Reporting

# Reporting
### Intro to Data Science with R <a href='https://therbootcamp.github.io'> The R Bootcamp @ Unibe </a> <a href='https://dwulff.github.io/Intro2R_Unibe_2021/'> </a>  <a href='https://therbootcamp.github.io'> </a>  <a href='mailto:therbootcamp@gmail.com'> </a>  <a href='https://www.linkedin.com/company/basel-r-bootcamp/'> </a>
### September 2021

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 <a href="https://therbootcamp.github.io/">
 
 
 www.therbootcamp.com
 
 
 </a>
 <a href="https://therbootcamp.github.io/">
 
 The R Bootcamp | September 2021
 
 </a>
 
 </div>

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# What is Markdown?

<ul>
 <li class="m1">Developed by John Gruber and Aaron Swartz in 2004. 
 "<high>easy-to-read</high> and <high>easy-to-write</high> plain text format, [...] convert it to structurally valid XHTML (or HTML)"</li> 
 <li class="m2">Simple <high>Syntax for the layout</high> of documents.</li> 
 <ul>
 <li>Text in bold and italics</li> 
 <li>Lists</li> 
 <li>Headings</li> 
 <li>Links</li>
 <li>Pictures</li>
 </ul>
</ul>

]

<img src="image/markdown.png" width=400px> 
 from <a href="https://de.wikipedia.org/wiki/Markdown">wikipedia.org</a>

]

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# What is RMarkdown?

<ul>
 <li class="m1">Markdown is used for <high>layout of dynamic documents</high> with embedded ...</li> 
 <ul>
 <li>R code chunks</li>
 <li>R inline code</li> 
 <li>Output from statistical models</li>
 <li>Tables</li>
 <li>Visualization</li>
 </ul>
</ul>

]

<img src="image/hex.png" height=300> 
 from <a href="https://rmarkdown.rstudio.com/docs/">rmarkdown.rstudio.com</a>

]

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# Types of documents

<ul>
 <li class="m1">RMarkdown allows the creation of different <high>document types</high>.</li> 
 <ul>
 <li>Text documents</li>
 <li>Presentations</li> 
 <li>Dashboards (Cockpits)</li>
 <li>Books</li>
 <li>Web-Pages</li>
 </ul>
</ul>

]

]

---

# Components of RMarkdown

<ul>
 <li class="m1">A RMarkdown script consists of multiple <high>components</high>.</li>
</ul>

<table style="cellspacing:0; cellpadding:0; border:none; padding-top:10px" width=100%>
 <col width="40%">
 <col width="60%">
<tr>
 <td bgcolor="white">
 Component
 </td>
 <td bgcolor="white">
 Description
 </td> 
</tr>
<tr>
 <td bgcolor="white">
 <mono>YAML</mono>
 </td>
 <td bgcolor="white">
 YAML Ain't Markup Language 
 <high>Document setup</high>
 </td> 
</tr>
<tr>
 <td bgcolor="white">
 <mono>Setup chunk</mono>
 </td>
 <td bgcolor="white">
 <high>Chunk</high> features 
 <high>Packages</high> load 
 <high>Data</high> load
 </td> 
</tr>
<tr>
 <td bgcolor="white">
 <mono>Markdown</mono>
 </td>
 <td bgcolor="white">
 <high>Headings</high> 
 <high>Text</high> with decoration 
 </td> 
</tr>
<tr>
 <td bgcolor="white">
 <mono>Code chunk</mono>
 </td>
 <td bgcolor="white">
 R <high>Code</high> 
 R <high>Outputs<high>
 </td> 
</tr>
</table>

]

]

---

# Pipeline

<ul>
 <li class="m1">One RMarkdown document can be translated into multiple output <high>formats</high>.</li> 
 <ul>
 <li>PDF</li>
 <li>HTML</li> 
 <li>Word</li>
 <li>PowerPoint</li>
 </ul> 
 <li class="m2">During theses steps RMarkdown will be translated <high>multiple times</high>. This process comes with certain restrictions.</li> 
</ul>

]

]

---

# HTML Pipeline

<ul>
 <li class="m1">HTML is the <high>universal framework</high> for documents, presentations and dashboards.</li>
 <li class="m2"><high>Export to PDF</high> is possible, with minimal restrictions.</li> 
</ul>

]

]

---

# HTML

<ul>
 <li class="m1">HyperText Markup Language.</li>
 <li class="m2">The lingua franca of the <high>World Wide Web</high>.</li>
 <li class="m3">Can be extended with <high>CSS</high> (Cascading Style Sheets) for specialized formats.</li>
</ul>

]

]

---

# Rendering

<ul>
 <li class="m1">HTML is interpreted by RStudio (or a browsern) and presented as a formatted document.</li>
 <li class="m2"><high>Rstudio</high> can show rendered documents in the viewer window. </li> 
</ul>

]

]

---

# Headings

<ul>
 <li class="m1">Different level headings are represented with one or multiple <mono>#</mono>.</li>
</ul>

<table style="cellspacing:0; cellpadding:0; border:none; padding-top:20px" width=100%>
 <col width="40%">
 <col width="60%">
<tr>
 <td bgcolor="white">
 Markdown
 </td>
 <td bgcolor="white">
 Description
 </td> 
</tr>
<tr>
 <td bgcolor="white">
 <mono># text</mono>
 </td>
 <td bgcolor="white">
 Level 1
 </td> 
</tr>
<tr>
 <td bgcolor="white">
 <mono>## text</mono>
 </td>
 <td bgcolor="white">
 Level 2
 </td> 
</tr>
<tr>
 <td bgcolor="white">
 <mono>...</mono>
 </td>
 <td bgcolor="white">
 ...
 </td> 
</tr>
<tr>
 <td bgcolor="white">
 <mono>##### text</mono>
 </td>
 <td bgcolor="white">
 Level 5
 </td> 
</tr>
</table>

