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<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8">
<title>Bonus Slides: Making pretty regression tables with pipes</title>
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<meta name="viewport" content="width=device-width, initial-scale=1.0, maximum-scale=1.0, user-scalable=no" />
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0;transform-origin:0 0;-webkit-transform:translate3d(0,100%,0) rotateX(-90deg);-moz-transform:translate3d(0,100%,0) rotateX(-90deg);-ms-transform:translate3d(0,100%,0) rotateX(-90deg);transform:translate3d(0,100%,0) rotateX(-90deg)}.reveal.page .slides{-webkit-perspective-origin:0 50%;-moz-perspective-origin:0 50%;-ms-perspective-origin:0 50%;perspective-origin:0 50%;-webkit-perspective:3000px;-moz-perspective:3000px;-ms-perspective:3000px;perspective:3000px}.reveal.page .slides section{padding:30px;min-height:700px;-webkit-box-sizing:border-box;-moz-box-sizing:border-box;box-sizing:border-box}.reveal.page .slides section.past{z-index:12}.reveal.page .slides section:not(.stack):before{content:'';position:absolute;display:block;width:100%;height:100%;left:0;top:0;background:rgba(0,0,0,.1);-webkit-transform:translateZ(-20px);-moz-transform:translateZ(-20px);-ms-transform:translateZ(-20px);-o-transform:translateZ(-20px);transform:translateZ(-20px)}.reveal.page .slides section:not(.stack):after{content:'';position:absolute;display:block;width:90%;height:30px;left:5%;bottom:0;background:0;z-index:1;border-radius:4px;box-shadow:0 95px 25px rgba(0,0,0,.2);-webkit-transform:translateZ(-90px) rotateX(65deg)}.reveal.page .slides>section.stack{padding:0;background:0}.reveal.page .slides>section.past{-webkit-transform-origin:0 0;-moz-transform-origin:0 0;-ms-transform-origin:0 0;transform-origin:0 0;-webkit-transform:translate3d(-40%,0,0) rotateY(-80deg);-moz-transform:translate3d(-40%,0,0) rotateY(-80deg);-ms-transform:translate3d(-40%,0,0) rotateY(-80deg);transform:translate3d(-40%,0,0) rotateY(-80deg)}.reveal.page .slides>section.future{-webkit-transform-origin:100% 0;-moz-transform-origin:100% 0;-ms-transform-origin:100% 0;transform-origin:100% 0;-webkit-transform:translate3d(0,0,0);-moz-transform:translate3d(0,0,0);-ms-transform:translate3d(0,0,0);transform:translate3d(0,0,0)}.reveal.page .slides>section>section.past{-webkit-transform-origin:0 0;-moz-transform-origin:0 0;-ms-transform-origin:0 0;transform-origin:0 0;-webkit-transform:translate3d(0,-40%,0) rotateX(80deg);-moz-transform:translate3d(0,-40%,0) rotateX(80deg);-ms-transform:translate3d(0,-40%,0) rotateX(80deg);transform:translate3d(0,-40%,0) rotateX(80deg)}.reveal.page .slides>section>section.future{-webkit-transform-origin:0 100%;-moz-transform-origin:0 100%;-ms-transform-origin:0 100%;transform-origin:0 100%;-webkit-transform:translate3d(0,0,0);-moz-transform:translate3d(0,0,0);-ms-transform:translate3d(0,0,0);transform:translate3d(0,0,0)}.reveal .slides section[data-transition=fade],.reveal.fade .slides section,.reveal.fade .slides>section>section{-webkit-transform:none;-moz-transform:none;-ms-transform:none;-o-transform:none;transform:none;-webkit-transition:opacity .5s;-moz-transition:opacity .5s;-ms-transition:opacity .5s;-o-transition:opacity .5s;transition:opacity .5s}.reveal.fade.overview .slides section,.reveal.fade.overview 