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

[Michael Dewey]

On 30/03/2026 15:18, peter dalgaard 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.
> 

Cumulative seems a good idea but since na.omit() returns the row numbers 
which data.frame will they refer to? Or have I misunderstood?

Michael

> 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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> 

-- 
Michael Dewey