Jonathan Greenberg
2013-Jun-01 20:01 UTC
[R] Official way to set/retrieve options in packages?
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@hotmail.com, Gchat: jgrn307, Skype: jgrn3007 [[alternative HTML version deleted]]
Anthony Damico
2013-Jun-01 21:44 UTC
[R] Official way to set/retrieve options in packages?
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--
> 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@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@hotmail.com, Gchat: jgrn307, Skype: jgrn3007
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help@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]]
Jonathan Greenberg
2013-Jun-02 16:06 UTC
[R] Official way to set/retrieve options in packages?
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@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@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@hotmail.com, Gchat: jgrn307, Skype: jgrn3007 > >> > >> [[alternative HTML version deleted]] > >> > >> ______________________________________________ > >> R-help@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@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@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@hotmail.com, Gchat: jgrn307, Skype: jgrn3007 [[alternative HTML version deleted]]
Jonathan Greenberg
2013-Oct-18 22:46 UTC
[R] Official way to set/retrieve options in packages?
Wanted to re-start this thread a bit, since I'm still not exactly sure the best approach to my problem -- basically, the parameters I'm try to make persistent are installation locations of a particular command line program that is not installed along with an R package I'm working on (GDAL, for those of you who are interested in the specifics). The function tries to dummy-proof this process by doing a (mostly) brute-force search of the user's drive for the program location the first time it executes, and then stores this information (the path to a given executable) in an option for use with other functions. This search process can take some time, so I'd prefer to have this option set in a semi-permanent way (so it persists between sessions). Now, Brian Ripley suggested modifying the .Rprofile, but Bert Guntner suggested this might not be a welcome behavior. Given that, on an operating system level, there are often per-program directories for preferences, would it follow that it might make sense to store package-options in some standardized location? If so, where might this be? Would it make sense to drop then in the package directory? Is this a discussion that should move over to r-developers? --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 259 Computing Applications Building, MC-150 605 East Springfield Avenue Champaign, IL 61820-6371 Phone: 217-300-1924 http://www.geog.illinois.edu/~jgrn/ AIM: jgrn307, MSN: jgrn307 at hotmail.com, Gchat: jgrn307, Skype: jgrn3007