[R-pkg-devel] Redefinition of generic for plot function breaks plot.formula

[Gavin Simpson]

...or have an object that is a data.frame but to which you add an
additional class

class(obj) <- c("my_df", "data.frame")

Then you can include plot.my_df() in your package, plus a function to
create a my_df object from a data frame, and you don't have to worry about
all this and your objects will still work like data frames

G
On Sep 1, 2015 07:15, "Hadley Wickham" <h.wickham at gmail.com> wrote:

> Why don't you just create your own function?
>
> Hadley
>
> On Tue, Sep 1, 2015 at 8:08 AM, Benjamin Hofner <benjamin.hofner at fau.de>
> wrote:
> > Dear Gavin,
> >
> > unfortunately, I cannot overwrite plot.data.frame only. If I do this I
> > get the following warning from R CMD check:
> >
> > * checking use of S3 registration ... WARNING
> > Registered S3 method from a standard package overwritten by 'papeR':
> > method from
> > plot.data.frame graphics
> >
> > The reason for this is given in the following statement by Prof. Ripley:
> >
> >> Do not replace registered S3 methods from base/recommended packages,
> >> something which is not allowed by the CRAN policies and will mean
> >> that everyone gets your method even if your namespace is unloaded.
> >
> > The route I am taking is one of the advised routes to go (see
> > https://github.com/hofnerb/papeR/issues/5). So I am still looking for a
> fix
> > of this issue.
> >
> > Your warning regarding the changed user experience is well noted.
> However, I
> > think (and am aware that this is my personal opinion) that a lot of users
> > will not miss the standard plot.data.frame method which is only well
> defined
> > for numerics anyway and not very informative in many situations. After
> your
> > comment I am thinking of adding an option to my plot.data.frame function
> > which allows to fall back to the original user experience.
> >
> > Thanks,
> > Benjamin
> >
> > Am 01.09.2015 um 04:37 schrieb Gavin Simpson:
> >>
> >> Why do you even need to take over `plot`, `plot.default`? You can just
> >> register/export the plot.data.frame method from our package without
> >> touching the generic or default method. The part of WRE that you refer
> >> to is about making functions that are *not* S3 methods in one of base R
> >> or it's packages into S3 generics. You are just providing a method for
> >> an existing generic so you don't need to follow that code.
> >>
> >> That said, it wouldn't be good form to fundamentally alter the way
> >> plot.data.frame worked as users might expect certain functionality.
> >>
> >> HTH
> >>
> >> G
> >>
> >> On 31 August 2015 at 04:03, Benjamin Hofner <benjamin.hofner at fau.de
> >> <mailto:benjamin.hofner at fau.de>> wrote:
> >>
> >>     Dear all,
> >>
> >>     CRAN policies do not allow that single methods (for generic
> >>     functions) which are defined in base or recommended packages are
> >>     replaced. They advice package authors to replace the standard
> >>     generic and use a xxx.default method which then calls the original
> >>     standard generic.
> >>
> >>     Using the following code
> >>
> >>
> >>     ## overwrite standard generic
> >>     plot <- function(x, y, ...)
> >>          UseMethod("plot")
> >>
> >>     ## per default fall back to standard generic
> >>     plot.default <- function(x, y, ...)
> >>          graphics::plot(x, y, ...)
> >>
> >>     ## now specify modified plot function for data frames
> >>     plot.data.frame <- function(x, variables = names(x), ...)
> >>
> >>
> >>     essentially works for all tested plot.xxx functions. Yet, it breaks
> >>     plot.formula. How can I proceed to overwrite plot.data.frame without
> >>     breaking plot.formula. Any help is greatly appreciated.
> >>
> >>     For a detailed description of the problem with syntax highlighting
> >>     and code to reproduce the problem please see:
> >>
> >>
> >>
> http://stackoverflow.com/questions/32246361/redefinition-of-generic-for-plot-function-breaks-plot-formula
> >>
> >>     Best,
> >>     Benjamin
> >>     --
> >>
> >>
> ******************************************************************************
> >>     Dr. rer. nat. Benjamin Hofner
> >>
> >>     Institut für Medizininformatik, Biometrie und Epidemiologie
> >>     Friedrich-Alexander-Universität Erlangen-Nürnberg
> >>     Waldstr. 6 - 91054 Erlangen - Germany
> >>
> >>     Tel: +49-9131-85-22707 <tel:%2B49-9131-85-22707>
> >>     Fax: +49-9131-85-25740 <tel:%2B49-9131-85-25740>
> >>
> >>     Büro:
> >>        Raum 3.036
> >>        Universitätsstraße 22
> >>        (Eingang linke Seite des Gebäudes; Wegweiser IMBE)
> >>
> >>     benjamin.hofner at fau.de <mailto:benjamin.hofner at fau.de>
> >>
> >>     http://www.imbe.med.uni-erlangen.de/cms/benjamin_hofner.html
> >>     http://www.benjaminhofner.de
> >>
> >>     ______________________________________________
> >>     R-package-devel at r-project.org <mailto:R-package-devel at r-project.org
> >
> >>     mailing list
> >>     https://stat.ethz.ch/mailman/listinfo/r-package-devel
> >>
> >>
> >>
> >>
> >> --
> >> Gavin Simpson, PhD
> >
> >
> > ______________________________________________
> > R-package-devel at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-package-devel
>
>
>
> --
> http://had.co.nz/
>

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