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<!DOCTYPE html>
<html>
<head>
<meta charset="utf-8">
<meta name="generator" content="pandoc">
<title>HELP!</title>
<meta name="apple-mobile-web-app-capable" content="yes">
<meta name="apple-mobile-web-app-status-bar-style" content="black-translucent">
<meta name="viewport" content="width=device-width, initial-scale=1.0, maximum-scale=1.0, user-scalable=no, minimal-ui">
<link rel="stylesheet" href="externals/reveal.js-3.3.0.1/css/reveal.css"/>
<style type="text/css">
a.sourceLine { display: inline-block; line-height: 1.25; }
a.sourceLine { pointer-events: none; color: inherit; text-decoration: inherit; }
a.sourceLine:empty { height: 1.2em; position: absolute; }
.sourceCode { overflow: visible; }
code.sourceCode { white-space: pre; position: relative; }
div.sourceCode { margin: 1em 0; }
pre.sourceCode { margin: 0; }
@media screen {
div.sourceCode { overflow: auto; }
}
@media print {
code.sourceCode { white-space: pre-wrap; }
a.sourceLine { text-indent: -1em; padding-left: 1em; }
}
pre.numberSource a.sourceLine
{ position: relative; }
pre.numberSource a.sourceLine:empty
{ position: absolute; }
pre.numberSource a.sourceLine::before
{ content: attr(data-line-number);
position: absolute; left: -5em; text-align: right; vertical-align: baseline;
border: none; pointer-events: all;
-webkit-touch-callout: none; -webkit-user-select: none;
-khtml-user-select: none; -moz-user-select: none;
-ms-user-select: none; user-select: none;
padding: 0 4px; width: 4em;
color: #aaaaaa;
}
pre.numberSource { margin-left: 3em; border-left: 1px solid #aaaaaa; padding-left: 4px; }
div.sourceCode
{ background-color: #f8f8f8; }
@media screen {
a.sourceLine::before { text-decoration: underline; }
}
code span.al { color: #ef2929; } /* Alert */
code span.an { color: #8f5902; font-weight: bold; font-style: italic; } /* Annotation */
code span.at { color: #c4a000; } /* Attribute */
code span.bn { color: #0000cf; } /* BaseN */
code span.cf { color: #204a87; font-weight: bold; } /* ControlFlow */
code span.ch { color: #4e9a06; } /* Char */
code span.cn { color: #000000; } /* Constant */
code span.co { color: #8f5902; font-style: italic; } /* Comment */
code span.cv { color: #8f5902; font-weight: bold; font-style: italic; } /* CommentVar */
code span.do { color: #8f5902; font-weight: bold; font-style: italic; } /* Documentation */
code span.dt { color: #204a87; } /* DataType */
code span.dv { color: #0000cf; } /* DecVal */
code span.er { color: #a40000; font-weight: bold; } /* Error */
code span.ex { } /* Extension */
code span.fl { color: #0000cf; } /* Float */
code span.fu { color: #000000; } /* Function */
code span.im { } /* Import */
code span.in { color: #8f5902; font-weight: bold; font-style: italic; } /* Information */
code span.kw { color: #204a87; font-weight: bold; } /* Keyword */
code span.op { color: #ce5c00; font-weight: bold; } /* Operator */
code span.ot { color: #8f5902; } /* Other */
code span.pp { color: #8f5902; font-style: italic; } /* Preprocessor */
code span.sc { color: #000000; } /* SpecialChar */
code span.ss { color: #4e9a06; } /* SpecialString */
code span.st { color: #4e9a06; } /* String */
code span.va { color: #000000; } /* Variable */
code span.vs { color: #4e9a06; } /* VerbatimString */
code span.wa { color: #8f5902; font-weight: bold; font-style: italic; } /* Warning */
</style>
<link rel="stylesheet" href="externals/reveal.js-3.3.0.1/css/theme/white.css" id="theme">
<!-- some tweaks to reveal css -->
<style type="text/css">
.reveal h1 { font-size: 2.0em; }
.reveal h2 { font-size: 1.5em; }
.reveal h3 { font-size: 1.25em; }
.reveal h4 { font-size: 1em; }
.reveal .slides>section,
.reveal .slides>section>section {
padding: 0px 0px;
}
.reveal table {
border-width: 1px;
border-spacing: 2px;
border-style: dotted;
border-color: gray;
border-collapse: collapse;
font-size: 0.7em;
}
.reveal table th {
border-width: 1px;
padding-left: 10px;
padding-right: 25px;
font-weight: bold;
border-style: dotted;
border-color: gray;
}
.reveal table td {
border-width: 1px;
padding-left: 10px;
padding-right: 25px;
border-style: dotted;
border-color: gray;
}
</style>
<style type="text/css">code{white-space: pre;}</style>
<link rel="stylesheet" href="reveal.css"/>
<!-- Printing and PDF exports -->
<script id="paper-css" type="application/dynamic-css">
/* Default Print Stylesheet Template
by Rob Glazebrook of CSSnewbie.com
Last Updated: June 4, 2008
Feel free (nay, compelled) to edit, append, and
manipulate this file as you see fit. */
@media print {
/* SECTION 1: Set default width, margin, float, and
background. This prevents elements from extending
beyond the edge of the printed page, and prevents
unnecessary background images from printing */
html {
background: #fff;
width: auto;
height: auto;
overflow: visible;
}
body {
background: #fff;
font-size: 20pt;
width: auto;
height: auto;
border: 0;
margin: 0 5%;
padding: 0;
overflow: visible;
float: none !important;
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This would include navigation, ads, sidebars, etc. */
.nestedarrow,
.controls,
.fork-reveal,
.share-reveal,
.state-background,
.reveal .progress,
.reveal .backgrounds {
display: none !important;
}
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Consider using a serif font for readability. */
body, p, td, li, div {
font-size: 20pt!important;
font-family: Georgia, "Times New Roman", Times, serif !important;
color: #000;
}
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Differentiate your headings from your body text.
