Inline R Code in Yaml for Rmarkdown Doesn't Run

Inline R code in YAML for rmarkdown doesn't run

This is how I solved this. I knit from RStudio. Curiously, I had to use one solution for the date and csl fields and a different solution for the bibliography field. !expr did not work in the date or csl lines (for me). And quoted r code didn't work in the bibliography line (for me). I have the bibliography and csl files in a package (inst/docs folder). rmarkdown files, which are not part of that package, use those.

---
title: "Title"
date: '`r format(Sys.time(), "%d %B, %Y")`'
output: html_document
bibliography: !expr system.file("docs", "my.bib", package = "MyPackage")
csl: '`r system.file("docs", "my.csl", package = "MyPackage")`'
---

# Introduction

Yada yada [@MyRef04].

# References

my.bib is the BibTex file with MyRef04. csl is the style file

This is a situation where one person maintains a package which has data, code, bibliography, etc. Others, potentially unknown to the package writer, install that package from GitHub and write or run rmarkdown files that use the package. The users almost certainly do not use Git or GitHub and I don't want them to have to download any extra files after installing the package from GitHub.

Update: After posting the above, I happened to install markdown from GitHub because I needed something in the development version. With version ‘1.7.5’ of rmarkdown on GitHub you can use r code in the bibliography line:

---
title: "Title"
date: '`r format(Sys.time(), "%d %B, %Y")`'
output: html_document
bibliography: '`r system.file("docs", "my.bib", package = "MyPackage")`'
csl: '`r system.file("docs", "my.csl", package = "MyPackage")`'
---

To install rmarkdown from GitHub

library(devtools)
install_github("rstudio/rmarkdown")

Quotes and inline R code in Rmarkdown YAML

The fontawesome::fa() function returns a SVG element.

For instance, the string returned by fontawesome::fa("twitter", fill = "steelblue") is:

<svg style="height:0.8em;top:.04em;position:relative;fill:steelblue;" viewBox="0 0 512 512">
  <path d="M459.37 151.716c.325 4.548.325 9.097.325 13.645 0 138.72-105.583 298.558-298.558 298.558-59.452 0-114.68-17.219-161.137-47.106 8.447.974 16.568 1.299 25.34 1.299 49.055 0 94.213-16.568 130.274-44.832-46.132-.975-84.792-31.188-98.112-72.772 6.498.974 12.995 1.624 19.818 1.624 9.421 0 18.843-1.3 27.614-3.573-48.081-9.747-84.143-51.98-84.143-102.985v-1.299c13.969 7.797 30.214 12.67 47.431 13.319-28.264-18.843-46.781-51.005-46.781-87.391 0-19.492 5.197-37.36 14.294-52.954 51.655 63.675 129.3 105.258 216.365 109.807-1.624-7.797-2.599-15.918-2.599-24.04 0-57.828 46.782-104.934 104.934-104.934 30.213 0 57.502 12.67 76.67 33.137 23.715-4.548 46.456-13.32 66.599-25.34-7.798 24.366-24.366 44.833-46.132 57.827 21.117-2.273 41.584-8.122 60.426-16.243-14.292 20.791-32.161 39.308-52.628 54.253z"/>
</svg>

This string contains double quotes: this is the reason why single quoting leads to a proper result and double quoting does not perform well.

It is clear if you inspect the intermediate markdown file using the keep_md option:

---
title: "Untitled"
subtitle: "`r fontawesome::fa('twitter', fill = 'steelblue')` @twitter handle"
author: "My Name"
date: "7/12/2018"
output: 
  html_document:
    keep_md: true
---

These quoting considerations can be done away using YAML literal or folded blocks:

subtitle: |
    `r fontawesome::fa('twitter', fill = 'steelblue')` @twitter handle

or

subtitle: >
    `r fontawesome::fa('twitter', fill = 'steelblue')` @twitter handle

Include YAML file in RMarkdown document

I think the easiest way is that you read the external file in an inline R expression, e.g.,

```yaml
`r xfun::file_string('envs/r40_tidyverse.yaml')`
```

Note that you should not use ```{yaml} (i.e., do not add {} to yaml), because that would change its meaning to knitr:

• With curly braces, it means a code chunk, and a knitr language engine needs to evaluate the code chunk (but there is not a yaml engine yet, and your first example worked just by chance).
• Without curly braces, it means a normal code block, which will not be processed by knitr.

Rmarkdown - python inline code in Rmarkdown

Not sure whether this is possible. All examples I have found use R inline code like so `r py$x` to achieve that. See e.g. the rmarkdown cookbook.

YAML current date in rmarkdown

This is a little bit tricky, but you just need to make the date field valid in YAML by quoting the inline R expression, e.g.

date: "`r format(Sys.time(), '%d %B, %Y')`"

Then the parsing error will be gone, and the date will be generated in the markdown output so Pandoc can use the value from Sys.time().

---

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