Header 3

Some text…

An identified header

• One can force unnumbered titles using {-} or {.unnumbered} (providing, of course, that the other headers are numbered).

Basic text formatting

• Bold using bold or bold

• Italic using italic or italic, but intra_word_underscore is not interpreted (use stars for that like in this word)

• Super^script, or sub_script. No space can occur inside super- or subscript. If you need it, backslash-escape the space like P_a cat.

• Strikethrough with this formatting.

• Formattings can be combined of course, like bold italic with super^script.

• Inline code like x <- 1, and if you need backquote inside it `@var` <- 2.

• Links are automatically detected like http://example.com, or can be explicitly indicated (with a different text) like some example. Note that Markdown uses also reference links. You can also put your links between angle brackets http://example.com.

• You can use any UTF-8 character (at least for HTML documents (examples: µm, Ω, Æ, ∫√)…

• You need to backshlash-escape punctuation you don’t want to be interpreted ad formatting code, like *foo*.

• A nonbreaking space is simply an escaped space, like between “Fig.” and “3” here: Fig. 3.

• A few sequences of characters produce special characters. Use of –dashes– and —em-dashes—. Three dots is ellipsis… and I can use any unicode, too, for special characters, like 😌.

Special paragraphs and other items

• Quoted text (need blank line before it to avoid misinterpretation of > inside a paragraph)

Some quoted text

With two paragraph…

More quoted
with a second paragraph within the same quote block.

And double quotation

with two paragraphs…

• Line blocks

• Preformatted text:

  Some preformatted text using indentation

• Preformatted or verbatim sections indented with four spaces of fenced (but only fenced blocks work in lists and are thus the preferred mean to do so). Fenced blocks are delimited by three or more tildes (~) or backticks (`) and they must be separated from the surrounding using blank lines. You can use identifiers too like in this block:

Some preformatted text (like for code blocks)
using a fenced block with backticks

It is very easy to indicate a language, and syntax highlighting will be used for it:

# Idem, but with R syntax highlighting
for (i in 1:100) {
  if (i > 1) stop("Got it!")
}

It can also be specified in a more complex way, and with marks allowing to link to it:

name = raw_input('What is your name?\n')
print 'Hi, %s.' % name

Then you can link to it like here.

• Horizontal rule or page break using four or more *, - or _ optionally separated by spaces

• Line breaks when ending with two or more spaces
  like this paragraph. However, this is not very visible, nor usable in table. So you can also use a backslash followed by a newline
  and this approach is the only way to do it in tables!

• You can escape special characters except in code block or inline code if you don’t want them to be interpreted as formatting marks like _here_.

• Non-breaking space is entered as a backslash-escaped space (\).

• Comment that do not appear in the final document are similar to HTML comments (<!-- comment-->), but can also be entered using the [//]: syntax.

• Smart punctuation is used and converts straight quotes into curly ones like ‘here’ or “here”. It will also interpret -- as en-dash –, --- as em-dash —, and ... as ellipses … Moreover, nonbreaking spaces are automatically used after certain items like Mr. Schmidt.

• Note that raw HTML (with or without interpretation of markdown inside it) can be included too.

• Footnotes¹ are easy to insert. Another example². And here, I use an inline footnote³.

Text after the long note…

Lists

• Unordered list (using *, + or -)

  • Second level

• Compact

• list

• of items

• Loose

• list

• of items

1. Ordered list

   1. Second level
   2. Second level, second item

2. Back to first level

3. There is a mechanism to include paragraphs inside the list using indentation (don’t forget the empty line in between to start a new paragraph):

   Some preformatted inside a list item

4. Fourth item

• The fancy list extension allow for using #. for ordered lists, as well as something like 1), or (I) for instance:

1. First item
2. Second item

1. First item
2. Second item
3. Third item
4. Fourth item

• Definition lists are also supported (definitions must start with : or ~) and blank lines are optional between the term and its definition (loose vs compact form), but not before the term. Finally, several defintions are allowed for the same term.

Term 1

Definition 1

Term 2 with inline markup

Definition 2

{ some code, part of Definition 2 }

Third paragraph of definition 2.

or

Term 1

Definition 1

Term 2

Definition 2a

Definition 2b

• Numbered example lists use a sequential numbering throughout the whole document and use the @. syntax:

1. First item
2. Second item

Some text

3. Third item

You can give them labels (alphanumeric + character + hyphen) and refer to them later on. You can also enclose it into parentheses, but it does not change how it is displayed:

4. This is a good example

As example 4 illustrates⁴, …

And what if I refer to it before the label like 5? Yes! It works! But unfortunately, there is no link to example 5.