Perhaps use a large sans-serif for distinction. */
h1,h2,h3,h4,h5,h6 {
color: #000!important;
height: auto;
line-height: normal;
font-family: Georgia, "Times New Roman", Times, serif !important;
text-shadow: 0 0 0 #000 !important;
text-align: left;
letter-spacing: normal;
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/* Need to reduce the size of the fonts for printing */
h1 { font-size: 28pt !important; }
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h3 { font-size: 22pt !important; }
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h5 { font-size: 21pt !important; }
h6 { font-size: 20pt !important; font-style: italic; }
/* SECTION 5: Make hyperlinks more usable.
Ensure links are underlined, and consider appending
the URL to the end of the link for usability. */
a:link,
a:visited {
color: #000 !important;
font-weight: bold;
text-decoration: underline;
}
/*
.reveal a:link:after,
.reveal a:visited:after {
content: " (" attr(href) ") ";
color: #222 !important;
font-size: 90%;
}
*/
/* SECTION 6: more reveal.js specific additions by @skypanther */
ul, ol, div, p {
visibility: visible;
position: static;
width: auto;
height: auto;
display: block;
overflow: visible;
margin: 0;
text-align: left !important;
}
.reveal pre,
.reveal table {
margin-left: 0;
margin-right: 0;
}
.reveal pre code {
padding: 20px;
border: 1px solid #ddd;
}
.reveal blockquote {
margin: 20px 0;
}
.reveal .slides {
position: static !important;
width: auto !important;
height: auto !important;
left: 0 !important;
top: 0 !important;
margin-left: 0 !important;
margin-top: 0 !important;
padding: 0 !important;
zoom: 1 !important;
overflow: visible !important;
display: block !important;
text-align: left !important;
-webkit-perspective: none;
-moz-perspective: none;
-ms-perspective: none;
perspective: none;
-webkit-perspective-origin: 50% 50%;
-moz-perspective-origin: 50% 50%;
-ms-perspective-origin: 50% 50%;
perspective-origin: 50% 50%;
}
.reveal .slides section {
visibility: visible !important;
position: static !important;
width: auto !important;
height: auto !important;
display: block !important;
overflow: visible !important;
left: 0 !important;
top: 0 !important;
margin-left: 0 !important;
margin-top: 0 !important;
padding: 60px 20px !important;
z-index: auto !important;
opacity: 1 !important;
page-break-after: always !important;
-webkit-transform-style: flat !important;
-moz-transform-style: flat !important;
-ms-transform-style: flat !important;
transform-style: flat !important;
-webkit-transform: none !important;
-moz-transform: none !important;
-ms-transform: none !important;
transform: none !important;
-webkit-transition: none !important;
-moz-transition: none !important;
-ms-transition: none !important;
transition: none !important;
}
.reveal .slides section.stack {
padding: 0 !important;
}
.reveal section:last-of-type {
page-break-after: avoid !important;
}
.reveal section .fragment {
opacity: 1 !important;
visibility: visible !important;
-webkit-transform: none !important;
-moz-transform: none !important;
-ms-transform: none !important;
transform: none !important;
}
.reveal section img {
display: block;
margin: 15px 0px;
background: rgba(255,255,255,1);
border: 1px solid #666;
box-shadow: none;
}
.reveal section small {
font-size: 0.8em;
}
}
</script>
<script id="pdf-css" type="application/dynamic-css">
/**
* This stylesheet is used to print reveal.js
* presentations to PDF.
