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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" />
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<title>Example of a Report made in Rmarkdown</title>
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<a class="navbar-brand" href="index.html">Basic R courses for FOOD UCPH</a>
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BASICs
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RePro
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<a href="RePro_report.html">An example of a report</a>
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<a href="RePro_presentation.html">An example of a presentation</a>
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<a href="https://github.com/mortenarendt/basicR4FOOD/tree/master/data">Data</a>
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<h1 class="title toc-ignore">Example of a Report made in Rmarkdown</h1>
<h4 class="author"><em>Morten Rasmussen</em></h4>
<h4 class="date"><em>February 19 - 2019</em></h4>
</div>
<div id="TOC">
<ul>
<li><a href="#setting-libraries">Setting libraries</a></li>
<li><a href="#importing-data">Importing Data</a><ul>
<li><a href="#relative-to-current-location">Relative to current location</a></li>
<li><a href="#when-the-data-is-in-the-same-folder">When the data is in the same folder</a></li>
<li><a href="#hard-coded-from-the-root-of-the-pc">Hard coded from the root of the PC</a></li>
</ul></li>
<li><a href="#a-table-of-data">A table of data</a></li>
<li><a href="#a-nice-plot">A nice Plot</a></li>
<li><a href="#anova-of-the-aromas">ANOVA of the aromas</a></li>
<li><a href="#toc-level-1">TOC level 1</a><ul>
<li><a href="#toc-level-2">TOC level 2</a><ul>
<li><a href="#toc-level-3">TOC level 3</a><ul>
<li><a href="#toc-level-4">TOC level 4</a><ul>
<li><a href="#toc-level-5">TOC level 5</a></li>
</ul></li>
</ul></li>
</ul></li>
</ul></li>
</ul>
</div>
<div id="setting-libraries" class="section level1">
<h1>Setting libraries</h1>
<pre class="r"><code>library(rio)
library(ggplot2)</code></pre>
</div>
<div id="importing-data" class="section level1">
<h1>Importing Data</h1>
<p>First we import data. this can be done in three ways.</p>
<div id="relative-to-current-location" class="section level2">
<h2>Relative to current location</h2>
<pre class="r"><code>X <- import('../BASICs/data/cheese_aromas.xlsx')</code></pre>
</div>
<div id="when-the-data-is-in-the-same-folder" class="section level2">
<h2>When the data is in the same folder</h2>
<pre class="r"><code>X <- import('cheese_aromas.xlsx')</code></pre>
</div>
<div id="hard-coded-from-the-root-of-the-pc" class="section level2">
<h2>Hard coded from the root of the PC</h2>
<pre class="r"><code>X <- import('~/Dropbox/Backup/MyDocumentsOnC/Course and teaching/FOOD_Rcourses/BASICs/data/cheese_aromas.xlsx')</code></pre>
</div>
</div>
<div id="a-table-of-data" class="section level1">
<h1>A table of data</h1>
<p>If we want nice tables in the report, then the two packages knirt and kableExtra is very useful.</p>
<pre class="r"><code>library(knitr)
library(kableExtra)
df <- head(X[,1:4],20)
kable(df,digits = 1, caption = 'Some caption for my nice table')</code></pre>
<table>
<caption>
Some caption for my nice table
</caption>
<thead>
<tr>
<th style="text-align:left;">
maturation_culture
</th>
<th style="text-align:right;">
time_weeks
</th>
<th style="text-align:left;">
time_culture
</th>
<th style="text-align:right;">
1Butanol
</th>
</tr>
</thead>
<tbody>
<tr>
<td style="text-align:left;">
culture
</td>
<td style="text-align:right;">
4
</td>
<td style="text-align:left;">
04uger_culture
</td>
<td style="text-align:right;">
7.5
</td>
</tr>
<tr>
<td style="text-align:left;">
culture
</td>
<td style="text-align:right;">
4
</td>
<td style="text-align:left;">
04uger_culture
</td>
<td style="text-align:right;">
7.5
</td>
</tr>
<tr>
<td style="text-align:left;">
culture
</td>
<td style="text-align:right;">
4
</td>
<td style="text-align:left;">
04uger_culture
</td>
<td style="text-align:right;">
7.6
</td>
</tr>
<tr>
<td style="text-align:left;">
culture
</td>
<td style="text-align:right;">
4
</td>
<td style="text-align:left;">
04uger_culture
</td>
<td style="text-align:right;">
7.6
</td>
</tr>
<tr>
<td style="text-align:left;">
none
</td>
<td style="text-align:right;">
4
