R help - Sep 2012 - R equivalent of python module structure and functionality?

summary: how to structure an R file such that it can be both

1. used as a script via, e.g., (from OS commandline)

$ Rscript foo.r bar=baz

2. imported and called as a function via, e.g. (from R commandline)
> source('./foo.r)
> foo(bar='baz')
? I'm looking for the 'R equivalent' of how python supports this
usecase.

details:

As discussed in the thread beginning

https://stat.ethz.ch/pipermail/r-help/2012-September/323255.html

I have a script

https://github.com/TomRoche/GEIA_to_netCDF/blob/master/netCDF.stats.to.stdout.r

that takes named arguments without undue pain. I would also like to be
able to call it as a function from other scripts. How to do that in R?
In case that's not specific enough :-) I know how to structure files/
modules in python like

http://python.net/~goodger/projects/pycon/2007/idiomatic/cmdline.py

(i.e., generically,

http://python.net/~goodger/projects/pycon/2007/idiomatic/handout.html#module-structure
> """module docstring"""
>
> # imports
> # constants
> # exception classes
> # interface functions
> # classes
> # internal functions & classes
>
> def main(...):
>     ...
>
> if __name__ == '__main__':
>     status = main()
>     sys.exit(status)
) so that the file/module is both

1. callable from the OS commandline via, e.g.,

$ /path/to/cmdline.py

2. importable without mere import causing execution of the script's
   functionality, e.g.,
>>> sys.path.append('/path/to')
>>> from cmdline import *
>>> process_command_line(...)
How to do this in R?

TIA, Tom Roche <Tom_Roche at pobox.com>

On Tue, Sep 11, 2012 at 6:00 PM, Tom Roche <Tom_Roche at pobox.com>
wrote:
>
> summary: how to structure an R file such that it can be both
>
> 1. used as a script via, e.g., (from OS commandline)
>
> $ Rscript foo.r bar=baz
>
> 2. imported and called as a function via, e.g. (from R commandline)
>
>> source('./foo.r)
>> foo(bar='baz')
>
> ? I'm looking for the 'R equivalent' of how python supports
this
> usecase.
>
> details:
>
> As discussed in the thread beginning
>
> https://stat.ethz.ch/pipermail/r-help/2012-September/323255.html
>
> I have a script
>
>
https://github.com/TomRoche/GEIA_to_netCDF/blob/master/netCDF.stats.to.stdout.r
>
> that takes named arguments without undue pain. I would also like to be
> able to call it as a function from other scripts. How to do that in R?
> In case that's not specific enough :-) I know how to structure files/
> modules in python like
>
> http://python.net/~goodger/projects/pycon/2007/idiomatic/cmdline.py
>
> (i.e., generically,
>
>
http://python.net/~goodger/projects/pycon/2007/idiomatic/handout.html#module-structure
>> """module docstring"""
>>
>> # imports
>> # constants
>> # exception classes
>> # interface functions
>> # classes
>> # internal functions & classes
>>
>> def main(...):
>>     ...
>>
>> if __name__ == '__main__':
>>     status = main()
>>     sys.exit(status)
>
> ) so that the file/module is both
>
> 1. callable from the OS commandline via, e.g.,
>
> $ /path/to/cmdline.py
>
> 2. importable without mere import causing execution of the script's
>    functionality, e.g.,
>
>>>> sys.path.append('/path/to')
>>>> from cmdline import *
>>>> process_command_line(...)
>
> How to do this in R?

Maybe take a look at littler.

"littler provides hash-bang (i.e. script starting with #!/some/path)
capability for GNU R, as well as simple command-line and piping use."

http://dirk.eddelbuettel.com/code/littler.html


James

On 11 September 2012 at 18:47, J Toll wrote:
| Maybe take a look at littler.
| 
| "littler provides hash-bang (i.e. script starting with #!/some/path)
| capability for GNU R, as well as simple command-line and piping use."
| 
| http://dirk.eddelbuettel.com/code/littler.html

Thanks for the plug. I also wanted to point Tom to CRAN packages

    getopt

    optparse

written specifically to support command-line argument parsing with R scripts
(ie via Rscript and littler).

Dirk

-- 
Dirk Eddelbuettel | edd at debian.org | http://dirk.eddelbuettel.com