The knitr language engines makes it possible to include an Rcpp chunk in your R Markdown document. This works perfectly when knitting the entire document.
However, it doesn't seem to be possible to execute (that is, compile) the Rcpp chunk interactively in RStudio (v. 1.1.364), or am I missing something?
I could keep the C++ code in a separate file and use sourceCpp in a chunk, which also works fine. However, for small examples I use in teaching it's more convenient to have everything in one document. I could then use cppFunction, but that doesn't give proper syntax highlighting.
I'm either looking for an answer that shows that I, indeed, missed how to interactively compile Rcpp chunks in RStudio, or answers that suggest good practices for i) having all code in one file, and ii) being able to execute chunks interactively.
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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.
I'm writing a publication manuscript for a new R package. The author guidelines expect a self-contained Sweave (Latex+R) project with self-contained executable code within R code chunks in the Sweave document. This allows for seamless reviewing. Recommendations are to use RStudio.
All is going well. However, some of my packaged R code prints to the terminal intermediate steps; notably in the parts that setup and execute parallel code. In terms of use, this is great. However, the intermediate output is bulking out the code chunks in the compiled PDF. Not great for a scientific manuscript with a limited page count (fine elsewhere, e.g., Github wiki etc).
I'm using the code chunk options:
<<eval=T, echo=T>>=
#R code to execute AND to display code here.
#But this print all internal R print() statements to the pdf document.
#
Is there a Sweave code chunk option (not a global option, as for some code chunks the current behaviour is fine) that executes and displays the code itself but halts the printing of any internal print statements in my R package?
In answer to my own question I figured this out through a process of elimination; I could have continued scrolling through online blogs and tutorial but I'm very much pressed for time.
To suppress the output of a calculation in an R code chunk whilst displaying the R code in the compiled pdf:
<<eval=T, echo=T,results=hide>>=
eval=T -- evaluate the code
echo=T -- spits the code into the pdf (and the code output)
results=hide -- overrides echo=T to prevent the code's output whilst maintaining the code display.
I've started using knitr (without pander) and I'm very impressed.
I can find instructions for writing inline knitr markdown – which will be processed even though a hash is written at the beginning of a line (which will be useful). However, it has occurred to me that if knitr can read and process such information, perhaps there is a way to write ALL markdown instructions e.g. ```{r} with a hash at the beginning of the line ? I.e., I would like it if ##```{r} also worked when run via knit.
This would allow me to create files which work without errors when run using R console and also when run via knit – which might be useful when files are submitted for review.
Is there any way to compile knitr subfiles separately? What I have in mind is something like the package subfiles for latex just in combination with R/knitr/Sweave?
This would be great in case one has two exercises a first exercise with heavy computations and
don't want to compile the entire exercise always while working and testing the second one.
The patchDVI package does this for Sweave. I imagine it would be possible (maybe even easy) to modify it to do the same for knitr.
For example, in Sweave, you define variables in a chunk like so:
<<>>=
.TexRoot <- "main.tex"
.SweaveFiles <- c("subfile1.Rnw", "subfile2.Rnw")
#
and after Sweave is finished running that file, patchDVI will check whether the files subfile1.Rnw and subfile2.Rnw also need to be run, then will run LaTeX on the main.tex file once everything is up to date.
You don't need to do anything difficult, just use the cache options. Lots of details here, but it's probably as simple as specifying cache = T in the chunk options of your first exercise.
I'm experimenting with using Markdown to write homework problems for a course that involves some R coding. Because these are homework sets, I intentionally write code that throws errors;. Is it possible to use Markdown to display R code in the code style without evaluating it (or to trap the errors somehow)?
If you're using R markdown, putting eval=FALSE in the chunk options should work. Or use try(). Or, if you're using knitr as well, I believe that the default chunk option error=FALSE doesn't actually stop the compilation when it encounters an error, but just proceeds to the next chunk (which sometimes drives me crazy).