</td>
<td style="text-align:left;">
04uger_none
</td>
<td style="text-align:right;">
7.6
</td>
</tr>
<tr>
<td style="text-align:left;">
none
</td>
<td style="text-align:right;">
4
</td>
<td style="text-align:left;">
04uger_none
</td>
<td style="text-align:right;">
7.6
</td>
</tr>
<tr>
<td style="text-align:left;">
none
</td>
<td style="text-align:right;">
4
</td>
<td style="text-align:left;">
04uger_none
</td>
<td style="text-align:right;">
7.5
</td>
</tr>
<tr>
<td style="text-align:left;">
none
</td>
<td style="text-align:right;">
7
</td>
<td style="text-align:left;">
07uger_none
</td>
<td style="text-align:right;">
7.7
</td>
</tr>
<tr>
<td style="text-align:left;">
none
</td>
<td style="text-align:right;">
7
</td>
<td style="text-align:left;">
07uger_none
</td>
<td style="text-align:right;">
7.8
</td>
</tr>
<tr>
<td style="text-align:left;">
none
</td>
<td style="text-align:right;">
7
</td>
<td style="text-align:left;">
07uger_none
</td>
<td style="text-align:right;">
7.7
</td>
</tr>
<tr>
<td style="text-align:left;">
culture
</td>
<td style="text-align:right;">
7
</td>
<td style="text-align:left;">
07uger_culture
</td>
<td style="text-align:right;">
7.4
</td>
</tr>
<tr>
<td style="text-align:left;">
culture
</td>
<td style="text-align:right;">
7
</td>
<td style="text-align:left;">
07uger_culture
</td>
<td style="text-align:right;">
7.3
</td>
</tr>
<tr>
<td style="text-align:left;">
culture
</td>
<td style="text-align:right;">
7
</td>
<td style="text-align:left;">
07uger_culture
</td>
<td style="text-align:right;">
7.4
</td>
</tr>
<tr>
<td style="text-align:left;">
culture
</td>
<td style="text-align:right;">
7
</td>
<td style="text-align:left;">
07uger_culture
</td>
<td style="text-align:right;">
7.4
</td>
</tr>
<tr>
<td style="text-align:left;">
culture
</td>
<td style="text-align:right;">
7
</td>
<td style="text-align:left;">
07uger_culture
</td>
<td style="text-align:right;">
7.4
</td>
</tr>
<tr>
<td style="text-align:left;">
none
</td>
<td style="text-align:right;">
7
</td>
<td style="text-align:left;">
07uger_none
</td>
<td style="text-align:right;">
7.7
</td>
</tr>
<tr>
<td style="text-align:left;">
none
</td>
<td style="text-align:right;">
7
</td>
<td style="text-align:left;">
07uger_none
</td>
<td style="text-align:right;">
7.8
</td>
</tr>
<tr>
<td style="text-align:left;">
none
</td>
<td style="text-align:right;">
7
</td>
<td style="text-align:left;">
07uger_none
</td>
<td style="text-align:right;">
7.7
</td>
</tr>
<tr>
<td style="text-align:left;">
none
</td>
<td style="text-align:right;">
10
</td>
<td style="text-align:left;">
10uger_none
</td>
<td style="text-align:right;">
7.9
</td>
</tr>
<tr>
<td style="text-align:left;">
none
</td>
<td style="text-align:right;">
10
</td>
<td style="text-align:left;">
10uger_none
</td>
<td style="text-align:right;">
8.0
</td>
</tr>
</tbody>
</table>
<pre class="r"><code>tb <- kable(df,digits = 1)
tb <- kable_styling(tb, "striped", full_width = F)
tb <- column_spec(tb, 1:2, bold = T)
tb <- row_spec(tb, c(7,19), bold = T, color = "white", background = "#D7261E")
tb <- row_spec(tb, c(3,20), bold = T, color = "white", background = "blue")
tb</code></pre>
<table class="table table-striped" style="width: auto !important; margin-left: auto; margin-right: auto;">
<thead>
<tr>
<th style="text-align:left;">
maturation_culture
</th>
<th style="text-align:right;">
time_weeks
</th>
<th style="text-align:left;">
time_culture
</th>
<th style="text-align:right;">
1Butanol
</th>
</tr>
</thead>
<tbody>
<tr>
<td style="text-align:left;font-weight: bold;">
culture
</td>
<td style="text-align:right;font-weight: bold;">
4
</td>
<td style="text-align:left;">
04uger_culture
</td>
<td style="text-align:right;">
7.5
</td>
</tr>
<tr>
<td style="text-align:left;font-weight: bold;">
culture
</td>
<td style="text-align:right;font-weight: bold;">
4
</td>
<td style="text-align:left;">
04uger_culture
</td>
<td style="text-align:right;">
7.5
</td>
</tr>
<tr>
<td style="text-align:left;font-weight: bold;font-weight: bold;color: white;background-color: blue;">
culture
</td>
<td style="text-align:right;font-weight: bold;font-weight: bold;color: white;background-color: blue;">
4
</td>
<td style="text-align:left;font-weight: bold;color: white;background-color: blue;">
04uger_culture
</td>
<td style="text-align:right;font-weight: bold;color: white;background-color: blue;">
