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

[Shu Fai Cheung]

Hi All,

I would like to share more about the behavior of na.omit() from my
previous email.

This is a test dataset:

> DF <- data.frame(x = c(1, 2, 3, 5), y = c(NA, 10, 1, 10))

One case omitted by na.omit()
> DF_omitted <- na.omit(DF)
> DF_omitted
  x  y
2 2 10
3 3  1
4 5 10
> na.action(DF_omitted)
1
1
attr(,"class")
[1] "omit"

Then I do regression on this DF_omitted (na.action can be omitted, but
I included it just to show that na.omit is used)

> out1 <- lm(y ~ x,
+            DF_omitted,
+            na.action = na.omit)
> summary(out1)

Call:
lm(formula = y ~ x, data = DF_omitted, na.action = na.omit)

Residuals:
     2      3      4
 3.857 -5.786  1.929

Coefficients:
            Estimate Std. Error t value Pr(>|t|)
(Intercept)   4.8571    11.8885   0.409    0.753
x             0.6429     3.3404   0.192    0.879

Residual standard error: 7.216 on 1 degrees of freedom
Multiple R-squared:  0.03571,   Adjusted R-squared:  -0.9286
F-statistic: 0.03704 on 1 and 1 DF,  p-value: 0.879

> na.action(out1)
NULL
> na.action(na.omit(DF_omitted))
1
1
attr(,"class")
[1] "omit"

The output of lm() states that no cases were removed. To me, this is a
correct message because no cases were removed when fitting the model,
that is, in *this call* of lm(). One case was deleted, but before
being processed by lm(). It is not done by this call of lm().

If the model is fitted to the original data set, then it will report,
again correctly, that *this call* of lm() removed one case:

> out2 <- lm(y ~ x,
+            DF,
+            na.action = na.omit)
> summary(out2)

Call:
lm(formula = y ~ x, data = DF, na.action = na.omit)

Residuals:
     2      3      4
 3.857 -5.786  1.929

Coefficients:
            Estimate Std. Error t value Pr(>|t|)
(Intercept)   4.8571    11.8885   0.409    0.753
x             0.6429     3.3404   0.192    0.879

Residual standard error: 7.216 on 1 degrees of freedom
  (1 observation deleted due to missingness)
Multiple R-squared:  0.03571,   Adjusted R-squared:  -0.9286
F-statistic: 0.03704 on 1 and 1 DF,  p-value: 0.879

> na.action(out2)
1
1
attr(,"class")
[1] "omit"

However, the behavior of na.omit() is different. If na.omit() is run
again on DF_omitted, it will say that Case 1 was removed.

> na.action(na.omit(DF))
1
1
attr(,"class")
[1] "omit"

This behavior, to me, can be misleading because no cases were removed
by *this call* of na.omit().

Moreover, from the help page of na.omit():

'If na.omit removes cases, the row numbers of the cases form the
"na.action" attribute of the result, of class "omit".'

It does not state what happens if na.omit() does not remove cases.
>From the example of lm() above, na.omit() will report/store that no
cases were removed, though this is actually the behavior of
model.frame()/lm(), not of na.omit()). However, when used alone,
na.omit() will do nothing.

Changing this behavior of na.omit() may break a lot of things. If this
behavior of na.omit(), doing nothing, is intended (though unnatural to
me), perhaps this should be stated in the help page?

Regards,
Shu Fai

On Fri, Mar 27, 2026 at 10:13 PM 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