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.
Probably a basic question but I can't see how to knit my RMarkdown document into a Word document. I've checked the various ReadMe's e.g. https://crsh.github.io/papaja_man/ but can't see anywhere where it is spelled out. Any help is appreciated.
If you are looking to produce a Word document in APA style using papaja you can change the default output specified in the YAML front matter to the following:
---
output: apa6_docx
---
This is also mentioned in the package manual.
I believe you have to specify it in your yaml header as such:
---
title: TITLE
author: AUTHOR
output: word_document
---
Also, the manual does note that there functions won't work when converting into word.
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 started using bookdown to generate a longer report, but came into some touble as I wanted to customize the pdf output. \documentclass[]{} does not work in the preamble.tex file. I think that comand is somehow executed by pandoc beforhand, unfortunately I did not find out how to pass options to it so far.
I worked around a few things like setting the fontsize via \usepackage[12pt]{moresize} but I was wondering how to acces the set up options properly. The bookdown documentation does not cover this subject in sufficient detail for me to understand.
Look at this BookDown Documentation,
You can just add following in your header yaml,
---
documentclass: book
bibliography: [book.bib, packages.bib]
biblio-style: apalike
---
I found the answer in the Pandoc documentation
I am writing a report in R markdown (using pdflatex to convert it into pdf) and I am trying to set the style of the different headers (color, size, interline before and after).
I am using this formalisation :
#H1
##H2
###H3
I have the basics of Markdown and LaTeX but I'm far to be an expert. Is there a way to do it without creating a LaTeX template ? For exemple with some YAML code in the head of the document ?
Mine for now :
---
title: "Guide"
output:
pdf_document:
fig_caption: yes
highlight: tango
toc: yes
toc_depth: 2
documentclass: report
---
Or by changing the R options ?
```{r set-options, echo=FALSE, cache=FALSE}
options(some stuff)
```
I've found some indications while searching that suggest it may be possible, but I could'nt manage to find any understandable exemple ...
Thanks for any feedback.
If you do not want to do any LaTeX, you could add your own CSS (see documentation) and set it that way, as in this answer.
You would then need to do: How to convert Markdown + CSS -> PDF?
However, your results may not be as faithfully rendered as if you create a LaTeX template.