I'm trying to use lua filters to capture images in my manuscript and list their caption in a special \section at the end of it.
I am working on a rmarkdown document that itself uses a .tex template.
I wasn't able to get anywhere, so I run a very simple filter:
function Header (head) print(pandoc.utils.stringify(head)) end
and noticed that just the headers in the markdown were recognized, not the ones in the ones in the template.
The only way I found to have lua filters recognize the elements in the template was to rerun the produced .tex file with pandoc:
pandoc -f latex -t latex -o test2.tex --lua-filter=my_filters.lua test.tex
but that removed all latex formatting and structure content outside the body, e.g., \documentclass, \usepackage and other custom commands. So it's a no go.
So the question is, is there a way to force lua filter to be applied after the integration of a latex template when knitting a rmarkdown document?
There might be a way, but it most likely won't do what you need.
When pandoc reads a document, it parses it and converts it into it's internal data structure. That internal structure can then be modified with a filter. LaTeX is a very expressive and complex document format, and any conversion from LaTeX into pandoc's internal format will result in a loss of (layout) information. That's good enough in most cases, but would be a problem in your case.
There are two possible ways to do this: one is to post-process the output, which is probably tedious and error-prone. The other is to find a way to generate the desired output, e.g. via a pandoc filter, without adding it to the template first.
I believe your other question is the right way to go.
I have to put all my code from a Rmarkdown document into pure LaTeX format in Overleaf. For this reason, I can't use my knitr code anymore to produce latex tables right away, but I need to write the LaTeX code by myself.
I through, although kable/kableExtra do now show LaTeX code in RStudio, the code must be produced in the background to make LaTeX able to read it.
Now my question: Is there any option to let me see the full LaTeX code produced by kable/kableExtra in order to take it and copy it into my pure LaTeX document?
I would be happy to hear your suggestions.
Best,
Moritz
There are different ways to get to the .tex file from an .Rmd file.
Convert only to LaTeX by using in your YAML header
---
[...]
output: rmarkdown::latex_document
---
Convert to PDF but keep the LaTeX file by using in your YAML header
---
[...]
output:
rmarkdown::pdf_document
keep_tex: yes
---
I prefer the second approach since it allows for previewing the document easily while editing the .Rmd file. Note that there are other output functions besides rmarkdown::pdf_function that support the keep_tex argument.
I want to convert Asciidoc to LaTeX, then use an existing toolchain that includes LaTeX modules to convert the resulting document further to the final format. Asciidoc's native LaTeX conversion is "experimental" according to their documentation, and it also doesn't work for me. There is another toolchain supported by Asciidoc, which is converting to Docbook first, then use dblatex to convert it further. However, it includes a lot of formatting in its LaTeX output, which clashes with the formatting of my toolchain.
Is there any way to convert Asciidoc to LaTex in a way that the content is included in the resulting document, but without any exact formatting rules (expect those explicitly specified in the document). I don't want the LaTeX result to contain any information about fonts, page layout and so on, because for those I already have a toolchain.
I get acceptable, almost good results with this toolchain using pandoc convertor:
edit your document in asciidoc or asciidoctor
convert your document to docbook: asciidoctor -b docbook5 your asciidoc document.
convert your docbook document to (xe)latex using pandoc: pandoc -f docbook your docbook document --pdf-engine=xelatex
You can customize your latex layout and modules in a pandoc configuration file or convert your docbook file into a latex file with pandoc. The converted latex file is quite clean (because its source is docbook).
The problem:
I have several Rmarkdown documents representing different sections of my thesis (e.g. chapter 1 results, chapter 2 results), and I would like to combine the knitted latex versions of these documents with other TeX files into a master TeX 'thesis' document. The problem is, that when knitting to PDF and keeping the TeX file to include in the master TeX document, Rstudio auto-generates a bunch of preamble that ends up clashing with my preamble in the master.TeX document.
A less than ideal, workaround:
I have been working around this issue by deleting this preamble by hand before including the knitted output into the master.tex file.
So far my current workflow is as follows:
set the output to pdf_document in the YAML header, with the keep_tex option set to true.
knitPDF using the Rstudio button
delete the preamble at the beginning of the knitted TeX files by hand.
include the files into my master.tex file using \include{}
The question:
I would like to convert Rmd to LaTeX, without having to delete the preamble manually before including the knitted TeX files into a master TeX file. How do I do this?
