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

[Hadley Wickham]

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:
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>>
>>     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
>>
>>     ______________________________________________
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>>
>>
>>
>>
>> --
>> Gavin Simpson, PhD
>
>
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