How can I force RStudio (v1.1.383) to evaluate R chunks always in console (instead of inline) when working with Rmarkdown documents, using a script?
I know I can set up Output chunks in Console by clicking on it:
According to this RStudio support post I could also un-check 'Show output inline for all R Markdown document' under 'Tools -> Global Options...':
But, is there a way to do it from a command line?
The reason I ask is that, I often work on my university machines and they all restore to defaults after each reset. Each time when in class, we have to manually go thru menus.
Knowing how to do it via a console command would as useful as starting each of my classes with
rm(list=ls())
There's not currently an elegant way to do this. This preference is stored inside an internal RStudio state file, in %localappdata%\RStudio-Desktop\monitored\user-settings. If you're sufficiently motivated you can write a script which sets the rmd_chunk_output_inline preference, but it's going to be unpleasant.
One thing you can do is set the chunk output type in the YAML header, like this:
---
editor_options:
chunk_output_type: console
---
You could also use an R Markdown document template with this set up for you (maybe your script could write this out).
Finally, there's an open issue for this on RStudio's github page which you might comment on and/or vote for:
https://github.com/rstudio/rstudio/issues/1607
Related
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.
In R Markdown if I have a chunk coded with the normal r chunk wrappers,
```{r}
[R code]
```
A play button will appear. However, when I run a chunk wrapped like so for other language engines:
```{python}
[python code]
```
or replacing python replaced with bash/sh, I don't get a play button on the right.
Is there a package I need to install? I restarted Rstudio, and even downloaded the Lesson 5: https://rmarkdown.rstudio.com/lesson-5.html , which even shows those play buttons, and I still don't get it. I am on a mac, and saw that someone on a Windows computer was able to see the play buttons.
I think you need to install the package "knitr". Try to check that first.
Second, you might need to state explitly where your interpreter for Python is, for instance. Use
{python, engine.path = '/usr/bin/python3'}
YOUR CODE
to see if it works.
I'm utilizing a Macbook pro running "El Capitan" and RStudio is version 0.99.902. I'm writing a Rmd document. I want to utilize the snippets that RStudio has built in and create my own also. By clicking Preference => Code; I can see that "Enable code snippets" is checked. However, while trying to utilize any snippet the completion is not performed. If I typed just r I should get this block of code, but nothing hapen
snippet r
```{r ${1:label}, ${2:options}}
${0}
```
I also create a simple snippet:
snippet dthen
%>%
None of the markdown snippet seems to work. Do I'm doing something wrong or any setting has to be done?
You can invoke code snippets in Markdown in RStudio using Shift+Tab after typing the snippet, but it will not currently prompt you to expand the snippet, either with Tab or by just waiting. I thought this was a bug, but the discussion in this GitHub issue says it's intended, just still-to-be-documented.
In Tools > Global Options > Code > Editing > Edit Snippets, go to the section "Markdown" and paste your snippet there. Save, OK, apply. Type r in your Rmd document (not within in a R code chunk) and click Shift+Tab. If it still does not work, try to create a new "R markdown" file (File > New file > R markdown) and check if it works there.
TL;DR
What are the (possibly unwanted) side-effects of using knit()/knit2pdf() instead of the "Compile PDF"1 button in RStudio?
Motivation
Most users of knitr seem to write their documents in RStudio and compile the documents using the "Compile PDF" / "Knit HTML" button. This works smoothly most of the time, but every once a while there are special requirements that cannot be achieved using the compile button. In these cases, the solution is usually to call knit()/knit2pdf()/rmarkdown::render() (or similar functions) directly.
Some examples:
How to knit/Sweave to a different file name?
Is there a way to knitr markdown straight out of your workspace using RStudio?
Insert date in filename while knitting document using RStudio Knit button
Using knit2pdf() instead of the "Compile PDF" button usually offers a simple solution to such questions. However, this comes at a price: There is the fundamental difference that "Compile PDF" processes the document in a separate process and environment whereas knit2pdf() and friends don't.
