Using R Markdown for reporting

Part 2

---

Background

We saw last time how to work with some of the basic formatting options when creating .html files in R Markdown. Here we will learn about some of the more advanced formatting options for creating nice looking documents. You should download the blank .Rmd template here, which contains some random text and other output options.

---

Basic info

The basic information in the YAML of a blank .Rmd document set for .pdf output includes the following.

title: "A catchy title"
author: "First Last"
date: "10 February 2025"
output: pdf_document

You can add a subtitle with the subtitle argument.

title: "A catchy title"
subtitle: "A pithy subtitle"  # a subtitle
author: "First Last"
date: "10 February 2025"
output: pdf_document

• You can set the date field to automatically update to the current date by using the R function Sys.Date() inline.

• You can use custom date formats as well.

For example, the following date option will print the current date as full-month-name day, four-digit-year (eg, February 10, 2025).

title: "A catchy title"
subtitle: "A pithy subtitle"
author: "First Last"
date: "`r format(Sys.time(), '%B %d, %Y')`"  # use current date with formatting
output: pdf_document

Type ?format() at the R command prompt to see options for various date formats.

---

Document layout

The default document layout for .pdf files in R Markdown is pretty good, but there are some options to improve it. These options are specified primarily in the document’s YAML, but some of them will be placed in the “chunk options” within R code blocks.

Appearance

We can change the overall appearance or class of the document with the documentclass argument, which you set in the YAML. The following subsections show some of the options.

Article

The article class is a basic layout that has relatively large margins.

title: "Example template for exploring formatting options"
author: "First Last"
date: "2/10/2025"
output: pdf_document
## use default article format
documentclass: article

Report

The report class will create a separate title page and insert page breaks between level-one section headings. It also has relatively large margins.

title: "Example template for exploring formatting options"
author: "First Last"
date: "2/10/2025"
output: pdf_document
## use default report format
documentclass: report

Two columns

You can create a document with two columns of text with the classoption argument. For example, here is an article with two columns.

title: "Example template for exploring formatting options"
author: "First Last"
date: "2/10/2025"
output: pdf_document
documentclass: report
## use 2-column text
classoption: twocolumn

Margins

You can set the margin spacing to be the same for all four sides, or set each of them separately, with the geometry argument. Here is an example of setting all of the margins in an article to 1.5 inches.

title: "Example template for exploring formatting options"
author: "First Last"
date: "2/10/2025"
output: pdf_document
documentclass: article
## set wider margins
geometry: margin=1.5in  

Here’s an example of setting the top and bottom margins in an article to 1 inch and the left and right margins to 1.25 inches.

title: "Example template for exploring formatting options"
author: "First Last"
date: "2/10/2025"
output: pdf_document
documentclass: article
## set different margins by location
geometry:
- top=1in
- bottom=1in
- left=1.25in
- right=1.25in

When using multiple settings in a YAML argument, we need to set them on separate lines preceded by a hyphen -.

You can also use metric units for margins.

Line spacing

You can increase the line spacing with the linestretch argument. For example, here is an article with 1-inch margins and double line spacing.

title: "Example template for exploring formatting options"
author: "First Last"
date: "2/10/2025"
output: pdf_document
documentclass: article
geometry: margin=1in
# use double-spaced text
linestretch: 2

Line numbers

You can add line numbers to .pdf documents, but it involves using an additional LaTeX package call lineno.

To use additional LaTeX packages, you have to set the header-includes argument in the YAML.

For example, here are the settings for a double-spaced article with 1-inch margins:

title: "Example template for exploring formatting options"
author: "First Last"
date: "2/10/2025"
output: pdf_document
## article
documentclass: article
## 1-in margins
geometry: margin=1in
## double-spaced
linestretch: 2
## include line numbers
header-includes:  
  - \usepackage{lineno}
  - \linenumbers

Fonts

Size

You can set the font size in your document with the fontsize argument. For example, here is a double-spaced article with 1-inch margins and 12-point font.

title: "Example template for exploring formatting options"
author: "First Last"
date: "2/10/2025"
output: pdf_document
documentclass: article
geometry: margin=1in
linestretch: 2
## use 12-pt font
fontsize: 12pt

Family

You can change the font family, but doing so depends on the LaTeX engine you are using.

You can check your LaTeX engine by examining the Global options in RStudio.

• Click on Tools > Global Opotions…

• In the dialogue box, select the Sweave option on the left and look at the setting for Typeset LaTeX into PDF using.

If your LaTeX distribution is TinyTeX and the required font packages have not been installed, they should be automatically installed when the document is knitted.

Settings for pdflatex

If you are using pdflatex, you can use the fontfamily argument to select a LaTeX font package to be loaded in your document to change the font. Also note that this requires you to use multi-line option specification for output like we saw for geometry above.

For example, this document will use the Arial font.

title: "Example template for exploring formatting options"
author: "First Last"
date: "2/10/2025"
output:
  pdf_document: 
    ## set LaTeX engine
    latex_engine: pdflatex
## set font to Arial
fontfamily: Arial
documentclass: article
geometry: margin=1in
linestretch: 2
fontsize: 12pt

Settings for XeLaTeX

If you using XeLaTeX or luaLaTeX, you will be able to select fonts that are available on your local computer, and do not have to install additional LaTeX packages. To do so, use the mainfont argument.

title: "Example template for exploring formatting options"
author: "First Last"
date: "2/10/2025"
output:
  pdf_document:
    ## set LaTeX engine
    latex_engine: xelatex
## set font to Arial
mainfont: Arial
documentclass: article
geometry: margin=1in
linestretch: 2
fontsize: 12pt

---

Front matter

You can add so-call front matter to your document, such as a table of contents.

Table of contents

To automatically create a table of contents, set the toc argument to true. You can control how many heading levels you want to display in the table of contents with the toc-depth argument. For example, here is a double-spaced report with 1-inch margins, 12-point font, and a table of contents that shows the first two heading levels.

title: "Example template for exploring formatting options"
author: "First Last"
date: "2/10/2025"
output: pdf_document
documentclass: report
geometry: margin=1in
linestretch: 2
fontsize: 12pt
## insert table of contents with level-2 headings
toc: TRUE
toc-depth: 2

Document version

For some documents, I prefer to set a custom version number based on the date rather than set the date argument explicitly. To do so, simply include a line in the main document (not in the YAML) similar to something like this:

This is version `r paste0('0.',format(Sys.time(), '%y.%m.%d'))`.

that will render to

This is version 0.25.07.19.

---

Figure placement

Unlike Microsoft Word, in which figures are placed directly where the user specifies, LaTeX will attempt to place a figure in a position that does not violate certain typographic rules. Thus, figures may “float away” from where they are referenced in the text. These so-called floats are used as containers for figures (and tables) that cannot be broken across pages.

In R Markdown, figures are actually generated with the figure environment in LaTeX. For example, Pandoc will convert the following Markdown code for specifying an image

![This is an image.](images/my_picture.jpg)

to the following LaTeX code:

\begin{figure}
  \includegraphics{images/my_picture.jpg}
  \caption{This is an image.}
\end{figure}

If the figure or table cannot be contained in the space remaining on the current page, LaTeX will try to place it at the top of the next page. If the figure is tall enough, it may occupy the whole next page, even if there is still space left for a few lines of text.

The float’s behavior can be controlled by using placement controls in square brackets like \begin{figure}[].

Here are some possible controls:

• h: Place the float here (or close to it)
  
• t: Position at the top of the page
  
• b: Position at the bottom of the page
  
• p: Put on a special page for floats only

You can override the default placement by prefacing the control with an exclamation point (eg, [!t]).

If you want to place the float at exactly the location in the LaTeX code, you will need to include a call to the float package in the YAML

title: "Example template for exploring formatting options"
author: "First Last"
date: "2/10/2025"
output: pdf_document
documentclass: article
geometry: margin=1in
linestretch: 2
fontsize: 12pt
toc: TRUE
toc-depth: 2
## use the {float} package
header-includes:
  - \usepackage{float}

---

Literature cited

You can create in-text citations and associated literature cited sections (bibliographies) in R Markdown with a few easy steps.

YAML setup

The first step in getting properly formatted citations and references in R Markdown documents is to add two fields to the document’s YAML:

1. bibliography: the name of of the .bib file containing the citation/reference information (see below);

2. csl: the name of the .csl style file that specifies how the references will be formatted in the printed docuement.

So, for example, the information for this document is

bibliography: "references.bib"
csl: "ecology.csl"

Each entry in the .bib file looks something like this:

@Book{Xie_2018,
  title = {R Markdown: The Definitive Guide},
  author = {Yihui Xie and J.J. Allaire and Garrett Grolemund},
  publisher = {Chapman and Hall/CRC},
  address = {Boca Raton, Florida},
  year = {2018},
  note = {ISBN 9781138359338},
  url = {https://bookdown.org/yihui/rmarkdown},
}

@Book specifies the reference is a book. Xie_2018 is the “citekey”, which is simply a short-hand name for the record (and can be alpha-numeric sequence); it’s used when making/creating in-text citations (see below). The rest of the fields contain metadata about the reference itself.