Sweave is not an option:
I'm sure I could achieve this by working with Sweave, however I like the flexibility of output formats that Rmarkdown offers: I can knit to html and view in my browser as I'm writing, to quickly view the progress of my work and ensure that there are no bugs, and I can also choose to knit to word to share with my supervisor who works only in word. Then, when I'm ready to compile everything into my master LaTeX document for printing, I can select knit to PDF in Rstudio to obtain the latex output.
I have since come up with a workaround:
create_latex <- function(f){
knitr::knit(f, 'tmp-outputfile.md');
newname <- paste0(tools::file_path_sans_ext(f), ".tex")
mess <- paste('pandoc -f markdown -t latex -p -o', shQuote(newname),"tmp-outputfile.md")
system(mess)}
The function above takes an Rmd file as its input, knits the file to md, and then converts it to TeX by calling pandoc from the command-line.
The secret ingredient lies in the pandoc call... When knitting using Rstudio, Rstudio must be calling the pandoc standalone -s flag when it compiles the pdf. This generates a 'standalone' document, i.e. one that contains latex preamble. This is obviously necessary when you want to view the PDF, but conflicts with my needs.
I am instead seeking to generate a latex 'fragment' from Rmd with knitr, that can be later incorporated into my master Latex file. So the solution was simply to create a pandoc command line call that omits the -s standalone flag. I achieved this by calling pandoc from R with system() inside the above function.
Hope this helps anyone out there having this problem, but would be great if I was able to change Rstudio's settings to avoid bothering with this hack. Suggestions and feedback welcome.
Here is a simpler solution using the LaTeX package docmute.
Your main Rmarkdown document, (e.g., main.Rmd) should load the docmute package and include your other files (e.g., part1.Rmd and part.Rmd), once knitted and located in the same directory, with \input or \includelike this:
---
title: "Main"
output: pdf_document
header-includes:
- \usepackage{docmute}
---
# Part 1
\input{part1.tex}
# Part 2
\input{part1.tex}
Then your other files just need to have a keep_tex argument in the YAML front matter. Like this:
---
title: "Part 1"
output:
pdf_document:
keep_tex: true
---
Something
and this:
---
title: "Part 2"
output:
pdf_document:
keep_tex: true
---
Something else
Then all you need to do is knit part*.Rmd's before main.Rmd and all the content will appear in main.tex and main.pdf. The docmute package strips the preamble from the input .tex files so you will need to make sure anything you need before \begin{docunent} in the input files is also in main.Rmd.
What is the best way to take care of citations in Ipython Notebook? Ideally, I would like to have a bibtex file, and then, as in latex, have a list of shorthands in Ipython markdown cells, with the full references at the end of the notebook.
The relevant material I found is this: http://nbviewer.ipython.org/github/ipython/nbconvert-examples/blob/master/citations/Tutorial.ipynb
But I couldn't follow the documentation very well. Can anyone explain it? Thanks so much!!
Summary
This solution is largely based on Sylvain Deville's excellent blog post. It allows you to simply write [#citation_key] in markdown cells. The references will be formatted after document conversion. The only requirements are LaTeX and pandoc, which are both widely supported. While there is never a guarantee, this approach should therefore still work in many years time.
Step-by-Step Guide
In addition to a working installation of jupyter you need:
LaTeX (installation guide).
Pandoc (installation guide).
A citation style language. Download a citation style, e.g., APA. Save the .csl file (e.g., apa.csl) into the same folder as your jupyter notebook (or specify the path to the .csl file later).
A .bib file with your references. I am using a sample bib file list.bib. Save to the same folder as your jupyter notebook (or specify the path to the .bib file later).
Once you completed these steps, the rest is easy:
Use markdown syntax for references in markdown cells in your jupyter notebook. E.g., [#Sh:1] where the syntax works like this: ([#citationkey_in_bib_file]). I much prefer this syntax over other solutions because it is so fast to type [#something].
At the end of your ipython notebook, create a code cell with the following syntax to automatically convert your document (note that this is R code, use an equivalent command to system() for python):
#automatic document conversion to markdown and then to word
#first convert the ipython notebook paper.ipynb to markdown
system("jupyter nbconvert --to markdown paper.ipynb")
#next convert markdown to ms word
conversion <- paste0("pandoc -s paper.md -t docx -o paper.docx",
" --filter pandoc-citeproc",
" --bibliography="listb.bib",
" --csl="apa.csl")
system(conversion)
Run this cell (or simply run all cells). Note that the 2nd system call is simply pandoc -s paper.md -t docx -o paper.docx --filter pandoc-citeproc --bibliography=listb.bib --csl=apa.csl. I merely used paste0() to be able to spread this over multiple lines and make it nicer to read.