*
* https://github.com/hakimel/reveal.js#pdf-export
*/
* {
-webkit-print-color-adjust: exact;
}
body {
margin: 0 auto !important;
border: 0;
padding: 0;
float: none !important;
overflow: visible;
}
html {
width: 100%;
height: 100%;
overflow: visible;
}
/* Remove any elements not needed in print. */
.nestedarrow,
.reveal .controls,
.reveal .progress,
.reveal .playback,
.reveal.overview,
.fork-reveal,
.share-reveal,
.state-background {
display: none !important;
}
h1, h2, h3, h4, h5, h6 {
text-shadow: 0 0 0 #000 !important;
}
.reveal pre code {
overflow: hidden !important;
font-family: Courier, 'Courier New', monospace !important;
}
ul, ol, div, p {
visibility: visible;
position: static;
width: auto;
height: auto;
display: block;
overflow: visible;
margin: auto;
}
.reveal {
width: auto !important;
height: auto !important;
overflow: hidden !important;
}
.reveal .slides {
position: static;
width: 100%;
height: auto;
left: auto;
top: auto;
margin: 0 !important;
padding: 0 !important;
overflow: visible;
display: block;
-webkit-perspective: none;
-moz-perspective: none;
-ms-perspective: none;
perspective: none;
-webkit-perspective-origin: 50% 50%; /* there isn't a none/auto value but 50-50 is the default */
-moz-perspective-origin: 50% 50%;
-ms-perspective-origin: 50% 50%;
perspective-origin: 50% 50%;
}
.reveal .slides section {
page-break-after: always !important;
visibility: visible !important;
position: relative !important;
display: block !important;
position: relative !important;
margin: 0 !important;
padding: 0 !important;
box-sizing: border-box !important;
min-height: 1px;
opacity: 1 !important;
-webkit-transform-style: flat !important;
-moz-transform-style: flat !important;
-ms-transform-style: flat !important;
transform-style: flat !important;
-webkit-transform: none !important;
-moz-transform: none !important;
-ms-transform: none !important;
transform: none !important;
}
.reveal section.stack {
margin: 0 !important;
padding: 0 !important;
page-break-after: avoid !important;
height: auto !important;
min-height: auto !important;
}
.reveal img {
box-shadow: none;
}
.reveal .roll {
overflow: visible;
line-height: 1em;
}
/* Slide backgrounds are placed inside of their slide when exporting to PDF */
.reveal section .slide-background {
display: block !important;
position: absolute;
top: 0;
left: 0;
width: 100%;
z-index: -1;
}
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.reveal section>* {
position: relative;
z-index: 1;
}
/* Display slide speaker notes when 'showNotes' is enabled */
.reveal .speaker-notes-pdf {
display: block;
width: 100%;
max-height: none;
left: auto;
top: auto;
z-index: 100;
}
/* Display slide numbers when 'slideNumber' is enabled */
.reveal .slide-number-pdf {
display: block;
position: absolute;
font-size: 14px;
}
</script>
<script>
var style = document.createElement( 'style' );
style.type = 'text/css';
var style_script_id = window.location.search.match( /print-pdf/gi ) ? 'pdf-css' : 'paper-css';
var style_script = document.getElementById(style_script_id).text;
style.innerHTML = style_script;
document.getElementsByTagName('head')[0].appendChild(style);
</script>
<link href="externals/font-awesome-5.0.13/css/fa-svg-with-js.css" rel="stylesheet" />
<script src="externals/font-awesome-5.0.13/js/fontawesome-all.min.js"></script>
<script src="externals/font-awesome-5.0.13/js/fa-v4-shims.min.js"></script>
</head>
<body>
<div class="reveal">
<div class="slides">
<section>
<h1 class="title">HELP!</h1>
</section>
<section id="got-problems" class="slide level2">
<h2>Got Problems?</h2>
<p><img data-src="https://imgs.xkcd.com/comics/error_code.png" /></p>
</section>
<section><section id="strange-errors" class="title-slide slide level1"><h1>Strange Errors</h1></section><section id="examples-from-stack-overflow" class="slide level2">
<h2>Examples from Stack Overflow</h2>
<p>This is the error messages I get…</p>
<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" data-line-number="1"><span class="op">></span><span class="st"> </span><span class="kw">setwd</span>(<span class="st">"H:/user/george"</span>)</a>
<a class="sourceLine" id="cb1-2" data-line-number="2"><span class="st">"Error: unexpected input in "</span><span class="kw">setwd</span>(<span class="st">"H:/XX/XXX"</span>)</a>
<a class="sourceLine" id="cb1-3" data-line-number="3"><span class="st">"Error: unexpected input in "</span></a>