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section:before{display:none!important}.reveal.overview .slides section>section{opacity:1;cursor:pointer}.reveal.overview .slides section:hover{background:rgba(0,0,0,.3)}.reveal.overview .slides section.present{background:rgba(0,0,0,.3)}.reveal.overview .slides>section.stack{padding:0;background:0;overflow:visible}.reveal .pause-overlay{position:absolute;top:0;left:0;width:100%;height:100%;background:#000;visibility:hidden;opacity:0;z-index:100;-webkit-transition:all 1s ease;-moz-transition:all 1s ease;-ms-transition:all 1s ease;-o-transition:all 1s ease;transition:all 1s ease}.reveal.paused .pause-overlay{visibility:visible;opacity:1}.no-transforms{overflow-y:auto}.no-transforms .reveal .slides{position:relative;width:80%;height:auto!important;top:0;left:50%;margin:0;text-align:center}.no-transforms .reveal .controls,.no-transforms .reveal .progress{display:none!important}.no-transforms .reveal .slides section{display:block!important;opacity:1!important;position:relative!important;height:auto;min-height:auto;top:0;left:-50%;margin:70px 0;-webkit-transform:none;-moz-transform:none;-ms-transform:none;-o-transform:none;transform:none}.no-transforms .reveal .slides section section{left:0}.no-transition{-webkit-transition:none;-moz-transition:none;-ms-transition:none;-o-transition:none;transition:none}.reveal .state-background{position:absolute;width:100%;height:100%;background:rgba(0,0,0,0);-webkit-transition:background 800ms ease;-moz-transition:background 800ms ease;-ms-transition:background 800ms ease;-o-transition:background 800ms ease;transition:background 800ms ease}.alert .reveal .state-background{background:rgba(200,50,30,.6)}.soothe .reveal .state-background{background:rgba(50,200,90,.4)}.blackout .reveal .state-background{background:rgba(0,0,0,.6)}.whiteout .reveal .state-background{background:rgba(255,255,255,.6)}.cobalt .reveal .state-background{background:rgba(22,152,213,.6)}.mint .reveal .state-background{background:rgba(22,213,75,.6)}.submerge .reveal .state-background{background:rgba(12,25,77,.6)}.lila .reveal .state-background{background:rgba(180,50,140,.6)}.sunset .reveal .state-background{background:rgba(255,122,0,.6)}.reveal.rtl .slides,.reveal.rtl .slides h1,.reveal.rtl .slides h2,.reveal.rtl .slides h3,.reveal.rtl .slides h4,.reveal.rtl .slides h5,.reveal.rtl .slides h6{direction:rtl;font-family:sans-serif}.reveal.rtl pre,.reveal.rtl code{direction:ltr}.reveal.rtl ol,.reveal.rtl ul{text-align:right}.reveal.rtl .progress span{float:right}.reveal aside.notes{display:none}.zoomed .reveal *,.zoomed .reveal :before,.zoomed .reveal :after{-webkit-transform:none!important;-moz-transform:none!important;-ms-transform:none!important;transform:none!important;-webkit-backface-visibility:visible!important;-moz-backface-visibility:visible!important;-ms-backface-visibility:visible!important;backface-visibility:visible!important}.zoomed .reveal .progress,.zoomed .reveal .controls{opacity:0}.zoomed .reveal .roll span{background:0}.zoomed .reveal .roll span:after{visibility:hidden}
</style>
<style type="text/css" >
/**
* A simple theme for reveal.js presentations, similar
* to the default theme. The accent color is darkblue.
*
* This theme is Copyright (C) 2012 Owen Versteeg, https://github.com/StereotypicalApps. It is MIT licensed.
