[Rd] na.omit inconsistent with is.na on list

[Toby Hocking]

Some relevant information from ?is.na: the behavior for lists is
documented,

     For is.na, elementwise the result is false unless that element
     is a length-one atomic vector and the single element of that
     vector is regarded as NA or NaN (note that any is.na method
     for the class of the element is ignored).

Also there are other functions anyNA and is.na<- which are consistent with
is.na. That is, anyNA only returns TRUE if the list has an element which is
a scalar NA. And is.na<- sets list elements to logical NA to indicate
missingness.

On Fri, Aug 13, 2021 at 1:10 AM Hugh Parsonage <hugh.parsonage using gmail.com>
wrote:

> The data.frame method deliberately skips non-atomic columns before
> invoking is.na(x) so I think it is fair to assume this behaviour is
> intentional and assumed.
>
> Not so clear to me that there is a sensible answer for list columns.
> (List columns seem to collide with the expectation that in each
> variable every observation will be of the same type)
>
> Consider your list L as
>
> L <- list(NULL, NA, c(NA, NA))
>
> Seems like every observation could have a claim to be 'missing' here.
> Concretely, if a data.frame had a list column representing the lat-lon
> of an observation, we might only be able to represent missing values
> like c(NA, NA).
>
> On Fri, 13 Aug 2021 at 17:27, Iñaki Ucar <iucar using fedoraproject.org> wrote:
> >
> > On Thu, 12 Aug 2021 at 22:20, Gabriel Becker <gabembecker using gmail.com>
> wrote:
> > >
> > > Hi Toby,
> > >
> > > This definitely appears intentional, the first  expression of
> > > stats:::na.omit.default is
> > >
> > >    if (!is.atomic(object))
> > >
> > >         return(object)
> >
> > I don't follow your point. This only means that the *default* method
> > is not intended for non-atomic cases, but it doesn't mean it shouldn't
> > exist a method for lists.
> >
> > > So it is explicitly just returning the object in non-atomic cases,
> which
> > > includes lists. I was not involved in this decision (obviously) but my
> > > guess is that it is due to the fact that what constitutes an
> observation
> > > "being complete" in unclear in the list case. What should
> > >
> > > na.omit(list(5, NA, c(NA, 5)))
> > >
> > > return? Just the first element, or the first and the last? It seems, at
> > > least to me, unclear. A small change to the documentation to to add
> "atomic
> >
> > > is.na(list(5, NA, c(NA, 5)))
> > [1] FALSE  TRUE FALSE
> >
> > Following Toby's argument, it's clear to me: the first and the last.
> >
> > Iñaki
> >
> > > (in the sense of is.atomic returning \code{TRUE})" in front of
> "vectors"
> > > or similar  where what types of objects are supported seems justified,
> > > though, imho, as the current documentation is either ambiguous or
> > > technically incorrect, depending on what we take "vector" to mean.
> > >
> > > Best,
> > > ~G
> > >
> > > On Wed, Aug 11, 2021 at 10:16 PM Toby Hocking <tdhock5 using gmail.com>
> wrote:
> > >
> > > > Also, the na.omit method for data.frame with list column seems to be
> > > > inconsistent with is.na,
> > > >
> > > > > L <- list(NULL, NA, 0)
> > > > > str(f <- data.frame(I(L)))
> > > > 'data.frame': 3 obs. of  1 variable:
> > > >  $ L:List of 3
> > > >   ..$ : NULL
> > > >   ..$ : logi NA
> > > >   ..$ : num 0
> > > >   ..- attr(*, "class")= chr "AsIs"
> > > > > is.na(f)
> > > >          L
> > > > [1,] FALSE
> > > > [2,]  TRUE
> > > > [3,] FALSE
> > > > > na.omit(f)
> > > >    L
> > > > 1
> > > > 2 NA
> > > > 3  0
> > > >
> > > > On Wed, Aug 11, 2021 at 9:58 PM Toby Hocking <tdhock5 using gmail.com>
> wrote:
> > > >
> > > > > na.omit is documented as "na.omit returns the object with
> incomplete
> > > > cases
> > > > > removed." and "At present these will handle vectors," so I
> expected that
> > > > > when it is used on a list, it should return the same thing as if we
> > > > subset
> > > > > via is.na; however I observed the following,
> > > > >
> > > > > > L <- list(NULL, NA, 0)
> > > > > > str(L[!is.na(L)])
> > > > > List of 2
> > > > >  $ : NULL
> > > > >  $ : num 0
> > > > > > str(na.omit(L))
> > > > > List of 3
> > > > >  $ : NULL
> > > > >  $ : logi NA
> > > > >  $ : num 0
> > > > >
> > > > > Should na.omit be fixed so that it returns a result that is
> consistent
> > > > > with is.na? I assume that is.na is the canonical definition of
> what
> > > > > should be considered a missing value in R.
> > > > >
> > > >
> > > >         [[alternative HTML version deleted]]
> > > >
> > > > ______________________________________________
> > > > R-devel using r-project.org mailing list
> > > > https://stat.ethz.ch/mailman/listinfo/r-devel
> > > >
> > >
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> > >
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> >
> >
> >
> > --
> > Iñaki Úcar
> >
> > ______________________________________________
> > R-devel using r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-devel
>
> ______________________________________________
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