R devel - Sep 2020 - Is it possible to simply the use of NULL slots (or at least improve the help files)?

Hi Martin,
Thankyou for your response.

I suspect that we're not going to agree on the main point.
Making it trivially simple (as say Java) to set slots to NULL.
So, I'll move on to the other points here.

***Note that cited text uses excerpts only.***
>   setClassUnion("character_OR_NULL", c("character",
"NULL"))
>   A = setClass("A", slots = c(x = "character_OR_NULL"))
I think the above construct needs to be documented much more clearly.
i.e. In the introductory and details pages for S4 classes.
This is something that many people will want to do.
And BasicClasses or NULL-class, are not the most obvious place to
start looking, either.

Also, I'd recommend the S4 authors, go one step further.
Include character_OR_NULL, numeric_OR_NULL, etc, or something similar,
in S4's predefined basic classes.
Otherwise, contributed packages will (eventually) end up with hundreds
of copies of these.
> setClassUnion("maybeNumber", c("numeric",
"logical"))
> every instance of numeric _is_ a maybeNumber, e.g.,
> > is(1, "maybeNumber")
> [1] TRUE
> which I think is consistent with the use of 'superclass'
Not quite.

    x <- structure (sqrt (37), class = c ("sqrt.prime",
"numeric") )
    is (x, "numeric") #TRUE
    is (x, "maybeNumber") #FALSE

So now, an object x, is a numeric but not a maybeNumber.
Perhaps a class union should be described as a partial imitation of a
superclass, for the purpose of making slots more flexible.


B.

Answering to convey the 'rules' as I know them, rather than to address
the underlying issues that I guess you are really after...

The S4 practice is to use setOldClass() to explicitly treat an S3 character()
vector of classes as an assertion of linear inheritance
> x <- structure (sqrt (37), class = c ("sqrt.prime",
"numeric") )
> is(x, "maybeNumber")
[1] FALSE
> setOldClass(class(x))
> is(x, "maybeNumber")
[1] TRUE

There are some quite amusing things that can go on with S3 classes, since the
class attribute is just a character vector. So
> x <- structure ("September", class = c
("sqrt.prime", "numeric") )
> is(x, "numeric")  ## similarly, inherits()
[1] TRUE
> x <- structure (1, class = c ("numeric",
"character"))
> is(x, "numeric")
[1] TRUE
> is(x, "character")
[1] TRUE

Perhaps the looseness of the S3 system motivated the use of setOldClass() for
anything more than assertion of simple relationships? At least in this context
setOldClass() provides some type checking sanity
> setOldClass(c("character", "numeric"))
Error in setOldClass(c("character", "numeric")) :
  inconsistent old-style class information for "character"; the class
is defined but does not extend "numeric" and is not valid as the data
part
In addition: Warning message:
In .validDataPartClass(cl, where, dataPartClass) :
  more than one possible class for the data part: using "numeric"
rather than "character"

Martin Morgan

?On 9/24/20, 4:51 PM, "Abby Spurdle" <spurdle.a at gmail.com>
wrote:

    Hi Martin,
    Thankyou for your response.

    I suspect that we're not going to agree on the main point.
    Making it trivially simple (as say Java) to set slots to NULL.
    So, I'll move on to the other points here.

    ***Note that cited text uses excerpts only.***

    >   setClassUnion("character_OR_NULL", c("character",
"NULL"))
    >   A = setClass("A", slots = c(x =
"character_OR_NULL"))

    I think the above construct needs to be documented much more clearly.
    i.e. In the introductory and details pages for S4 classes.
    This is something that many people will want to do.
    And BasicClasses or NULL-class, are not the most obvious place to
    start looking, either.

    Also, I'd recommend the S4 authors, go one step further.
    Include character_OR_NULL, numeric_OR_NULL, etc, or something similar,
    in S4's predefined basic classes.
    Otherwise, contributed packages will (eventually) end up with hundreds
    of copies of these.