7.6
</td>
</tr>
<tr>
<td style="text-align:left;font-weight: bold;">
culture
</td>
<td style="text-align:right;font-weight: bold;">
4
</td>
<td style="text-align:left;">
04uger_culture
</td>
<td style="text-align:right;">
7.6
</td>
</tr>
<tr>
<td style="text-align:left;font-weight: bold;">
none
</td>
<td style="text-align:right;font-weight: bold;">
4
</td>
<td style="text-align:left;">
04uger_none
</td>
<td style="text-align:right;">
7.6
</td>
</tr>
<tr>
<td style="text-align:left;font-weight: bold;">
none
</td>
<td style="text-align:right;font-weight: bold;">
4
</td>
<td style="text-align:left;">
04uger_none
</td>
<td style="text-align:right;">
7.6
</td>
</tr>
<tr>
<td style="text-align:left;font-weight: bold;font-weight: bold;color: white;background-color: #D7261E;">
none
</td>
<td style="text-align:right;font-weight: bold;font-weight: bold;color: white;background-color: #D7261E;">
4
</td>
<td style="text-align:left;font-weight: bold;color: white;background-color: #D7261E;">
04uger_none
</td>
<td style="text-align:right;font-weight: bold;color: white;background-color: #D7261E;">
7.5
</td>
</tr>
<tr>
<td style="text-align:left;font-weight: bold;">
none
</td>
<td style="text-align:right;font-weight: bold;">
7
</td>
<td style="text-align:left;">
07uger_none
</td>
<td style="text-align:right;">
7.7
</td>
</tr>
<tr>
<td style="text-align:left;font-weight: bold;">
none
</td>
<td style="text-align:right;font-weight: bold;">
7
</td>
<td style="text-align:left;">
07uger_none
</td>
<td style="text-align:right;">
7.8
</td>
</tr>
<tr>
<td style="text-align:left;font-weight: bold;">
none
</td>
<td style="text-align:right;font-weight: bold;">
7
</td>
<td style="text-align:left;">
07uger_none
</td>
<td style="text-align:right;">
7.7
</td>
</tr>
<tr>
<td style="text-align:left;font-weight: bold;">
culture
</td>
<td style="text-align:right;font-weight: bold;">
7
</td>
<td style="text-align:left;">
07uger_culture
</td>
<td style="text-align:right;">
7.4
</td>
</tr>
<tr>
<td style="text-align:left;font-weight: bold;">
culture
</td>
<td style="text-align:right;font-weight: bold;">
7
</td>
<td style="text-align:left;">
07uger_culture
</td>
<td style="text-align:right;">
7.3
</td>
</tr>
<tr>
<td style="text-align:left;font-weight: bold;">
culture
</td>
<td style="text-align:right;font-weight: bold;">
7
</td>
<td style="text-align:left;">
07uger_culture
</td>
<td style="text-align:right;">
7.4
</td>
</tr>
<tr>
<td style="text-align:left;font-weight: bold;">
culture
</td>
<td style="text-align:right;font-weight: bold;">
7
</td>
<td style="text-align:left;">
07uger_culture
</td>
<td style="text-align:right;">
7.4
</td>
</tr>
<tr>
<td style="text-align:left;font-weight: bold;">
culture
</td>
<td style="text-align:right;font-weight: bold;">
7
</td>
<td style="text-align:left;">
07uger_culture
</td>
<td style="text-align:right;">
7.4
</td>
</tr>
<tr>
<td style="text-align:left;font-weight: bold;">
none
</td>
<td style="text-align:right;font-weight: bold;">
7
</td>
<td style="text-align:left;">
07uger_none
</td>
<td style="text-align:right;">
7.7
</td>
</tr>
<tr>
<td style="text-align:left;font-weight: bold;">
none
</td>
<td style="text-align:right;font-weight: bold;">
7
</td>
<td style="text-align:left;">
07uger_none
</td>
<td style="text-align:right;">
7.8
</td>
</tr>
<tr>
<td style="text-align:left;font-weight: bold;">
none
</td>
<td style="text-align:right;font-weight: bold;">
7
</td>
<td style="text-align:left;">
07uger_none
</td>
<td style="text-align:right;">
7.7
</td>
</tr>
<tr>
<td style="text-align:left;font-weight: bold;font-weight: bold;color: white;background-color: #D7261E;">
none
</td>
<td style="text-align:right;font-weight: bold;font-weight: bold;color: white;background-color: #D7261E;">
10
</td>
<td style="text-align:left;font-weight: bold;color: white;background-color: #D7261E;">
10uger_none
</td>
<td style="text-align:right;font-weight: bold;color: white;background-color: #D7261E;">
7.9
</td>
</tr>
<tr>
<td style="text-align:left;font-weight: bold;font-weight: bold;color: white;background-color: blue;">
none
</td>
<td style="text-align:right;font-weight: bold;font-weight: bold;color: white;background-color: blue;">
10
</td>
<td style="text-align:left;font-weight: bold;color: white;background-color: blue;">
10uger_none
</td>