### Chunk option example

```{r}
install.packages(forecast)
library(forecast)
```

### Chunk option example
```{r message=FALSE}
library(forecast)
```

If you need to convert files from one markup format into another, pandoc is your swiss-army knife.

--About pandoc (http://pandoc.org/index.html)

When you create a new R Markdown file in RStudio next to the prefilled text, there are also four lines of code between three dashes at the beginning of each new .Rmd file. After knitting the file, this so-called YAML header will not appear in the output, but R Markdown will take some information out of it.

The final HTML file takes the given title, the author name, and the date out of the YAML header and includes them in the compiled report.

Output formats

You change the output format by clicking on the down-facing arrowhead next to the Knit button, and choosing HTML, PDF, or Word; you can also change it in the YAML header. To do so, write the format after the output argument, as shown as follows:

• output: html_document: This creates an HTML file
• output: pdf_document: This produces a PDF document
• output: word_document: This generates a Microsoft Word file
• output: md_document: This outputs a Markdown file

All output formats will be saved into your existing working directory.

Changing the look of the output

By overwriting and adding new arguments to the YAML header, you can easily change the final look of your report. A lot of change options can be made with the help of the respective output settings.

In the previous example, we changed the syntax highlighting to espresso, and we applied a CSS theme called journal. These default themes are collected from the well-known Twitter bootstrap theme. The effects of these small adjustments can be inspected in the following screenshot. On the left-hand side, we see the normal output with default syntax and the default CSS theme, and on the right-hand side is our new output with the changed syntax and theme.

There are countless options to modify the YAML header, and hence, the output of the R Markdown file. Of course, you can change everything in the header manually, but you need to pay attention to the right indentation:

---
title: "My Report"
output:
  html_document:
    toc: yes
    number_sections: yes
    theme: united
---

The preceding header will generate a working HTML file with a table of contents and numbered headings; it uses a CSS theme called united.

The indentation for the YAML header is very strict. If you're using, for example, an incorrect indentation in the YAML header, an error message will appear in the R Markdown console. Thus, you can quickly find and fix those errors:

1 ---
2 title: "My Report"
3 output:
4   html_document:
5     toc: yes
6       number_sections: yes
7     theme: united
8 ---

The error message looks as follows:

Error in yaml::yaml.load(front_matter) : 
  Scanner error: mapping values are not allowed in this context at line 5, column 22

You can learn more about YAML at http://yaml.org/.

Using a custom CSS style sheet

As already learned, for the HTML output format, you can change the whole look by applying one of the inbuilt CSS themes. But RStudio also makes it possible to use a custom CSS file. As a result, R Markdown reports can be adapted to an existing corporate design, for example.

In the settings window of the HTML output, which opens after a click on the gear icon, you need to uncheck the Apply theme box and check the Apply CSS file box instead. Then, you can add your custom CSS file.

Using R Markdown templates

RStudio offers the option to use completely custom templates for R Markdown. This makes sense if you want to use a template again and again. In contrast to the possibility of applying a style sheet with its own CSS file, you can adjust basically everything with a Markdown template. So, you can adjust not only the fonts and color schemes, but also the complete formatting and the corresponding special formats. In general, these templates are installed or distributed through R packages. RStudio has installed two templates by default. One is the package vignette, and the other the so-called Tufte Handout.

You can open these templates by creating a new R Markdown file and clicking on From Template in the selection menu on the left-hand side.

Package vignette

Compiling R Notebooks

R Markdown also offers a quick way to render a so-called R Notebook, which is in fact equal to the normal HTML output of a knitted .Rmd file. Just type rmarkdown::render("yourfilename.R") into the RStudio console and an HTML version of your R script will be generated.

Generating R Markdown presentations

In conjunction with R Markdown, RStudio also offers the possibility of building presentations. When you click on New File and choose R Markdown..., you need to select the item called Presentation in the popup window. RStudio offers three default output formats to choose from.

But you can also change the YAML header of existing R Markdown documents from this:

---
title: "My Report"
author: "Your Name"
output: html_document
---

To the following header, which for example, creates a slidy presentation:

---
title: "My Report"
author: "Your Name"
output: slidy_presentation
---

The same applies to beamer_presentation and ioslides_presentation. All R Markdown presentations will not open in the Viewer pane, but in a new window.

ioslides

An ioslides presentation is an HTML document, and to start a new slide, you use the # hash sign. If you use one hash sign to start a new slide, the background of the slide will be dark, and if you use two hash signs, the background looks bright. The content of the first slide will be taken from the YAML header. The following lines demonstrate this in code:

This will be the content of your first slide:
--
title: "My Report"
author: "Your Name"
output: ioslides_presentation
--

# Next slide (background will be dark)
… content …

## Next slide (background will be bright)
… content … 

# Next slide (background will be dark)
… and so on …

Slidy

Slidy presentations are also HTML documents after knitting, but they are somewhat more sophisticated than ioslides. For example, slidy offers an inbuilt table of contents from the beginning. Moreover, you can see the number of total slides, and so, it is no blind flight for the viewers.

Again, you use hash signs to create a new slide. But, this time, you need to decide if you use one hash sign or two hash signs. Also, the background is always bright.

Beamer

Beamer presentations are compiled to PDF. To start a new slide or sheet, you use one or two hash signs, as we already know from slidy presentations. Beamer Presentations allow a lot of customizations with LaTeX, such as macros and others.