Re: [Rd] Defining a method in two packages

From: Prof Brian Ripley <ripley_at_stats.ox.ac.uk>
Date: Sat, 06 Mar 2010 20:17:23 +0000 (GMT)

On Sat, 6 Mar 2010, Uwe Ligges wrote:

> Terry,
>
> this happens since the ranef in coxme is a S3 generic and the one in lme4 is
> a S4 generic.

But the packages could be more cooperative. There is also a S3 generic for ranef in package nlme. Ideally the S4 generic in lme4 would have a default method which dispatched on S3 methods: that would be easy to achieve if there was just one other ranef, but not so if there are 2 or more -- but read on.

Indeed, the situation is pretty much the same if you load nlme after coxme:

> library(nlme)

Attaching package: 'nlme'

The following object(s) are masked from 'package:coxme':

     fixed.effects, fixef, random.effects, ranef

> ranef(fit)

Error in UseMethod("ranef") :

   no applicable method for 'ranef' applied to an object of class "coxme"

The situation can be alleviated by making S3 methods visible. Thus if coxme exported coxme:::ranef.coxme and lme4 had a default method

function (object, ...) UseMethod("ranef")

loading lme4 (or nlme) after coxme would work.

My solution would though be NOT to reuse a name that is already established in another package (nlme has used it for many years).

The design problem is that generic foo() in package B might have nothing to do with foo() in package A. When it does, we expect B to import the generic from A, but that can be a 'which came first' problem unless a base package is involved. But here nlme is a long-established recommended package, so it would be reasonable to expect both coxme and lme4 to import from it.

> Of course, after loading lme4, you can still use the ranef from coxme:
>
> coxme::ranef(fit)
>
> and get the desired result.
>
> If you write your own code, you might want to use that call explicitly (i.e.
> accessing from the correct namepsace). In your own package, you could simply

> import the generic from coxme.

> Best wishes,
> Uwe
>
>
>
>
>
>
> On 05.03.2010 17:47, Terry Therneau wrote:
>> The coxme package has a ranef() method, as does lme4. I'm having
>> trouble getting them to play together, as shown below. (The particular
>> model in the example isn't defensible, but uses a standard data set.)
>>
>> The problem is that most of the time only one of lme4 or coxme will be
>> loaded, so each needs to define the basic ranef function as well as a
>> method for it. But when loaded together the last one wins. The coxme
>> object is an S3 class BTW. (Suggestions to convert it to S4 will not be
>> well recieved -- but that's a different and unnecessary thread.)
>>
>> Odds are that this has a simple solution which I have missed.
>> Terry Therneau
>>
>>
>> tmt935% R --vanilla
>>
>> R version 2.10.0 (2009-10-26)
>> Copyright (C) 2009 The R Foundation for Statistical Computing
>> ISBN 3-900051-07-0
>>
>> R is free software and comes with ABSOLUTELY NO WARRANTY.
>> You are welcome to redistribute it under certain conditions.
>> Type 'license()' or 'licence()' for distribution details.
>>
>> Natural language support but running in an English locale
>>
>> R is a collaborative project with many contributors.
>> Type 'contributors()' for more information and
>> 'citation()' on how to cite R or R packages in publications.
>>
>> Type 'demo()' for some demos, 'help()' for on-line help, or
>> 'help.start()' for an HTML browser interface to help.
>> Type 'q()' to quit R.
>>
>>> library(coxme)
>> Loading required package: survival
>> Loading required package: splines
>> Loading required package: bdsmatrix
>>
>>> fit<- coxme(Surv(time, status) ~ age + (1|ph.ecog), lung)
>>> ranef(fit)
>> $ph.ecog
>> Intercept
>> 0.1592346
>>
>>> library(lme4)
>> Loading required package: Matrix
>> Loading required package: lattice
>>
>> Attaching package: 'lme4'
>>
>>
>> The following object(s) are masked from package:coxme :
>>
>> fixef,
>> ranef
>>
>>> ranef(fit)
>> Error in function (classes, fdef, mtable) :
>> unable to find an inherited method for function "ranef", for signature
>> "coxme"
>>> q()
>>
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>
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-- 
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

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