Writing articles • memoiR

Markdown is a very simple language for producing various types of documents: HTML, PDF, and Word among others. Its documentation is available at the RStudio website¹.

Markdown is extended by Bookdown², which allows for book writing and more efficient syntax for articles. Articles of the memoiR package are made with Markdown in RStudio: knitr processes the Markdown code, passes it to Pandoc for transformation into LaTeX, finally LaTeX compiles it into PDF.

Motivation

Markdown is very easy to learn.

Markdown allows you to integrate your R code for a reproducible result.

Markdown allows to produce, without rewriting the text, a document in different formats: HTML, LaTeX or Word for example.

How to do it

In RStudio, create a new document of type Document R Markdown. The wizard allows you to choose between different formats.

Click on From template: from templates installed by packages. The memoiR package templates are displayed: choose aither Simple Article or Stylish Article.

It is better to create an RStudio project to benefit from all the possibilities: File / New Project then use the wizard to create a project from an existing folder.

Write the document in RStudio.

Clicking the Knit button in RStudio generates the document in the requested format.

Code

The main features of R Markdown are summarized here.

R code

R code is included in code chunks:

```{r cars, echo=FALSE}
head(cars)
```

head(cars)

##   speed dist
## 1     4    2
## 2     4   10
## 3     7    4
## 4     7   22
## 5     8   16
## 6     9   10

Tables

The horizontal - and vertical separators | allow you to draw a table according to Markdown syntax, but this is not the best method.

Tables can also be produced by R code. The content of the table is in a dataframe. The kbl() function in the kableExtra package (which enhances the original kable() function from knitr) prepares the table for display and passes the result to the kable_styling function for final formatting.

```{r iris, echo=FALSE, warning=FALSE}
library("kableExtra")
names(iris) <- c("Sepal length", "Width", "Petal length", "Width", "Species")
kbl(head(iris), caption="Table created by R", longtable = TRUE, booktabs = TRUE) %>%
  kable_styling(bootstrap_options = "striped", full_width = FALSE)
```

## 
## Attaching package: 'kableExtra'

## The following object is masked from 'package:dplyr':
## 
##     group_rows

Table created by R
Sepal length	Width	Petal length	Width	Species
5.1	3.5	1.4	0.2	setosa
4.9	3.0	1.4	0.2	setosa
4.7	3.2	1.3	0.2	setosa
4.6	3.1	1.5	0.2	setosa
5.0	3.6	1.4	0.2	setosa
5.4	3.9	1.7	0.4	setosa

The caption is specified by the caption argument and referencing is possible because the table receives a label whose name is tab: followed by the name of the code snippet: write something like see table \@ref(tab:iris)). Always use the booktabs = TRUE argument so that the thickness of the separator lines is optimal in LaTeX. The bootstrap_options = "striped" option provides more readable tables in HTML.

In LaTeX, tables can have the width of the column and possibly span multiple pages, or use the width of the page.

```{r Paracou, echo=FALSE, warning=FALSE}
Intervention <- data.frame(
  Treatment=c("Control", "T1", "T2", "T3"),
  Timber=c("", 
           "DBH $\\geq$ 50 cm, commercial species, $\\approx$ 10 trees/ha", 
           "DBH $\\geq$ 50 cm, commercial species, $\\approx$ 10 trees/ha",
           "DBH $\\geq$ 50 cm, commercial species, $\\approx$ 10 trees/ha"),
  Thinning=c("", 
             "", 
             "DBH $\\geq$ 40 cm, non-valuable species, $\\approx$ 30 trees/ha", 
             "DBH $\\geq$ 50 cm, non-valuable species, $\\approx$ 15 trees/ha  "),
  Fuelwood=c("", 
             "", 
             "", 
             "40 cm $\\leq$ DBH $\\leq$ 50 cm, non-valuable species, $\\approx$ 15 trees/ha"),
  AGBLost=c(0, "$[12\\%-33\\%]$", "$[33\\%-56\\%]$", "$[35\\%-56\\%]$")
)
names(Intervention)[5] <- "\\%AGB lost"
kbl(
  Intervention, 
  caption = "Summary of the disturbance intensity for the 4 plot treatments in Paracou.", 
  longtable = FALSE,
  booktabs = TRUE, 
  escape = FALSE
) %>%
  kable_styling(bootstrap_options = "striped", full_width = TRUE)
```

Summary of the disturbance intensity for the 4 plot treatments in Paracou.
Treatment	Timber	Thinning	Fuelwood	%AGB lost
Control				0
T1	DBH $\geq$ 50 cm, commercial species, $\approx$ 10 trees/ha			$[12\%-33\%]$
T2	DBH $\geq$ 50 cm, commercial species, $\approx$ 10 trees/ha	DBH $\geq$ 40 cm, non-valuable species, $\approx$ 30 trees/ha		$[33\%-56\%]$
T3	DBH $\geq$ 50 cm, commercial species, $\approx$ 10 trees/ha	DBH $\geq$ 50 cm, non-valuable species, $\approx$ 15 trees/ha	40 cm $\leq$ DBH $\leq$ 50 cm, non-valuable species, $\approx$ 15 trees/ha	$[35\%-56\%]$

This table contains mathematics: the escape = FALSE option is necessary.

Finally, the full_width = FALSE option adjusts the width of the table to its content instead of occupying all the available width. It must be TRUE for correct formatting of two-column tables in LaTeX.

Figures

Figures can be created by some R code.

```{r pressure, fig.cap="Figure title"}
plot(pressure)
```

Figure title

With Bookdown, a label is associated with each figure: its name is fig:xxx where xxx is the name of the R code snippet. Cross-references are made with the command \@ref(fig:xxx).

In the PDF output of Stylish Articles, a figure can use the full width of the page by adding the following options to the header of the code snippet that generates it: fig.env="figure*" and out.extra="".