This document is set to use the style guidelines for the journal Ecology, as specified in ecology.csl.

You can download just about any journal’s style file here.

At this point there are two options for setting up your BibTeX file and creating in-text citations.

Option 1: Standard Markdown

Creating a .bib file

One option for creating a .bib file is to copy/paste records from other sources (e.g., the result of call to citation()). Online databases such as Web of Science also allow you to export references based upon saved searches, and there are several methods for exporting references from reference management software, such as Zotero, Mendeley, or EndNote.

Export from Zotero

To export your citations from Zotero, do the following

• Select the library you wish to export
  
• From the menu, choose File > Export Library
  
• On the next screen, choose BibTeX from the dropdown menu & click OK
  
• Navigate to the directory where you want to save your file & save it with a .bib suffix

Export from Mendeley

To export a reference library from Mendeley, do the following

• Go to the Mendeley Preferences menu

• Click on the BibTeX tab

• Check the box next to Enable BibTeX syncing

• Click the radio button next to Create one BibTeX file per group

• Change the Path to your desired location for the library files

• Click OK when you are finished

Export from EndNote

To export a reference library from EndNote, do the following

• From the main menu, select Edit > Output Styles > Open Style Manager...

• Enter “bibtex” into the search bar at the top of the pop-up window and check the box next to BibTeX Export

• Close the window when you’re finished

• From the main menu, select Edit > Output Styles and check the BibTeX Export option

• From the main menu, select File > Export...

• Make sure to give your filename a .bib suffix and verify that the options Text only and BibTeX Export are selected

• Click Save when you’re finished

In-text citations

There are two options for citations in R Markdown documents, both based upon the standard Author Year format. For example, if we had this reference in our .bib library:

@Article{Smith_2021,
  year = {2021},
  publisher = {The Ecological Society of America},
  volume = {123},
  number = {2},
  pages = {1-10},
  author = {Sarah Smith and Joe Johnson},
  title = {Probably the best paper ever written},
  journal = {Ecology},
}

we could use [@Smith_2021] to format the in-text reference as “(Smith and Johnson 2021)”, or we could use @Smith_2021 without the brackets to format the in-text reference as “Smith and Johnson (2021)”.

---

Option 2: {knitcitations}

Carl Boettiger and colleagues have created a really neat package called {knitcitations} for creating and citing BibTeX-style references via several mechanisms.

For this method to work properly, the .bib file you specify in the YAML must not exist in the working directory.

Initial setup

Place the following code block somewhere near the top of your document. For example, you could even include it within the default {r setup} block beneath the YAML.

## load the package
library("knitcitations")

## clear out any cached refs
cleanbib()

## set pandoc for formatting
options("citation_format" = "pandoc")

Creating a .bib file

Rather than creating a .bib file ahead of time, {knitcitations} actually creates it dynamically based upon the in-text citation calls when the .Rmd document is knit.

In-text citations

With {knitcitations}, you use R commands to both create an entry in the .bib file as well as create the in-text citation.

Cite by DOI

You can cite an article by its DOI, using either citep() or citet(), and the full citation information will be gathered automatically. For example, the inline command

`r citep("10.1890/11-0011.1")`

will do two things:

1. create an (Author[s] Year) inline citation that looks like “(Abrams et al. 2012)”;

2. create the following BibTeX reference that can be cited elsewhere using [@Abrams_2012] or @Abrams_2012:

@Article{Abrams_2012,
  doi = {10.1890/11-0011.1},
  url = {https://doi.org/10.1890/11-0011.1},
  year = {2012},
  month = {feb},
  publisher = {Wiley},
  volume = {93},
  number = {2},
  pages = {281--293},
  author = {Peter A. Abrams and Lasse Ruokolainen and Brian J. Shuter and Kevin S. McCann},
  title = {Harvesting creates ecological traps: consequences of invisible mortality risks in predator{\textendash}prey metacommunities},
  journal = {Ecology},
}

On the other hand, the inline command

`r citet("10.1098/rspb.2013.1372")`

will do two things:

1. create an Author[s] (Year) inline citation that looks like “Boettiger and Hastings (2013)”;

2. create the following BibTeX reference that can be cited elsewhere using [@Boettiger_2013] or @Boettiger_2013:

@Article{Boettiger_2013,
  doi = {10.1098/rspb.2013.1372},
  url = {https://doi.org/10.1098/rspb.2013.1372},
  year = {2013},
  month = {sep},
  publisher = {The Royal Society},
  volume = {280},
  number = {1766},
  pages = {20131372},
  author = {Carl Boettiger and Alan Hastings},
  title = {No early warning signals for stochastic transitions: insights from large deviation theory},
  journal = {Proceedings of the Royal Society B: Biological Sciences},
}

