Use additional Latex packages for math expressions in RMarkdown `output = "html_document"` - r-markdown

I`m aware how to use additional Latex-packages for pdf-format output from .Rmd files using
---
header-includes:
- \usepackage{mathtools}
---
in the YAML header.
However, this does (of course) not work if one specifies output: html_document.
---
output: html_document
header-includes:
- \usepackage{mathtools}
---
Using additional Latex-Packages could be of interest for output: html_document, too - especially in math expressions (MWE below)
---
title: "MWE"
output: html_document
header-includes:
- \usepackage{mathtools}
---
## Use "Defined by" Symbol
$$sin(x) \coloneqq \frac{opposite}{hypothenuse}$$

MathJax offer a number of extensions, and there are third-party extensions as well. If your desired package is not available in this way, then things get difficult.
Simple commands, such as \coloneqq, can be recreated using \newcommand. The simplest way is to add these via the include-before option. Using your MWE with a solution from Mathematics Meta SE, one gets:
---
title: "MWE"
output:
html_document: default
include-before:
- '$\newcommand{\coloneqq}{\mathrel{=}}$'
---
## Use "Defined by" Symbol
$$sin(x) \coloneqq \frac{opposite}{hypothenuse}$$
Output:
Background
RMarkdown is build around pandoc, which performs most of the format conversions. Pandoc creates PDF via LaTeX (by default), and will simply include any raw LaTeX commands which are given in the source. When seeing \usepackage{mathtools}, the package is not parsed, but the command is simply added verbatim to the intermediate LaTeX. However, when exporting to HTML, it wouldn't make sense to pass through LaTeX commands, so any such command will simply be omitted from the output, so any \usepackage in your document won't effect the HTML output.
Alternative solution
If you are using very complex LaTeX-packages, then you could consider setting up a complex pipeline to still use it: E.g, one could use a pandoc filter to extract all equations, compile each equation as a separate document, and then convert the resulting PDF to SVG. Finally, that SVG can then be included in the HTML output. This is non-trivial and probably not worth the effort. A similar approach is recommended to include TikZ pictures.