Existing figures are integrated into a piece of code by the include_graphics function.

```{r cover, fig.cap="A figure from a file", echo=FALSE, out.width='60%'}
knitr::include_graphics("images/trim.png")
```

A figure from a file

Systematically place these files in the images folder for the automation of GitHub pages.

Captions

Figure and table captions can be long, include formatted text, maths, references… The only limit is they cannot contain more than a single paragraph. Such captions must be stored in a separate paragraph starting with (ref:ChunkName)and a space. The text of the caption follows.

In the figure chunk heading, the caption is called in the fig.cap field:

(ref:ChunkName) This *is* a figure legend.
```{r ChunkName, fig.cap="(ref:ChunkName)"}
plot(pressure)
```

In tables, the caption argument of the kbl() function is used the same way.

Lists

Lists are indicated by *, + and - (three hierarchical levels) or numbers 1., i. and A. (numbered lists). Indentation of lists indicates their level: *, + and - may be replaced by - at all levels, but four spaces are needed to nest a list into another.

First element of a list
- sub-list
Second element
Continuation of the list

Leave an empty line before and after the list, but not between its items.

Math

Equations in LaTeX format can be inserted in line, like $A=\pi r^2$ or isolated like $e^{i \pi} = -1.$

They can be numbered using the equation environment:

\begin{equation}
  A = \pi r^2.
  (\#eq:disk)
\end{equation}

Cross referencing is supported: see equation \@ref(eq:disk).

Cross-references

Figures and tables have an automatically generated label, identical to the name of the code snippet prefixed with fig: and tab:.

For equations, the label is added manually by the code (\#eq:xxx) before the end of the equation.

Sections can be tagged by ending their title with {#yyy}.

In all cases, the call to the reference is made by the command \@ref().

Bibliography

Bibliographic references included in the references.bib file can be called by [@CitationKey], in parentheses (Xie 2016), or without square brackets, in the text, as Xie, Allaire, and Grolemund (2018) .

The bibliography is processed by Pandoc when producing Word or HTML documents. The bibliographic style can be specified, by adding the line

csl:file_name.csl

in the document header and copying the .csl style file to the project folder. More than a thousand styles are available³.

For PDF documents, the bibliography is managed by natbib. The style is declared in the header:

biblio-style: chicago

It can be changed as long as the appropriate .bst file (by default: chicago.bst) is included in the project.

Specificities of document types

The templates are designed to produce documents in PDF, HTML or Word format. Use the list of choices in the Knit button to choose the output format.

HTML

While writing, prefer knitting to HTML format for its speed of execution.

The standard HTML output formats are “HTML document” and “GitBook”, both optimized for on-screen reading. More specific formats are from the rmdformats and distill packages.

Specific instructions apply to each format:

GitBook: A download button is available in the document menu bar. It will work if the document is also knitted in PDF format and if the file name is entered in the download field of the YAML header.
rmdformats: read the documentation of the package.
distill articles: read the documentation of the package.
- the date item in the HTML header must be formatted as “year/month/day” to be interpreted correctly. The current date must be changed from its default format in templates '%d %B %Y' to '%Y %B %d'.
- sections may be numbered by adding a specific pandoc option in the YAML header, but cross references to section numbers are not supported yet.

output:
  bookdown::html_document2:
    base_format: distill::distill_article
    pandoc_args: ["--number-sections"]

PDF

The document is formatted for self-archiving of well-formatted articles (Stylish Article) or a simpler, LaTeX-article-style output (Simple Article).

LaTeX preamble

LaTeX commands can be added in the preamble of the produced LaTeX file, for example to load additional packages. These commands are in the preamble: section of the Markdown file header.

The default commands allow to show the use of the hyphenation command:

\hyphenation%
  {bio-di-ver-si-ty sap-lings}

Other commands can be added as needed. Warning:

Comments are not allowed.
Complex commands (e.g. \renewenvironment) must be entered on a single line otherwise they will be destroyed by knitr at the first knitting in HTML.

Forcing line breaks

Hyphenation is handled automatically in LaTeX. If a word is not hyphenated correctly, add its hyphenation in the preamble of the file with the command hyphenation (words are separated by spaces, hyphenation locations are represented by dashes).

If LaTeX can’t find a solution for the line break, for example because some code is too long a non-breaking block, add the LaTeX command \break to the line break location. Do not leave a space before the command. The HTML document ignores LaTeX commands.

Languages

Languages are declared in the document header.

The main language of the document (lang) changes the name of some elements, such as the table of contents. The change of language in the document (one of otherlangs) is managed in LaTeX but not in HTML by inserting on a new line the following command:

\selectlanguage{english}

The current language has an effect only in LaTeX output: a space is added before double punctuation in French, the size of spaces is larger at the beginning of sentences in English, etc. The \selectlanguage command is simply ignored in HTML.

Language codes are used in the header, such as en-US but language names are necessary in `. Name matches are listed in table 3 of the polyglossia package documentation⁴.

Word

Word outputs can be formatted or copied into a template. The standard text styles are “First Paragraph” and “Body Text” rather than “Normal”.

The Word format allows to produce a manuscript for journals that do not support LaTeX. The bibliographic style of the journal is most likely available in .csl format, which minimizes manual preparation.

The level 1 title References must be added manually to Word files.

References

Xie, Yihui. 2016. Bookdown: Authoring Books and Technical Documents with R Markdown. Boca Raton, Florida: Chapman; Hall/CRC. https://github.com/rstudio/bookdown.

Xie, Yihui, J. J. Allaire, and Garrett Grolemund. 2018. R Markdown: The Definitive Guide. Boca Raton, Florida: Chapman; Hall/CRC. https://bookdown.org/yihui/rmarkdown.