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slides_intro_to_R.html
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<!DOCTYPE html>
<html lang="en"><head>
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</head>
<body class="quarto-light">
<div class="reveal">
<div class="slides">
<section id="title-slide" class="quarto-title-block center">
<h1 class="title">Intro to R with RStudio</h1>
<div class="quarto-title-authors">
<div class="quarto-title-author">
<div class="quarto-title-author-name">
Abner Heredia Bustos, CSCAR
</div>
</div>
</div>
</section>
<section id="about-this-workshop" class="slide level2">
<h2>About this workshop</h2>
<p>For novice or inexperienced coders that want to use <strong>R</strong>. We will learn:</p>
<ul>
<li class="fragment">How to use the RStudio interface and scripts to code in R.</li>
<li class="fragment">What are and how to use “objects”.</li>
<li class="fragment">How to use and write basic functions.</li>
<li class="fragment">How to work with numerical vectors.</li>
<li class="fragment">But <em>NOT</em> statistical modeling.</li>
</ul>
</section>
<section id="workshop-format" class="slide level2">
<h2>Workshop format</h2>
<ul>
<li class="fragment">From 2:30 to 4:45 pm.</li>
<li class="fragment">Breaks every 45 minutes.</li>
<li class="fragment">A few slides for context and extra information.</li>
<li class="fragment">A lot of hands-on coding and live demonstrations.</li>
<li class="fragment">All materials will be available after the workshop ends.</li>
</ul>
<aside class="notes">
<p>This workshop runs from 2:30 to 4:45 pm, with breaks every 45 minutes. Right now I will use a few slides for context and extra information. But this is a WORKshop, so there will be plenty of hands-on coding and live demonstrations. All materials will be available after the workshop ends, so don’t worry about copying these slides.</p>
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</section>
<section id="tips-for-this-workshop" class="slide level2">
<h2>Tips for this workshop</h2>
<ul>
<li class="fragment">Coding along with me is the best way to learn.</li>
<li class="fragment">Ask questions at any time.</li>
<li class="fragment">During exercises, interact with your peers.</li>
</ul>
<aside class="notes">
<p>Coding along with me is the best way to learn. If you just watch, you will not remember anything after you leave today. Feel free to ask questions at any time. Code can be confusing and mistakes are easy to make, but I’m here to help, so don’t be afraid to interrupt me. During exercises, interact with your peers. We all struggle with computers, but it’s easier if we can help each other.</p>
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</section>
<section id="what-is-cscar" class="slide level2">
<h2>What is CSCAR?</h2>
<ul>
<li class="fragment">Full name: Consulting for Statistics, Computing and Analytics Research.</li>
<li class="fragment">A unit of the Office of the Vice President of Research (OVPR).</li>
<li class="fragment">Guides and trains researchers in data collection, management, and analysis.</li>
<li class="fragment">Also helps researchers to use technical software and advanced computing.</li>
</ul>
<aside class="notes">
<p>Before we get to the coding part, let me tell you a little bit about the people behind this workshop: CSCAR.</p>
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</section>
<section id="cscar-is-here-to-help-you" class="slide level2">
<h2>CSCAR is here to help you</h2>
<ul>
<li class="fragment">Free, one-hour consultations with full-time statistical consultants.</li>
<li class="fragment">GSRAs are available for walk-in consultations Monday through Friday, between 9am and 5pm (we close on Tuesdays between noon and 1pm).</li>
<li class="fragment">All of our scheduled appointments can be either remote or in-person.</li>
</ul>
<aside class="notes">
<p>All of our scheduled appointments can be either remote or in-person. So, if you live out of town, work in a different campus or just don’t want to deal with bad weather, you can still ask CSCAR for help.</p>
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</section>
<section id="contact-cscar" class="slide level2">
<h2>Contact CSCAR</h2>
<ul>
<li class="fragment">To request a consultation: email <a href="mailto:[email protected]" class="email">[email protected]</a>, or fill <a href="https://docs.google.com/forms/d/e/1FAIpQLSei-twcjFkoobUrVwSQTmSxdKKEc1Ub8w5LHmeIZUmTV1wmIg/viewform?pli=1">this form</a>. Or visit <a href="cscar.research.umich.edu">cscar.research.umich.edu</a>.</li>
<li class="fragment">Self-schedule a consultation with a GSRA using <a href="https://calendar.google.com/calendar/u/0/appointments/AcZssZ1DT776EMK1EGFFmBRyW-FrQrzo35QnU2nIv1E=">this link</a>.</li>
<li class="fragment">Address: The University of Michigan, 3560 Rackham, 915 E. Washington St., Ann Arbor, MI 48109-1070.</li>
</ul>
<aside class="notes">
<p>There are several ways to contact CSCAR. You can request a consultation by email or by filling this form. You can also self-schedule a consultation with a GSRA using this link. Our office is at 3560 Rackham, 915 E. Washington St., Ann Arbor, Michigan.</p>
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</section>
<section id="who-am-i" class="slide level2">
<h2>Who am I?</h2>
<ul>
<li class="fragment">Abner Heredia Bustos, a data science consultant at CSCAR.</li>
