Re^2: Passing parameters to R script

Thank you all for your input! I did eventually work it out and my solution looks like so:

# test.R
# Parse and use command line arguments
# Invoke % R --slave --args 100 < test.R 

Args <- commandArgs();      # retrieve args
x <- c(1:as.real(Args[4])); # get the 4th argument
y <- c(x^2);                # work out square
png(filename="image.png");  # create image file
plot(x,y);                  # plot image
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This creates the image file image.png which contains a plot of an exponential curve =)

The variable Args contains the following:

[1] "/usr/lib/R/bin/exec/R" 
[2] "--slave" 
[3] "--args"               
[4] "100"
[download]

We only require the 4th element for our graph. You can add more arguments and just pick them off accordingly =)

I hope someone else finds this useful.

Smoothie, smoothie, hundre prosent naturlig!

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Re^3: Passing parameters to R script by Anonymous Monk on Apr 22, 2009 at 14:37 UTC
Yes, this was very useful and worked right away! Thanks a lot!	[reply]
Re^3: Passing parameters to R script by Anonymous Monk on Jun 08, 2010 at 09:39 UTC
That works fine, but there's a slightly neater way to do it; if you provide a TRUE value to the commandArgs function, it ignores any commandline parameters before (and including) --args. So with `Args <- commandArgs(TRUE)`, `Args[1]` is `"100"`, and is the only element of the vector. It's also possible to use a simpler syntax to call the script on the command line, which implicitly assumes that any arguments are given after the script name: `Rscript test.R 100` Cheers, Julio	[reply] [d/l] [select]
Re^4: Passing parameters to R script by Anonymous Monk on Jan 09, 2011 at 14:28 UTC
In Bash shell `# a=1 # b=10 # Rscript -e "args<-commandArgs(TRUE);x=args[1]:args[2];x;mean(x);sd(x +)" $a $b [1] 1 2 3 4 5 6 7 8 9 10 [1] 5.5 [1] 3.027650` [download] So you can control variables on the command line R script and you can feed these variables into R itself using commandArgs(TRUE), and manipulate the variables as args1 and args2. So if I imagine if you are doing a system call in perl, you can also construct a similar Rscript on the command line, and get the output accordingly, which you can manipulate further within perl (or any other script).	[reply] [d/l]
Re^4: Passing parameters to R script by Anonymous Monk on Jan 06, 2011 at 03:53 UTC
Here is simple function to parse unix way of parsing argument from R. `# # # EXAMPLE: # R --test=mydata.csv #> getopt('test') #[1] "mydata.csv" # getting numeric argument # R --N=123 #> getopt('N',numeric=T) #[1] 123 # getopt <- function(argname, numeric = F) { args <- commandArgs() argexp = sprintf('^--%s=',argname) idx <- regexpr(argexp, args); ret <- NA if ( any(idx > 0) ) { # found matching argument found <- args[idx > 0] value <- strsplit(found,"=") ret <- unlist(value)[2] } if ( numeric ) ret <- as.numeric(ret) ret }` [download] cheers, c.okugami	[reply] [d/l]
Re^3: Passing parameters to R script by Anonymous Monk on Feb 01, 2012 at 19:25 UTC
In Rscript/R `require(plyr) ## get and parse any commandline options/args cmd.args <- commandArgs(trailingOnly=TRUE) ## this assumes trailingOnly in commandArgs() mk.cmd.args.list <- function(args) { if (length(args)>1) { split.list <- strsplit( args[-1], '\\=' ) ## exclude "--args" values <- llply( split.list, '[[', 2 ) names(values) <- laply( split.list, '[[', 1 ) values } else list() ## the possible returns } cmd.args.list <- mk.cmd.args.list(cmd.args)` [download]	[reply] [d/l]