I'm writing a document in rmarkdown with the thesisdown template.
Related to the issue thesisdown-41: how can I add a new language for highlighting which is currently not supported?
The project mentioned in the link is derived from bookdown
Under the hood bookdown uses pandoc for tranforming markdown to HTML/PDF/.... From pandoc's manual at http://pandoc.org/MANUAL.html#syntax-highlighting we get:
The library used for highlighting is skylighting.
The list of available languages can be retrieved with pandoc --list-highlight-languages
Slightly off topic, but I just worked out how to do this in RMarkdown rather than Bookdown. I suspect you'll need this and maybe a little more.
Passing extra arguments to Pandoc via the YAML front-matter:
output:
html_document:
highlight: haddock
pandoc_args: ["--syntax-definition", "cobol.xml"]
Obtain the XML syntax definition file from somewhere (or create it). I got my COBOL one from:
wget http://kde.6490.n7.nabble.com/attachment/1163657/0/cobol.xml.gz
The syntax of the highliting file is as used by the Kate project in KDE.
Obtain the pre-req language.dtd file, this is some deep dependency with pandoc.
wget https://raw.githubusercontent.com/jgm/highlighting-kate/master/xml/language.dtd
If've just added the two files to my git repo, plus the YAML lines to my RMarkdown, and everything then worked on other developers machines.
Related
I am using exams2moodle() to create exam quizzes. I would like to use some math symbols which require the LaTeX package amssymb. How should I proceed?
TL;DR: amssymb LaTeX symbols are supported by MathJax which is the default renderer in a standard Moodle installation. So these symbols should work out of the box when using exams2moodle(..., converter = "pandoc-mathjax") which is the default sinc R/exams 2.3.3 (released in July 2019).
Details: As already pointed out by the answer of #Hack-R, there are various ways of including mathematical notation written in LaTeX in HTML-based exercises. An overview is given in this blog post: http://www.R-exams.org/tutorials/math/
It is important to note that in this case the LaTeX code is not actually processed by LaTeX itself. It can either be converted to MathML (using pandoc or ttm) or rendered in the browser by the MathJax JavaScript library. In any case it depends on the converter/renderer which LaTeX commands can be successfully displayed. All of them support basic LaTeX commands plus some extra commands from certain packages. Which additional commands from which packages are supported depends on the converter/renderer. In any case, the capabilities can not be extended by style files!
In a standard Moodle installation MathJax is enabled which suports the AMS LaTeX package (because MathJax was developed by/for the AMS!). So the best strategy is to simply keep the LaTeX in the HTML for Moodle. This can be done with exams2moodle(..., converter = "pandoc-mathjax") which is actually the default converter since R/exams 2.3.3 released in July 2019. In previous versions of R/exams, the default was converter = "ttm" which did not support all the amssymb symbols.
In general, you input your symbols into either .Rmd or .Rnw and you can have it rendered with any available engine (e.g. pandoc, mathjax, knitr, etc).
install.packages("exams")
require(exams)
xWeave is called on each exercise file and creates LaTeX code
elearn_exam <- c("swisscapital.Rmd", "deriv.Rmd", "ttest.Rmd",
"boxplots.Rmd", "function.Rmd", "lm.Rmd", "fourfold2.Rmd")
set.seed(2020-04-16)
exams2moodle() produces an XML file that may be uploaded into Moodle
It goes from LaTeX to HTML then HTML to XML
exams2moodle(elearn_exam, n = 3, name = "R-exams")
To add custom LaTeX packages you can modify the preamble as per the answers in this post, i.e. \usepackage
As described in the linked post, that can either be done direct, i.e.
---
title: "Title"
author: "Me"
header-includes:
- \usepackage{mypackage}
output:
pdf_document
---
or via a mystyles.sty file in the same directory.
I'm writing a paper using R Markdown and TinyTex, using Biblatex for referencing. It works fine with default referencing styles, but I need to add a custom bibliography and citation style for the journal I'm writing for.
I need to follow the Unified Stylesheet for Linguistics, for which there is a Biblatex implementation available on Github here, containing a .bbx and .cbx file.
I've tried adding those .bbx and .cbx files to my local copy of TinyTex, inside Library/TinyTex/texmf-local/tex/latex/biblatex. My YAML header includes:
output:
pdf_document:
citation_package: biblatex
biblatexoptions: [bibstyle=biblatex-sp-unified, citestyle=sp-authoryear-comp]
When I knit the document, I get the following error:
tlmgr search --file --global '/biblatex-dm.cfg'
! Package keyval Error: bibstyle undefined.
I don't have a biblatex-dm.cfg file (nor do I really understand what that would be). I would have thought the .bbx and .cbx files would be sufficient, based on the regular installation instructions in the style's Github repo.
Where should I put .bbx and .cbx files, so that tlmgr can find them? And/or what additional steps do I need to take to use this style with my paper?
====================================================================
UPDATE: The problem seems to be coming from the Pandoc LaTeX template that R Markdown uses.