* reveal.js is Copyright (C) 2011-2012 Hakim El Hattab, http://hakim.se
*/
/*********************************************
* GLOBAL STYLES
*********************************************/
body {
background: white;
background-color: white; }
.reveal {
font-family: "Lato", sans-serif;
font-size: 36px;
font-weight: 200;
letter-spacing: -0.02em;
color: black; }
::selection {
color: white;
background: rgba(0, 0, 0, 0.99);
text-shadow: none; }
/*********************************************
* HEADERS
*********************************************/
.reveal h1,
.reveal h2,
.reveal h3,
.reveal h4,
.reveal h5,
.reveal h6 {
margin: 0 0 20px 0;
color: black;
font-family: "News Cycle", Impact, sans-serif;
line-height: 0.9em;
letter-spacing: 0.02em;
text-transform: none;
text-shadow: none; }
.reveal h1 {
text-shadow: 0px 0px 6px rgba(0, 0, 0, 0.2); }
/*********************************************
* LINKS
*********************************************/
.reveal a:not(.image) {
color: darkblue;
text-decoration: none;
-webkit-transition: color .15s ease;
-moz-transition: color .15s ease;
-ms-transition: color .15s ease;
-o-transition: color .15s ease;
transition: color .15s ease; }
.reveal a:not(.image):hover {
color: #0000f1;
text-shadow: none;
border: none; }
.reveal .roll span:after {
color: #fff;
background: #00003f; }
/*********************************************
* IMAGES
*********************************************/
.reveal section img {
margin: 15px 0px;
background: rgba(255, 255, 255, 0.12);
border: 4px solid black;
box-shadow: 0 0 10px rgba(0, 0, 0, 0.15);
-webkit-transition: all .2s linear;
-moz-transition: all .2s linear;
-ms-transition: all .2s linear;
-o-transition: all .2s linear;
transition: all .2s linear; }
.reveal a:hover img {
background: rgba(255, 255, 255, 0.2);
border-color: darkblue;
box-shadow: 0 0 20px rgba(0, 0, 0, 0.55); }
/*********************************************
* NAVIGATION CONTROLS
*********************************************/
.reveal .controls div.navigate-left,
.reveal .controls div.navigate-left.enabled {
border-right-color: darkblue; }
.reveal .controls div.navigate-right,
.reveal .controls div.navigate-right.enabled {
border-left-color: darkblue; }
.reveal .controls div.navigate-up,
.reveal .controls div.navigate-up.enabled {
border-bottom-color: darkblue; }
.reveal .controls div.navigate-down,
.reveal .controls div.navigate-down.enabled {
border-top-color: darkblue; }
.reveal .controls div.navigate-left.enabled:hover {
border-right-color: #0000f1; }
.reveal .controls div.navigate-right.enabled:hover {
border-left-color: #0000f1; }
.reveal .controls div.navigate-up.enabled:hover {
border-bottom-color: #0000f1; }
.reveal .controls div.navigate-down.enabled:hover {
border-top-color: #0000f1; }
/*********************************************
* PROGRESS BAR
*********************************************/
.reveal .progress {
background: rgba(0, 0, 0, 0.2); }
.reveal .progress span {
background: darkblue;
-webkit-transition: width 800ms cubic-bezier(0.26, 0.86, 0.44, 0.985);
-moz-transition: width 800ms cubic-bezier(0.26, 0.86, 0.44, 0.985);
-ms-transition: width 800ms cubic-bezier(0.26, 0.86, 0.44, 0.985);
-o-transition: width 800ms cubic-bezier(0.26, 0.86, 0.44, 0.985);
transition: width 800ms cubic-bezier(0.26, 0.86, 0.44, 0.985); }
</style>
<style type="text/css">
.reveal h1 {
font-size: 2.5em;
}
.reveal h1,
.reveal h2,
.reveal h3,
.reveal h4,
.reveal h5,
.reveal h6 {
margin-bottom: .6em;
}
.reveal p,
.reveal table {
margin-bottom: 1em;
}
.reveal li {
margin-bottom: .4em;
}
.reveal ul ul,
.reveal ul ol,
.reveal ol ol,
.reveal ol ul {
margin-top: .4em;
}
.reveal .slides {
text-align: left;
}
.reveal small {
font-size: 0.85em;
}
.reveal pre {
margin-top: 0;
max-width: 95%;
border: 1px solid #ccc;
white-space: pre-wrap;
margin-bottom: 1em;
}
.reveal pre code {
display: block; padding: 0.5em;
font-size: 1.6em;
line-height: 1.1em;
background-color: white;
overflow: visible;
max-height: none;
word-wrap: normal;
}
.reveal code {
overflow: visible;
max-height: none;
}
.reveal code.r {
background-color: #F8F8F8;
}
.reveal code.cpp {
background-color: #F8F8F8;
}
.reveal section del {
text-decoration: none;
color: #AAB1BA;
