I'm trying to improve my workflow when working with R and generating documentation. I've been going between TeXStudio, JupyterLab and RStudio for a while, and I'm trying to improve my workflow. TeXStudio has limited R support, and RStudio limited support for LaTeX.
VS Code has support for multiple languages, including R and LaTeX. The fact that it can run both Jupyter notebooks, R notebooks, and LaTeX, and has plugins for other languages as well, makes it seem desirable. However, I am unable to find documentation on how to configure it to work with R and LaTeX code in the same file. In addition, I am unable to configure R notebooks to allow inline code execution output.
However, I am unable to (a) set up code execution output under the code for .Rmd notebooks, and (b) I can't figure out how to weave .Rnw (R/LaTeX) documents with Sweave/knitr.
I'm trying to find an IDE that would include features like:
Markdown, code and code execution output in the same document
Auto R and LaTeX code completion
Automatic display of R function documentation
Spell check
Simple R console access
Compile .Rnw
Syntax highlighting for both R code and LaTeX code
I am, primarily, requesting ways to configure VS Code, or, secondly, way to configure another IDE that can meet my requirements. A tutorial on this would be much appreciated.
After a bit of digging around, I found that VS Code does nearly all the things I need.
Auto R and LaTeX code completion, Display of R function documentation in a tab in VS Code, Simple R console access, and Syntax highlighting for both R code and LaTeX code:
The R and LaTeX Workshop extensions, will provide highlighting and autocompletion of code in both languages. By installing R, you can easily open a session in a terminal window in VS Code, and from there open documentation inside VS Code.
Spell check
Code Spell Checker offers spell check for multiple languages. Install the extension and any desired dictionaries, and set the langauges you want to be included in the extension settings.
Compile .Rnw files
Turns out LaTeX Workshop can actually do this by default.
Markdown, code and code execution output in the same document
This is the only thing VS Code doesn't do as far as I can tell. It can compile .Rmd files, however, but the output can only be seen in the compiled PDF. I consider this less important, since I can use Jupyter notebooks instead.
How to use inline code in markdown in Jupyter with R?
CODE CELL
n <- 8
MARKDOWN CELL
The Number is {{n}}
What would be the correct syntax in Jupyter Markdown for R? Is it even possible?
In case you haven't done it already, you might want to give the python markdown extension a shot, that adds the markdown inline code functionality for Python to Jupyter notebooks. On their github they claim:
The Python Markdown extension allows displaying output produced by the current kernel in markdown cells. The extension is basically agnostic to the kernel language, however most testing has been done using Python.
Installation instructions are on the github page of the nbextensions. Make sure you'll enable the python markdown extension using a jupyter command or the extension configurator.
Calling variables then should work inside a markdown cell with the {{var-name}} syntax that you've already given (described in the readme of the corresponding github page (linked in the wiki)).
If this doesn't help, you might want to join the discussion of the corresponding issues in the issue trackers for ipython and jupyter.
I haven't been able to use the neater knitter package with the code chunks.
Basically there's only a few number of occasions in which it interprets them well, but for the most of it the chunks are not recognized as such. That is:
Running a markdown from RStudio only renders chunks before the file is saved. If the file has been saved, then it will show the code as is: no R output.
I also tried using knitr from within LyX, and this presented other problems. The simplest example knitr.lyx was rendered correctly as a pdf, but not html. Using more complicated documents, like the RJournal template showed other errors.
Rscript --verbose --no-save --no-restore
At first I thought it had to do with my Rstudio installation, but now I'm not so sure anymore.
By the way, I'm on Ubuntu 15.04 and the files that I'm using are examples from the documentation:
Rstudio > New File > Rmarkdown... renders R output only before it's saved.
knitr's manual in LyX from Github repo.
I found the answer for this.
It's very obvious and yet easy to overlook if you don't know it.
The problem was in saving the file with the wrong extension.
If you're using R code chunks you need .Rmd extension in Rstudio.
As I was starting with markdown I was using .md. Pfff.
I have an RMarkdown file that I use to generate a nice HTML report.
