I'm having some trouble to compile an entire document from many Rmd files by using the bookdown approach.
If I knit individual .Rmd files then 'preamble.tex' included in YAML options is taken into account.
If I render the book (with both approaches described here), then 'preamble.tex' is ignored.
To make things concrete, consider the following mwe:
preamble.tex:
\usepackage{times}
index.Rmd:
---
title: "My paper"
site: "bookdown::bookdown_site"
output:
bookdown::pdf_document2:
includes:
in_header: "preamble.tex"
---
01-intro.Rmd:
# Introduction
This chapter is an overview of the methods that we propose to solve an **important problem**.
Then, by knitting 'index.Rmd' or '01-intro.Rmd' the font indicated in 'preamble.tex' is used.
However when rendering with bookdown::render_book('index.Rmd',"bookdown::pdf_book", new_session = T) it is simply ignored.
What is more, in my actual project there are other output options that end up ignored. For example, I use toc: false and it works when knitting single files, but fails when rendering the document.
In this simple example it would be okay to use a single file, but my actual project has many chapters with R chunks within each of them. Thus, building a single file doesn't seem a good idea.
I appreciate any hints on what I am missing here.
Thanks in advance.
What you are missing here is that in your YAML header, preamble.tex is included for the bookdown::pdf_document2 output format and not bookdown::pdf_book, the format you pass to the output_format argument in bookdown::render_book(). For this reason, other YAML options (like toc: true) do not work either.
Running
bookdown::render_book('index.Rmd', "bookdown::pdf_document2", new_session = T)
instead should work.
Related
I need the output to be portable so all the file paths need to be relative to the root directory of the project not absolute paths. I also need to set the figure size so I can't fall back on markdown and just use but knitr insists on creating an absolute path in my output. I've tried setting root.dir & base.dir and fig.path in various combinations but I keep getting an absolute path in my output. Setting root.dir = "/" does change the path in my output but setting it to "" or "./" still results in an abs path so this is not helping produce a portable output.
My rmarkdown::render is being run from the same directory as the Rmd file, the output is to this same directory and the graphics files are in a sub-directory of the one with the notebook. Is the a way I can make knitr just us the paths I give it and not try to transform them in any way?
Issues with knitr & paths seem to be a common problem and there are a lot of stub Q&As out there in search results which often don't satisfactorily resolve the problem, or if they do resolve it the questioner and/or answer seem unclear on why it worked.
I've referred to https://yihui.org/knitr/ & https://bookdown.org/yihui/rmarkdown/ and I still don't have a satisfactory understanding of how to control output paths with knitr could someone help me understand how to control this or point me in the direction of a resource that can?
OK so calmed down and I tried to make a reprex, I found some interesting behaviour.
The graphics folder is a symlink to a folder in the parent directory and this works fine if I use as basic html_document output but when I use the revealjs::revealjs_presentation output I get different results in the basics document the img tag contains:
src="data:image/jpeg;base64,/9j/4AAQSkZJRgABAQAAAQABAAD......."
and in the presentation contains:
src="/home/richardjacton/project/graphics_test/example.jpg"
Now this does not work because I need to be able to move the directory containing the presentation and it's assets to somewhere else and have it work once built.
If I go in with inspect element and edit it to src="./graphics/example.jpg" that works.
Also If I make a real directory instead of a symlink to the a directory in the parent then I get src="graphics/example.jpg" in the revealjs output
---
title: "Example"
author: "Richard J. Acton"
date: "`r Sys.Date()`"
# output:
# html_document:
# df_print: paged
output:
revealjs::revealjs_presentation:
theme: dark
highlight: zenburn
center: true
self_contained: false
reveal_plugins: ["notes"]
reveal_options:
slideNumber: true
previewLinks: true
fig_caption: true
---
# Example
```{r, echo=FALSE, include=FALSE, message=FALSE}
fs::dir_create("../graphics_test/")
download.file("https://i.ytimg.com/vi/0hMr5-05bFc/maxresdefault.jpg", "../graphics_test/example.jpg")
fs::link_create("../graphics_test", "graphics")
# fs::dir_create("graphics")
# download.file("https://i.ytimg.com/vi/0hMr5-05bFc/maxresdefault.jpg", "graphics/example.jpg")
```
```{r, out.width='80%', echo=FALSE}
knitr::include_graphics("graphics/example.jpg")
```
In my real case I'm creating a presentation from inside a {targets} project that's also has a {bookdown} project in it that produces a report based on the pipeline. So the presentation lives in a sub-directory so I can exclude it from the bookdown build. I explicitly built the presentation with an rmarkdown::render call as the knit button in the gui wants to try and render the book: rmarkdown::render("test.Rmd",envir = new.env()). Also this is all in a directory mounted to a docker container that's running my RStudio server instance so I have a portable and reproducible working environment for any non-R dependencies of my pipeline.
