http://ggorjan.blogspot.ca/2013/07/parse-arguments-of-r-script.html?utm_source=feedburner&utm_medium=feed&utm_campaign=Feed:+GregorGorjancsBlog+(Gregor+Gorjanc's+blog)
R can be used also as a scripting tool. We just need to add shebang in the first line of a file (script):#!/usr/bin/Rscriptand then the R code should follow.
Often we want to pass arguments to such a script, which can be collected in the script by the commandArgs() function. Then we need to parse the arguments and conditional on them do something. I came with a rather general way of parsing these arguments using simply these few lines:
## Collect arguments
args <- a="" href="http://inside-r.org/r-doc/base/commandArgs" style="color: #b81909; text-decoration: none;">commandArgs
(TRUE)
## Default setting when no arguments passed
if(length(args) <
1) {
args <- a="" href="http://inside-r.org/r-doc/base/c" style="color: #b81909; text-decoration: none;">
c("--help")
}
## Help section
if("--help" %in%
args) {
cat("
The R Script
Arguments:
--arg1=someValue - numeric, blah blah
--arg2=someValue - character, blah blah
--arg3=someValue - logical, blah blah
--help - print this text
Example:
./test.R --arg1=1 --arg2="output.txt
" --arg3=TRUE \n\n")
q(save=
"no")
}
## Parse arguments (we expect the form --arg=value)
parseArgs <- a="" href="http://inside-r.org/r-doc/base/function" style="color: #b81909; text-decoration: none;">
function(x
) strsplit(sub("^--", "", x
), "=")
argsDF <- a="" href="http://inside-r.org/r-doc/base/as.data.frame" style="color: #b81909; text-decoration: none;">
as.data.frame(do.call("rbind", parseArgs
(args)))
argsL <- a="" href="http://inside-r.org/r-doc/base/as.list" style="color: #b81909; text-decoration: none;">
as.list(as.character(argsDF$V2
))
names(argsL
) <- argsdf="" nbsp="" span="" style="font-style: italic;">## Arg1 default
if(is.null(args$arg1
)) {
## do something
}
## Arg2 default
if(is.null(args$arg2
)) {
## do something
}
## Arg3 default
if(is.null(args$arg3
)) {
## do something
}
## ... your code here ...
Created by Pretty R at inside-R.orgIt is some work, but I find it pretty neat and use it for quite a while now. I do wonder what others have come up for this task. I hope I did not miss some very general solution.
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