The problem is, I want to be able to automate it so that it can run on a headless server. As such there will be nobody there to start Rstudio and press the 'knithtml' button and it seems that Rstudio is doing a LOT of additional magic like having it's own version of pandoc, running all the necessary commands, applying css styles etc.
How can I take this report and generate the same thing Rstudio is generating when I press the 'knithtml' button, but by just running an R script?
Thanks.
Try using
rmarkdown::render("/PATH/TO/YOUR.Rmd", output_file="/PATH/TO/YOUR/OUTPUT.html")
instead. This assumes you've got the rmarkdown library loaded on your headless box. It will use the system pandoc, but make sure it's 1.12 or higher.
Here's what knit2html does (via the "R Markdown" tab near "Console"):
Here's a side-by-side. Left is clicking the button, right is running the command:
I had the same issue. After a lot of brute force, I got the same result as RStudio with this command line:
"path\to\Rscript.exe" -e "rmarkdown::find_pandoc(dir='path/to/RStudio/bin/pandoc'); rmarkdown::render('file.Rmd')"
I've now got everything to work properly on my Mac OS X 10.6 machine so that I can create decent looking LaTeX documents with Sweave that include snippets of R code, output, and LaTeX formatting together. Unfortunately, I feel like my work-flow is a bit clunky and inefficient:
Using TextWrangler, I write LaTeX code and R code (surrounded by <<>>= above and # below R code chunk) together in one .Rnw file.
After saving changes, I call the .Rnw file from R using the Sweave command
Sweave(file="/Users/mymachine/Documents/Assign4.Rnw",
syntax="SweaveSyntaxNoweb")
In response, R outputs the following message:
You can now run LaTeX on 'Assign4.tex'
So then I find the .tex file (Assign4.tex) in the R directory and copy it over to the folder in my documents ~/Documents/ where the .Rnw file is sitting (to keep everything in one place).
Then I open the .tex file (e.g. Assign4.tex) in TeXShop and compile it there into pdf format. It is only at this point that I get to see any changes I have made to the document and see if it 'looks nice'.
Is there a way that I can compile everything with one button click? Specifically it would be nice to either call Sweave / R directly from TextWrangler or TeXShop. I suspect it might be possible to code a script in Terminal to do it, but I have no experience with Terminal.
Please let me know if there's any other things I can do to streamline or improve my work flow.
I use a Makefile of the following form for my Sweave documents:
pdf: myfile.tex
R CMD texi2pdf myfile.tex
myfile.tex: myfile.Rnw
R CMD Sweave myfile.Rnw
Then I can build the document in one step in the Mac OS Terminal by running the command make pdf
I'm sure there is a way to bring this closer to your one-click goal in Mac OS X, but this works well enough for me.
One-click Sweaving is easy to do in TeXShop using the Sweave.sh script by Gregor Gorjanc.
Get it from http://cran.r-project.org/contrib/extra/scripts/Sweave.sh and put it in your ~/Library/TeXShop/bin/ folder.
Then add the following files to your ~/Library/TeXShop/engines/ folder:
As Sweave.engine:
#!/bin/bash
~/Library/TeXShop/bin/Sweave.sh -ld "$1"
As SweaveNoClean.engine:
#!/bin/bash
~/Library/TeXShop/bin/Sweave.sh -nc -ld "$1"
You'll have to set the permissions on Sweave.sh and the two engine files to allow execution.
To Sweave with one click, restart TeXShop after adding these files, open the Sweave document (with Rnw extension) and in the dropdown menu above the document window, change it from LaTeX to Sweave or SweaveNoClean.
BEWARE: The "Sweave" option wll clean up after itself, deleting all the extra files LaTeX and Sweave creates. If your file is called myfile.Rnw, this will include files called myfile.R and myfile.tex. So a word to the wise: make sure the basename of your Rnw file is unique; then nothing unexpected will be written over and then deleted.
The SweaveNoClean option does not clean up after itself. This makes sure you don't delete anything unexpected; though it could still write over a file called myfile.tex if you Sweave a myfile.Rnw. This also doesn't delete any graphics that have been created, in case you want to have them separate from your full typeset document.