<a class="sourceLine" id="cb1-4" data-line-number="4"><span class="op">></span><span class="st"> </span>GWS <-<span class="st"> </span><span class="kw">read.csv</span>(<span class="st">"X.csv"</span>, <span class="dt">header =</span> <span class="ot">TRUE</span>, <span class="dt">sep =</span> <span class="st">","</span>, <span class="dt">stringsAsFactors =</span></a>
<a class="sourceLine" id="cb1-5" data-line-number="5"><span class="ot">FALSE</span>, <span class="dt">na.strings=</span><span class="kw">c</span>(<span class="st">""</span>,<span class="st">""</span>,<span class="st">"NA"</span>))</a>
<a class="sourceLine" id="cb1-6" data-line-number="6"><span class="st">"Error: unexpected input in "</span>GWS <-<span class="st"> </span><span class="kw">read.csv</span>(<span class="st">"X.csv"</span>, <span class="dt">header =</span> <span class="ot">TRUE</span>, <span class="dt">sep =</span></a>
<a class="sourceLine" id="cb1-7" data-line-number="7"><span class="st">","</span>, <span class="dt">stringsAsFactors =</span> <span class="ot">FALSE</span>, <span class="dt">na.strings=</span><span class="kw">c</span>(<span class="st">""</span>,<span class="st">""</span>,<span class="st">"NA"</span>))</a>
<a class="sourceLine" id="cb1-8" data-line-number="8"><span class="op">></span><span class="st"> </span>GWS <-<span class="st"> </span>GWS[<span class="kw">with</span>(GWS, <span class="kw">order</span>(d)), ]; <span class="kw">row.names</span>(GWS) <-<span class="st"> </span><span class="ot">NULL</span></a>
<a class="sourceLine" id="cb1-9" data-line-number="9">Error<span class="op">:</span><span class="st"> </span>object <span class="st">'GWS'</span> not found</a></code></pre></div>
</section><section id="another-one" class="slide level2">
<h2>Another one</h2>
<p>“Help, I’m getting an error and I don’t know what it means”</p>
<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb2-1" data-line-number="1"><span class="op">></span><span class="st"> </span>lm1=<span class="kw">lm</span>(cr<span class="op">~</span>tn,<span class="dt">data=</span>x)</a>
<a class="sourceLine" id="cb2-2" data-line-number="2">Error <span class="cf">in</span> <span class="kw">lm.fit</span>(x, y, <span class="dt">offset =</span> offset, <span class="dt">singular.ok =</span> singular.ok, ...) <span class="op">:</span><span class="st"> </span></a>
<a class="sourceLine" id="cb2-3" data-line-number="3"><span class="st"> </span><span class="ot">NA</span><span class="op">/</span><span class="ot">NaN</span><span class="op">/</span><span class="ot">Inf</span> <span class="cf">in</span> <span class="st">'y'</span></a>
<a class="sourceLine" id="cb2-4" data-line-number="4">In addition<span class="op">:</span><span class="st"> </span>Warning message<span class="op">:</span></a>
<a class="sourceLine" id="cb2-5" data-line-number="5">In <span class="kw">storage.mode</span>(v) <-<span class="st"> "double"</span> <span class="op">:</span><span class="st"> </span>NAs introduced by coercion</a></code></pre></div>
</section></section>
<section><section id="finding-help" class="title-slide slide level1"><h1>Finding Help</h1></section><section id="basic-resources" class="slide level2">
<h2>Basic Resources</h2>
<p><a href="https://www.r-project.org/help.html">Getting Help with R</a></p>
<iframe width="100%" height="500px" src="https://www.r-project.org/help.html">
</iframe>
</section><section id="help-files" class="slide level2">
<h2>Help Files</h2>
<iframe width="100%" height="500px" src="https://www.rdocumentation.org/packages/base/versions/3.5.1/topics/mean">
</iframe>
</section><section id="vignettes" class="slide level2">
<h2>Vignettes</h2>
<p><a href="https://cran.r-project.org/web/packages/sf/index.html">sf: Simple Features for R</a></p>
<div class="embed-responsive embed-responsive">
<iframe class="embed-responsive-item" width="100%" height="500px" src="https://cran.r-project.org/web/packages/sf/index.html" allowfullscreen>
</iframe>
</div>
</section></section>
<section><section id="effective-problem-solving" class="title-slide slide level1"><h1>Effective Problem Solving</h1></section><section id="step-one-break-down-your-problem" class="slide level2">
<h2>Step one: Break down your problem</h2>
<ul>
<li>Break down your code (run bit by bit)!</li>
<li>Understand the data/inputs</li>
<li>Read the help files carefully</li>
<li>Try <code>traceback()</code></li>
</ul>
</section><section id="r-is-very-picky" class="slide level2">
<h2>R is very picky</h2>
<p>It expects you to give accurate instructions…</p>