Setting aside R Markdown, I created a smaller minimal LaTeX example:
main.tex
references.bib
Where main.tex is:
\documentclass{article}
\usepackage[utf8]{inputenc}
\usepackage[bibstyle=biblatex-sp-unified,citestyle=sp-authoryear-comp]{biblatex}
\addbibresource{references.bib}
\begin{document}
Something something \citep{darwin_origin_1859}.
\printbibliography
\end{document}
And references.bib is:
#book{darwin_origin_1859,
location = {London},
title = {On the Origin of Species by Means of Natural Selection},
publisher = {J. Murray},
author = {Darwin, Charles},
date = {1859}
}
I had success compiling this example using the sequence of commands pdflatex, biber, pdflatex, pdflatex. Thus it seems my local TeX installation knows about the biblatex-sp-unified.bbx and sp-authoryear-comp.cbx files I added and can use them just fine.
Subsequently, I created an equivalent minimal R Markdown document with the YAML header:
title: "Untitled"
output:
pdf_document:
citation_package: biblatex
bibliography: references.bib
biblatexoptions: [bibstyle=biblatex-sp-unified, citestyle=sp-authoryear-comp]
and body:
Something something [#darwin_origin_1859].
This time, I got the same old error message from before:
tlmgr search --file --global '/biblatex-dm.cfg'
! Package keyval Error: bibstyle undefined.
This would seem to suggest that the problem is caused by something in Pandoc's LaTeX template, but I don't know what.
Just to confirm that it's definitely the Pandoc template and not my own installation/setup, I took the .tex file that gets produced when I knit the minimal R Markdown example above, and tried to compile it in Overleaf (with biblatex-sp-unified.bbx and sp-authoryear-comp.cbx files added). I reproduced the same error.
Although I think I've localised the problem, I'd still very much like to understand what and where the problem is in the Pandoc template. I'd also be keen to hear if anyone has any fixes (other than just using a different template or writing my own).
UPDATE: This seems to be an issue with using an out-of-date version of R Markdown and/or Pandoc.
I was using rmarkdown package v.1. At time of writing, the most up-to-date version is 2.1.
I updated all my packages and updated Rstudio (which currently ships with Pandoc v2.3.1) and no longer experience problems. I also upgraded R (from 3.5.something to 3.6.2) and did a fresh re-install of tinytex while I was at it, but I'm not sure whether those things had an effect for this particular problem.
Now, when I put biblatexoptions: [bibstyle=biblatex-sp-unified, citestyle=sp-authoryear-comp] in my YAML header, it's correctly converted into the LaTeX command \usepackage[bibstyle=biblatex-sp-unified,citestyle=sp-authoryear-comp]{biblatex}, rather than the \ExecuteBibliographyOptions command as described below.
Ralf Stubner initially suggested I check my R Markdown/Pandoc versions in the comments. Please give his comments an upvote if you them useful as well.
Problem recap:
I'm writing a document in R Markdown and I have a particular referencing style that I'd like to use with biblatex. I have a .bbx and .cbx file defining the style, available on Github (linked above). The problem is that the document fails to compile, saying biblio/citation styles are undefined (even when the style files are in the project folder itself).
I've found that the problem was caused by the way I was passing options to biblatex. In my YAML Header, the line:
biblatexoptions: [bibstyle=biblatex-sp-unified, citestyle=sp-authoryear-comp]
gets converted to the latex command:
\ExecuteBibliographyOptions{bibstyle=biblatex-sp-unified,citestyle=sp-authoryear-comp}
I'm not sure why, but when this command is included, it produces the errors I was observing.
Installing new Biblatex style:
I'm finding that TeX doesn't know about the .bbx and .cbx files when they're in my ~/Library/TinyTex/texmf-local/tex/latex/biblatex directory (which is where I expected to put them based on the Github installation instructions).
To get the referencing style recognised by the system, I placed .bbx and .cbx files inside ~/Library/TinyTex/texmf-dist/tex/latex/biblatex/bbx and ~/Library/TinyTex/texmf-dist/tex/latex/biblatex/cbx respectively. Then, in the terminal, I ran sudo mktexlsr.
(Alternatively, for use only with a particular document, the .bbx and .cbx files could simply be kept in the project directory with the R Markdown file)
Original hacky answer (but see update above):
Instead of using biblatexoptions in the YAML header of the R Markdown document, I simply knitted it with citation_package: biblatex (and no extra options). I also added keep_tex: yes. Then, I opened the resulting tex file, found the \usepackage{bibtex} command and added the desired options, so it read \usepackage[bibstyle=biblatex-sp-unified,citestyle=sp-authoryear-comp]{biblatex}.
Finally, I ran pdflatex and biber on the tex file in the terminal. Clearly far from ideal, but it will technically produce the desired output.
I have a problem with the preamble.tex file used in the Rmarkdown rticles template for R Journal Submission. This is the procedure I'm following:
Create a new Rmarkdown rticles template for submission to the R Journal
Knit the document and everything seems to be fine
Add some latex code to preamble.tex (like \usepackage{subfig})
Knit the document and it doesn't compile anymore.