So this is why I was looking for a resource with a more in depth explanation of what exactly happens when I make a knitr::include_graphics call because this is the sort of weird edge case I seem to encounter a lot and get stuck trying to debug. Thanks for the response #YihuiXie I love your work and use it daily - sorry for offering you the opportunity to engage with this particular headache.
I'd like to include LaTeX environments (e.g., algorithmic from algorithmicx, mini from optidef, dcases from mathtools, etc.) in my .Rmd bookdown file. This is no problem for pdf output. But these do not render for html or docx output.
My current hack solution:
Generate the .pdf output.
Screen shot, edit, save images of interest as png
Include images conditional on output not being LaTeX
Downsides:
Obviously doesn't scale
Images are ugly in docx and html output
Screws with figure cross-referencing
There has to be a better approach, right? I was thinking that there's a way to tell rmarkdown/LaTeX that, when rendering as pdf, certain code chunks should be saved in some image format. That way they could be added back into the document as images conditional on the output document being docx or html. Is that even possible?
UPDATE: An answer to Standalone diagrams with TikZ suggests an approach involving the LaTeX standalone package. But unfortunately, it's discovered over at standalone does not work with algorithms that this does not work for the algorithm environment. Any ideas?
index.Rmd
---
title: "Bookdown"
header-includes:
- \usepackage{float}
- \floatplacement{figure}{!htb}
- \usepackage{algorithm}
- \usepackage{algpseudocode}
output:
bookdown::gitbook:
split_by: none
bookdown::pdf_book:
fig_caption: yes
keep_tex: yes
toc: no
bookdown::word_document2: default
site: bookdown::bookdown_site
---
```{r setup, include=FALSE, }
knitr::opts_chunk$set(echo = TRUE)
```
Hello zero
# First Chapter
Hello one
\begin{algorithm}
\caption{My Algo}
\begin{algorithmic}[1]
\State Do this.
\State Do that.
\end{algorithmic}
\end{algorithm}
```{r myalgo, echo=FALSE, eval = !knitr:::is_latex_output(), fig.cap="Must have text here. For cross-referencing to work."}
knitr::include_graphics("myalgo.png")
```
Hello two.
Check out this picture: \#ref(fig:myalgo)
myalgo.png
For math, R Markdown uses MathJax, and only a subset of LaTeX is available. This subset includes the basic math macros and environments, and allows you to define new macros, but doesn't support everything necessary to let you use arbitrary LaTeX packages. See http://docs.mathjax.org/en/latest/tex.html for details.
You might be able to create an environment that looks something like algorithm or algorithmic, but it's going to be a lot of work, and likely won't look as nice.
You should probably choose between PDF output with all of LaTeX available for formatting, or some flavour of HTML output with less style. For example, you could write your algorithm as
******
**Algorithm 1**: My algo
******
1. Do this.
2. Do that.
******
and it will display as
Algorithm 1: My algo
Do this.
Do that.
Is it possible to have multiple sets of shared options for R Markdown?
This is my problem: I have a folder with a bunch of markdown files. The files can be divided into two groups:
html_document and
revealjs::revealjs_presentation.
I would like to factor out common YAML code from each of these groups. Now I know that I can create a _output.yaml file which would capture common YAML, but I essentially need to have two of these files, one for each of the output formats.
I saw the use of pandoc_args suggested here and I gave it a try as follows:
---
title: Document Type 1
output:
html_document:
pandoc_args: './common-html.yaml'
---
and
---
title: Document Type 2
output:
revealjs::revealjs_presentation:
pandoc_args: './common-reveal.yaml'
---
However using this setup the options from the included YAML files don't get processed.