<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" data-line-number="1">reallystrangenme <-<span class="st"> </span><span class="kw">rnorm</span>(<span class="dv">10</span>)</a>
<a class="sourceLine" id="cb3-2" data-line-number="2">anothrstrngenme <-<span class="st"> </span><span class="dv">3</span><span class="op">+</span><span class="dv">5</span><span class="op">*</span>reallystrangenme<span class="op">+</span><span class="kw">rnorm</span>(<span class="dv">10</span>)</a>
<a class="sourceLine" id="cb3-3" data-line-number="3"><span class="kw">lm</span>(reallystrngenme<span class="op">~</span>anothrstrngenme)</a></code></pre></div>
<ul>
<li class="fragment"><code># Error: object 'reallystrngenme' not found</code></li>
</ul>
</section><section id="break-down-your-code" class="slide level2">
<h2>Break down your code</h2>
<p>Run bit by bit:</p>
<p><img data-src="img/run_part.png" /></p>
</section><section id="traceback" class="slide level2">
<h2>traceback</h2>
<p>Prints the call stack of the last uncaught error, i.e., the sequence of calls that lead to the error. This is useful when an error occurs with an unidentifiable error message.</p>
<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" data-line-number="1">pets=<span class="kw">c</span>(<span class="st">"dog"</span>,<span class="st">"cat"</span>,<span class="st">"fish"</span>)</a>
<a class="sourceLine" id="cb4-2" data-line-number="2"><span class="kw">lm</span>(pets<span class="op">~</span><span class="dv">1</span><span class="op">:</span><span class="dv">5</span>)</a>
<a class="sourceLine" id="cb4-3" data-line-number="3"></a>
<a class="sourceLine" id="cb4-4" data-line-number="4">Error <span class="cf">in</span> <span class="kw">terms.formula</span>(formula, <span class="dt">data =</span> data) <span class="op">:</span></a>
<a class="sourceLine" id="cb4-5" data-line-number="5"><span class="st"> </span>invalid model formula <span class="cf">in</span> ExtractVars</a>
<a class="sourceLine" id="cb4-6" data-line-number="6"></a>
<a class="sourceLine" id="cb4-7" data-line-number="7"><span class="kw">traceback</span>()</a>
<a class="sourceLine" id="cb4-8" data-line-number="8"></a>
<a class="sourceLine" id="cb4-9" data-line-number="9"> <span class="dv">7</span><span class="op">:</span><span class="st"> </span><span class="kw">terms.formula</span>(formula, <span class="dt">data =</span> data)</a>
<a class="sourceLine" id="cb4-10" data-line-number="10"> <span class="dv">6</span><span class="op">:</span><span class="st"> </span><span class="kw">terms</span>(formula, <span class="dt">data =</span> data)</a>
<a class="sourceLine" id="cb4-11" data-line-number="11"> <span class="dv">5</span><span class="op">:</span><span class="st"> </span><span class="kw">model.frame.default</span>(<span class="dt">formula =</span> pets <span class="op">~</span><span class="st"> </span><span class="dv">1</span><span class="op">:</span><span class="dv">5</span>, <span class="dt">drop.unused.levels =</span> <span class="ot">TRUE</span>)</a>
<a class="sourceLine" id="cb4-12" data-line-number="12"> <span class="dv">4</span><span class="op">:</span><span class="st"> </span>stats<span class="op">::</span><span class="kw">model.frame</span>(<span class="dt">formula =</span> pets <span class="op">~</span><span class="st"> </span><span class="dv">1</span><span class="op">:</span><span class="dv">5</span>, <span class="dt">drop.unused.levels =</span> <span class="ot">TRUE</span>)</a>
<a class="sourceLine" id="cb4-13" data-line-number="13"> <span class="dv">3</span><span class="op">:</span><span class="st"> </span><span class="kw">eval</span>(mf, <span class="kw">parent.frame</span>())</a>
<a class="sourceLine" id="cb4-14" data-line-number="14"> <span class="dv">2</span><span class="op">:</span><span class="st"> </span><span class="kw">eval</span>(mf, <span class="kw">parent.frame</span>())</a>
<a class="sourceLine" id="cb4-15" data-line-number="15"> <span class="dv">1</span><span class="op">:</span><span class="st"> </span><span class="kw">lm</span>(pets <span class="op">~</span><span class="st"> </span><span class="dv">1</span><span class="op">:</span><span class="dv">5</span>)</a></code></pre></div>
</section></section>
<section><section id="rstudio-features-can-help" class="title-slide slide level1"><h1>RStudio features can help</h1></section><section id="tab-completion" class="slide level2">
<h2>TAB completion</h2>