The output is a word document. If you prefer another document, check out this guide for alternative syntax.
#Extras
If you do not like that your converted document includes the syntax for the document conversion, insert a markdown cell above and below the code cell with the syntax for the conversion. In the cell above, enter <!-- and in the cell below enter -->. This is a regular HTML command for a comment, so the syntax will in between these two cells will be evaluated but not printed.
You can also include a yaml header in your first cell. E.g.,
---
title: This is a great title.
author: Author Name
abstract: This is a great abstract
---
You can use the Document Tools of the Calico suite, which can be installed separately with:
sudo ipython install-nbextension https://bitbucket.org/ipre/calico/downloads/calico-document-tools-1.0.zip
Read the tutorial and watch the YouTube video for more details.
Warning: only the cited references are processed. Therefore, if you fail to cite an article, it won't appear in the References section. As a little working example, copy the following in a Markdown cell and press the "book" icon.
<!--bibtex
#Article{PER-GRA:2007,
Author = {P\'erez, Fernando and Granger, Brian E.},
Title = {{IP}ython: a System for Interactive Scientific Computing},
Journal = {Computing in Science and Engineering},
Volume = {9},
Number = {3},
Pages = {21--29},
month = may,
year = 2007,
url = "http://ipython.org",
ISSN = "1521-9615",
doi = {10.1109/MCSE.2007.53},
publisher = {IEEE Computer Society},
}
#article{Papa2007,
author = {Papa, David A. and Markov, Igor L.},
journal = {Approximation algorithms and metaheuristics},
pages = {1--38},
title = {{Hypergraph partitioning and clustering}},
url = {http://www.podload.org/pubs/book/part\_survey.pdf},
year = {2007}
}
-->
Examples of citations: [CITE](#cite-PER-GRA:2007) or [CITE](#cite-Papa2007).
This should result in the following added Markdown cell:
References
^ Pérez, Fernando and Granger, Brian E.. 2007. IPython: a System for Interactive Scientific Computing. URL
^ Papa, David A. and Markov, Igor L.. 2007. Hypergraph partitioning and clustering. URL
I was able to run it with the following approach:
Insert the html citation as in the tutorial you mentioned.
Create ipython.bib in the "standard" bibtex format. It goes into the same file as your *.ipynb notebook file.
Create the template file as in the tutorial, also in the same directory or else in the (distribution dependent) directory with the other templates. On my system, that's /usr/local/lib/python2.7/dist-packages/IPython/nbconvert/templates/latex.
The tutorial has the template extend latex_article.tplx. On my distribution, it's article.tplx (without latex_).
Run nbconvert with --to latex; that generates an .aux file among other things. Latex will complain about missing references.
Run bibtex yournotebook.aux; this generates yournotebook.bbl. You only need to re-run this if you change references.
Re-run nbconvert either with --to latex or with --to pdf. This generates a .tex file, or else runs all the way to a .pdf.
If you want html output, you can use pandoc to assemble the references into a tidy citation page. This may require some hand-editing to make an html page you can reference from your main document.
If you know that you will be converting your notebook to latex anyway, consider simply adding a "Raw" cell (Ctrl+M R) to the end of the document, containing the bibliography just as you would put it in pure LaTeX.
For example, when I need to reference a couple of external links, I would not even care to do a proper BibTeX thing and simply have a "Raw" cell at the end of the notebook like that:
\begin{thebibliography}{1}
\bibitem{post1}
Holography in Simple Terms. K.Tretyakov (blog post), 2015.\\
\url{http://fouryears.eu/2015/07/24/holography-in-simple-terms/}
\bibtem{book1}
The Importance of Citations. J. Smith. 2010.
\end{thebibliography}
The items can be cited in other Markdown cells using the usual <cite data-cite="post1">(KT, 2015)</cite>
Of course, you can also use proper BibTeX as well. Just add the corresponding Raw cell, e.g:
\bibliographystyle{unsrt}
\bibliography{papers}
This way you do not have to bother editing a separate template file (at the price of cluttering the notebook's HTML export with raw Latex, though).
You should have a look at the latex_envs extension in https://github.com/ipython-contrib/IPython-notebook-extensions (install from this repo, it is the most recent version). This extension contains a way to integrate bibliography using bibtex files and standard latex notation, and generates a bibliography section at the end of the notebook. Style of citations can be (to some extent) customized. Some documentation here https://rawgit.com/jfbercher/latex_envs/master/doc/latex_env_doc.html