I want to know if there is a way to run R code (train, mutate, search, ...) in the background, without the need to wait for execution to end or to manually transfer related data to a new session.
Multiple tabs in R-Studio or running multiple sessions in a Jupyer notebook from localhost:8888, localhost:8889, localhost:8890, localhost:8891, etc. is another crude way.
Be mindful of system compute strengths/limitations.
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.
I'm running Rstudio on a mac and my code slows down greatly when I place it between the brackets of a system.time command.
However system.time appears to report the actual time it takes to run the code without being placed in system.time(). Thus although it takes 2 or 3 minutes for the command to run within system.time(), it will report only a few seconds of elapsed time.
I'm not sure how to diagnose this behavior further.
One possible cause might be that I'm working with very large data tables and running efficient data.table commands that would take a long time to run in base r. Would this interfere with system.time()?
Try running it in the RGUI. One issue with RStudio (I have seen this same problem on my code) is that RStudio will want to update its Environment after each execution and this may take some time. I usually try to run large batch jobs in RGUI to avoid this issue.
Try it and report back.
I often include View() statements in my R scripts. If I accidentally forget the closing bracket at the end of the line, and then run the line of code from the script window using ctrl-enter, R just keeps trying to execute the remainder of my script. I don't know why it does that (rather than using the + symbol to prompt me to provide further input).
Moreover, I've tried to stop this by setting break points in my code - I can click on the LHS of the page and a little red circle appears. But the breakpoints don't seem to work - R just ignores them and keeps going.
The only way I can get out of it is by killing the process in the Windows task manager and then going back in afterwards. But it's wasting a lot of time.
Does anyone know how I can fix this please?
Thank you.
In effect, what your function is processing looks like that:
... %>% View(
lm(am~cyl, mtcars)
...
...
As R can't find the bracket for ) it includes remaining statements as input to View and searches for the bracket.
Solutions
Kind of depends on what you want to do with those scripts but if the intention is to run them in the background consider using callr. This package lets you run R from R and offers kill methods to kill the process you started that way.
On Windows pressing Esc should enable you to get back to the console but if it's a memory intense process it may be difficult.
You may try pressing Ctrl+c in order to kill the process.
I want an R script to continuously run and check for files in a folder and do something with those files.
The code simply checks for a file, then moves the file to somewhere else and renames it, deleting the old file (in reality it's a bit more elabore than this).
If I run the script it works fine, however I want R to automatically detect for the files. In other words, is there a way to have R run the script continuously so that I don't have to run the script if I put files in that folder?
In pure R you just need an infinite repeat loop...
repeat {
print('Checking files')
# Your code to do file manipulation
Sys.sleep(time=5) # to stop execution for 5 sec
}
However there may be better tools suitable to do this kind of file manipulation depending on your OS.
You can use the function tclTaskSchedule from the tcltk2 package to schedule a function or expression to run on a regular interval. You can have multiple such tasks scheduled and still work in the R session (just be careful not to modify something that the scheduled task could also modify or you can get unpredictable results).
Though an OS based solution that runs a given rscript may still be a better approach.
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.