R markdown: PDF, Word, and more
Sébastien Renaut
2018-09-06
Outputs
- We can output the same information in different ways
- .Rmd: The
R markdowndocument. - .html: A webpage.
- .docx: A MS Word document.
- .tex: A LaTeX document.
- .pdf: A Portable Document Format.
- .Rmd: The
1 html document
---
title: "rmarkdown_pdf"
author: "Sébastien Renaut"
date: '2018-09-06'
output:
html_document:
toc: yes
theme: cerulean
--- You can specify it when you create a new
Rmarkdowndocument.You can also specify it later in the header.
Then, it’s just a matter of kniting the document!
2 Microsoft Word
---
title: "rmarkdown_docx"
author: "Sébastien Renaut"
date: '2018-09-06'
output:
word_document:
toc: yes
--- Little documentation, few options & configurations are possible (This is probably not the format that should be promoted, as it moves away from an open source environment).
Can specify a LibreOffice OpenDocument Text (
output: odt_document) or Rich Text Format (output: rtf_document) instead.FYI, there is a spellchecker in
Rstudio: Edit >Check Spelling…
3 Portable Document Format (.pdf)
---
title: "rmarkdown_pdf"
author: "Sébastien Renaut"
date: '2018-09-06'
output:
pdf_document:
keep_tex: true
toc: yes
--- - You need an extra step to go from a LaTeX (.tex) format to a .pdf. This is handled by the
R tinytex pdflatexfunction in R.
3.1 LaTeX
LaTeX software is a high-quality typesetting system.
It is the de facto standard for the communication and publication of scientific documents.
LaTeX is available as a free software.
If interested, follow this discussion: Why LaTeX is such a bloated system?
- So…TinyTeX
- A custom LaTeX distribution that is small in size (~150MB) but functions well in most cases, especially for
Rusers . tinytex
is an R studio package that installs TinyTeX.
- A custom LaTeX distribution that is small in size (~150MB) but functions well in most cases, especially for
You should now have all the tools to generate your fully reproducible manuscripts in
R!
4 Exercice 1
- If you haven’t done so, install the
tinytexR package from the console and runinstall_tinytex()to install TinyTeX (It may take a few minutes to download and compile, ~150MB).
install.packages("tinytex")
library(tinytex)
install_tinytex() - Create a new document, compile it as .pdf.
- Add a Table of Content.
- Add a graphic.
Now compile it as a Word document (.docx)
Add some references by specifying the
csl(eg. csl : ../csl/peerj.csl) andbibliography(eg. bibliography : ../biblio/test_library.bib in the header.
5 Further customization
5.1 rticles
- R packages
rticlesis a (potentially) useful package to format articles according to the specification of a journal.
install.packages("rticles")- Once installed, you can start a new R markdown document according to your journal of interest.
Right now, few templates available.
Some templates may be slower to render, depending on what LaTeX package need to be installed.
5.2 LaTeX template: manuscript
This allows further options in the .Rmd file when going from .tex file to .pdf.
You can build your own .tex template if you know LaTeX…
But, there are also many templates available on the web that you can use.
Here is one I like for manuscripts (Thanks svmiller on
)For example, using this template, I am writing a scientific paper entirely in R markdown.
The only real objection I see against writing manuscript in
R markdownis integrating the comments of co-authors.
5.3 LaTeX template: CV
Here is a template I like for Curriculum Vitae
- For example, using this template, I re-wrote my CV to give it a fresh look!
- For example, using this template, I re-wrote my CV to give it a fresh look!
- Let’s briefly examine and knit the svm-rmarkdown-cv.Rmd file in the reference_material directory.
6 Presentations
---
title: "Untitled"
author: "Sebastien Renaut"
date: "27/02/2019"
output: ioslides_presentation
---- You can also generate Powerpoint-like presentations.
7 Bookdown
- Bookdown
is an open-source R package that facilitates writing books and long-form articles/reports with R Markdown.