Any other suggestions would be appreciated!
You can specify multiple output formats in the same _output.yaml file like this (just some example options):
html_document:
self_contained: false
revealjs::revealjs_presentation:
incremental: true
Then you have to render all output formats which cannot be done directly using the RStudio GUI. Instead you have to enter the following into the R console:
rmarkdown::render(input = "your.Rmd",
output_format = "all")
Ideally make sure that there's no output key in the YAML front matter of the .Rmd document itself. Otherwise the output options in _output.yaml file might get overridden. Unfortunately I couldn't find a comprehensive documentation of the exact behavior. Some of my observations so far:
Output options defined in the YAML front matter of the .Rmd document itself always override those specified in the shared options file _output.yaml.
Specifying an output format using the default option set (like pdf_document: default) in the YAML front matter of the .Rmd document itself completely overrides all options specified in _output.yaml. But if you don't explicitly specify the default options (like output: pdf_document; which is only possible for a single output format at once), the _output.yaml content is fully regarded.
If you have specified options for multiple output formats in _output.yaml, only the first one gets rendered when pressing the knit button in RStudio (even if you explicitly press knit to HTML/PDF/Word). You have to use rmarkdown::render(output_format = "all") to render the other formats, too.
When trying to knit a PDF using a template from package rticles output: rticles::acm_article I get the following error:
! LaTeX Error: Environment Shaded undefined.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
l.76 \begin{Shaded}
This appears to only happen when I include code chunks within the output document.
Reproducible example:
You will need to start a new R Markdown document using the New Document -> From Template -> Association for Computing Machinery. Here is the R Markdown file:
---
title: Short Paper
author:
- name: I Am Me
email: me#email.com
affiliation: Fictional University
abstract: |
This is the abstract.
It consists of two paragraphs.
output:
rticles::acm_article:
keep_tex: true
---
## Simple test
Code chuck follows:
```{r}
plot(rnorm(10))
```
This above example, however, works if I set echo=FALSE in the header. You won't get code in the output, but for an academic paper you probably don't need it anyway, an if you do you can display it in a different manner.
Notes:
R version 3.3.1 (2016-06-21)
Platform: x86_64-pc-linux-gnu (64-bit),
running Ubuntu 16:10
I made sure I have the texlive-latex-base, texlive-latex-recommended, and texlive-latex-extra package installed, but still no luck
I also tried generating a pdf from the intermediate .tex file, as suggested here, but I get the same error.
I considered this approach, but it didn't work, I still got an error (maybe I need to tweak to work in my context, but not sure how)
So, the issue here is the rticles templates sometimes omit a means for pandoc to inject code highlighting environments, e.g. Shaded. To get around this, you would have to insert into the template.tex preamble:
$if(highlighting-macros)$
$highlighting-macros$
$endif$
I struggled with fixing the error and actually raised another question which I was able to answer after quite some experimentation and searching for other related questions/answers.
In short the solution presented above by coatless works perfect given you know the location of the template.tex file. Obviously, I played around with the wrong files before I came across a related question on rticles and how to embed (missing) LATEX.
The longer answer can be found in my "another question". For reference here are the key steps:
locate the template.tex file in your R package rticles library. If you do not know where you have your package library use .libPaths() in your RStudio console. Then work your way to the resources subfolder of your rticle template. In my case:
R-3.5.0/library/rticles/rmarkdown/templates/ieee_article/resources.
add the fix proposed by coatless above in the preamble of the template.tex. The preamble is anything before the line \begin{document}:
$if(highlighting-macros)$
$highlighting-macros$
$endif$
save template.tex and go back to R/RStudio and hit the knit button. R code chunks are now nicely displayed, if you do not suppress their printing with echo = FALSE.
I know the post is old, but I'll put this here for reference for others who have the same problem.
The reason is that in the latex template the environment Shaded is trying to be redefined. However the environment only exists if you are using R chunks in your pdf. So if you don't have any r chunks in the pdf, it tries to redefine something which was never defined - causing the error.
The solution is to modify the \renewenvironment{Shaded} command in the latex template.
https://github.com/yihui/bookdown-chinese/commit/a3e392593b464ba31a7eceb0cd60f7e0bd112798
I found a work around. If I hide the code with chunk option echo = FALSE, a PDF is generated with no issues.