    > setClassUnion("maybeNumber", c("numeric",
"logical"))
    > every instance of numeric _is_ a maybeNumber, e.g.,
    > > is(1, "maybeNumber")
    > [1] TRUE

    > which I think is consistent with the use of 'superclass'

    Not quite.

        x <- structure (sqrt (37), class = c ("sqrt.prime",
"numeric") )
        is (x, "numeric") #TRUE
        is (x, "maybeNumber") #FALSE

    So now, an object x, is a numeric but not a maybeNumber.
    Perhaps a class union should be described as a partial imitation of a
    superclass, for the purpose of making slots more flexible.


    B.

It seems one of the primary reasons to use the S4 system is *to be strict
about types.*

IMO the documentation is quite clear on this point, if NULL is not a
subclass of character, which it isn't because inherits(NULL,
"character")
is FALSE then everything is behaving exactly as expected and documented.

Between making the calling function responsible for passing an object of
the correct type and setClassUnion, it doesn't seem that complicated to
handle the use case.

On Thu, Sep 24, 2020 at 5:26 PM Martin Morgan <mtmorgan.bioc at gmail.com>
wrote:
> Answering to convey the 'rules' as I know them, rather than to
address the
> underlying issues that I guess you are really after...
>
> The S4 practice is to use setOldClass() to explicitly treat an S3
> character() vector of classes as an assertion of linear inheritance
>
> > x <- structure (sqrt (37), class = c ("sqrt.prime",
"numeric") )
> > is(x, "maybeNumber")
> [1] FALSE
> > setOldClass(class(x))
> > is(x, "maybeNumber")
> [1] TRUE
>
> There are some quite amusing things that can go on with S3 classes, since
> the class attribute is just a character vector. So
>
> > x <- structure ("September", class = c
("sqrt.prime", "numeric") )
> > is(x, "numeric")  ## similarly, inherits()
> [1] TRUE
> > x <- structure (1, class = c ("numeric",
"character"))
> > is(x, "numeric")
> [1] TRUE
> > is(x, "character")
> [1] TRUE
>
> Perhaps the looseness of the S3 system motivated the use of setOldClass()
> for anything more than assertion of simple relationships? At least in this
> context setOldClass() provides some type checking sanity
>
> > setOldClass(c("character", "numeric"))
> Error in setOldClass(c("character", "numeric")) :
>   inconsistent old-style class information for "character"; the
class is
> defined but does not extend "numeric" and is not valid as the
data part
> In addition: Warning message:
> In .validDataPartClass(cl, where, dataPartClass) :
>   more than one possible class for the data part: using "numeric"
rather
> than "character"
>
> Martin Morgan
>
> ?On 9/24/20, 4:51 PM, "Abby Spurdle" <spurdle.a at
gmail.com> wrote:
>
>     Hi Martin,
>     Thankyou for your response.
>
>     I suspect that we're not going to agree on the main point.
>     Making it trivially simple (as say Java) to set slots to NULL.
>     So, I'll move on to the other points here.
>
>     ***Note that cited text uses excerpts only.***
>
>     >   setClassUnion("character_OR_NULL",
c("character", "NULL"))
>     >   A = setClass("A", slots = c(x =
"character_OR_NULL"))
>
>     I think the above construct needs to be documented much more clearly.
>     i.e. In the introductory and details pages for S4 classes.
>     This is something that many people will want to do.
>     And BasicClasses or NULL-class, are not the most obvious place to
>     start looking, either.
>
>     Also, I'd recommend the S4 authors, go one step further.
>     Include character_OR_NULL, numeric_OR_NULL, etc, or something similar,
>     in S4's predefined basic classes.
>     Otherwise, contributed packages will (eventually) end up with hundreds
>     of copies of these.
>
>     > setClassUnion("maybeNumber", c("numeric",
"logical"))
>     > every instance of numeric _is_ a maybeNumber, e.g.,
>     > > is(1, "maybeNumber")
>     > [1] TRUE
>
>     > which I think is consistent with the use of 'superclass'
>
>     Not quite.
>
>         x <- structure (sqrt (37), class = c ("sqrt.prime",
"numeric") )
>         is (x, "numeric") #TRUE
>         is (x, "maybeNumber") #FALSE
>
>     So now, an object x, is a numeric but not a maybeNumber.
>     Perhaps a class union should be described as a partial imitation of a
>     superclass, for the purpose of making slots more flexible.
>
>
>     B.
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
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