R devel - Nov 2000 - Problem with NAs using chisq.test() (PR#748)

Full_Name: Kjetil Kjernsmo
Version: 1.1.1.1 (patched the rpois :-))
OS: osf4.0e
Submission from: (NULL) (129.240.28.227)


Dear all,

I have just gotten through a debugging session of my code, being confused
for a few days. I sent what I thought was a straightforward matrix to
chisq.test() and once in a while got the error message:
> chisq.test(t2)
Error in chisq.test(t2) : missing value where logical needed

Now, it turned out that a fairly deep bug in my code occasionally produced
NAs in the matrix, and that was the source of the confusion. Looking at
the code, it is apparent that the test
    if (any(x < 0) || any(is.na(x)))
        stop("all entries of x must be nonnegative and finite")
was designed to catch this, but it doesn't seem to, because the first
any()-call is NA and so when using the operator ||, well, I bet you
understand this better than I... :-)

I figured, perhaps turn this around:
    if (any(is.na(x)) || any(x < 0))
        stop("all entries of x must be nonnegative and finite")
That seems to work: 
> chisq.test(t2)
Error in chisq.test(t2) : all entries of x must be nonnegative and finite

Now, I hope this was a true bug, not just one of my misunderstandings, and that
this is a real fix too.... :-)

Kjetil

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On Sun, 26 Nov 2000 kjetikj@astro.uio.no wrote:
> Full_Name: Kjetil Kjernsmo
> 
> 
> Now, it turned out that a fairly deep bug in my code occasionally produced
> NAs in the matrix, and that was the source of the confusion. Looking at
> the code, it is apparent that the test
>     if (any(x < 0) || any(is.na(x)))
>         stop("all entries of x must be nonnegative and finite")
> was designed to catch this, but it doesn't seem to, because the first
> any()-call is NA and so when using the operator ||, well, I bet you
> understand this better than I... :-)
> 
> I figured, perhaps turn this around:
>     if (any(is.na(x)) || any(x < 0))
>         stop("all entries of x must be nonnegative and finite")
> That seems to work: 
> > chisq.test(t2)
> Error in chisq.test(t2) : all entries of x must be nonnegative and finite
> 
> Now, I hope this was a true bug, not just one of my misunderstandings, and
that
> this is a real fix too.... :-)
This is a real fix; it may be a real bug.

any(x<0) correctly returns NA with NAs in x, that is, it doesn't know
whether there are any negative entries because some are missing.

any(x<0) || any(is.na(x)) returns NA because of short-circuit
evaluation.  That is, we do sequential if()s on each element from left to
right. The first one fails because of NAs.  Reversing the expression is
more sensible because you would expect to rule out NAs before testing
for x<0.

However, it would also be reasonable for NA || B to evaluate B and return
TRUE or NA depending on the value.  This is what S-PLUS 5 does, so at
least it's an incompatibility. 

The R documentation says 
    The longer form [ie ||]evaluates left to right examining only the first
    element of each vector.  Evaluation proceeds only until the result
    is determined. 
which at least seems incomplete as NA | TRUE gives TRUE, but
NA || TRUE gives an error.


	-thomas

Thomas Lumley
Assistant Professor, Biostatistics
University of Washington, Seattle

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