R devel - Jul 2020 - Methods for objects inheriting from lme (nlme package)

Dear R developers,

One function in my mkin package [1] returns an object that is originally 
created by nlme(), but contains some additional information. Its class is 
c("mmkin.nlme", "nlme", "lme").

Now I would like to use the anova() method for lme objects for comparing such 
S3 objects. Unfortunately, anova.lme currently does not check for inheritance, 
but checks the  first element of the class attribute (as obtained by 
data.class()) against a hardcoded list of classes in order to decide if it 
will work or not.

Therefore, I created a bug report [2], containing a patch [3] for nlme that 
makes anova.lme check for inheritance.

Encouraged by a kind comment by Elin Waring in the BTS, I have now revisited 
my bug report, and discovered that the help page for data.class() claims that 
its return value (the first element of the class attribute vector) is "what
is
typically useful for method dispatching".

However, I think that this use case illustrates that it would be useful not 
only to check for the primary class, but rather for class inheritance.

Do you agree that it is preferable for the S3 method to check for inheritance 
instead of checking against a hardcoded list in this case?

Kind regards,

Johannes Ranke


[1]  https://github.com/jranke/mkin/blob/master/R/nlme.mmkin.R
[2]  https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17761
[3]  https://bugs.r-project.org/bugzilla/attachment.cgi?id=2578

Am Montag, 20. Juli 2020, 11:12:25 CEST schrieb Johannes
Ranke:
> Dear R developers,
> 
> One function in my mkin package [1] returns an object that is originally
> created by nlme(), but contains some additional information. Its class is
> c("mmkin.nlme", "nlme", "lme").
> 
> Now I would like to use the anova() method for lme objects for comparing
> such S3 objects. Unfortunately, anova.lme currently does not check for
> inheritance, but checks the  first element of the class attribute (as
> obtained by data.class()) against a hardcoded list of classes in order to
> decide if it will work or not.
> 
> Therefore, I created a bug report [2], containing a patch [3] for nlme that
> makes anova.lme check for inheritance.
> 
> Encouraged by a kind comment by Elin Waring in the BTS, I have now
revisited
> my bug report, and discovered that the help page for data.class() claims
> that its return value (the first element of the class attribute vector) is
> "what is typically useful for method dispatching".
> 
> However, I think that this use case illustrates that it would be useful not
> only to check for the primary class, but rather for class inheritance.
> 
> Do you agree that it is preferable for the S3 method to check for
> inheritance instead of checking against a hardcoded list in this case?
> 
> Kind regards,
> 
> Johannes Ranke
> 
> 
> [1]  https://github.com/jranke/mkin/blob/master/R/nlme.mmkin.R
> [2]  https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17761
> [3]  https://bugs.r-project.org/bugzilla/attachment.cgi?id=2578
P.S.: I have updated the patch [4] based on comments provided by Sebastian 
Meyer.

[4] https://bugs.r-project.org/bugzilla/attachment.cgi?id=2656
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