I found R markdown/knitr useful tool to document my work and generate summary document.
I work with .Rmd (R markdown) files in RStudio.
It seems that knitr provide appropriate functionality to generate .odt (Open Document Text) and .tex (LaTeX) documents from .Rmd.
However, R studio allows to choose .docx, .html and .pdf formats only.
I would like to avoid MS Word format since I prefer open standards and working under Linux.
Is it possible to add .odt and .tex options to Rstudio menu?
It doesn't seem possible to output odt directly in RStudio, but you can always use knitr::knit to produce a markdown document and pandoc to produce the odt:
library(knitr)
knit("myDoc.Rmd")
system("pandoc myDoc.md -o myDoc.odt")
You may have to adjust the pandoc options and adapt the template to get a nice looking result.
As for latex, you can keep the tex sources when compiling to pdf with the following option in your yaml front matter:
---
output:
pdf_document:
keep_tex: true
---
Related
I would like to convert a rmarkdown .Rmd document to a jupyter notebook .ipynb.
I found that converting from jupyter to rmd is easy using as described in reference page but for some reason (...) the Rstudio team did not do the other way.
For instance I would like to convert
---
title: "Untitled"
author: "statquant"
date: "03/09/2019"
output: html_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
## R Markdown
This is an R Markdown document. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see <http://rmarkdown.rstudio.com>.
When you click the **Knit** button a document will be generated that includes both content as well as the output of any embedded R code chunks within the document. You can embed an R code chunk like this:
```{r cars}
summary(cars)
```
## Including Plots
You can also embed plots, for example:
```{r pressure, echo=FALSE}
plot(pressure)
```
Note that the `echo = FALSE` parameter was added to the code chunk to prevent printing of the R code that generated the plot.
After checking, the silver bullet seems to be jupytext
It allows you to convert from or to markdown, rmarkdown, python, ipynb, etc.
This can actually allow you a pretty neat workflow
write a simple R script, script.R, that you can spin into a Rmd document
use knitr::spin('script.R', knit = FALSE) to transform it to Rmd
use jupytext --to notebook script.Rmd to create script.ipynb
share or execute the notebook
sos-rmarkdown provides yet another Rmarkdown to Jupyter notebook converter. The unique features include its support for inline expressions using markdown-kernel, use of multiple kernels in one notebook (using a SoS kernel) to accommodate code blocks in multiple languages, and the ability to execute generated notebook using sos-papermill. It also uses cell meta data to control the display of input and output of code blocks in Jupyter Lab and exported HTML reports.
To use this tool, you can install sos-rmarkdown from pip or conda-forge, then run the converter with command
sos convert input.Rmd output.ipynb
or use option --execute to execute the converted notebook
sos convert input.Rmd output.ipynb --execute
Disclaimer: I am the author of sos-rmarkdown.
Here is another way.
The detailed answer (to convert .rmd to .ipynb) is described here: https://gist.github.com/ramnathv/10012123
TL;DR
Use a 3rd-party Python package notedown with sed command as follows:
1) Install a 3rd-party python package which does the conversion for us
$ pip install notedown
2) Use the installed package to convert from your *.Rmd file (or *.md) to *.ipynb and run the terminal command:
$ notedown example.Rmd | sed '/%%r/d' > example.ipynb
I use rstudio to write r-markdown, but sometimes it is not compatible with markdown support by pandoc(math for example. If there is a way allow me to convert r-markdown to pandoc markdown, then it will be convenient to export my articles to pdf, org, rts, latex...
https://pandoc.org/ also seems doesn't mention rmarkdown support.
I have tried to export .html form rstudio and use pandoc convert the html file back to markdown, but it seems doesn't work.
Actually pandoc is used to create pdf and other formats from r-markdown. Therefore there is an intermediate file with pandoc compatible markdown. You could retain this file by:
rmarkdown::render("document.Rmd", output_format = "pdf_document", run_pandoc = FALSE)
Using RStudio's "Compile Notebook to html" feature, I noticed that a temporary .md file was created in the process, but deleted automatically. At one point I was lucky enough to see its content, and it is exactly what I need: the code chunks alternate with output chunks, all perfectly formatted.
So my question is: how do I generate such an .md file directly form an R script?
You could also run knitr::spin() directly from the R console.
If you run "Knit to HTML", a markdown file is temporarily created and deleted. To keep the markdown file, add the following to the YAML code at the top of the RMD file.
---
output:
html_document:
keep_md: true
---
Here is a helpful reference: https://bookdown.org/yihui/rmarkdown/html-document.html#keeping-markdown
So I have a vignette, vignettes/test-vignette3.Rmd:
---
title: "Sample Document"
output:
html_document:
highlight: kate
theme: spacelab
toc: yes
pdf_document:
toc: yes
---
Header
=========
When I hit the knit HTML button, I get the following:
processing file: test-vignette3.Rmd
output file: test-vignette3.knit.md
Output created: /tmp/RtmpKVpegL/preview-5ef42271c0d5.dir/test-vignette3.html
However, if I copy this file to inst/doc and hit the knit HTML button, I get:
processing file: test-vignette3.Rmd
output file: test-vignette3.knit.md
Output created: test-vignette3.html
My questions are:
How do I get RStudio to save the output from knit HTML on vignettes/test-vignette3.Rmw to the vignettes directory?
How do I get RStudio to not delete test-vignette3.knit.md during the knit HTML procedure? (I'd like to have the .md so people can read it on my github repo.)
I'm running RStudio version 0.98.836, rmarkdown version 0.1.98 and knitr version 1.5.
Actually you should not keep the .html output under vignettes/, because the vignette output is supposed to be generated by R CMD build. R may fail to recompile your vignettes if the HTML output files have already been there when you build the source package, which means you are likely to see old (and possibly wrong) results because the HTML file was not generated from the latest version of the .Rmd file. Therefore RStudio intentionally avoid writing the HTML files in the vignetttes directory.
If you choose to ignore the warning above, you can certainly run rmarkdown::render('your-vignette.Rmd') in the R console.
For the second question, I do not recommend you to do that, either, because Github renders the markdown to HTML differently (compared to the Pandoc conversion done through the rmarkdown package). Normally the package vignettes are shown on CRAN, see, for example, the knitr page on CRAN. However, because the rmarkdown package is not on CRAN yet, you cannot use the vignette engine knitr::rmarkdown at the moment (I guess we are not too far away from the CRAN release now). You can consider pushing the HTML files to Github pages, though.
I have been saving some example R markdown html output to Word using pandoc. I actually only do this so I can add some page breaks for easier printing:
system("pandoc -s Exercise1.html -o Exercise1.docx")
Although the output is acceptable I was wondering if there is a way to keep the original syntax highlighting of the R chunks (just as they are in the original knit HTML document)?
Also, I seem to be loosing all images in the conversion process and have to stick them into Word by hand. Is that normal?
Using the rmarkdown package (baked into RStudio Version 0.98.682, the current preview release) it's very simple to convert Rmd to docx, and code highlighting is included in the docx file.
You just need to include this at the top of your markdown text:
---
title: "Untitled" # obviously you can change this
output: word_document # specifies docx output
---
However, it seems that page breaks are still not supported in this conversion.
Why not convert the markdown directly to Word format?
Anyway, Pandoc does not support syntax highlighting in Word: "Currently, the only output formats that uses this information are HTML and LaTeX."
About the images: the Word file would definitely include those if you'd convert the markdown to Word directly. I am not sure about the HTML source, but I suppose you might have a path issue.