<p>Hit <code>TAB</code> key after typing the first few letters.</p>
<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" data-line-number="1"><span class="kw">lm</span>(reallystrangenme<span class="op">~</span>anothrstrngenme)</a></code></pre></div>
</section><section id="find" class="slide level2">
<h2>“Find”</h2>
<p>Or use ctrl-F to ‘find’ variables with the same name. <img data-src="img/run_find.png" /></p>
</section><section id="rename-in-scope" class="slide level2">
<h2>Rename in Scope</h2>
<p>Rename all instances of a variable. Tool is context aware; changing ’m’ to ‘m1’ won’t change ‘mtcars’ to ‘m1tcars’.</p>
<p><img data-src="img/tip_rename_in_scope.gif" /></p>
</section><section id="command-history" class="slide level2">
<h2>Command History</h2>
<p>Scroll through the command history by clicking Ctrl/Cmd and ↑, then filter by typing.</p>
<p><img data-src="img/tip_console.gif" /></p>
</section><section id="history-pane" class="slide level2">
<h2>History Pane</h2>
<p>Searchable list of past commands. Commands can be written to the source pane or the console.</p>
<p><img data-src="img/tip_history.gif" /></p>
</section><section id="file-navigation" class="slide level2">
<h2>File Navigation</h2>
<p>Tab complete can find files and remove the hassle of writing out long path locations. Hit tab in between two double quotes (” “) to open a file explorer.</p>
<p><img data-src="img/tip_file_nav.gif" /></p>
</section><section id="debugging" class="slide level2">
<h2>Debugging</h2>
<p><a href="https://support.rstudio.com/hc/en-us/articles/205612627-Debugging-with-RStudio">Debugging in RStudio</a></p>
<ol type="1">
<li>Begin running the code</li>
<li>Stop the code at the point where you suspect the problem is arising, and</li>
<li>Look at and/or walk through the code, step-by-step at that point.</li>
</ol>
</section></section>
<section><section id="building-a-workflow" class="title-slide slide level1"><h1>Building a workflow</h1></section><section id="grandmas-recipe-book" class="slide level2">
<h2>Grandma’s Recipe Book</h2>
<ul>
<li class="fragment">Grandma writes the recipe for our favorite chocolate chip cookies</li>
<li class="fragment">We make a batch and they come out awful!</li>
<li class="fragment">Grandma makes another batch and they are delicious!</li>
<li class="fragment">Grandma says, “Well you didn’t add the sugar, of course you need about 2 cups of sugar!”</li>
<li class="fragment">No sugar in the recipe!</li>
<li class="fragment">Always, always, always think about the ‘flow’ of the script.</li>
</ul>
</section><section id="your-script-is-your-product" class="slide level2">
<h2>Your script is your product</h2>
</section><section id="it-worked-before-but-now-it-doesnt" class="slide level2">
<h2>“It worked before, but now it doesn’t”</h2>
<p>Possible explanations:</p>
<ul>
<li>Running commands in a different order</li>
<li>Skipping commands</li>
<li>Missing/incorrect/conflicts with packages</li>
<li>Different objects in environment (playing on the console?)</li>
</ul>
</section><section class="slide level2">
<div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb6-1" data-line-number="1"><span class="kw">library</span>(spData); <span class="kw">library</span>(rasterVis)</a>
<a class="sourceLine" id="cb6-2" data-line-number="2"><span class="kw">data</span>(elev)</a>
<a class="sourceLine" id="cb6-3" data-line-number="3"><span class="co"># change values!=20 to NA</span></a>
<a class="sourceLine" id="cb6-4" data-line-number="4">elev=<span class="kw">mask</span>(elev,<span class="dt">mask =</span> elev<span class="op">==</span><span class="dv">20</span>, <span class="dt">maskvalue=</span><span class="dv">0</span>) </a>
<a class="sourceLine" id="cb6-5" data-line-number="5"><span class="kw">gplot</span>(elev)<span class="op">+</span><span class="kw">geom_raster</span>(<span class="kw">aes</span>(<span class="dt">fill=</span>value))</a></code></pre></div>
<p><img data-src="day_12_help_files/figure-revealjs/unnamed-chunk-8-1.png" /></p>
<div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb7-1" data-line-number="1">distance_to_<span class="dv">20</span>=<span class="kw">distance</span>(elev) <span class="co">#works fine</span></a>
<a class="sourceLine" id="cb7-2" data-line-number="2"><span class="kw">data</span>(elev)</a>
<a class="sourceLine" id="cb7-3" data-line-number="3"><span class="kw">gplot</span>(distance_to_<span class="dv">20</span>)<span class="op">+</span><span class="st"> </span><span class="kw">geom_raster</span>(<span class="kw">aes</span>(<span class="dt">fill=</span>value))</a></code></pre></div>