Reproducible example 1:
title: Short Paper
author:
- name: I Am Me
email: me#email.com
affiliation: Fictional University
abstract: |
This is the abstract.
It consists of two paragraphs.
bibliography: sigproc.bib
output:
rticles::acm_article:
keep_tex: true
---
## Simple test
Code chuck follows:
```{r}
plot(rnorm(10))
```
Knit to PDF fails with ! LaTeX Error: Environment Shaded undefined.
Example 2:
---
title: Short Paper
author:
- name: I Am Me
email: me#email.com
affiliation: Fictional University
abstract: |
This is the abstract.
It consists of two paragraphs.
bibliography: sigproc.bib
output:
rticles::acm_article:
keep_tex: true
---
## Simple test
Code chuck follows:
```{r echo=FALSE}
plot(rnorm(10))
```
Knit to PDF works!.
The only difference between the two examples is adding echo=FALSE to the code chunk header. You won't get code in the output, but for an academic paper you probably don't need it anyway, an if you do you can display it in a different manner.
The rticles templates typically do not directly allow shading of code. As a result,
the required $highlighting-macros$ which is used to control the shading is not included.
If for any reason, you cannot (or do not) want to directly edit the template.tex file as suggested by #coatless, you can alternatively consider include the code directly in the acm_proc_article-sp.cls file:
\usepackage{color}
\usepackage{fancyvrb}
\newcommand{\VerbBar}{|}
\newcommand{\VERB}{\Verb[commandchars=\\\{\}]}
\DefineVerbatimEnvironment{Highlighting}{Verbatim}{commandchars=\\\{\}}
% Add ',fontsize=\small' for more characters per line
\usepackage{framed}
\definecolor{shadecolor}{RGB}{248,248,248}
\newenvironment{Shaded}{\begin{snugshade}}{\end{snugshade}}
\newcommand{\KeywordTok}[1]{\textcolor[rgb]{0.13,0.29,0.53}{\textbf{#1}}}
\newcommand{\DataTypeTok}[1]{\textcolor[rgb]{0.13,0.29,0.53}{#1}}
\newcommand{\DecValTok}[1]{\textcolor[rgb]{0.00,0.00,0.81}{#1}}
\newcommand{\BaseNTok}[1]{\textcolor[rgb]{0.00,0.00,0.81}{#1}}
\newcommand{\FloatTok}[1]{\textcolor[rgb]{0.00,0.00,0.81}{#1}}
\newcommand{\ConstantTok}[1]{\textcolor[rgb]{0.00,0.00,0.00}{#1}}
\newcommand{\CharTok}[1]{\textcolor[rgb]{0.31,0.60,0.02}{#1}}
\newcommand{\SpecialCharTok}[1]{\textcolor[rgb]{0.00,0.00,0.00}{#1}}
\newcommand{\StringTok}[1]{\textcolor[rgb]{0.31,0.60,0.02}{#1}}
\newcommand{\VerbatimStringTok}[1]{\textcolor[rgb]{0.31,0.60,0.02}{#1}}
\newcommand{\SpecialStringTok}[1]{\textcolor[rgb]{0.31,0.60,0.02}{#1}}
\newcommand{\ImportTok}[1]{#1}
\newcommand{\CommentTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{\textit{#1}}}
\newcommand{\DocumentationTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{\textbf{\textit{#1}}}}
\newcommand{\AnnotationTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{\textbf{\textit{#1}}}}
\newcommand{\CommentVarTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{\textbf{\textit{#1}}}}
\newcommand{\OtherTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{#1}}
\newcommand{\FunctionTok}[1]{\textcolor[rgb]{0.00,0.00,0.00}{#1}}
\newcommand{\VariableTok}[1]{\textcolor[rgb]{0.00,0.00,0.00}{#1}}
\newcommand{\ControlFlowTok}[1]{\textcolor[rgb]{0.13,0.29,0.53}{\textbf{#1}}}
\newcommand{\OperatorTok}[1]{\textcolor[rgb]{0.81,0.36,0.00}{\textbf{#1}}}
\newcommand{\BuiltInTok}[1]{#1}
\newcommand{\ExtensionTok}[1]{#1}
\newcommand{\PreprocessorTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{\textit{#1}}}
\newcommand{\AttributeTok}[1]{\textcolor[rgb]{0.77,0.63,0.00}{#1}}
\newcommand{\RegionMarkerTok}[1]{#1}
\newcommand{\InformationTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{\textbf{\textit{#1}}}}
\newcommand{\WarningTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{\textbf{\textit{#1}}}}
\newcommand{\AlertTok}[1]{\textcolor[rgb]{0.94,0.16,0.16}{#1}}
\newcommand{\ErrorTok}[1]{\textcolor[rgb]{0.64,0.00,0.00}{\textbf{#1}}}
\newcommand{\NormalTok}[1]{#1}
You may also wish to see my answer to a similar question, whereby the same code is put into a header.tex file in the same directory as your project.