<li class="fragment">I want to make coding as simple and effortless as possible…</li>
<li class="fragment">…which means learning it well from the beginning.</li>
</ul>
<aside class="notes">
<p>My name is Abner Heredia Bustos. I am a data science consultant at CSCAR. Apart from this, all you need to know is that, for me, coding is just a means to an end. So, I will try hard to make coding as simple and effortless as possible for you; but to achieve this you will need to put some effort in learning the basics.</p>
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</section>
<section>
<section id="why-do-you-want-to-learn-r" class="title-slide slide level1 center">
<h1>Why do you want to learn R?</h1>
</section>
<section id="r-is-cheap-and-powerful" class="slide level2">
<h2>R is cheap and powerful</h2>
<ul>
<li class="fragment"><strong>R</strong> is gratis ($0) and it runs on Windows, MacOS, and several Unix platforms.</li>
<li class="fragment">You can start with this:</li>
</ul>
</section>
<section class="slide level2">
<div class="cell">
<div class="cell-output cell-output-stdout">
<pre><code> treat nitrogen block height weight leaf_area shoot_area flowers
1 tip medium 1 7.5 7.62 11.7 31.9 1
2 tip medium 1 10.7 12.14 14.1 46.0 10
3 tip medium 1 11.2 12.76 7.1 66.7 10
4 tip medium 1 10.4 8.78 11.9 20.3 1
5 tip medium 1 10.4 13.58 14.5 26.9 4</code></pre>
</div>
</div>
</section>
<section class="slide level2">
<p>and, in 8 lines of code or less, make this:</p>
<img data-src="slides_intro_to_R_files/figure-revealjs/height%20by%20nitrogen%20boxplots-1.png" class="quarto-figure quarto-figure-center r-stretch" width="595"><aside class="notes">
<p>You can change the colors, the order of the boxes, the names, and much more. Doing all of this will be straightforward once you are familiar with R’s syntax.</p>
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</section>
<section id="r-is-an-environment-not-a-package" class="slide level2">
<h2>R is an <em>environment</em>, not a package</h2>
<ul>
<li class="fragment">A package is a fixed set of tools.</li>
<li class="fragment">An environment is for combining, modifying, and creating tools.</li>
</ul>
<aside class="notes">
<p>R is very powerful because it is an environment, not a package. A package is a fixed set of tools—what you see is what you get and that’s it. An environment is for combining, modifying, and creating tools. So, even if a tool is not readily available in an environment, chances are there is a way to make it.</p>
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</section>
<section id="r-has-plenty-of-statistical-tools-and-models" class="slide level2">
<h2>R has plenty of statistical tools and models</h2>
<ul>
<li class="fragment">Generalized linear models (including linear regression).</li>
<li class="fragment">Survival analysis.</li>
<li class="fragment">Time series analysis.</li>
<li class="fragment">Multilevel models.</li>
<li class="fragment">Classification and clustering.</li>
<li class="fragment">Sample size and power calculations.</li>
<li class="fragment">Multivariable analysis (e.g., factor analysis, PCA, and SEM).</li>
</ul>
<aside class="notes">
<p>Luckily for us, other people have already built tools and models to do a lot of statistics. We have…</p>
<p>Better yet, people add more tools every day.</p>
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</section>
<section id="even-more-tools-and-models" class="slide level2">
<h2>Even more tools and models</h2>
<ul>
<li class="fragment">Users constantly publish their own code packages: more than 13 thousand in the Comprehensive <strong>R</strong> Archive Network (CRAN) as of March 2019.</li>
<li class="fragment">Many complex statistical routines are not (and may never be) available in other statistical software.</li>
</ul>
<aside class="notes">
<p>As of March 2019, users like you and I have published more than 13 thousand packages in CRAN. Many of these packages implement complex statistical routines that are not (and may never be) available in other statistical software.</p>
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</section>
<section id="why-isnt-everyone-a-user" class="slide level2">
<h2>Why Isn’t Everyone a Use<strong>R</strong>?</h2>
<ul>
<li class="fragment">Some people only use the software they learned first, which is not always <strong>R</strong>.</li>
<li class="fragment">Each package in R has its own rules to learn.</li>
<li class="fragment">Help pages and error messages may be hard to understand.</li>
</ul>
<aside class="notes">
<p>But if R is so good, why isn’t everyone a user? Some people only use whatever they learned first. They took a course in statistics years ago that used SPSS or STATA and that has been enough for them. Also, each package in R has its own rules to learn. You can find a lot of good help for popular packages written by professional developers, but not so much for smaller packages written by other common users. Worst of all, some of the error messages in R are uninformative, so fixing problems can be difficult. Still, I think the advantages are well worth the effort.</p>
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</section>
<section id="suggestions-for-learning-r" class="slide level2">
<h2>Suggestions for Learning <strong>R</strong></h2>
<ul>
<li class="fragment">Learn interactively.</li>