<p><img data-src="day_12_help_files/figure-revealjs/unnamed-chunk-8-2.png" /></p>
<div class="sourceCode" id="cb8"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb8-1" data-line-number="1">distance_to_<span class="dv">20</span>=<span class="kw">distance</span>(elev) <span class="co">#returns an error:</span></a>
<a class="sourceLine" id="cb8-2" data-line-number="2">Error <span class="cf">in</span> <span class="kw">.local</span>(x, y, ...) <span class="op">:</span><span class="st"> </span></a>
<a class="sourceLine" id="cb8-3" data-line-number="3">RasterLayer has no <span class="ot">NA</span> <span class="kw">cells</span> (<span class="cf">for</span> which to compute a distance)</a></code></pre></div>
</section><section id="goals-while-coding" class="slide level2">
<h2>Goals while coding</h2>
<ol type="1">
<li>Figure out how to complete your task</li>
<li>Build the script that will do it again (and again)</li>
</ol>
</section><section id="suggestions-for-building-clean-scripts" class="slide level2">
<h2>Suggestions for building clean scripts</h2>
<ol type="1">
<li>Try to keep your script ‘clean’ - it should always run from beginning to end</li>
<li>Comment exploratory lines such as <code>View(iris)</code>, <code>str(iris)</code>, etc.</li>
</ol>
<div class="sourceCode" id="cb9"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb9-1" data-line-number="1"><span class="co"># str(iris)</span></a></code></pre></div>
<ol start="3" type="1">
<li>If you want a little playground, try</li>
</ol>
<div class="sourceCode" id="cb10"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb10-1" data-line-number="1"><span class="cf">if</span>(F){</a>
<a class="sourceLine" id="cb10-2" data-line-number="2"><span class="kw">View</span>(iris)</a>
<a class="sourceLine" id="cb10-3" data-line-number="3"><span class="kw">str</span>(iris)</a>
<a class="sourceLine" id="cb10-4" data-line-number="4"><span class="co"># Whatever you want</span></a>
<a class="sourceLine" id="cb10-5" data-line-number="5">}</a></code></pre></div>
<ol start="4" type="1">
<li>Use the console (lower left) for testing, quick plots, temporary things.</li>
<li>Never do something important in the console without putting it in the script.</li>
</ol>
</section></section>
<section><section id="asking-for-help" class="title-slide slide level1"><h1>Asking for help</h1></section><section id="rs-community" class="slide level2">
<h2>R’s Community</h2>
<p>R has a large and generous community of users, help them help you.</p>
</section><section id="issue-posted-on-tidyrs-github-page" class="slide level2">
<h2>“Issue” posted on tidyr’s github page:</h2>
<p><a href="https://github.com/tidyverse/tidyr/issues/297">Separate() causes R to crash with fatal error</a> I have 11 primary variables, each one appears in the dataset in 72 columns: once for each month, for 6 years. Each variable name ends in “.YYYY_M”, where YYYY is a 4-digit year and M is month.</p>
<div class="sourceCode" id="cb11"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb11-1" data-line-number="1"><span class="op">></span><span class="st"> </span>vnms <-<span class="st"> </span><span class="kw">names</span>(outs_TN_wide)</a>
<a class="sourceLine" id="cb11-2" data-line-number="2"><span class="op">></span><span class="st"> </span>vars_tv <-<span class="st"> </span><span class="kw">grepl</span>(<span class="st">"20[01]</span><span class="ch">\\</span><span class="st">d"</span>, vnms)</a>
<a class="sourceLine" id="cb11-3" data-line-number="3"></a>
<a class="sourceLine" id="cb11-4" data-line-number="4"><span class="op">></span><span class="st"> </span>outs_TN_long <-<span class="st"> </span>outs_TN_wide <span class="op">%>%</span></a>
<a class="sourceLine" id="cb11-5" data-line-number="5"><span class="st"> </span><span class="kw">gather</span>(Variable, Value, <span class="kw">one_of</span>(vnms[vars_tv])) <span class="op">%>%</span></a>
<a class="sourceLine" id="cb11-6" data-line-number="6"><span class="st"> </span><span class="kw">separate</span>(Variable, <span class="kw">c</span>(<span class="st">"Variable"</span>, <span class="st">"Time"</span>), <span class="dt">sep =</span> <span class="st">"</span><span class="ch">\\</span><span class="st">."</span>)</a>
<a class="sourceLine" id="cb11-7" data-line-number="7"></a>
