On Linstat, you can use R to process an entire script at once or you can use R interactively. Processing an entire R script at once begins at a linux prompt. To use R interactively log in to RStudio Server from a web browser.
To process lengthy, large, computationally intensive jobs, batch processing is generally preferred.
There are three commands you can use to process R scripts from a linux prompt.
(The > is the linux prompt. Items in square brackets, [ ] are optional.)
Rscript
> Rscript [options] infile [> outfile]
R
> R {--save|--no-save} [options*] < infile [> outfile]
R CMD BATCH
> R CMD BATCH [options] infile [outfile]
Any of these alternatives may be put in the background by adding an ampersand, "&", at the end of the command.
Note: All three of these commands automatically restore (load) the default R workspace (.RData). Use the --no-restore option to prevent this.
In addition, Rscript and R CMD BATCH automatically save the R workspace at the end of your script. Use the --no-save option to prevent this.
(The R command requires you to specify --save, --no-save, or --vanilla.)
The following table summarizes the differences among these commands.
| Feature | Rscript | R | R CMD BATCH |
|---|---|---|---|
| output goes to | terminal or file | terminal or file | file |
| errors go to | terminal | terminal | file |
| commands | no echo | echo | file |
| R banner | none | optional | file |
| restore workspace | default | default | default |
| save workspace | default | user specified | default |
All of these commands save graphics in a file named Rplots.pdf by default.
The first command, Rscript infile > outfile, sends only the printed output to the specified output file. Warning and error messages are sent to the terminal. If no output file is specified, output is also sent to the terminal.
Suppose we have a script with the R statements
x <- rnorm(15, mean=1)
t.test(x)saved in a file names example.r.
At the linstat command prompt we can issue the command
> Rscript --no-save example.r > example.logThen the file example.log contains these lines
One Sample t-test
data: x
t = 5.6398, df = 14, p-value = 6.101e-05
alternative hypothesis: true mean is not equal to 0
95 percent confidence interval:
0.7829532 1.7439090
sample estimates:
mean of x
1.263431
The second command, R --no-save < infile > outfile is similar to Rscript infile > outfile. In addition to the printed output, this command also begins with the R banner messages, and echos each R statement.
To suppress the R banner, we use the --quiet option
> R --no-save --quiet < example.r > example2.logThen the file example2.log contains these lines
> x <- rnorm(15, mean=1)
> t.test(x)
One Sample t-test
data: x
t = 2.601, df = 14, p-value = 0.02094
alternative hypothesis: true mean is not equal to 0
95 percent confidence interval:
0.09341475 0.97177368
sample estimates:
mean of x
0.5325942
> The third command, R CMD BATCH infile, saves the R banner, the infile commands, the printed results they produce, and any warning or error messages, all interleaved in a single file.
Automatic capture of error messages is perhaps the chief advantage of this command. It's biggest drawback is that it lacks a --quiet option.
Issue the command
> R CMD BATCH --no-save example.rThen the default output file, example.r.Rout, contains these lines
R version 4.1.0 (2021-05-18) -- "Camp Pontanezen"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> x <- rnorm(15, mean=1)
> t.test(x)
One Sample t-test
data: x
t = 4.9306, df = 14, p-value = 0.0002213
alternative hypothesis: true mean is not equal to 0
95 percent confidence interval:
0.6738831 1.7115150
sample estimates:
mean of x
1.192699
>
> proc.time()
user system elapsed
0.20 0.14 0.36 unlink("example.r")
unlink("example.r.Rout")