[R] Using na.omit() on the output of na.omit()

[Shu Fai Cheung]

Thanks for the comment. Just to share a little bit more. I used lm()
in another post, but I will use model.frame here because it is
model.frame that uses the na.action argument.

This is the example:

dat <- data.frame(
  x = 1:5,
  y = 1:5,
  z = 1:5
)
dat[1, "x"] <- NA
dat[2, c("y", "z")] <- NA
dat_omitted <- na.omit(dat)
head(dat)
#>    x  y  z
#> 1 NA  1  1
#> 2  2 NA NA
#> 3  3  3  3
#> 4  4  4  4
#> 5  5  5  5
head(dat_omitted)
#>   x y z
#> 3 3 3 3
#> 4 4 4 4
#> 5 5 5 5

tmp1 <- model.frame(y ~ x + z, dat, na.action = na.omit)
tmp2 <- model.frame(y ~ x + z, dat_omitted, na.action = na.omit)

na.action(tmp1)
#> 1 2
#> 1 2
#> attr(,"class")
#> [1] "omit"
na.action(tmp2)
#> NULL

tmp3 <- na.omit(dat)
tmp4 <- na.omit(dat_omitted)

na.action(tmp3)
#> 1 2
#> 1 2
#> attr(,"class")
#> [1] "omit"
na.action(tmp4)
#> 1 2
#> 1 2
#> attr(,"class")
#> [1] "omit"

This example has two data frames: dat with missing data, and
dat_omitted with cases omitted by na.omit, with an na.action
attribute.

When the input is dat_omitted, model.frame, which also stores cases
removed, if any, does not report that cases were omitted by it.

For na.omit, on the the other hand, it will pass the original object
(dat_omitted) unchanged, including the na.action attributes, if any.
Therefore, when na.action is used on the output (tmp4), or the
na.action attributes retrieved, there is no way to know whether the
cases were omitted by this call of na.omit or by a previous call,
unlike model.frame.

After studying this example, what puzzled me was no longer the
behavior of na.omit, but the difference in the behaviors of these two
functions when processing an object with the na.action attribute.

But I now think it was designed that way. I will do my work taking
into account the current behavior of na.omit. I'm sharing this
observation, which is new to me (and probably only me), in case it is
useful to others.

Regards,
Shu Fai


On Mon, Mar 30, 2026 at 10:18 PM peter dalgaard <pdalgd using gmail.com> wrote:
>
> I'm fairly sure that this is deliberate, although hardly something that I bump into every day. na.omit & friends are designed to work in connection with modeling code and there may be code down the line that wants to know about omitted cases. So na.omit cleans the original data by removing some cases and attaching a list of omitted cases; if you do it again, you still have a dataframe and some omitted cases.
>
> If anything, I would contend that omissions should be cumulative, so if you (say) add a column with some missing values and na.omit again, then the omission list should be augmented rather than replaced.
>
> Also, from a pragmatic viewpoint, there is a chance that na.omit gets called repeatedly by coincidence in the labyrinth of interrelated lm functions.
>
> -pd
>
> > On 27 Mar 2026, at 15.13, Shu Fai Cheung <shufai.cheung using gmail.com> wrote:
> >
> > Hi All,
> >
> > I noticed a behavior of na.omit() that I am not sure is intended.
> >
> > This is adapted from the example of na.omit()
> >
> >> DF <- data.frame(x = c(1, 2, 3), y = c(NA, 10, 1))
> >> DF_omitted <- na.omit(DF)
> >> attr(DF_omitted, "na.action")
> > 1
> > 1
> > attr(,"class")
> > [1] "omit"
> >> DF_omitted2 <- na.omit(DF_omitted)
> >> attr(DF_omitted2, "na.action")
> > 1
> > 1
> > attr(,"class")
> > [1] "omit"
> >
> > In the first call to na.omit(), the output, DF_omitted, correctly has only
> > two rows, with Row 1 removed, and 'na.action' stores the removed row number.
> >
> > In the second call of na.omit(), no cases are removed because DF_omitted
> > has no missing data. However, the attribute 'na.action' is retained,
> > indicating that Row 1 was removed.
> >
> > To my understanding of na.omit(), this occurred because, in the second call
> > of na.omit(), no rows were omitted, and so the original object was
> > returned, along with the attribute 'na.action' from the first call.
> >
> > From the "perspective" of the second call, no rows were omitted.
> > Should 'na.action'
> > be NULL (i.e., not set), as in the following example?
> >
> >> DF2 <- data.frame(x = c(1, 2, 3), y = c(3, 10, 1))
> >> DF2_omitted <- na.omit(DF2)
> >> attr(DF2_omitted, "na.action")
> > NULL
> >
> > Or is this behavior of na.omit() intended?
> >
> > Regards,
> > Shu Fai
> >
> > [[alternative HTML version deleted]]
> >
> > ______________________________________________
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>
> --
> Peter Dalgaard, Professor,
> Center for Statistics, Copenhagen Business School
> Solbjerg Plads 3, 2000 Frederiksberg, Denmark
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