I just got ESS set up in EMACS (I'm a relative newbie in this area). I have figured out how to take an R script and fire up an interactive R shell and evaluate a whole buffer ("C-c C-b"). But I'd also like to have the ability to submit an R script via RScript in the way that you can with Perl or Python with `compile-dwim-run', which I have bound to "C-c r", and have the whole output returned to me in a separate buffer without keeping open an interactive R shell.
I can't seem to find a default way to do this, and I'd like to leverage whatever ESS has to work that (I assume there is) before I go off and attempt to roll my own.
Thank you,
Matt
C-c C-l is what you are looking for? Use C-c C-h to see all the keys that are bound on C-c map (an even better approach is to install helm-descrbind from emacs package manager - you will be pleasantly surprised :).
[edit:] Sorry, misread your post slightly. You want batch evaluation. That is not available for R. The reason, the analysis in R is usually a complex process which you don't want to execute again and again. So you keep your interactive session open and iteratively achieve what you want.
There have been talks inside ESS to add some batch functionality, but it seems like very few people really need that.
Related
I have just started to learn to code on R, so I apologize for the very simple question. I understand it is best to type your code in as a Script so you can edit and save it. However, when I try to make an object in the script section, it does not work. If I make an object in the console, R saves the object and it appears in my environment. I am typing in a very simple code to try a quick exercise on rolling dice:
die <- 1:6
But it only works in the console and not when typed as a script. Any help/explanation appreciated!
Essentially, you interact with R environment differently when running an .R script via RScript.exe or via console with R.exe, Rterm, etc. and in GUI IDEs like RGui or RStudio. (This applies to any programming language with interactive compilers not just R).
The script does save thedie object in R environment but only during the run or lifetime of that script (i.e., from beginning to end of code lines). Your code line is simply an assignment of object. You do nothing with it. Apply some function, output results, and other actions in that script to see.
On the console, the R environment persists interactively until you quit it with q(). So assigned objects remains for lifetime of your console session. After assigning, you can afterwards apply function, output results, or other actions in line by line calls.
Ultimately, scripts gathers all line by line code in advance of run for automated execution without relying on user to supply lines. Imagine running 1,000 lines of code with nested if/then or for/while loops, apply functions on console! Therefore, have all your R coding needs summarily handled in scripts.
It is always better to have the script, as you say, you can save edit correct, without having to rewrite the code to change a variable or number.
I recommend using Rstudio, it is very practical and will help you to program more efficiently and allows you to see, among other things, the different objects that you have created.
Is there an easy way to have R record all input and output from your R session to disk while you are working with R interactively?
In R.app on Mac OS X I can do a File->Save..., but it isn't much help in recovering the commands I had entered when R crashes.
I have tried using sink(...,split=T), but it doesn't seem to do exactly what I am looking for.
Many of us use ESS / Emacs for this very reason. Saving old sessions with extension '.Rt' even gives you mode-specific commands for re-running parts of your session.
Greg Snow wrote recently on the R-help list (a very valuable resource, SO R people!):
"You may also want to look at ?TeachingDemos::txtStart as an alternative to sink, one advantage is that the commands as well as the output can be included. With a little more work you can also include graphical output into a transcript file."
r-help
Check out the savehistory() command
I'm not sure yet how to answer an answer, but there is an updated version of Ranke's vim r-plugin called r-plugin2 available here. It seems more user-friendly and robust than the original.
Emacs is good, but for those of us with a vi preference there's the vim-r plugin at:
http://www.uft.uni-bremen.de/chemie/ranke/index.php?page=vim_R_linux
It works brilliantly and has a tiny memory footprint.
I am running a set of selected code on R. Like
source("/tmp/r-plugin-honli/Rsource-2704-quantmod.R")
There is no output. Only the prompt '>' flickered there.
I use 'killall' to kill the R session. But I don't know where is wrong on the code. Because R did not give any output. How could I know what's going on about the code.
I'd try two things:
Run the code interactively. As in, open the Rsource-2704 file and run its lines one by one.
If that doesn't replicate the problem or is not possible, you can take Joshua Ulrich's suggestion or use:
R CMD BATCH --vanilla Rsource-2704-quantmod.R out.log
Which will run the code in a batch mode and output the usual console lines to a file called out.log (you can name it whatever you like).
Instead of using print statements, you could also take a look at the browser() command. This drops you into an interactive session at the point where the command is put. This works particularly well when trying to figure out what is happening inside a function, although I don't know if your script contains them.
I have about 5 scripts that are all part of a project to be run one after the other. I would like to open the first script, run it and then be prompted at the end, "Do you want to run XrefGenetic.r?" If yes, then XrefGenetic.r should open and run. I am 100% certain R can do this, in fact I think I used to know how but have forgotten and cannot find it anywhere.
How do I open another r script from within an r script?
Are you thinking of source() ?
My usual recommendation is to create a package, as that alleviates all these issues: functions and symbols are known (or hidden if you chose not to export them) and you have generally much better control.
Is there an easy way to have R record all input and output from your R session to disk while you are working with R interactively?
In R.app on Mac OS X I can do a File->Save..., but it isn't much help in recovering the commands I had entered when R crashes.
I have tried using sink(...,split=T), but it doesn't seem to do exactly what I am looking for.
Many of us use ESS / Emacs for this very reason. Saving old sessions with extension '.Rt' even gives you mode-specific commands for re-running parts of your session.
Greg Snow wrote recently on the R-help list (a very valuable resource, SO R people!):
"You may also want to look at ?TeachingDemos::txtStart as an alternative to sink, one advantage is that the commands as well as the output can be included. With a little more work you can also include graphical output into a transcript file."
r-help
Check out the savehistory() command
I'm not sure yet how to answer an answer, but there is an updated version of Ranke's vim r-plugin called r-plugin2 available here. It seems more user-friendly and robust than the original.
Emacs is good, but for those of us with a vi preference there's the vim-r plugin at:
http://www.uft.uni-bremen.de/chemie/ranke/index.php?page=vim_R_linux
It works brilliantly and has a tiny memory footprint.