Why is it important? My collaborators would like to be able to modify my .pdf reports and they are not able to modify the actual .tex code. They are sooo used to word !
How I write my reports? I use knitr. What a great and useful tool; thanks Yihui :)
What I'm looking for? convert the generated pdf report into .doc (my collaborators favorite !)
a solution might help: Pandoc (http://johnmacfarlane.net/pandoc/). As it's explained in the introduction of page of Pandoc, it can be used to convert LaTex to .docx and to markup. I then thought converting the .tex file of each of my reports (a .tex file is generated when I run my knitr .Rnw file) and convert it to .docx using pandoc:
pandoc -s myTexRepot.tex -o aDocReport.docx
issue: 1) Figures are missing in my .docx file. 2) I generate all my tables in my reports using xtable(), none of them can be converted! 3) Also, I lose all table of contents, section numbering.
Markup to Word: Issue (1) above is still an issue in converting Markup code to .doc
Is there any better idea to approach the issue of converting latex to doc. If Pandoc is the best, would you know how I can solve the issues above?
I really appreciate your help.
since you are already using knitr, you can call the rmarkdown:render() function to knit the document.
there is a parameter in render() called output_format[1]. the parameter along with the YAML header in your knitr document will allow you do generate the pdf and word document simultaneously
[1] output_format
R Markdown output format to convert to. Pass "all" to render all formats defined within the file. Pass the name of a format (e.g. "html_document") to render a single format or pass a vector of format names to render multiple formats. Alternatively you can pass an output format object; e.g. html_document(). If NULL is passed then the output format is the first one defined in the YAML metadata of the input file (defaulting to HTML if none is specified).
Related
So I just recently started to learn how to use RStudio for my Bio class. For my latest submission, I knitted my lab, which was made as an R Markdown, into an HTML file. For some reason, I might have deleted my RMD file, which was also needed in the submission. Is there any way to convert my HTML (PDF or even Word) file back into an R Markdown file?
Thank you so much!
-SuperEli
No, one rmarkdown file generates a unique word/html/pdf
however, different rmarkdown files may generate same output results.
In LaTeX I can create conditionals in the following manner
\iftoggle{ebook}{
\newcommand{\textbreak}{\newline\hrule\newline}
}{
\newcommand{\textbreak}{\begin{center}\LARGE{$\Psi\quad\Psi\quad\Psi$}\end{center}}
}
Can I do the same while knitting R Markdown, depending on if the output, is say HTML or PDF.
If you just need to include a short command in your target format, then you could use raw elements for your target format:
`<br><hr><br>`{=html}
`\begin{center}\LARGE{$\Psi\quad\Psi\quad\Psi$}\end{center}`{=latex}
The first line will only be included in HTML formats (like epub), while the latter will be used when exporting to or via LaTeX.
For longer text, or if you don't want to write in the target format directly, I'd recommend using fenced divs in combination with a pandoc filter, e.g. a Lua filter; this works both with raw pandoc as well as with RMarkdown.
rmarkdown, following {xe|lua}latex, allows to specify fonts for main text, sans-serif text, monspaced text (most notably code chunks !) and math fonts in the YAML header. At least for PDF rendering via xetex, this works.
However, I found no (documented) way to pass options to the underlying setxxxfont \LaTeX command. For example, the YAML fragment :
```
monofont: Inconsolata
```
generates the following \LaTeX fragment :
\setmonofont[Mapping=tex-ansi]{Inconsolata}
I have two questions with this:
why is the Mapping=tex-ansi added ? And how to control it ? (I'm working in UTF8...).
How could I set additional arguments for the font options i.e. \setmonofont[Scale=0.91]{TeX Gyre Cursor}?
The R Markdown book and the Pandoc's User's Guide did not reveal anything pertinent.
Background:
When R Markdown converts the knitted code to the output format (PDF), a pandoc template is used. The template is stored within the package, and any variables which get replaced by the YAML variables are contained in the $$ Notation
1. Encoding
The Mapping=tex-ansi is added to the code as a workaround an issue as reported on GitHub. Therefore I would be cautious of deleting this for potential side effects.
If you do indeed wish to change this code, you will have to make a copy of the LaTeX template file used to convert the document. You can find the default template here. See here for some more information on providing custom templates.
2. Additional Font Options
You can use the monofontoptions YAML argument to add additional arguments to the font options.
Documentation of the variables which can be parsed by the LaTeX output are available in the pandoc documentation
I would like to be able to use knitr to produce a structured PDF file. I did not see anything unless the input file is Sweave format. This question may be too vague but I really like to know right from knitr, is it possible to create a structured PDF output file without using any Sweave or LaTeX?
Try using command knit2pdf if you haven't already.
Is there a simple way to create R documentation file for simple R functions?
I know I can edit a .Rd file in R-studio and preview it in HTML file. But how to put it into latex to edit and preview? Is there some latex package producing R documentation format?
There is the Rd2latex function in the tools package that will convert from the .Rd format to LaTeX format. This will let you preview the documentation in LaTeX. However this does not allow converting edits to the LaTeX document back to the .Rd document.
Look at Sweave, maybe it helpful for you.
Sweave is a tool that allows to embed the R code for complete data analyses in latex documents.
The purpose is to create dynamic reports, which can be updated automatically if data or analysis change. Instead of inserting a prefabricated graph or table into the report, the master document contains the R code necessary to obtain it. When run through R, all data analysis output (tables, graphs, etc.) is created on the fly and inserted into a final latex document.
The report can be automatically updated if data or analysis change, which allows for truly reproducible research.
Check out printr http://yihui.name/printr/ . It should do what you need if you are using knitr.
The problem with Rd2latex is that i haven't figured out which style file I need to use, otherwise it works fine.
When you generate the latex code with the Rd2latex function, make sure that you copy the Rd.sty file from the R directory, paste it and somewhere that latex can see it and use \usepackage{Rd}.
Try the knitr package, an easy way to generate flexible and fast dynamic reports with R for LaTex.