This has implications and the problem is that not all of these implications are obvious. Take the fact that knit() uses objects from the global environment (whereas "Compile PDF" does not) as an example. This might be obvious and the desired behavior in cases like the second example above, but it is an unexpected consequence when knit() is used to overcome problems like in example 1 and 3.
Moreover, there are more subtle differences:
The working directory might not be set as expected.
Packages need to be loaded.
Some options that are usually set by RStudio may have unexpected values.
The Question and it's goal
Whenever I read/write the advice to use knit2pdf() instead of "Compile PDF", I think "correct, but the user should understand the consequences …".
Therefore, the question here is:
What are the (possibly unwanted) side-effects of using knit()/knit2pdf() instead of the "Compile PDF" button in RStudio?
If there was a comprehensive (community wiki?) answer to this question, it could be linked in future answers that suggest using knit2pdf().
Related Questions
There are dozens of related questions to this one. However, they either propose only code to (more or less) reproduce the behavior of the RStudio button or they explain what "basically" happens without mentioning the possible pitfalls. Others look like being very similar questions but turn out to be a (very) special case of it. Some examples:
Knit2html not replicating functionality of Knit HTML button in R Studio: Caching issue.
HTML outputs are different between using knitr in Rstudio & knit2html in command line: Markdown versions.
How to convert R Markdown to HTML? I.e., What does “Knit HTML” do in Rstudio 0.96?: Rather superficial answer by Yihui (explains what "basically" happens) and some options how to reproduce the behavior of the RStudio button. Neither the suggested Sys.sleep(30) nor the "Compile PDF" log are insightful (both hints point to the same thing).
What does “Knit HTML” do in Rstudio 0.98?: Reproduce behavior of button.
About the answer
I think this question raised many of the issues that should be part of an answer. However, there might be many more aspects I don't know about which is the reason why I am reluctant to self-answer this question (though I might try if nobody answers).
Probably, an answer should cover three main points:
The new session vs. current session issue (global options, working directory, loaded packages, …).
A consequence of the first point: The fact that knit() uses objects from the calling environment (default: envir = parent.frame()) and implications for reproducibility. I tried to tackle the issue of preventing knit() from using objects from outside the document in this answer (second bullet point).
Things RStudio secretly does …
… when starting an interactive session (example) --> Not available when hitting "Compile PDF"
… when hitting "Compile PDF" (anything special besides the new session with the working directory set to the file processed?)
I am not sure about the right perspective on the issue. I think both, "What happens when I hit 'Compile PDF' + implications" as well as "What happens when I use knit() + implications" is a good approach to tackle the question.
1 The same applies to the "Knit HTML" button when writing RMD documents.
First of all, I think this question is easier to answer if you limit the scope to the "Compile PDF" button, because the "Knit HTML" button is a different story. "Compile PDF" is only for Rnw documents (R + LaTeX, or think Sweave).
I'll answer your question following the three points you suggested:
Currently RStudio always launch a new R session to compile Rnw documents, and first changes the working directory to the directory of the Rnw file. You can imagine the process as a shell script like this:
cd path/to/your-Rnw-directory
Rscript -e "library(knitr); knit('your.Rnw')"
pdflatex your.tex
Note that the knitr package is always attached, and pdflatex might be other LaTeX engines (depending on your RStudio configurations for Sweave documents, e.g., xelatex). If you want to replicate it in your current R session, you may rewrite the script in R:
owd = setwd("path/to/your-Rnw-directory")
system2("Rscript", c("-e", shQuote("library(knitr); knit('your.Rnw')"))
system2("pdflatex", "your.tex")
setwd(owd)
which is not as simple as knitr::knit('path/to/your.Rnw'), in which case the working directory is not automatically changed, and everything is executed in the current R session (in the globalenv() by default).