I have a few Rmd documents that all have the same YAML frontmatter except for the title. How can I keep this frontmatter in one file and have it used for all the documents? It is getting rather large and I don't want to keep every file in step every time I tweak the frontmatter.
I want to still
use the Knit button/Ctrl+Shift+K shortcut in RStudio to do the compile
keep the whole setup portable: would like to avoid writing a custom output format or overriding rstudio.markdownToHTML (as this would require me to carry around a .Rprofile too)
Example
common.yaml:
author: me
date: "`r format (Sys.time(), format='%Y-%m-%d %H:%M:%S %z')`"
link-citations: true
reference-section-title: References
# many other options
an example document
----
title: On the Culinary Preferences of Anthropomorphic Cats
----
I do not like green eggs and ham. I do not like them, Sam I Am!
Desired output:
The compiled example document (ie either HTML or PDF), which has been compiled with the metadata in common.yaml injected in. The R code in the YAML (in this case, the date) would be compiled as a bonus, but it is not necessary (I only use it for the date which I don't really need).
Options/Solutions?
I haven't quite got any of these working yet.
With rmarkdown one can create a _output.yaml to put common YAML metadata, but this will put all of that metadata under output: in the YAML so is only good for options under html_document: and pdf_document:, and not for things like author, date, ...
write a knitr chunk to import the YAML, e.g.
----
title: On the Culinary Preferences of Anthropomorphic Cats
```{r echo=F, results='asis'}
cat(readLines('common.yaml'), sep='\n')
```
----
I do not like green eggs and ham. I do not like them, Sam I Am!
This works if I knitr('input.Rmd') and then pandoc the output, but not if I use the Knit button from Rstudio (which I assume calls render), because this parses the metadata first before running knitr, and the metadata is malformed until knitr has been run.
Makefile: if I was clever enough I could write a Makefile or something to inject common.yaml into input.Rmd, then run rmarkdown::render(), and somehow hook it up to the Knit button of Rstudio, and perhaps somehow save this Rstudio configuration into the .Rproj file so that the whole thing is portable without me needing to edit .Rprofile too. But I'm not clever enough.
EDIT: I had a go at this last option and hooked up a Makefile to the Build command (Ctrl+Shift+B). However, this will build the same target every time I use it via Ctrl+Shift+B, and I want to build the target that corresponds with the Rmd file I currently have open in the editor [as for Ctrl+Shift+K].
Have found two options to do this portably (ie no .Rprofile customisation needed, minimal duplication of YAML frontmatter):
You can provide common yaml to pandoc on the command-line! d'oh!
You can set the knit: property of the metadata to your own function to have greater control over what happens when you Ctrl+Shift+K.
Option 1: common YAML to command line.
Put all the common YAML in its own file
common.yaml:
---
author: me
date: "`r format (Sys.time(), format='%Y-%m-%d %H:%M:%S %z')`"
link-citations: true
reference-section-title: References
---
Note it's complete, ie the --- are needed.
Then in the document you can specify the YAML as the last argument to pandoc, and it'll apply the YAML (see this github issue)
in example.rmd:
---
title: On the Culinary Preferences of Anthropomorphic Cats
output:
html_document:
pandoc_args: './common.yaml'
---
I do not like green eggs and ham. I do not like them, Sam I Am!
You could even put the html_document: stuff in an _output.yaml since rmarkdown will take that and place it under output: for all the documents in that folder. In this way there can be no duplication of YAML between all documents using this frontmatter.