On the bash shell command line:
R CMD Sweave foo.Rnw && pdflatex foo.tex
Runs Sweave, and if that succeeds it goes on to do pdflatex. Out pops a pdf. If you've got this in a bash Terminal then just hit up-arrow to get it back and do it again. And again. And Again.
Makefile solution also good.
RStudio has a button that does this in one go. One caveat is that it runs in its own session, so any workspace variables you may have set are ignored.
Just a note: you can actually call things like pdflatex etc. directly from R using texi2dvi (in the tools package). For example:
Sweave(file="/Users/mymachine/Documents/Assign4.Rnw")
texi2pdf("Assign4.tex")
would compile your Rnw file into a pdf. Thus, no need to leave R to handle the tex->pdf step.
I use these (saved as sweave.engine and sweavebibtex.engine) for custom engines in texshop. I usually work up a code chunk in R, then copy the block into the rnw file I have open in texshop. I'd love a solution that lets me do syntax highlighting and spelling correction of R and tex in the same document (that isnt emacs).
#!/bin/bash
echo 'SWEAVE | PDFLATEX. Custom engine--Akasurak-16Nov2009'
export PATH=$PATH:/usr/texbin:/usr/local/bin
R CMD Sweave "$1"
pdflatex "${1%.*}"
and the second, for doing bibtex as well:
#!/bin/bash
date
before="$(date +%s)"
echo 'SWEAVE | PDFLATEX | BIBTEX | PDFLATEX | PDFLATEX. Custom engine--Akasurak-16Nov2009'
#Updated 20Jul2010 for auto including Sweave.sty
export PATH=$PATH:/usr/texbin:/usr/local/bin
R CMD Sweave "$1"
R CMD pdflatex "${1%.*}"
bibtex "${1%.*}.aux"
R CMD pdflatex "${1%.*}"
R CMD pdflatex "${1%.*}"
after="$(date +%s)"
elapsed_seconds="$(expr $after - $before)"
date
echo Elapsed time '(m:s)': $(date -r $elapsed_seconds +%M:%S)
Can't say they are the best way of doing things, but they do work.
I use either Aquamacs or Eclipse to do the editing of the .Rnw file, then I use the following shell function to compile & view it:
sweaveCache () {
Rscript -e "library(cacheSweave); setCacheDir(getwd());
Sweave('$1.Rnw', driver = cacheSweaveDriver)" &&
pdflatex --shell-escape $1.tex &&
open $1.pdf
}
Notice that I'm using the cacheSweave driver, which helps avoid constantly re-executing code sections that take a long time to run.
BTW, I'm also trying to switch over to Babel instead of Sweave; not sure which I'll end up using more often, but there are definitely aspects of Babel that I like.
The best solution is here: you create a new *.engine for TeXShop to use, then typeset using the shortcut or the 1 button.
http://cameron.bracken.bz/sweave-for-texshop
Cameron is also very responsive, so I highly recommend his solution.
If you are open to switching to a (paid) solution, TextMate has a Sweave plugin that takes you from .Rnw to PDF in one step: Sweave, typeset, and view. Combined with Skim, which can be configured to reload PDFs, it makes tweaking files pretty easy.
I had this same issue (I use Mac OSX) and I opted to download Eclipse Classic 3.6.2. and then installed the StatET plugin. It's a bit hairy to get set up but once you do this environment is nice because you can one-click compile your .Rwn Sweave document using pdflatex and set options for your favorite viewer so the .pdf automatically pops up when you compile like it does in TeXShop. You can do this in TeXShop as well, but TeXShop is lousy for debugging .Rnw files and it doesn't highlight the R-code in the .Rwn file. In Eclipse you can customize the syntax highlighting (not the greatest from the Texclipse end, but ok) so that you can easily distinguish between your R and LaTeX code. You can also launch the R console from within Eclipse and it has a graphical object browser. Anyway, I could go on. If you want details about how to get it all installed, message me.
Guess I'm late to the party on this, but I put together a webpage that documents my Sweave workflow based on Eclipse (with one-touch sweave):
http://www.stanford.edu/~messing/ComputationalSocialScienceWorkflow.html