]

]

---

# Headings

<ul>
 <li class="m1">Different level headings are represented with one or multiple <mono>#</mono>.</li>
</ul>

]

]

---

# Emphasize text

<ul>
 <li class="m1">The usage of special characters allows <high>text- and code-related</high> emphasis</li>
</ul>

<table style="cellspacing:0; cellpadding:0; border:none; padding-top:20px" width=100%>
 <col width="50%">
 <col width="50%">
<tr>
 <td bgcolor="white">
 Markdown
 </td>
 <td bgcolor="white">
 Description
 </td> 
</tr>
<tr>
 <td bgcolor="white">
 &ast;<mono>text</mono>&ast;
 </td>
 <td bgcolor="white">
 italic
 </td> 
</tr>
<tr>
 <td bgcolor="white">
 &ast;&ast;<mono>text</mono>&ast;&ast;
 </td>
 <td bgcolor="white">
 bold
 </td> 
</tr>
<tr>
 <td bgcolor="white">
 &ast;&ast;&ast;<mono>text</mono>&ast;&ast;&ast;
 </td>
 <td bgcolor="white">
 italic and bold 
 </td> 
</tr>
<tr>
 <td bgcolor="white">
 &grave;<mono>text</mono>&grave;
 </td>
 <td bgcolor="white">
 code
 </td> 
</tr>
<tr>
 <td bgcolor="white">
 &grave;<mono>r "text"</mono>&grave;
 </td>
 <td bgcolor="white">
 inline code
 </td> 
</tr>
</table>

]

]

---

# Emphasize text

<ul>
 <li class="m1">The usage of special characters allows <high>text- and code-related</high> emphasis</li>
</ul>

]

]

---

# Emphasize text

<ul>
 <li class="m1">The usage of special characters allows <high>text- and code-related</high> emphasis</li>
</ul>

]

]

---

# Inline Code

<ul>
 <li class="m1"><high>Number and word </high> can be parameterised with inline code .</li>
 <li class="m2">inline code can contain any R code, similar to <high>code <mono>chunks</mono></high></li>
</ul>

]

]

---

# Chunks

<ul>
 <li class="m1">A <high>code <mono>chunk</mono></high> can contain any R Code.</li>
 <li class="m2">Code chunks are fine tuned with <high>additional arguments</high></li>
</ul>

]

]

---

# Chunks

<table style="cellspacing:0; cellpadding:0; border:none; padding-top:60px" width=100%>
 <col width="60%">
 <col width="40%">
<tr>
 <td bgcolor="white">
 Argument
 </td>
 <td bgcolor="white">
 Description
 </td> 
</tr>
<tr>
 <td bgcolor="white">
 <mono>echo=T/F</mono>
 </td>
 <td bgcolor="white">
 show/hide <high>code</high>
 </td> 
</tr>
<tr>
 <td bgcolor="white">
 <mono>eval=T/F</mono>
 </td>
 <td bgcolor="white">
 execute/don't execute <high>code</high>
 </td> 
</tr>
<tr>
 <td bgcolor="white">
 <mono>include=T/F</mono>
 </td>
 <td bgcolor="white">
 include/exclude <high>output</high> 
 </td> 
</tr>
<tr>
 <td bgcolor="white">
 <mono>message=T/F</mono>
 </td>
 <td bgcolor="white">
 include/exclude <highm>messages</highm>
 </td> 
</tr>
<tr>
 <td bgcolor="white">
 <mono>warning=T/F</mono>
 </td>
 <td bgcolor="white">
 include/exclude <highm>warnings</highm>
 </td> 
</tr>
</table>

<mono>T/F = TRUE/FALSE</mono>

]

]

---

# Chunks

<mono>T/F = TRUE/FALSE</mono>

]

]

---

# Chunks

<mono>T/F = TRUE/FALSE</mono>

]

]

---

# Setup-Chunk

<ul>
 <li class="m1">In the setup-chunk global <high>settings for all other chunks </high> can be defined.</li>
</ul>

]

]

---

# Setup-Chunk

<ul>
 <li class="m1">In the setup-chunk global <high>settings for all other chunks </high> can be defined.</li>
</ul>
]

]

---

# Setup-Chunk

<ul>
 <li class="m1">In the setup-chunk global <high>settings for all other chunks </high> can be defined.</li>
</ul>

]

]

---

# Setup-Chunk

<ul>
 <li class="m1">In the setup-chunk global <high>settings for all other chunks </high> can be defined.</li>
</ul>

]

]

---

# Setup-Chunk

<ul>
 <li class="m1">In the setup-chunk global <high>settings for all other chunks </high> can be defined.</li>
</ul>
]

]

---

# Relative path

<ul>
 <li class="m1">Markdown documents do not access the regular <high>working directory</high>.</li> 
 <li class="m2">Paths in RMarkdown have to be <high>relative to the .Rmd</high> file.</li>
</ul>

```R
# Read Data
read_csv("../1_Data/daten.csv")
```

]

]

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<h1><a href="https://dwulff.github.io/Intro2R_Unibe_2021/_sessions/Reporting/Reporting_practical.html">Practical</a></h1>