Because the Rnw document is always compiled in a new R session, it won't use any objects in your current R session. This is hard to replicate only through the envir argument of knitr::knit() in the current R session. In particular, you cannot use knitr::knit(envir = new.env()) because although new.env() is a new environment, it has a default parent environment parent.frame(), which is typically the globalenv(); you cannot use knitr::knit(envir = emptyenv()), either, because it is "too clean", and you will have trouble with objects even in the R base package. The only reliable way to replicate what the "Compile PDF" button does is what I said in 1: system2("Rscript", c("-e", shQuote("library(knitr); knit('your.Rnw')")), in which case knit() uses the globalenv() of a new R session.
I'm not entirely sure about what RStudio does for the repos option. It probably automatically sets this option behind the scenes if it is not set. I think this is a relatively minor issue. You can set it in your .Rprofile, and I think RStudio should respect your CRAN mirror setting.
Users have always been asking why the Rnw document (or R Markdown documents) are not compiled in the current R session. To us, it basically boils down to which of the following consequences is more surprising or undesired:
If we knit a document in the current R session, there is no guarantee that your results can be reproduced in another R session (e.g., the next time you open RStudio, or your collaborators open RStudio on their computers).
If we knit a document in a new R session, users can be surprised that objects are not found (and when they type the object names in the R console, they can see them). This can be surprising, but it is also a good and early reminder that your document probably won't work the next time.
To sum it up, I think:
Knitting in a new R session is better for reproducibilty;
Knitting in the current R session is sometimes more convenient (e.g., you try to knit with different temporary R objects in the current session). Sometimes you also have to knit in the current R session, especially when you are generating PDF reports programmatically, e.g., you use a (for) loop to generate a series of reports. There is no way that you can achieve this only through the "Compile PDF" button (the button is mostly only for a single Rnw document).
BTW, I think what I said above can also apply to the Knit or Knit HTML buttons, but the underlying function is rmarkdown::render() instead of knitr::knit().
When compiling with sweave/pgfsweave, every time a figure is created in R it is shown in a graphics windows (during the sweave compilation process). This is helpful in many cases as I can see what the figures look like as the document is being compiled.
But when I compile through ssh a large document this can be very slow. Is there a way to tell sweave/pgfsweave to avoid displaying the figure during the compilation (I still want the figure in the final pdf document though).
For interactive sessions, the figs.only Sweave option controls this behavior. To plot figures only to the target graphics files (and not to a console graphical window) set figs.only=TRUE.
As explained in the RweaveLatex help file:
figs.only: logical (‘FALSE’). By default each figure chunk is run
once, then re-run for each selected type of graphics. That
will open a default graphics device for the first figure
chunk and use that device for the first evaluation of all
subsequent chunks. If this option is true, the figure chunk
is run only for each selected type of graphics, for which a
new graphics device is opened and then closed.
As with other Sweave options, you can set this option: (1) for the current compilation (e.g. Sweave("example.Rnw", figs.only=TRUE); (2) within the .Rnw file, using \SweaveOpts{figs.only=TRUE}; or (3) as a global default, by putting SWEAVE_OPTIONS="figs.only=TRUE" in, e.g., $R_HOME/etc/Renviron.site
figs.only is the correct way to go, and I also want to mention the default graphical device in R here:
For now you may look at this: http://yihui.name/en/2010/12/a-special-graphics-device-in-r-the-null-device/
After R 2.14.1 (not released yet) you will be able to set the default device to a null PDF device, which is both safe and fast: https://github.com/yihui/knitr/issues/9
If you sweave from the command line instead of in an interactive session, graphics aren't produced in an interactive graphic window.
You can run R from the command line by just typing R CMD Sweave mydoc.Rnw or via a batch file, or a makefile for larger projects. I've started to use makefiles for many of my sweave documents as it handles dependencies, can clear up after itself and much more.
One option could be
<<label=myplotlabel, fig=TRUE, include=FALSE>>=
graph code
#
then
\begin{figure}[h]
\includegraphics[width=6cm, height=6cm]{myplotlabel}
\caption{My Plot}
\label{fig:label}
\end{figure}