If I just remove \usepackage{subfig} from preamble.tex then everything works fine. I think the problem is related to the fact that the \usepackage{...} code isn't put in the preamble of the .tex document but I don't know how to fix that.
If you want to test I created I git repo here with all the Rmarkdown files up to point 3 of the previous list. If I knit the Rmd document that I get an error.
Hope it's clear
This is due to a bug in the rticles package, which I just resolved on Github. If you install the Github version, it should work now:
remotes::install_github('rstudio/rticles')
I would like to convert a *.Rmd to document to PDF without rstudio being available.
Current approach
Current approach follows the following steps:
*.Rmd document is passed to knitr: knit(input = "report.Rmd"))
Obtained md is converted via pandoc:
# Convert
pandoc --smart --to latex \
--latex-engine pdflatex \
-s report.md \
-o report.PDF
Problems
This results in the following problems, the top section of the Rmarkdown document:
---
title: "Report Title"
author: "Person"
output: pdf_document
classoption: landscape
---
and shows as:
all text is centered, whereas I would like for it to be left-aligned:
Possible approach
I would like to make use of the rmarkdown::render; however, despite setting RSTUDIO_PANDOC (as discussed here), the command fails on pandoc not being available.
Desired outcome
I don't care much whether the utilised mechanism makes use of the rmarkdown::render, what I want to achieve is:
Landscape page layout across all pages
Left-aligned text
Ability to exercise minimum control over the document by controlling default fonts
Ideally, I would like to do as much as in the *.Rmd file as possible without the need to add parameters to the pandoc command.
Updates, following comments
I'm working on Linux and pandoc is installed, I can execute pandoc command pass files and generate exports with no problems. It only doesn't work with the rmarkdown::render package.
Concerning the hooks and *.Rmd files, this is what I'm trying to understand as I see that that the first section of my *.Rmd file is ignored. The current process looks as follows:
*.Rmd (not much in it, just title section and dummy text and code that renders but wrongly justified) >
*.R file running one line knit(input = "report.Rmd")) >
*.sh file running pandoc command and generating PDF
Concerning:
if all that is in place, it is indeed just a call to
rmarkdown::render(...)
The rmarkdown::render(...) fails:
Error: pandoc version 1.12.3 is required and was not found ...
However:
>> rmarkdown::pandoc_available()
[1] TRUE
and:
$ pandoc -v
pandoc 1.9.4.1 (...)
The RSTUDIO_PANDOC points to pandoc.
A few things:
"the command fails on pandoc not being available." well you must have pandoc installed in order to call it -- but you didn't say what OS you have. On Linux it is pretty trivial to install pandoc from the package manager; otherwise jgm has binaries for you on the site; "should" be similar on OS X
for different styling you need to modify the LaTeX code which you can via numerous hooks to include macro files; see the RMarkdown cheat sheets for detail
if you want to exercise more control, you can supply your own template; I have done so in the tint package
(which is also on CRAN)
if all that is in place, it is indeed just a call to rmarkdown::render(...)
Error: pandoc version 1.12.3 is required and was not found
I think the error says it plainly: you need pandoc 1.12.3 and you have pandoc 1.9.4.1
I do not know, however, why such a specific version is required.
Edit
Thanks to some SO (i.e., #tmpname12345) users, I've come to the conclusion that my problem (described below) is likely caused by the differences between v0.2.64 and v0.3.11 of rmarkdown. The question now becomes:
Is there a way I can prevent rmarkdown version 0.3.11 and knitr from adding a line after the title of a .pdf file?
Original Question
I've come across a curious difference between compiling a .pdf document with the same yaml header block on two different computers with Rstudio and knitr. The difference is that on one computer, an additional line is inserted after the title while on the other, the line is not inserted (the preferred behavior). I would like to prevent the line from being inserted regardless of where the document is compiled.
I am using 32-bit R 3.1.2 on both computers. The yaml block is identical between both computers.
Here is the .Rmd file:
---
title: Header Test
output: pdf_document
---
My#gmail.com\hfill \hfill Address
Phone number\hfill \hfill Town, State, ZIP
Evidence of no additional line after the title, generated from my laptop with rmarkdown version 0.2.64:
Evidence of the additional line after the title, generated from my desktop with rmarkdown version 0.3.11:
Initially, I thought it may have been a function of the knitr package version, so I upgraded the package in the second image from 1.7 to the newest available version on CRAN, 1.9, but the extra line still remains.
I have also considered that this is an artifact of the Rstudio version on my laptop but if it is, I don't want to upgrade as the first image is the preferred.
I routinely edit .Rmd files in my Google Drive folder from both a desktop computer and my laptop, accessing the same file. Unfortunately, they compile differently. I prefer that there is no line added after the title. At this point, I don't want to change anything on my laptop, fearing that compilation will start to include the extra line.
Is there some way I can force knitr to not add the additional line?
One way is to create your own latex template that formats the header like you want. You can use the default template as a starting point here. Then save the file as .tex in the same directory as your Rmd file and add this to the yaml header:
output:
pdf_document:
template: mytemplate.tex