}
.reveal section img {
border: none;
}
.reveal section .fieldError {
margin-bottom: 25px;
}
.reveal section .fieldError span {
color: red;
}
.prompt .reveal .state-background {
background: #C6D7DC;
}
.quiz-multichoice .reveal .state-background {
background: rgba(254,220,179,1);
}
.quiz-multichoice .reveal ul {
list-style-type: none;
margin-bottom: 30px;
}
.quiz-multichoice .reveal li {
margin-top: 15px;
}
.quiz-multichoice .reveal .quizFeedback {
margin-bottom: 30px;
}
.quiz-multichoice .reveal .quizFeedback img {
border: none;
box-shadow: none;
background: transparent;
float: left;
margin-top: -15px;
}
.quiz-multichoice .reveal .quizFeedback span {
font-size: 1.4em;
margin-left: 12px;
}
.section .reveal .state-background {
background: #96A2B6;
}
.section .reveal h1,
.section .reveal h2,
.section .reveal p {
color: white;
margin-top: 50px;
}
.sub-section .reveal .state-background {
background: #E7E8EA
}
.sub-section .reveal h2,
.sub-section .reveal p {
color: #63717B;
margin-top: 50px;
}
.reveal strong {
color: #25679E;
}
.reveal .controls {
right: -20px;
bottom: 5px;
}
.reveal .controls div.navigate-left {
top: 75px;
}
.reveal .controls div.navigate-right {
left: 54px;
top: 75px;
}
.reveal .controls div.navigate-up {
display: none;
}
.reveal .controls div.navigate-down {
display: none;
}
/*********************************************
* NAVIGATION CONTROLS
*********************************************/
.reveal .controls div.navigate-left,
.reveal .controls div.navigate-left.enabled {
border-right-color: #25679E;
}
.reveal .controls div.navigate-right,
.reveal .controls div.navigate-right.enabled {
border-left-color: #25679E;
}
.reveal .controls div.navigate-up,
.reveal .controls div.navigate-up.enabled {
border-bottom-color: #25679E;
}
.reveal .controls div.navigate-down,
.reveal .controls div.navigate-down.enabled {
border-top-color: #25679E;
}
.reveal .controls div.navigate-left.enabled:hover {
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<h1>Bonus Slides: Making pretty regression tables with pipes</h1><p>Tristan Mahr, @tjmahr<br/>March 18, 2015</p>
<div class="slideContent" >
<p>Madison R Users Group</p>
<p>Repository for this talk: <a href="https://github.com/tjmahr/MadR_Pipelines">https://github.com/tjmahr/MadR_Pipelines</a></p>
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<h3>Plan</h3>
<div class="slideContent" >
<p>Earlier, I <a href="http://rpubs.com/tjmahr/pipelines_2015">covered pipelines</a>.</p>
<p>Then, I <a href="http://rpubs.com/tjmahr/dplyr_2015">used pipelines with dplyr</a>.</p>
<p>Now, I will demonstrate off how I use pipelines to make
pretty-printed regression tables.</p>
<pre><code class="r">library("magrittr")
library("dplyr")
library("broom")
library("stringr")
library("knitr")
</code></pre>
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<section data-transition="linear" data-transition-speed="default">
<div class="slideContent noTitle" >
<p>I want to print a regression summary table.</p>
<pre><code class="r">model <- lm(Sepal.Length ~ Sepal.Width, iris)
summary(model)
</code></pre>
<pre><code>
Call:
lm(formula = Sepal.Length ~ Sepal.Width, data = iris)
Residuals:
Min 1Q Median 3Q Max
-1.5561 -0.6333 -0.1120 0.5579 2.2226
Coefficients:
Estimate Std. Error t value
(Intercept) 6.5262 0.4789 13.63
Sepal.Width -0.2234 0.1551 -1.44
Pr(>|t|)
(Intercept) <2e-16 ***
Sepal.Width 0.152
---
Signif. codes:
0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
Residual standard error: 0.8251 on 148 degrees of freedom
Multiple R-squared: 0.01382, Adjusted R-squared: 0.007159
F-statistic: 2.074 on 1 and 148 DF, p-value: 0.1519
</code></pre>
</div>
</section>
<section data-transition="linear" data-transition-speed="default">
<h3>broom::tidy</h3>
<div class="slideContent" >
<p><code>broom</code>'s <code>tidy</code> function extracts summary values into a data-frame.</p>
<pre><code class="r">m_table <- tidy(model)
m_table %>% print(digits = 3)
</code></pre>
<pre><code> term estimate std.error statistic
1 (Intercept) 6.526 0.479 13.63
2 Sepal.Width -0.223 0.155 -1.44
p.value
1 6.47e-28
2 1.52e-01
</code></pre>
</div>
</section>
<section data-transition="linear" data-transition-speed="default">
