I want to generate from an rmarkdown file (using RStudio) a Gitlab flavored markdown(GFM), so the file is displayed properly on a gitlab server.
I am especially interested in having Latex formula to be displayed properly.
In the gitlab documentation specify that the formulas should be written between $` and `$
$`a^2+b^2=c^2`$
But Rmarkdown require the $ $ synthax (no `)
$a^2+b^2=c^2$
Currently I have tryied to create github flavored markdown with the following yaml in the preamble:
output:
html_document:
keep_md: false
md_document:
variant: markdown_github
but when entering the following in my Rmd file:
$A=\displaystyle\sum_{b} c_b$
I get the following in the markdown:
*A* = ∑<sub>*b*</sub>*c*<sub>*b*</sub>
How can I configure my Rmarkdown or Rstudio so I will get this in the md file:
$`A=\displaystyle\sum_{b} c_b`$
Related
In R, when compiling a markdown document using rmarkdown::render(...), how can I retain the intermediate .tex file that is produced from knitting.
I have tried setting the clean=FALSE argument, but this retains the figures, not the final tex file or auxiliary files, which I need to inspect for debugging purposes.
You can specify it in your YML header with:
output:
pdf_document:
keep_tex: true
---
More options on the rmarkdown site.
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
Is there a YAML option, which sets knit directory for an Rmd file? I.e. does the same as illustrated in Fig.1.
The problem is that every time I copy files or share a project with other people (which usually have different default RStudio options than I do), the knit directory should be reset manually in each file.
I'm aware of the global option (Fig.2), but I need a more reproducible solution which works for individual Rmd files in both both RStudio notebook and knitting modes.
And, for instance, I know that there is an option such as:
editor_options:
chunk_output_type: console
Any ideas?
Fig. 1 Setting knit directory via menu commands.
Fig. 2 Global option to set default knit directory in RStudio.
You could try to specify the knit field in the front-matter of our .Rmd file. Example .Rmd that would knit into "some_dir" created in your home directory:
---
title: "Untitled"
output: html_document
knit: (function(inputFile, encoding) {
rmarkdown::render(inputFile, encoding = encoding, output_dir = "~/some_dir/")
})
---
# Some content
Some content
Is it possible to use pandoc-crossref in bookdown?
I tried to change the yaml header to:
output:
bookdown::tufte_book2:
toc: yes
highlight: tango
pandoc_args: -F /usr/local/bin/pandoc-crossref
Which should pass the filter to pandoc, but I get the error:
pandoc: Error running filter pandoc-crossref:
Could not find executable ' pandoc-crossref'.
The above error does not make sense, as I entered the correct path. What kind of env is bookdown using, which is precluding the access to the filter file?
Here is an example
---
output: bookdown::html_document2
---
# Section name {#id}
```{r pressure, echo=FALSE, fig.cap='test plot'}
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. To cross-reference the figure, use `\#ref(fig:pressure)` to produce Figure \#ref(fig:pressure). All this is found within the section \#ref(id).
Which produces...
See https://bookdown.org/yihui/bookdown/figures.html for the official documentation.
I had a similar issue while I was trying to put numbers to equations in Word files (SO question). I got the same error Could not find executable 'pandoc-crossref'.
My RStudio installation (on Windows) did not come with pandoc-crossref. Here is what I did:
Downloaded pandoc-crossref from here.
Find the path where RStudio saved the file pandoc.exe:
rmarkdown::find_pandoc()
Put the pandoc-crossref.exe in the folder I got in (2).
I am practicing data analysis using R programming. I want my files to be on github. I am unable to figure out why github is not showing the output of .rmd files.
Here is the link to the file in my github repository Data Analysis Practice
I want the output including plots to be shown on github.
Instead of:
output: html_document
make it:
output: rmarkdown::github_document
(assuming you have the latest rmarkdown installed which you should if you're using RStudio — which I suspect you are — and keep it updated or update packages regularly).
It will create Exploring_one_variable.md and render the images as files.
When you browse to that markdown file, the images will render.
An alternative is to use:
output:
html_document:
keep_md: true
and it will render to both Exploring_one_variable.md and Exploring_one_variable.html so you'll have the best of both worlds without the local github-esque preview that the former provides.
You can get fancier and put something like the following as the first code section in the Rmd:
```{r, echo = FALSE}
knitr::opts_chunk$set(
fig.path = "README_figs/README-"
)
```
which will put the figures in a directory of your choosing.
You can see this in action here as the README.md was generated with knitr from the README.Rmd in the same directory.
There is now output: github_document