Cite BibTeX objects directly

We can also cite BibTeX objects directly, such as those that R provides for citing packages using the citation() function. So, for example, here are the citations for the {knitr} package

citation("knitr")

## To cite package 'knitr' in publications use:
## 
##   Xie Y (2025). _knitr: A General-Purpose Package for Dynamic Report
##   Generation in R_. R package version 1.50, <https://yihui.org/knitr/>.
## 
##   Yihui Xie (2015) Dynamic Documents with R and knitr. 2nd edition.
##   Chapman and Hall/CRC. ISBN 978-1498716963
## 
##   Yihui Xie (2014) knitr: A Comprehensive Tool for Reproducible
##   Research in R. In Victoria Stodden, Friedrich Leisch and Roger D.
##   Peng, editors, Implementing Reproducible Computational Research.
##   Chapman and Hall/CRC. ISBN 978-1466561595
## 
## To see these entries in BibTeX format, use 'print(<citation>,
## bibtex=TRUE)', 'toBibtex(.)', or set
## 'options(citation.bibtex.max=999)'.

We can use the following inline command

`r citep(citation("knitr"))`

to generate the 3 BibTeX objects as

@InCollection{Xie_2014,
  booktitle = {Implementing Reproducible Computational Research},
  editor = {Victoria Stodden and Friedrich Leisch and Roger D. Peng},
  title = {knitr: A Comprehensive Tool for Reproducible Research in {R}},
  author = {Yihui Xie},
  publisher = {Chapman and Hall/CRC},
  year = {2014},
  note = {ISBN 978-1466561595},
  url = {http://www.crcpress.com/product/isbn/9781466561595},
}

@Book{Xie_2015,
  title = {Dynamic Documents with {R} and knitr},
  author = {Yihui Xie},
  publisher = {Chapman and Hall/CRC},
  address = {Boca Raton, Florida},
  year = {2015},
  edition = {2nd},
  note = {ISBN 978-1498716963},
  url = {https://yihui.org/knitr/},
}

@Manual{Xie_2020,
  title = {knitr: A General-Purpose Package for Dynamic Report Generation in R},
  author = {Yihui Xie},
  year = {2020},
  note = {R package version 1.30},
  url = {https://yihui.org/knitr/},
}

and also create the formatted in-text citation

(Xie 2014, 2015, 2025).

We can now cite the package with normal BibTeX entries and pandoc will correctly avoid duplicating the author’s name. For example,

[@Xie_2014; @Xie_2015]

will produce a formatted in-text citation

(Xie 2014, 2015).

Similarly, we can cite references that are already included in our .bib file using the standard notation, such that

[@Boettiger_2013] or @Boettiger_2013

will render as

(Boettiger and Hastings 2013) or Boettiger and Hastings (2013).

Re-using BibTeX keys

When citep() or citet() are called, they automatically generate a BibTeX key in the format AuthorLastName_Year. We can then use this key to cite a reference without remembering its DOI. For example,

`r citep("Abrams_2012")`

will simply create the citation

(Abrams et al. 2012).

Creating the References section

Creating the References section is straightforward with {knitcitations}.

At the end of your document, insert a code block with a call to write.bibtex(file = "filename.bib"), where filename.bib is the name of the .bib file to which you would like the references written.

The function will then create the reference cited section using the formatting specified in the .csl file supplied in the document’s YAML.

For example, we can generate the references cited section from the citations in this tutorial with the following:

## create ref cited section
write.bibtex(file = "references.bib")

---

References

Abrams, P. A., L. Ruokolainen, B. J. Shuter, and K. S. McCann. 2012. Harvesting creates ecological traps: Consequences of invisible mortality risks in predator–prey metacommunities. Ecology 93:281–293.

Boettiger, C., and A. Hastings. 2013. No early warning signals for stochastic transitions: Insights from large deviation theory. Proceedings of the Royal Society B: Biological Sciences 280:20131372.

Xie, Y. 2014. Knitr: A comprehensive tool for reproducible research in R. in V. Stodden, F. Leisch, and R. D. Peng, editors. Implementing reproducible computational research. Chapman; Hall/CRC.

Xie, Y. 2015. Dynamic documents with R and knitr. 2nd edition. Chapman; Hall/CRC, Boca Raton, Florida.

Xie, Y. 2025. Knitr: A general-purpose package for dynamic report generation in R.

Placement of references

By default, formatted references in an R Markdown document will always be placed at the very end, but sometimes you might want to place them before other content like tables and figures.

You can specify a specific location for the reference cited section with the following code.

::: {#refs}
:::