1957 30.332 9240934 820.8530
## 3 Afghanistan Asia 1962 31.997 10267083 853.1007
## 4 Afghanistan Asia 1967 34.020 11537966 836.1971
## 5 Afghanistan Asia 1972 36.088 13079460 739.9811
## 6 Afghanistan Asia 1977 38.438 14880372 786.1134
## 7 Afghanistan Asia 1982 39.854 12881816 978.0114
## 8 Afghanistan Asia 1987 40.822 13867957 852.3959
## 9 Afghanistan Asia 1992 41.674 16317921 649.3414
## 10 Afghanistan Asia 1997 41.763 22227415 635.3414
## .. ... ... ... ... ... ...</code></pre>
<p>Compare with some base R code to accomplish the same things</p>
<pre class="r"><code>gapminder[gapminder$lifeExp < 29, ] ## repeat `gapminder`, [i, j] indexing is distracting
subset(gapminder, country == "Rwanda") ## almost same as filter ... but wait ...</code></pre>
</div>
<div id="meet-the-new-pipe-operator" class="section level3">
<h3>Meet the new pipe operator</h3>
<p>Before we go any further, we should exploit the new pipe operator that <code>dplyr</code> imports from the <a href="https://github.com/smbache/magrittr"><code>magrittr</code></a> package by Stefan Bache. This is going to change your data analytical life. You no longer need to enact multi-operation commands by nesting them inside each other, like so many <a href="http://blogue.us/wp-content/uploads/2009/07/Unknown-21.jpeg">Russian nesting dolls</a>. This new syntax leads to code that is much easier to write and to read.</p>
<p>Here’s what it looks like: <code>%>%</code>. The RStudio keyboard shortcut: Ctrl + Shift + M (Windows), Cmd + Shift + M (Mac).</p>
<p>Let’s demo then I’ll explain:</p>
<pre class="r"><code>gapminder %>% head</code></pre>
<pre><code>## country continent year lifeExp pop gdpPercap
## 1 Afghanistan Asia 1952 28.801 8425333 779.4453
## 2 Afghanistan Asia 1957 30.332 9240934 820.8530
## 3 Afghanistan Asia 1962 31.997 10267083 853.1007
## 4 Afghanistan Asia 1967 34.020 11537966 836.1971
## 5 Afghanistan Asia 1972 36.088 13079460 739.9811
## 6 Afghanistan Asia 1977 38.438 14880372 786.1134</code></pre>
<p>This is equivalent to <code>head(gapminder)</code>. This pipe operator takes the thing on the left-hand-side and <strong>pipes</strong> it into the function call on the right-hand-side – literally, drops it in as the first argument.</p>
<p>Never fear, you can still specify other arguments to this function! To see the first 3 rows of Gapminder, we could say <code>head(gapminder, 3)</code> or this:</p>
<pre class="r"><code>gapminder %>% head(3)</code></pre>
<pre><code>## country continent year lifeExp pop gdpPercap
## 1 Afghanistan Asia 1952 28.801 8425333 779.4453
## 2 Afghanistan Asia 1957 30.332 9240934 820.8530
## 3 Afghanistan Asia 1962 31.997 10267083 853.1007</code></pre>
<p>I’ve advised you to think “gets” whenever you see the assignment operator, <code><-</code>. Similary, you should think “then” whenever you see the pipe operator, <code>%>%</code>.</p>
<p>You are probably not impressed yet, but the magic will soon happen.</p>
</div>
<div id="use-select-to-subset-the-data-on-variables-or-columns." class="section level3">
<h3>Use <code>select()</code> to subset the data on variables or columns.</h3>
<p>Back to <code>dplyr</code> …</p>
<p>Use <code>select()</code> to subset the data on variables or columns. Here’s a conventional call:</p>
<pre class="r"><code>select(gtbl, year, lifeExp) ## tbl_df prevents TMI from printing</code></pre>
<pre><code>## Source: local data frame [1,704 x 2]
##
## year lifeExp
## (dbl) (dbl)
## 1 1952 28.801
## 2 1957 30.332
## 3 1962 31.997
## 4 1967 34.020
## 5 1972 36.088
## 6 1977 38.438
## 7 1982 39.854
## 8 1987 40.822
## 9 1992 41.674
## 10 1997 41.763
## .. ... ...</code></pre>
<p>And here’s similar operation, but written with the pipe operator and piped through <code>head</code>:</p>
<pre class="r"><code>gtbl %>%
select(year, lifeExp) %>%
head(4)</code></pre>
<pre><code>## Source: local data frame [4 x 2]
##
## year lifeExp
## (dbl) (dbl)
## 1 1952 28.801
## 2 1957 30.332
## 3 1962 31.997
## 4 1967 34.020</code></pre>
<p>Think: “Take <code>gtbl</code>, then select the variables year and lifeExp, then show the first 4 rows.”</p>
</div>
<div id="revel-in-the-convenience" class="section level3">
<h3>Revel in the convenience</h3>
<p>Here’s the data for Cambodia, but only certain variables:</p>
<pre class="r"><code>gtbl %>%
filter(country == "Cambodia") %>%
select(year, lifeExp)</code></pre>
<pre><code>## Source: local data frame [12 x 2]
