YAML Header

The header is on top of every .Rmd file. The code is enclosed with 3 dashes. Your Header contains meta data about your .Rmd file, such as the author, date and output format. You can add additional stuff such as gloabal variables. But don't worry about your header too much for now. Let it just be there.

--- 
title: "My first R Markdown document"
author: "Heike W"
date: '2018-11-05'
output: html_document
---

Markdown (Text)

Markdown is a simple textformatting language. Similar to HTML or Latex, you write plain text. Punctuation characters indicate the formating. For example a # header1 indicates a header on the top level. You can make you text italic by enclosing it in 2 asterisk (*italic*). If you have never worked with HTML, Latex or Markdown before, this may appear strange to you: Your text appears to have no format. You cannot see how your formatting looks like until you compile the document. You have to click on the "Knit" button to compile your R Markdown. Then you will see the formating of your output file.The good thing is that you can be sure, that a header level 1 is a header level 1 and all header level 1 will look the same in the final document. Here is an overview of the most common formating:

Source RMarkdown Cheat Sheet

R Code Chunks

Just write your R code and wrap it around 3 apostrophies followed by {r}. This tells R Markdown that you want to write R code (You could also insert for example python {python}, bash {bash} or sql {sql}). Insert as many code chunks as you want. Instead of typing 3 apostrophies and the curly braces everytime, you can simply press command-option-I on the Mac and Ctrl-Alt-I on Windows to create a new code chunk. Per default, R will execute this code chunk and display the code and the results in the output file when you "knit" your .Rmd file.

```{r headCars}
summary(cars)
```

You have previously executed the example code by clicking on the "Knit" button in R Studio. This opens a new session and runs the entire .Rmd file. This means you're starting with a new clean environment. You can also run single R code chunks separately. Click on the little green triange in the right corner of your code chunk and only this chunk will run. You can see, that the results are shown directly below your code.

You can give names to your code chunks within the curly braces of your R code chunks. I named our first code chunk "headCars". In addition, you can pass options. Options tell R what it should do with this code chunk. For example, for not displaying any R code in the output file pass echo = FALSE:

```{r headCars, echo = FALSE}
summary(cars)
```

Or you can tell R not to run a code chunk by setting eval = FALSE.

```{r headCars, eval = FALSE}
summary(cars)
```

You can use as many options as neccessary. The order of options does not matter, but you have to separate them with a comma.

```{r headCars, echo = TRUE, eval = FALSE}
summary(cars)
```

Here is a brief overview of the options, I use the most.

You can find a comprehensive overview about code chunk options on Yihui Xie's website

You're wondering whether you have to pass the same options to all your code chunks? You don't. You can determine global options at the beginning of your .Rmd file Here in this example, where I told R Markdown to not print any code.

```{r globaloptions, include=FALSE}
knitr::opts_chunk$set(echo = FALSE)
```

The code chunk options overwrite the global options. So if there is one code chunk, where you want to display code, you can pass the option echo = TRUE to this code chunk and the code will be shown in the output document.