Pros:
no duplication of YAML frontmatter.
very clean
Cons:
the common YAML is not passed through knit, so the date field above will not be parsed. You will get the literal string "r format(Sys.time(), format='%Y-%m-%d %H:%M:%S %z')" as your date.
from the same github issue:
Metadata definitions seen first are kept and left unchanged, even if conflicting data is parsed at a later point.
Perhaps this could be a problem at some point depending on your setup.
Option 2: override the knit command
This allows for much greater control, though is a bit more cumbersome/tricky.
This link and this one mention an undocumented feature in rmarkdown: the knit: part of the YAML will be executed when one clicks the "Knit" button of Rstudio.
In short:
define a function myknit(inputFile, encoding) that would read the YAML, put it in to the RMD and call render on the result. Saved in its own file myknit.r.
in the YAML of example.rmd, add
knit: (function (...) { source('myknit.r'); myknit(...) })
It seems to have to be on one line. The reason for source('myknit.r') instead of just putting the function definition int he YAML is for portability. If I modify myknit.r I don't have to modify every document's YAML. This way, the only common YAML that all documents must repeat in their frontmatter is the knit line; all other common YAML can stay in common.yaml.
Then Ctrl+Shift+K works as I would hope from within Rstudio.
Further notes:
myknit could just be a system call to make if I had a makefile setup.
the injected YAML will be passed through rmarkdown and hence knitted, since it is injected before the call to render.
Preview window: so long as myknit produces a (single) message Output created: path/to/file.html, then the file will be shown in the preview window.
I have found that there can be only one such message in the output [not multiple], or you get no preview window. So if you use render (which makes an "Output created: basename.extension") message and the final produced file is actually elsewhere, you will need to suppress this message via either render(..., quiet=T) or suppressMessages(render(...)) (the former suppresses knitr progress and pandoc output too), and create your own message with the correct path.
Pros:
the YAML frontmatter is knitted
much more control than option 1 if you need to do custom pre- / post-processing.
Cons:
a bit more effort than option 1
the knit: line must be duplicated in each document (though by source('./myknit.r') at least the function definition may be stored in one central location)
Here is the setup for posterity. For portability, you only need to carry around myknit.r and common.yaml. No .Rprofile or project-specific config needed.
example.rmd:
---
title: On the Culinary Preferences of Anthropomorphic Cats
knit: (function (...) { source('myknit.r'); myknit(...) })
---
I do not like green eggs and ham. I do not like them, Sam I Am!
common.yaml [for example]:
author: me
date: "`r format (Sys.time(), format='%Y-%m-%d %H:%M:%S %z')`"
link-citations: true
reference-section-title: References
myknit.r:
myknit <- function (inputFile, encoding, yaml='common.yaml') {
# read in the YAML + src file
yaml <- readLines(yaml)
rmd <- readLines(inputFile)
# insert the YAML in after the first ---
# I'm assuming all my RMDs have properly-formed YAML and that the first
# occurence of --- starts the YAML. You could do proper validation if you wanted.
yamlHeader <- grep('^---$', rmd)[1]
# put the yaml in
rmd <- append(rmd, yaml, after=yamlHeader)
# write out to a temp file
ofile <- file.path(tempdir(), basename(inputFile))
writeLines(rmd, ofile)
# render with rmarkdown.
message(ofile)
ofile <- rmarkdown::render(ofile, encoding=encoding, envir=new.env())
# copy back to the current directory.
file.copy(ofile, file.path(dirname(inputFile), basename(ofile)), overwrite=T)
}
Pressing Ctrl+Shift+K/Knit from the editor of example.rmd will compile the result and show a preview. I know it is using common.yaml, because the result includes the date and author whereas example.rmd on its own does not have a date or author.
The first solution proposed by #mathematical.coffee is a good approach, but the example it gave did not work for me (maybe because the syntax had changed). As said so, this is possible by providing pandoc arguments in the YAML header. For example,
It's the content of a header.yaml file:
title: "Crime and Punishment"
author: "Fyodor Dostoevsky"
Add this to the beginning of the RMarkdown file:
---
output:
html_document:
pandoc_args: ["--metadata-file=header.yaml"]
---
See the pandoc manual for the --metadata-file argument.