[R] fisher.test - can I use non-integer expected values?

[David Winsemius]

On Dec 10, 2013, at 2:04 PM, bakerwl wrote:

> I seem to be able to use expected values that are decimal (e.g., 1.33) when
> using chisq.test but not when using fisher.test.

There are no expected values in the input to fisher.test. 

> This happens when using an
> array/matrix as input. Fisher.test returns: Error in sprintf(gettext(fmt,
> domain = domain), ...) : invalid format '%d'; use format %s for character
> objects.
> 
> Thus, it appears fisher.test is looking for integers only.

That would seem to be a very reasonable assumption.

> 
> I tried putting the data in x and y factor objects, but that does not work
> either.
> 
> Is there another way to use non-integer expected values with fisher.test or
> is that a limitation of fisher.test?

> If I must use integer expected values, I suppose one option would be round
> the expected value down or up to an integer. But, which? I tried that, but
> they produce different p values.

Well, of course. First, you tell us why you need `fisher.test` at all. It says very clearly it is for count data and you clearly want to do something with input that is not counts. `prop.test` will test a distribution of counts against expected proportions and `binom.test` will do an exact test of a Bernoulli experiment against (one) proportion. 

> 
> Thanks for any help!
> 
> View this message in context: http://r.789695.n4.nabble.com/fisher-test-can-I-use-non-integer-expected-values-tp4681976.html
> Sent from the R help mailing list archive at Nabble.com.
> 
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-- 
David Winsemius
Alameda, CA, USA