Appendix 1. Markdown Syntax

Many of the descriptions of Markdown syntaxes presented here can be obtained directly in the Markdown quick reference section of the RStudio help menu.

Format text with Pandoc

Format for bold, italics and code

**bold**, *italics* and `code`

Section and subsection header format

 # Section title
 ## Subsection title
 ### Subsubsection title

Format numbered lists

1.item 1
1.item 2

Compiled result:

  1. item 1
  2. item 2

Format lists with dots

+ item 1
+ item 2

Compiled result:

  • item 1
  • item 2

Format nested lists

1.item 1
     + item 1.1 # leave 4 blank spaces as margin on the left
     +item 1.2
1.item 2

Compiled result:

  1. item 1
    • item 1.1
    • item 1.2
  2. item 2

Horizontal line format

****

Compiled result:

Table format

+---------------+---------------+--------------------+
| A             | B             | C                  |
+===============+===============+====================+
| A0            | B1            | - C10              |
|               |               | - C11              |
+---------------+---------------+--------------------+
| A1            | B2            | - C20              |
|               |               | - C21              |
+---------------+---------------+--------------------+

Compiled result:

A B C
A0 B1
  • C10
  • C11
A1 B2
  • C20
  • C21

Building a table from a tibble structure

tibble(
   year=c(1985,2000,2015),
   Spain=c(38.734,40.75,46.122),
   France=c(55.38,59.387,64.395),
   Germany=c(77.57,81.896,80.689)) %>%
   knitr::kable( caption = "Annual population in millions")
Table 8.1: Annual population in millions
year Spain France Germany
1985 38.734 55.380 77.570
2000 40.750 59.387 81.896
2015 46.122 64.395 80.689

Image insertion format

![Image title](https://ctim.es/Delmond.png){ width=50% }

Compiled result:

Image title
Image title

Codes in the Markdown file

Mardown file header

---
title: "My job title"
author: "My name and surname"
date: "`r Sys.Date()`"
output: html_document
---

Chunks

The syntax of the chunks is as follows

```{r, comma-separated chunk options}
    code
```

Chunk Options

  • include = FALSE neither the code nor the results appear in the compiled file. R Markdown still runs the code in the chunk and the results can be used by other chunks.

  • echo = FALSE the code does not appear in the compiled file but the results do.

  • message = FALSE prevents messages generated by the code from appearing in the compiled file.

  • warning = FALSE prevents warnings generated by the code from appearing in the compiled file.

  • cache = TRUE saves the execution of the chunk and is not executed again unless it is modified. This is interesting to speed up the execution of the Knit.

  • fig.cap = "..." adds a legend to the graphical results.

  • out.width='60%' sets the width of the shape as a percentage of the width of the text area.

  • fig.asp=1.2 sets the height/width ratio of the figure

  • fig.align='center' sets the alignment of the figure

Additionally, we can associate a label (label) to each chunk by writing it at the beginning, after ```{r. Let’s look at this with an example of a bar chart figure (in this example the instructions on how to construct the bar chart are not relevant).

```{r chunk-label,fig.cap = "Figure legend",out.width='50%',fig.asp=0.8,fig.align='center',cache=TRUE}
tibble(var=c("A","B","C"),value=1:3) %>%
   ggplot(aes(x=var,y=value,fill=var)) +
     geom_bar(stat = "identity")
```
Figure legend

Figure 8.1: Figure legend

If we want to adjust the default options that the chunk will use, we can put an instruction like the following at the beginning of the document, which will ensure that, by default, the chunk code is not included in the text. This is interesting when we want to generate text without R codes.

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

```

Interactive execution of R code

To debug code errors, it is useful to be able to execute the code line by line. To do this, simply place the cursor over it and press Ctrl-Enter (on Windows and Linux), or Cmd-Enter (on Mac). To execute several lines, we can select them with the mouse and do the same. To execute the entire content of a chunk, simply place the mouse anywhere in the chunk and press Alt-Ctrl-C (on Windows) or Alt-Cmd-Enter (on Mac).