Command-line argument parser

Description

argparser provides functions for parsing command-line arguments.

Details

To use the parser,

1. create an arg.parser object with arg_parser;

2. add arguments to the parser with add_argument;

3. call parse_args to parse the command line arguments.

To execute the script, invoke Rscript. Alternatively on Linux, insert a shebang on the first line (#!/usr/bin/env Rscript) and chmod +x the script,

See Also

Useful links:

• https://bitbucket.org/djhshih/argparser

• Report bugs at https://bitbucket.org/djhshih/argparser/issues

Add an argument to a parser.

Description

This function is deprecated. Use add_argument instead.

Usage

add.argument(
  parser,
  arg,
  help,
  default = NULL,
  type = NULL,
  flag = NULL,
  short = NULL
)

Arguments

Value

an arg.parser object with the argument added

Add an argument to a parser.

Description

This function adds an argument to an arg.parser object and returns the modified object.

Usage

add_argument(
  parser,
  arg,
  help,
  default = NULL,
  type = NULL,
  nargs = NULL,
  flag = NULL,
  short = NULL
)

Arguments

Details

This function supports multiple arguments in a vector. To ensure that the argument variable type is set correctly, either specify type directly or supply default argument values as a list. Custom types are supported by defining a new class and a S4 method for coerce, see the examples section.

Value

an arg.parser object with the argument added

Note

Dashes - that occur in the stem of the argument names (e.g. –argument-name) will be converted to underscores _ (e.g. argument_name) in the name of the corresponding variable.

Examples

p <- arg_parser("A text file modifying program")

# Add a positional argument
p <- add_argument(p, "input", help="input file")

# Add an optional argument
p <- add_argument(p, "--output", help="output file", default="output.txt")

# Add a flag
p <- add_argument(p, "--append", help="append to file", flag=TRUE)

# Add multiple arguments together
p <- add_argument(p,
    c("ref", "--date", "--sort"),
    help = c("reference file", "date stamp to use", "sort lines"),
    flag = c(FALSE, FALSE, TRUE))

# Print the help message
print(p)

# Example of custom type, using the example from pythons argparse
setClass("perfectSquare")
setMethod("coerce", c(from = "ANY", to = "perfectSquare"),
    function(from, to) {
      from <- as.numeric(from)
      if (!all.equal(from, as.integer(from))) {
        stop("Type error: ", from, " is not an integer!")
      }
      sqt <- sqrt(from)
      if (sqt != as.integer(sqt)) {
         stop("Type error: ", from, " is not a perfect square!")
      }
      from
    }
)

p2 <- arg_parser("Perfect square checker")
p2 <- add_argument(p2, arg = c("--perfect-square"), 
                   help = "A perfect square integer",
                   type = "perfectSquare")

parse_args(p2, c("--perfect-square", 144))

Create an argument parser.

Description

This function is deprecated. Use arg_parser instead.

Usage

arg.parser(description, name = NULL)

Arguments

Value

a new arg.parser object

Create an argument parser.

Description

This function creates an arg.parser object. It infers the program name from the file name of the invoked script.

Usage

arg_parser(description, name = NULL, hide.opts = FALSE)

Arguments

Details

The argument parser will be created by default with two arguments: --help and --opts. The latter argument can be used for loading a list of argument values that are saved in a RDS file.

Value

a new arg.parser object

Examples

p <- arg_parser("A test program")

Include R script file

Description

Include R script with behaviour similar to C++ #include "header.h", by searching in the directory where the current script file resides.

Usage

include(file)

Arguments

Parse arguments with a parser.

Description

This function is deprecated. Use parse_args instead.

Usage

parse.args(parser, argv = commandArgs(trailingOnly = TRUE))

Arguments

Value

a list with argument values

Parse arguments with a parser.

Description

This function uses an arg.parser object to parse command line arguments or a character vector.

Usage

parse_args(parser, argv = NULL)

Arguments

Value

a list with argument values

Examples

p <- arg_parser('pi')
p <- add_argument(p, "--digits",
  help="number of significant digits to print", default=7)

## Not run: 
# If arguments are passed from the command line,
# then we would use the following:
argv <- parse_args(p)

## End(Not run)

# For testing purposes, we can pass a character vector:
argv <- parse_args(p, c("-d", "30"))

# Now, the script runs based on the passed arguments
digits <- if (argv$digits > 22) 22 else argv$digits
print(pi, digits=digits)

## Not run: 
# We can also save an argument list for later use
saveRDS(argv, "arguments.rds")

# To use the saved arguments, use the --opts argument at the command line
#$ ./script.R --opts arguments.rds

## End(Not run) 

Print the help message for an arg.parser.

Description

This function prints the help message.

Usage

## S3 method for class 'arg.parser'
print(x, ...)

Arguments

Details

At the command line, we would use the --help or -help flag to print the help message: $ script --help

Extract label and help strings from parser.

Description

Extract label and help strings from parser.

Usage

show_arg_labels(parser)

Arguments

Value

a list containing a reg.args, flags, and opt.args list, which each containing a label string and a help string

Space string.

Description

Space string.

Usage

spaces(n)

Arguments

Value

a character string containing n spaces