[R] Official way to set/retrieve options in packages?

[Bert Gunter]

Have you read

?Startup

which explains startup procedures, including reading of .Rprofile.

I cannot speak for Brian Ripley, but I can tell you that I would
prefer that packages did not mess with my .Rprofile files.

OTOH, I have no objections if packages suggest that I set certain
options in them or even give me lines of code that I can add if I
choose ( or give me an option to call a function to do so).

I understand that this is not the automatic procedure you seem to be seeking...

Cheers,
Bert

On Sun, Jun 2, 2013 at 9:06 AM, Jonathan Greenberg <jgrn at illinois.edu> wrote:
> What would be an example of setting, saving, and re-loading an option to a
> user's .Rprofile -- and would this be a no-no in a CRAN package?
>
> --j
>
>
> On Sat, Jun 1, 2013 at 4:57 PM, Prof Brian Ripley <ripley at stats.ox.ac.uk>wrote:
>
>> On 01/06/2013 22:44, Anthony Damico wrote:
>> > hope this helps..  :)
>> >
>> >      # define an object `x`
>> >      x <- list( "any value here" , 10 )
>> >
>> >      # set `myoption` to that object
>> >      options( "myoption" = x )
>> >
>> >      # retrieve it later (perhaps within a function elsewhere in the
>> package)
>> >      ( y <- getOption( myoption ) )
>> >
>> >
>> > it's nice to name your options `mypackage.myoption` so users know what
>> > package the option is associated with in case they type `options()`
>> >
>> >
>> > here's the `.onLoad` function in the R survey package.  notice how the
>> > options are only set *if* they don't already exist--
>>
>> But a nicer convention is that used by most packages in R itself: if the
>> option is not set, the function using it assumes a suitable default.
>> That would make sense for all the FALSE defaults below.
>>
>> Note though that this is not 'persistent': users have to set options in
>> their startup files (see ?Startup).   There is no official location to
>> store package configurations.  Users generally dislike software saving
>> settings in their own file space so it seems very much preferable to use
>> the standard R mechanisms (.Rprofile etc).
>>
>> >
>> >> survey:::.onLoad
>> >
>> > function (...)
>> > {
>> >      if (is.null(getOption("survey.lonely.psu")))
>> > options(survey.lonely.psu = "fail")
>> >      if (is.null(getOption("survey.ultimate.cluster")))
>> > options(survey.ultimate.cluster = FALSE)
>> >      if (is.null(getOption("survey.want.obsolete")))
>> > options(survey.want.obsolete = FALSE)
>> >      if (is.null(getOption("survey.adjust.domain.lonely")))
>> > options(survey.adjust.domain.lonely = FALSE)
>> >      if (is.null(getOption("survey.drop.replicates")))
>> > options(survey.drop.replicates = TRUE)
>> >      if (is.null(getOption("survey.multicore")))
>> > options(survey.multicore = FALSE)
>> >      if (is.null(getOption("survey.replicates.mse")))
>> > options(survey.replicates.mse = FALSE)
>> > }
>> > <environment: namespace:survey>
>> >
>> >
>> >
>> >
>> > On Sat, Jun 1, 2013 at 4:01 PM, Jonathan Greenberg <jgrn at illinois.edu
>> >wrote:
>> >
>> >> R-helpers:
>> >>
>> >> Say I'm developing a package that has a set of user-definable options
>> that
>> >> I would like to be persistent across R-invocations (they are saved
>> >> someplace).  Of course, I can create a little text file to be
>> written/read,
>> >> but I was wondering if there is an "officially sanctioned" way to do
>> this?
>> >>   I see there is an options() and getOptions() function, but I'm
>> unclear how
>> >> I would use this in my own package to create/save new options for my
>> >> particular package.  Cheers!
>> >>
>> >> --j
>> >>
>> >> --
>> >> Jonathan A. Greenberg, PhD
>> >> Assistant Professor
>> >> Global Environmental Analysis and Remote Sensing (GEARS) Laboratory
>> >> Department of Geography and Geographic Information Science
>> >> University of Illinois at Urbana-Champaign
>> >> 607 South Mathews Avenue, MC 150
>> >> Urbana, IL 61801
>> >> Phone: 217-300-1924
>> >> http://www.geog.illinois.edu/~jgrn/
>> >> AIM: jgrn307, MSN: jgrn307 at hotmail.com, Gchat: jgrn307, Skype: jgrn3007
>> >>
>> >>          [[alternative HTML version deleted]]
>> >>
>> >> ______________________________________________
>> >> R-help at r-project.org mailing list
>> >> https://stat.ethz.ch/mailman/listinfo/r-help
>> >> PLEASE do read the posting guide
>> >> http://www.R-project.org/posting-guide.html
>> >> and provide commented, minimal, self-contained, reproducible code.
>> >>
>> >
>> >       [[alternative HTML version deleted]]
>> >
>> > ______________________________________________
>> > R-help at r-project.org mailing list
>> > https://stat.ethz.ch/mailman/listinfo/r-help
>> > PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html
>> > and provide commented, minimal, self-contained, reproducible code.
>> >
>>
>>
>> --
>> Brian D. Ripley,                  ripley at stats.ox.ac.uk
>> Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
>> University of Oxford,             Tel:  +44 1865 272861 (self)
>> 1 South Parks Road,                     +44 1865 272866 (PA)
>> Oxford OX1 3TG, UK                Fax:  +44 1865 272595
>>
>
>
>
> --
> Jonathan A. Greenberg, PhD
> Assistant Professor
> Global Environmental Analysis and Remote Sensing (GEARS) Laboratory
> Department of Geography and Geographic Information Science
> University of Illinois at Urbana-Champaign
> 607 South Mathews Avenue, MC 150
> Urbana, IL 61801
> Phone: 217-300-1924
> http://www.geog.illinois.edu/~jgrn/
> AIM: jgrn307, MSN: jgrn307 at hotmail.com, Gchat: jgrn307, Skype: jgrn3007
>
>         [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.



-- 

Bert Gunter
Genentech Nonclinical Biostatistics

Internal Contact Info:
Phone: 467-7374
Website:
http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm