# Tools that allow to write markdown, latex and R code (knitr) in the same document and convert to pdf?

I have been searching the internet for hours but I think I am looking in the wrong direction. Hopefully this is the right place for asking, otherwise please point me in the right direction :)

I write markdown documents. I use latex inside these documents for equations and figures. I save these as .txt and use pandoc to convert to .pdf and such,

pandoc example.txt -o example.pdf --bibligraphy library.bib


to be precise. I have now started using knitr as well. I played around with it for a bit and tried to create more markdown .txt documents with latex embedded (as described above) as well as R code chunks. I then converted this to .pdf using pandoc but this didn't produce the desired result.

My question: are there any tools that will allow me to write markdown, latex and Rcode (knitr) in the same document and convert to proper pdf (and .docx) versions?

• It would reallly help to know how the results differed from your desired results. – Steve Barnes Jun 17 '15 at 4:56
• Do you want to typeset these R code chunks, or do you want to execute them and typeset their output (graphs?)? – Gilles 'SO- stop being evil' Jun 17 '15 at 8:05
• There is a workaround if you use org-mode instead of markdown. It supports embedded Latex and R code snippets, and its syntax is similar to markdown and easy to learn. Documents can be directly exported to pdf from within Emacs. – Tymric Jun 17 '15 at 19:22
• @SteveBarnes It just didn't look nice. I sorry that is very vague, but what happened was that the R code/R markdown wansn't understood by pandoc as such an it turned it nonsense. – rosannavh Jun 19 '15 at 2:21
• @rosannav I have added a note and link on how to do R in ipython. Unless you tell ipython that a cell is R with the magic it will be assumed to be either python or Markdown. – Steve Barnes Jun 19 '15 at 5:14

I suggest taking a look at the ipython notebook.

It lets you mix via your browser

• Markdown
• Formulae with MathJax
• Python code
• R code
• Several other programming languages
• Bash Scripts
• The results of all of the above including graphs etc
• Syntax highlighted code in 100s of other languages

It allows export as html and pdf as well as sharing as notebooks.

• Free and open source.
• Cross Platform.

You will need to install r2py and use the rmagic command as explained here.

• Thanks heaps! I'm going to look into that – rosannavh Jun 19 '15 at 2:25