<h3>knitr::kable</h3>
<div class="slideContent" >
<p><code>knitr</code>'s <code>kable</code> function prints a data-frame as a Markdown table,
which rmarkdown/pandoc can convert to HTML or Word.</p>
<pre><code class="r">kable(m_table, digits = 3,
col.names = c("Param", "B", "SE", "t", "p"))
</code></pre>
<p>Raw Markdown output</p>
<pre><code>
|Param | B| SE| t| p|
|:-----------|------:|-----:|------:|-----:|
|(Intercept) | 6.526| 0.479| 13.628| 0.000|
|Sepal.Width | -0.223| 0.155| -1.440| 0.152|
</code></pre>
</div>
</section>
<section data-transition="linear" data-transition-speed="default">
<div class="slideContent noTitle" >
<p>Which renders as:</p>
<pre><code class="r">kable(m_table, digits = 3,
col.names = c("Param", "B", "SE", "t", "p"))
</code></pre>
<table><thead>
<tr>
<th align="left">Param</th>
<th align="right">B</th>
<th align="right">SE</th>
<th align="right">t</th>
<th align="right">p</th>
</tr>
</thead><tbody>
<tr>
<td align="left">(Intercept)</td>
<td align="right">6.526</td>
<td align="right">0.479</td>
<td align="right">13.628</td>
<td align="right">0.000</td>
</tr>
<tr>
<td align="left">Sepal.Width</td>
<td align="right">-0.223</td>
<td align="right">0.155</td>
<td align="right">-1.440</td>
<td align="right">0.152</td>
</tr>
</tbody></table>
</div>
</section>
<section data-transition="linear" data-transition-speed="default">
<h3>Almost there</h3>
<div class="slideContent" >
<p>Two more things that I want.</p>
<ol>
<li class="fragment">APA style for printing numbers
<ul>
<li class="fragment">Two digits of precision for estimates, errors and statistics.</li>
<li class="fragment">Three digits for p-values.</li>
<li class="fragment">Bounded values (correlations, p-values) don't need leading zero.</li>
<li class="fragment">Tiny p-values should not be 0.000. Use <code>< .001</code> instead.</li>
</ul></li>
<li class="fragment">Flexibility for many related models. (I don't know the
final in-text model beforehand.)</li>
</ol>
</div>
</section>
<section data-transition="linear" data-transition-speed="default">
<h3>Approach</h3>
<div class="slideContent" >
<ul>
<li class="fragment">Build a set of generic, reusable functions for formatting numbers.</li>
<li class="fragment">Make a custom pipeline to format the <code>term</code> column.</li>
<li class="fragment">Assemble a pipeline to convert a model into a pretty table.</li>
</ul>
</div>
</section>
<section data-transition="linear" data-transition-speed="default">
<h3>Digit Formatters</h3>
<div class="slideContent" >
<p>The <code>formatC</code> function is big and confusing, but after I
figured out something that works well enough, I extracted a
function. Now I don't have to worry about solving that
problem again.</p>
<pre><code class="r"># Print with n digits of precision
fixed_digits <- function(xs, n = 2) {
formatC(xs, digits = n, format = "f")
}
# Want .100 to print with two digits
c(1000.012, 0.0001, 0.100) %>% fixed_digits(2)
</code></pre>
<pre><code>[1] "1000.01" "0.00" "0.10"
</code></pre>
</div>
</section>
<section data-transition="linear" data-transition-speed="default">
<h3>Remove leading zeros</h3>
<div class="slideContent" >
<p>Here I do a sanity check to see if this operation is necessary.</p>
<pre><code class="r"># Don't print leading zero on bounded numbers.
remove_leading_zero <- function(xs) {
# Problem if any value is greater than 1.0
digit_matters <- xs %>% as.numeric %>%
abs %>% is_greater_than(1)
if (any(digit_matters)) {
warning("Non-zero leading digit")
}
str_replace(xs, "^(-?)0", "\\1")
}
c(1.00, -0.12, 0.87, 0.82) %>% remove_leading_zero
</code></pre>
<pre><code>[1] "1" "-.12" ".87" ".82"
</code></pre>
</div>
</section>
<section data-transition="linear" data-transition-speed="default">
<h3>p-value formatter</h3>
<div class="slideContent" >
<p>I format p-values with the previous two functions and overwrite the
really small ones with the <code>< .001</code> template.</p>
<pre><code class="r"># Print three digits of a p-value, but use
# the "< .001" notation on tiny values.
format_pval <- function(ps, html = FALSE) {
tiny <- ifelse(html, "&lt;&nbsp;.001", "< .001")
ps_chr <- ps %>% fixed_digits(3) %>%
remove_leading_zero
ps_chr[ps < 0.001] <- tiny
ps_chr