<li class="fragment">Don’t worry about getting errors.</li>
<li class="fragment">Ask other <strong>R</strong> users for help.</li>
</ul>
<aside class="notes">
<p>Learn interactively. Retype, experiment, go crazy with sample code. Today I will show you many examples that you can use and you can find many more online. Also, don’t worry about making mistakes. Even professional coders make errors all the time, and you can learn a lot from error messages. Besides you can always ask other users for help. Take advantage of R’s popularity to tap into our collective knowledge. It’s also a good excuse to get up from your desk every once in a while.</p>
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</section>
<section id="some-useful-links" class="slide level2">
<h2>Some useful links</h2>
<div>
<ul>
<li><a href="https://www.r-project.org" class="uri">https://www.r-project.org</a>: Here you will find links for downloading <strong>R</strong>, downloading additional packages for <strong>R</strong>, and more.</li>
<li><a href="https://cran.r-project.org/web/views/" class="uri">https://cran.r-project.org/web/views/</a>: Summaries of important packages by subject field or analysis type.</li>
<li><a href="https://journal.r-project.org" class="uri">https://journal.r-project.org</a>: The <strong>R</strong> Journal.</li>
<li><a href="https://stats.stackexchange.com" class="uri">https://stats.stackexchange.com</a>: Cross-Validated.</li>
<li><a href="https://www.r-bloggers.com" class="uri">https://www.r-bloggers.com</a></li>
</ul>
</div>
</section>
<section id="more-useful-links" class="slide level2">
<h2>More useful links</h2>
<div>
<ul>
<li><a href="https://stats.idre.ucla.edu/r/" class="uri">https://stats.idre.ucla.edu/r/</a>: Institute for Digital Research and Education at UCLA.</li>
<li><a href="https://socialsciences.mcmaster.ca/jfox/" class="uri">https://socialsciences.mcmaster.ca/jfox/</a>: John Fox’s home page.</li>
<li><a href="https://sas-and-r.blogspot.com/" class="uri">https://sas-and-r.blogspot.com/</a>: Examples of code to perform same task in SAS and R.</li>
</ul>
</div>
</section></section>
<section>
<section id="lets-start-coding" class="title-slide slide level1 center">
<h1>Let’s start coding</h1>
</section>
<section id="practice-your-arithmetic" class="slide level2">
<h2>Practice your arithmetic</h2>
<p>Think of an integer, double it, add six, divide it in half, subtract the number you started with, and then square it. If your code is correct, the answer should be nine.</p>
</section>
<section id="object-names-have-rules" class="slide level2">
<h2>Object names have rules</h2>
<ul>
<li class="fragment">Names can be a combination of letters, digits, periods <code>.</code> and underscores <code>_</code>.</li>
<li class="fragment">Names can <em>not</em> include white spaces.</li>
<li class="fragment">If a name starts with a period <code>.</code>, it can <em>not</em> be followed by a digit.</li>
<li class="fragment">Names can <em>not</em> start with a number or an underscore <code>_</code>.</li>
</ul>
</section>
<section id="object-names-have-rules-1" class="slide level2">
<h2>Object names have rules</h2>
<ul>
<li class="fragment">Names are case-sensitive (<code>age</code>, <code>Age</code> and <code>AGE</code> are three different objects).</li>
<li class="fragment">Reserved words (<code>TRUE</code>, <code>FALSE</code>, <code>NULL</code>, <code>if</code>, …) can <em>not</em> be used as names</li>
</ul>
</section>
<section id="tips-for-naming-objects" class="slide level2">
<h2>Tips for naming objects</h2>
<ul>
<li class="fragment">Avoid giving your object the same name as a built-in function.</li>
<li class="fragment">To separate words, use an underscore (<code>my_object</code>) or a dot (<code>my.object</code>), or capitalize the different words (<code>MyObject</code>). Choose your favorite way, but <em>be consistent</em> with it.</li>
<li class="fragment">Use names that illustrate what you want to do with the objects.</li>
</ul>
</section>
<section id="exercise" class="slide level2">
<h2>Exercise</h2>
<p>Write a function that can simulate the roll of two six-sided dice, one red and one blue, an arbitrary number of times. This function should return a vector with the values of the red die that were strictly larger than the corresponding values of the blue die.</p>
</section>
<section id="exercise-step-by-step-part-1" class="slide level2">
<h2>Exercise step by step (part 1)</h2>
<ul>
<li class="fragment">Step 1: define a function that takes one argument, <code>num_rolls</code>, representing the number of times to roll the dice.</li>
<li class="fragment">Step 2: create two objects called <code>red</code> and <code>blue</code> to store the results from the dice rolls.</li>
<li class="fragment">Step 3: simulate the dice rolls using function <code>sample()</code> (read its help page if you need to).</li>
</ul>
</section>
<section id="exercise-step-by-step-part-2" class="slide level2">
<h2>Exercise step by step (part 2)</h2>
<ul>
<li class="fragment">Step 4: create a vector of indices that identifies the values in the red die that were larger than the values in the blue die.</li>
<li class="fragment">Step 5: use this vector of indices to extract the values from the red die.</li>
<li class="fragment">Step 6: make sure that your function returns the values you extracted in step 5.</li>
</ul>
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