Related

Dynamic footnote referencing in rmarkdown / bookdown

I am combining several .Rmd-files into one large document using bookdown. The individual files all contain footnotes, starting with ^[1]. This obviously leads to duplicate footnotes in the final document, with bookdown unable to assert which reference belongs to which footnote.
As a consequence, I am wondering whether there is a way to dynamically generate footnotes when the document is rendered, but I could not find anything related to that in the bookdown docs.
I have this working solution using a custom function:
---
title: "Untitled"
output:
html_document:
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
footnote.nr <- 0
footnote.counter <- function(){
footnote.nr <- footnote.nr + 1
.GlobalEnv$footnote.nr <- footnote.nr
return(footnote.nr)
}
```
Lorem ipsum.[^`r footnote.counter()`]
[^`r footnote.nr`]: Test
Lorem ipsum.[^`r footnote.counter()`]
[^`r footnote.nr`]: Test2
However, this would result in me having to retrofit the entire document which would be just as much manual labor as starting footnote numbering completely anew (though it is probably less error prone). Are there any other solutions? I would also be okay with footnotes being rendered for each individual chapter, meaning that the first footnote in each chapter starts with a 1.
In my humble opinion, #jtbayly's answer is only partially correct as using Rstudio's visual editing mode can indeed prompt it to make automatic changes to your text by adding a unique identifier before the citation (ex: [^love1]).
However, that did not initially work for me, and I had to add, for each child document the following option in the yaml header :
editor_options:
markdown:
references:
prefix: "[insert the unique identifier you want for this child document]"
This should then work, and would allow you to compile multiple .Rmd files into a single large document without RMarkdown/Pandoc messing with the citations. However, don't forget to go back to "Source" mode and "Visual" mode once after editing the yaml header for the editor to make the change.
Another option is to use Rstudio to edit your files, and turn on visual editing. If you do, it will make some automatic changes to your text, including giving your footnotes unique names.

Rmarkdown rticles - MDPI template. How to print your own abbreviations

I am using the MDPI template (from the rticles package), and keen to also use the glossaries packages so I don't have to manually feed all the abbreviation on the appropriate YAML field.
For such, I have loaded the LaTex package glossaries using the header-includes:
header-includes:
\usepackage{inputenc}
\usepackage[acronym, section=section]{glossaries}
\setacronymstyle{long-short}
\makeglossaries
\makeindex
\input{glossary}
after creating several acronyms within the Rmarkdown body, I would be willing to either input the latex commands and have it printed in within the "Abbreviations" section of the template.
Currently, I am able to hack it through the following steps (I am sure there is a better way):
1- keep all the aux files chunk with :
options(tinytex.clean = FALSE)
2- cmd makeglossaries "filename"
3- Raw Latex on Rmarkdown file:
\begin{abbreviations}
\setabbreviationstyle[acronym]{long-short}
\printglossary[type=\acronymtype,title={}]
\end{abbreviations}
However, I would be keen to know if I could insert something on the YAML and use the MDPI formatting.
Alternatively, I could edit the rticles MDPI template (but I am not sure how).
Any ideas?
Cheers,
Include in YAML:
include-after: glossary.tex
I tried without success, but it seems reasonable that this approach might work with a few modifications

Bookdown: Password protect a *single* page/chapter in HTML

I am producing a Tutorial Workbook for my class using bookdown. I have a large class (500+), and so have a couple of other people helping me with the course.
So I would like to produce the answers for these tutorial questions.
I can produce a whole new document... but then it would be tricky to (automatically) cross-reference the exercise numbers.
So I wondered: Is there a way to password-protect a single page, or a single chapter, in bookdown? (Thinking HTML here; in PDF I can just not include that page/chapter.)
Is this possible? If so how? If not... any other ideas...?
P.
This solution does not use a password, but since you say that for PDF you can simply distribute a version that does not include the material in question, perhaps the following simple approach might help
Inspired by this question on how to conditionally input material as well as the option to use parameters in Rmarkdown, consider two Rmarkdown files:
main.Rmd, which contains what you want to show everyone.
protected.Rmd, which should only be shown to some people.
These files look as follows:
main.Rmd:
---
output: html_document
params:
include:
label: "Include extra material?"
value: ""
input: select
choices: [True, False]
---
```{r, include=FALSE}
print(params)
show_all <- as.logical(params$include)
```
```{r conditional_print, child="protected.Rmd", eval = show_all}
```
protected.Rmd:
Hello World!
Assuming you are in RStudio, if you choose "Knit with parameters" on main.Rmd, you will be asked to select either TRUE or FALSE from an interactive dropdown. If and only if you choose TRUE, the output will include "Hello World". More generally, code blocks with eval = show_all will only be displayed when selecting to include extra material. Therefore, you can of course have multiple sections (each contained in a separate .Rmd file) that are only conditionally included.
In this way, you could knit the same document twice: once with questions only, and once with questions and answers both. Since this is the same for both pdf and html, it also gives you a consistent workflow for both of these output types.

Chapter(s) before table of contents in Bookdown PDF output

I'd like for a chapter to appear before the table of contents (but after the title page) in the pdf_book output of Bookdown.
One way to do this is to add the chapter to a .tex file and and link it using before_body:. However, this means the chapter will not appear in gitbook (which I also need). I'd prefer not to keep both a .tex and .Rmd version of the same chapter.
An ideal solution would be if the chapter could be kept in a .Rmd file, and its contents extracted into the before_body for pdf_book. That way it's still available for gitbook. Though I'm not sure how I might do that, or indeed if it's possible?
Is there a solution? Or is it exceeding the limits of Bookdown's flexibility?
Any help would be greatly appreciated, thanks!
One can trigger ToC creation manually in the document, which gives more control over its placement. Of course, automatic table of contents creation should be disabled:
---
title: "MWE"
output:
bookdown::pdf_book:
toc: False
---
```{r child = 'file-you-want-to-include.Rmd'}
```
```{=latex}
% Trigger ToC creation in LaTeX
\tableofcontents
```
# Rest of your document starts here
The downside is that this only works with PDF output, not HTML.

Compiling reveal.js-based R markdown presentation without RStudio

Fairly recently, RStudio has added support for beautiful reveal.js-based HTML presentations generated from RMarkdown (with some extensions). These are different from earlier HTML presentation formats provided by the rmarkdown R package, which relied on ioslides or Slidy.
Is it possible to compile such a presentation to HTML without having recourse to RStudio? I.e. is there a pure R function which will, given an R presentation source file, generate the same result as the IDE?
P.S. I suppose the underlying R package doing the conversion is revealjs by JJ Allaire, but on its own, it doesn't recognize some of the syntax extensions (e.g. those for customizing appearance by putting css: custom.css under the title of the first slide), which makes me think there must be an additional wrapper around it.
You can use the standard rmarkdown::render() function with the revealjs::revealjs_presentation format in the YAML header. Resources like custom.css are referenced relative to the Rmd location so there is no need to specify these within the render() step.
User notes on specific implementation diffs between native RStudio & scripted version
It's not a drop-in replacement though. The revealjs package, as it's available from CRAN, ships with a different (newer) version of the reveal.js library than the one used internally by RStudio (3.2 vs 2.4 as of March 8th, 2016). The default settings (e.g. transitions) are also different, so they need tweaking.
Circumspection is also warranted with the version of pandoc used as the workhorse for the Markdown → HTML conversion, as RStudio may internally be using an older one with different templates. All of this means that you may need to rework your customizations (e.g. css tweaks).
There are also syntax differences -- the metadata can't go under the first heading of the presentation (i.e. the title):
Presentation title
==================
author: Foo Bar
css: custom.css
Instead, they have to be put in a traditional RMarkdown YAML header:
---
author: Foo Bar
css: custom.css
---
I'm not sure whether per-slide special settings like incremental: true (which are put under the respective slide's heading in the RPresentation format) are recognized at all.
I use a script like this that I source to render my reveal.js markdown slides:
library(rmarkdown)
library(revealjs)
file.name <- "index"
path.to.file <- "."
rmarkdown::render(file.path(path.to.file, paste0(file.name, ".Rmd")),
revealjs_presentation(theme="white", highlight="tango", slideNumber = TRUE),
encoding = "UTF-8")
# Open the generated HTML file in the browser
browseURL( file.path(path.to.file, paste0(file.name, ".html")))