##
## year lifeExp
## (dbl) (dbl)
## 1 1952 39.417
## 2 1957 41.366
## 3 1962 43.415
## 4 1967 45.415
## 5 1972 40.317
## 6 1977 31.220
## 7 1982 50.957
## 8 1987 53.914
## 9 1992 55.803
## 10 1997 56.534
## 11 2002 56.752
## 12 2007 59.723</code></pre>
<p>and what a typical base R call would look like:</p>
<pre class="r"><code>gapminder[gapminder$country == "Cambodia", c("year", "lifeExp")]</code></pre>
<pre><code>## year lifeExp
## 217 1952 39.417
## 218 1957 41.366
## 219 1962 43.415
## 220 1967 45.415
## 221 1972 40.317
## 222 1977 31.220
## 223 1982 50.957
## 224 1987 53.914
## 225 1992 55.803
## 226 1997 56.534
## 227 2002 56.752
## 228 2007 59.723</code></pre>
<p>or, possibly?, a nicer look using base R’s <code>subset()</code> function:</p>
<pre class="r"><code>subset(gapminder, country == "Cambodia", select = c(year, lifeExp))</code></pre>
<pre><code>## year lifeExp
## 217 1952 39.417
## 218 1957 41.366
## 219 1962 43.415
## 220 1967 45.415
## 221 1972 40.317
## 222 1977 31.220
## 223 1982 50.957
## 224 1987 53.914
## 225 1992 55.803
## 226 1997 56.534
## 227 2002 56.752
## 228 2007 59.723</code></pre>
</div>
<div id="pause-to-reflect" class="section level3">
<h3>Pause to reflect</h3>
<p>We’ve barely scratched the surface of <code>dplyr</code> but I want to point out key principles you may start to appreciate. If you’re new to R or “programming with data”, feel free skip this section and <a href="block010_dplyr-end-single-table.html">move on</a>.</p>
<p><code>dplyr</code>’s verbs, such as <code>filter()</code> and <code>select()</code>, are what’s called <a href="http://en.wikipedia.org/wiki/Pure_function">pure functions</a>. To quote from Wickham’s <a href="http://adv-r.had.co.nz/Functions.html">Advanced R Programming book</a>:</p>
<blockquote>
<p>The functions that are the easiest to understand and reason about are pure functions: functions that always map the same input to the same output and have no other impact on the workspace. In other words, pure functions have no side effects: they don’t affect the state of the world in any way apart from the value they return.</p>
</blockquote>
<p>In fact, these verbs are a special case of pure functions: they take the same flavor of object as input and output. Namely, a data.frame or one of the other data receptacles <code>dplyr</code> supports. And finally, the data is <strong>always</strong> the very first argument of the verb functions.</p>
<p>This set of deliberate design choices, together with the new pipe operator, produces a highly effective, low friction <a href="http://adv-r.had.co.nz/dsl.html">domain-specific language</a> for data analysis.</p>
<p>Go to the next block, <a href="block010_dplyr-end-single-table.html"><code>dplyr</code> functions for a single dataset</a>, for more <code>dplyr</code>!</p>
</div>
<div id="resources" class="section level3">
<h3>Resources</h3>
<p><code>dplyr</code> official stuff</p>
<ul>
<li>package home <a href="http://cran.r-project.org/web/packages/dplyr/index.html">on CRAN</a>
<ul>
<li>note there are several vignettes, with the <a href="http://cran.r-project.org/web/packages/dplyr/vignettes/introduction.html">introduction</a> being the most relevant right now</li>
<li>the <a href="http://cran.rstudio.com/web/packages/dplyr/vignettes/window-functions.html">one on window functions</a> will also be interesting to you now</li>
</ul></li>
<li>development home <a href="https://github.com/hadley/dplyr">on GitHub</a></li>
<li><a href="https://www.dropbox.com/sh/i8qnluwmuieicxc/AAAgt9tIKoIm7WZKIyK25lh6a">tutorial HW delivered</a> (note this links to a DropBox folder) at useR! 2014 conference</li>
</ul>
<p><a href="https://www.rstudio.com/wp-content/uploads/2015/02/data-wrangling-cheatsheet.pdf?version=0.99.687&mode=desktop">RStudio <code>dplyr</code> and <code>tidyr</code> cheatsheet</a>. Remember you can get to these via <em>Help > Cheatsheets.</em></p>
<p><a href="https://github.com/tjmahr/MadR_Pipelines">Excellent slides</a> on pipelines and <code>dplyr</code> by TJ Mahr, talk given to the Madison R Users Group.</p>
<p>Blog post <a href="http://www.dataschool.io/dplyr-tutorial-for-faster-data-manipulation-in-r/">Hands-on dplyr tutorial for faster data manipulation in R</a> by Data School, that includes a link to an R Markdown document and links to videos</p>
<p><a href="bit001_dplyr-cheatsheet.html">Cheatsheet</a> I made for <code>dplyr</code> join functions (not relevant yet but soon)</p>
</div>
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