commandArgs {R.utils}

Extract command-line arguments

Description

Provides access to a copy of the command-line arguments supplied when this R session was invoked. This function is backward compatible with commandArgs() of the base package, but adds more features.

Usage

commandArgs(trailingOnly=FALSE, asValues=FALSE, defaults=NULL, always=NULL, adhoc=FALSE,
  unique=FALSE, excludeReserved=FALSE, excludeEnvVars=FALSE, os=NULL, .args=NULL, ...)

Arguments

trailingOnly

If TRUE, only arguments after --args are returned.

asValues

If TRUE, a named list is returned, where command line arguments of type --foo will be returned as TRUE with name foo, and arguments of type -foo=value will be returned as character string value with name foo. In addition, if -foo value is given, this is interpreted as -foo=value, as long as value does not start with a double dash (--).

defaults

A character vector or a named list of default arguments. Any command-line or fixed arguments will override default arguments with the same name.

always

A character vector or a named list of fixed arguments. These will override default and command-line arguments with the same name.

adhoc

(ignored if asValues=FALSE) If TRUE, then additional coercion of character command-line arguments to more specific data types is performed, iff possible.

unique

If TRUE, the returned set of arguments contains only unique arguments such that no two arguments have the same name. If duplicates exists, it is only the last one that is kept.

excludeReserved

If TRUE, arguments reserved by R are excluded, otherwise not. Which the reserved arguments are depends on operating system. For details, see Appendix B on "Invoking R" in An Introduction to R.

excludeEnvVars

If TRUE, arguments that assigns environment variable are excluded, otherwise not. As described in R --help, these are arguments of format <key>=<value>.

os

A vector of character strings specifying which set of reserved arguments to be used. Possible values are "unix", "mac", "windows", "ANY" or "current". If "current", the current platform is used. If "ANY" or NULL, all three OSs are assumed for total cross-platform compatibility.

args

A named list of arguments.

.args

A character vector of command-line arguments.

...

Passed to commandArgs() of the base package.

Value

If asValue is FALSE, a character vector is returned, which contains the name of the executable and the non-parsed user-supplied arguments.

If asValue is TRUE, a named list containing is returned, which contains the the executable and the parsed user-supplied arguments.

The first returned element is the name of the executable by which R was invoked. As far as I am aware, the exact form of this element is platform dependent. It may be the fully qualified name, or simply the last component (or basename) of the application. The returned attribute isReserved is a logical vector specifying if the corresponding command-line argument is a reserved R argument or not.

Backward compatibility

This function should be fully backward compatible with the same function in the base package, except when littler is used (see below).

Compatibility with littler

The littler package provides the r binary, which parses user command-line options and assigns them to character vector argv in the global environment. The commandArgs() of this package recognizes argv arguments as well.

Coercing to non-character data types

When asValues is TRUE, the command-line arguments are returned as a named list. By default, the values of these arguments are character strings. However, any command-line argument that share name with one of the 'always' or 'default' arguments, then its value is coerced to the corresponding data type (via as). This provides a mechanism for specifying data types other than character strings.

Furthermore, when asValues and adhoc are TRUE, any remaining character string command-line arguments are coerced to more specific data types (via type.convert), if possible.

Author(s)

Henrik Bengtsson

See Also

For a more user friendly solution, see cmdArgs(). Internally commandArgs() is used.

Examples

######################################################################
# Non-parsed command-line arguments
######################################################################
# Display how this instance of R was invoked.
cmd <- paste(commandArgs(), collapse=" ")
cat("How R was invoked:\n");
cat(cmd, "\n")

# Get all arguments
args <- commandArgs()
print(args)

# Get only "private" arguments and not the name of the R executable.
args <- commandArgs(excludeReserved=TRUE)[-1]
print(args)

# Assert backward compatibility
args0 <- base::commandArgs()
args <- commandArgs()
stopifnot(all.equal(args, args0, check.attributes=FALSE))


######################################################################
# Parsed command-line arguments
######################################################################
# Get all arguments as a named list, e.g. if R is started as:
#
#   R DATAPATH=../data --args --root="do da" --foo bar --details --a=2
#
# then 'args' below will equal
#
#   list(R=NA, DATAPATH="../data" args=TRUE, root="do da",
#        foo="bar", details=TRUE, a="2")
args <- commandArgs(asValues=TRUE)
str(args)

# Turn arguments into R variables
args <- commandArgs(asValues=TRUE, excludeReserved=TRUE)[-1]
keys <- attachLocally(args)
cat("Command-line arguments attached to global environment:\n");
print(keys);
str(mget(keys, envir=globalenv()))