r - An NA in subsetting a data.frame does something unexpected

Question

Consider the following code. When you don't explicitly test for NA in your condition, that code will fail at some later date then your data changes.

>   # A toy example
>   a <- as.data.frame(cbind(col1=c(1,2,3,4),col2=c(2,NA,2,3),col3=c(1,2,3,4),col4=c(4,3,2,1)))
>   a
  col1 col2 col3 col4
1    1    2    1    4
2    2   NA    2    3
3    3    2    3    2
4    4    3    4    1
>   
>   # Bummer, there's an NA in my condition
>   a$col2==2
[1]  TRUE    NA  TRUE FALSE
> 
>   # Why is this a good thing to do?
>   # It NA'd the whole row, and kept it
>   a[a$col2==2,]
   col1 col2 col3 col4
1     1    2    1    4
NA   NA   NA   NA   NA
3     3    2    3    2
>   
>   # Yes, this is the right way to do it
>   a[!is.na(a$col2) & a$col2==2,]
  col1 col2 col3 col4
1    1    2    1    4
3    3    2    3    2
>     
>   # Subset seems designed to avoid this problem
>   subset(a, col2 == 2)
  col1 col2 col3 col4
1    1    2    1    4
3    3    2    3    2

Can someone explain why the behavior you get without the is.na check would ever be good or useful?

Answer 1

I definitely agree that this isn't intuitive (I made that point before on SO). In defense of R, I think that knowing when you have a missing value is useful (i.e. this is not a bug). The == operator is explicitly designed to notify the user of NA or NaN values. See ?"==" for more information. It states:

Missing values ('NA') and 'NaN' values are regarded as non-comparable even to themselves, so comparisons involving them will always result in 'NA'.

In other words, a missing value isn't comparable using a binary operator (because it's unknown).

Beyond is.na(), you could also do:

which(a$col2==2) # tests explicitly for TRUE

Or

a$col2 %in% 2 # only checks for 2

%in% is defined as using the match() function:

'"%in%" <- function(x, table) match(x, table, nomatch = 0) > 0'

This is also covered in "The R Inferno".

Checking for NA values in your data is crucial in R, because many important operators don't handle it the way you expect. Beyond ==, this is also true for things like &, |, <, sum(), and so on. I am always thinking "what would happen if there was an NA here" when I'm writing R code. Requiring an R user to be careful with missing values is "by design".

Update: How is NA handled when there are multiple logical conditions?

NA is a logical constant and you might get unexpected subsetting if you don't think about what might be returned (e.g. NA | TRUE == TRUE). These truth tables from ?Logic may provide a useful illustration:

outer(x, x, "&") ## AND table
#       <NA> FALSE  TRUE
#<NA>     NA FALSE    NA
#FALSE FALSE FALSE FALSE
#TRUE     NA FALSE  TRUE

outer(x, x, "|") ## OR  table
#      <NA> FALSE TRUE
#<NA>    NA    NA TRUE
#FALSE   NA FALSE TRUE
#TRUE  TRUE  TRUE TRUE