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

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

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--
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