<a class="sourceLine" id="cb11-8" data-line-number="8">R encountered a fatal error.<span class="op">/</span>The session was terminated.</a></code></pre></div>
</section><section id="jun-23-2017-hadley-replies" class="slide level2">
<h2>Jun 23, 2017 <span class="citation" data-cites="hadley">@hadley</span> replies</h2>
<p>“Can you please provide a minimal reprex (reproducible example)? The goal of a reprex is to make it as easy as possible for me to recreate your problem so that I can fix it: please help me help you! If you’ve never heard of a reprex before, start by reading <a href="http://reprex.tidyverse.org/articles/reprex.html">"What is a reprex"</a>…”</p>
<p><img data-src="https://nypdecider.files.wordpress.com/2014/08/help-me-help-you.gif" /></p>
</section><section id="nov-14-2017-hadley-closes-this-issue" class="slide level2">
<h2>Nov 14, 2017 <span class="citation" data-cites="hadley">@hadley</span> closes this issue</h2>
<p>I’ve closed this issue due to lack of requested reprex. If you still care about this bug, please open a new issue with a reprex.</p>
<h3 id="the-more-helpful-you-are-the-more-likely-you-will-get-help.">The more helpful you are, the more likely you will get help.</h3>
</section><section id="build-a-reproducible-example-reprex" class="slide level2">
<h2>Build a Reproducible Example (REPREX)</h2>
<p>Break the problem down to the simplest possible illustation (preferably using built-in datasets).</p>
</section><section id="reprex-package" class="slide level2">
<h2>REPREX package</h2>
<p>Write a bit of code and copy it to the clipboard:</p>
<div class="sourceCode" id="cb12"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb12-1" data-line-number="1">(y <-<span class="st"> </span><span class="dv">1</span><span class="op">:</span><span class="dv">4</span>)</a>
<a class="sourceLine" id="cb12-2" data-line-number="2"><span class="kw">mean</span>(y)</a></code></pre></div>
<p>Type <code>reprex()</code> in the R Console. In RStudio, you’ll see a preview of your rendered reprex:</p>
<div class="sourceCode" id="cb13"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb13-1" data-line-number="1">(y <-<span class="st"> </span><span class="dv">1</span><span class="op">:</span><span class="dv">4</span>)</a>
<a class="sourceLine" id="cb13-2" data-line-number="2"><span class="co">#> [1] 1 2 3 4</span></a>
<a class="sourceLine" id="cb13-3" data-line-number="3"><span class="kw">mean</span>(y)</a>
<a class="sourceLine" id="cb13-4" data-line-number="4"><span class="co">#> [1] 2.5</span></a></code></pre></div>
<p>Paste it into GitHub issue, StackOverflow, email, etc.</p>
</section><section id="this-is-a-lot-of-work" class="slide level2">
<h2>This is a lot of work!</h2>
<p>Yes! You are asking other people to do work too. It’s a partnership.</p>
<ul>
<li>You will often solve your own problem while developing the reprex!</li>
<li>If you don’t, you will create a reprex that will help others help you!</li>
</ul>
</section><section id="general-questions-stack-overflow" class="slide level2">
<h2>General Questions: Stack Overflow</h2>
<p><a href="https://stackoverflow.com/questions/tagged/r">R topics</a></p>
</section><section id="specific-bug-feature-request" class="slide level2">
<h2>Specific Bug / Feature Request</h2>
<p>Github “Issues” <a href="https://github.com/tidyverse/tidyr/issues" class="uri">https://github.com/tidyverse/tidyr/issues</a></p>
</section></section>
</div>
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68: function() { RevealChalkboard.download() }, // downlad recorded chalkboard drawing when 'd' is pressed
},
// Optional reveal.js plugins
dependencies: [
{ src: 'externals/reveal.js-3.3.0.1/plugin/search/search.js', async: true },
{ src: 'externals/reveal.js-3.3.0.1/plugin/zoom-js/zoom.js', async: true },
{ src: 'externals/reveal.js-3.3.0.1/plugin/chalkboard/chalkboard.js', async: true },
]
});
</script>
<!-- dynamically load mathjax for compatibility with self-contained -->
<script>
(function () {
var script = document.createElement("script");
script.type = "text/javascript";
script.src = "https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML";
document.getElementsByTagName("head")[0].appendChild(script);
})();
</script>
<script>
(function() {
if (window.jQuery) {
Reveal.addEventListener( 'slidechanged', function(event) {
window.jQuery(event.previousSlide).trigger('hidden');
window.jQuery(event.currentSlide).trigger('shown');
});
}
})();
</script>
</body>
</html>