[R-pkg-devel] Exporting S3 methods for base generics

Mon Jun 26 20:01:59 CEST 2017

Ah, good point :-)  You can avoid that by using inheritance, but now you're
on a route to refactoring your entire package actually. See also this
question on stackoverflow for a nice example of how this can be done:

https://stackoverflow.com/questions/26963900/generalizing-three-dots-argument-dispatch-s4-methods-for-argument-set-i

If neither class can inherit from the other in a logical way, you could
define a virtual "superclass" they both inherit from, and define the pmax
method for that virtual class. In R you do this using setClassUnion(), see
also ?setClassUnion and the section on virtual classes in ?setClass.

Hope this helps
Cheers
Joris

On Mon, Jun 26, 2017 at 7:56 PM, Charles Determan <cdetermanjr at gmail.com>
wrote:

> Ah, I see now.  I came across this previous post (
> http://r.789695.n4.nabble.com/override-pmin-pmax-for-my-
> own-matrix-td4715903.html) which mentioned the caveat that all the
> elements passed to ... must be the same.  When I pass two of the same class
> it works but I believe I will need to go back to the S3 if I want different
> classes passed to the call.
>
> Charles
>
> On Mon, Jun 26, 2017 at 12:42 PM, Charles Determan <cdetermanjr at gmail.com>
> wrote:
>
>> Could you point to one of these packages you refer to?  I'm still having
>> problems and not sure why at the moment.
>>
>> Thanks
>>
>> On Mon, Jun 26, 2017 at 12:32 PM, Joris Meys <Joris.Meys at ugent.be> wrote:
>>
>>> Hi Charles,
>>>
>>> my mistake. I forgot that pmax has an extra argument na.rm. I'm
>>> surprised you could define the method, as this normally should return an
>>> error from conformMethod().
>>>
>>> So:
>>> #' @rdname pmax
>>> setGeneric("pmax", signature = "...")
>>>
>>> should work. I've used this myself in quite a number of packages.
>>>
>>> Cheers
>>> Joris
>>>
>>> On Mon, Jun 26, 2017 at 7:20 PM, Charles Determan <cdetermanjr at gmail.com
>>> > wrote:
>>>
>>>> Thanks for the reply Joris, although I am not sure what I could be
>>>> doing wrong.  I implement exactly the lines you show and yet I just get the
>>>> following error when I call 'pmax' on the class.
>>>>
>>>> > pmax(x, 0)
>>>>
>>>> Error in mmm < each :
>>>>   comparison (3) is possible only for atomic and list types
>>>> In addition: Warning message:
>>>> In is.na(mmm) : is.na() applied to non-(list or vector) of type 'S4'
>>>>
>>>> Regards,
>>>> Charles
>>>>
>>>> On Mon, Jun 26, 2017 at 12:10 PM, Joris Meys <Joris.Meys at ugent.be>
>>>> wrote:
>>>>
>>>>> Hi Charles,
>>>>>
>>>>> if a generic exists already in the base, you only have to export the
>>>>> actual S3 method. Your problem is that base::pmax() is not a generic S3
>>>>> function. So R gives you the correct warning: the S3 generic in your
>>>>> package will always mask the base pmax function. And that's not really a
>>>>> problem, especially since you ensured the base functionality with your
>>>>> default method.
>>>>>
>>>>> If you want to avoid that warning, use S4.
>>>>>
>>>>> #' @rdname
>>>>> setGeneric("pmax")
>>>>>
>>>>> #' @rdname pmax
>>>>> #' @method pmax myclass
>>>>> #' @export
>>>>> setMethod("pmax",
>>>>>                   "myclass",
>>>>>                   function(...){
>>>>>                      # do some stuff
>>>>> })
>>>>>
>>>>> More information on how to deal with dots can be found on the help
>>>>> page ?dotsMethods.
>>>>>
>>>>> If you have a generic in the base package (eg plot is such one), you
>>>>> only define the method and use:
>>>>>
>>>>> #' @export
>>>>> plot.myclass <- function(x, y, ...){
>>>>>    # do some more stuff
>>>>> }
>>>>>
>>>>> Cheers
>>>>> Joris
>>>>>
>>>>>
>>>>>
>>>>> On Mon, Jun 26, 2017 at 6:28 PM, Charles Determan <
>>>>> cdetermanjr at gmail.com> wrote:
>>>>>
>>>>>> Greetings R users,
>>>>>>
>>>>>> I was wondering how others are exporting S3 methods in their packages
>>>>>> when
>>>>>> the generic is in 'base'.  For example, let's say I want to export a
>>>>>> new
>>>>>> pmax method.  The only way I have found to get this to work is by
>>>>>> redefining the function with 'UseMethod' and setting the default
>>>>>> method.
>>>>>>
>>>>>> #' @export
>>>>>> pmax <- function(...){ UseMethod("pmax") }
>>>>>> #' @export
>>>>>> pmax.default <- function(..., na.rm=FALSE){ base::pmax(...,
>>>>>> na.rm=FALSE) }
>>>>>>
>>>>>> setClass("myclass")
>>>>>>
>>>>>> #' @export
>>>>>> pmax.myclass <- function(..., na.rm = FALSE){
>>>>>>     print('myclass pmax!')
>>>>>> }
>>>>>>
>>>>>> Although this works, I get the 'warning'
>>>>>>
>>>>>> The following objects are masked from 'package:base':
>>>>>>
>>>>>>     pmax
>>>>>>
>>>>>>
>>>>>> I would like the package build and loading to be as clean as possible
>>>>>> but
>>>>>> if this is acceptable and not considered a problem I will let it go.
>>>>>> It
>>>>>> just seems odd that one would to redefine a the generic when in
>>>>>> states in
>>>>>> the docs for 'pmax' that it will also work on classed S3 objects but
>>>>>> perhaps I am reading this incorrectly.
>>>>>>
>>>>>> Thanks,
>>>>>> Charles
>>>>>>
>>>>>>         [[alternative HTML version deleted]]
>>>>>>
>>>>>> ______________________________________________
>>>>>> R-package-devel at r-project.org mailing list
>>>>>> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>>>>>>
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Joris Meys
>>>>> Statistical consultant
>>>>>
>>>>> Ghent University
>>>>> Faculty of Bioscience Engineering
>>>>> Department of Mathematical Modelling, Statistics and Bio-Informatics
>>>>>
>>>>> tel : +32 9 264 59 87 <+32%209%20264%2059%2087>
>>>>> Joris.Meys at Ugent.be
>>>>> -------------------------------
>>>>> Disclaimer : http://helpdesk.ugent.be/e-maildisclaimer.php
>>>>>
>>>>
>>>>
>>>
>>>
>>> --
>>> Joris Meys
>>> Statistical consultant
>>>
>>> Ghent University
>>> Faculty of Bioscience Engineering
>>> Department of Mathematical Modelling, Statistics and Bio-Informatics
>>>
>>> tel : +32 9 264 59 87 <+32%209%20264%2059%2087>
>>> Joris.Meys at Ugent.be
>>> -------------------------------
>>> Disclaimer : http://helpdesk.ugent.be/e-maildisclaimer.php
>>>
>>
>>
>

-- 
Joris Meys
Statistical consultant

Ghent University
Faculty of Bioscience Engineering
Department of Mathematical Modelling, Statistics and Bio-Informatics

tel : +32 9 264 59 87
Joris.Meys at Ugent.be
-------------------------------
Disclaimer : http://helpdesk.ugent.be/e-maildisclaimer.php

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