5. A bad example

Finally, to force ending a list, just add a comment where you want to end it (same trick applies for restarting another numbered list):

1. list item

2. another item

   Formatted block with spaces does not work inside lists

3. third list item

Formatted block with spaces work now

1. New list item #1

Indent paragraphs or blocks or chunks (see hereunder) following a list item to include it in the list:

1. The area of a circle with a given radius is:

   radius <- 3.5
   pi * radius ^ 2

   ## [1] 38.48451

2. As you can see, the R chunk and its associated results are included in the list element!

Equations

• Inline equations like \(\frac{1}{n} \sum_{i=1}^{n} x_{i} + \beta\), or \(f(\alpha, \beta) \propto x^{\alpha-1}(1-x)^{\beta-1}\).

• Display equation

\[ \frac{1}{n} \sum_{i=1}^{n} x_{i} + \beta \]

Here is a more complex example spanning on several lines:

\[ \begin{aligned} \dot{x} & = \sigma(y-x) \\ \dot{y} & = \rho x - y - xz \\ \dot{z} & = -\beta z + xy \end{aligned}\]

If you feel difficult to write LaTeX equations, there are inline LateX equation editors like this one, and you don’t need to install anything on your computer to used them. Also, there is a R Studio addin provided with the bookdown R package to ease entering LaTeX equations in your R Markdown document.

R chunks

• A few R commands:

# This is a comment (don't use ##, since it is reserved for output!)
a <- 1 + 1 # Another comment
TRUE; NA; "Some text"

## [1] TRUE

## [1] NA

## [1] "Some text"

summary(cars) # A table

##      speed           dist       
##  Min.   : 4.0   Min.   :  2.00  
##  1st Qu.:12.0   1st Qu.: 26.00  
##  Median :15.0   Median : 36.00  
##  Mean   :15.4   Mean   : 42.98  
##  3rd Qu.:19.0   3rd Qu.: 56.00  
##  Max.   :25.0   Max.   :120.00

• Normal output versus message versus warning versus error:

# Normal output
cat("Some text...\n")

## Some text...

# A message
message("My very nice message")

## My very nice message

# Output with a warning
1:2 + 1:3

## Warning in 1:2 + 1:3: longer object length is not a multiple of shorter object
## length

## [1] 2 4 4

# An error
non_existing_object

## Error in eval(expr, envir, enclos): object 'non_existing_object' not found

• R chunk with option to generate a plot⁵:

Figure 1: An example figure generated by R, from the cars dataset.

My plot is here.

• Another plot:

library(ggplot2)
qplot(speed, dist, data = cars) + geom_smooth(method = "loess")

## `geom_smooth()` using formula 'y ~ x'

Figure 2: Distance in function of speed for the cars data set.

I can now reference this figure in the text (see this plot).

• R chunk with option to generate a table :

Now, I can refer to this table (see this Table).

Tables using xtable

The xtable R package offers an alternative to output well-formatted tables in an R Markdown document:

library(xtable)
data(tli)
## Demonstrate data.frame... can also export many objects!
tli.table <- xtable(tli[1:10, ])
digits(tli.table)[c(2, 6)] <- 0
## Choose one of these!
print(tli.table, floating = FALSE, type = "html")

Tables using pander

The pander package can output various objects in pandoc:

library(pander)
# You can change default pander options:
panderOptions('table.alignment.default', function(df)
  ifelse(sapply(df, is.numeric), 'right', 'left'))
panderOptions('table.split.table', Inf)
panderOptions('big.mark', ",")
panderOptions('keep.trailing.zeros', TRUE)
pander(head(iris))

Tables using flextable

The flextable package allows for fine customization of the formatted table:

library(flextable)

## 
## Attaching package: 'flextable'

## The following objects are masked from 'package:xtable':
## 
##     align, display

library(dplyr)

## 
## Attaching package: 'dplyr'

## The following objects are masked from 'package:stats':
## 
##     filter, lag

## The following objects are masked from 'package:base':
## 
##     intersect, setdiff, setequal, union

library(flow)
mtcars %>.%
  group_by(., cyl, am) %>.%
  summarise(., avg = mean(mpg)) %>.%
  flextable(.) %>.%
  bg(., bg = '#c7deff', part = 'header')

There are many other packages to output well-formatted tables from R objects, like: stargazer, table1, tables, formattable, htmlTable, huxtable, kableExtra, pixiedust, tangram, texreg, ztable, etc.

Inline R expressions and special chunks

• Inline R expression like 2, or R version 3.6.3 (2020-02-29).

• Rcpp code chunks can also be included in your document:

#include <Rcpp.h>

// [[Rcpp::export]]
int fibonacci(const int x) {
    if (x == 0 || x == 1) return(x);
    return (fibonacci(x - 1)) + fibonacci(x - 2);
}

Because fibonacci was defined with the Rcpp::export attribute it can now be called as a normal R function:

fibonacci(10L)

## [1] 55

fibonacci(20L)

## [1] 6765

• An R chunk that is displayed, but not executed:

library(knitr)
knit('R Markdown V2 Syntax.Rmd')

• A Python chunk:

import sys
print(sys.version)

## 2.7.16 (default, Apr 17 2020, 18:29:03) 
## [GCC 4.2.1 Compatible Apple LLVM 11.0.3 (clang-1103.0.29.20) (-macos10.15-objc-