Hi,
I received a bug report for my exact2x2 package that seems to apply to
fisher.test in the stats package also.
Here is some code which creates the error:
>x<-factor(c(0,1,1),levels=c(0,1))
> y<-factor(c(1,1,1),levels=c(0,1))
> fisher.test(x,y)
Error in fisher.test(x, y) : 'x' and 'y' must have at least 2 levels
>
The help says that x and y could be factors, and technically y does have 2
levels, although both are not observed. There is no problem statistically with
y not having 2 observed levels, and
> fisher.test(table(x,y))
Produces the correct p-value of 1 and no errors.
There is an easy solution. In fisher.test replace
x <- factor(x[OK])
y <- factor(y[OK])
with
x <- as.factor(x[OK])
y <- as.factor(y[OK])
(similar to how it is done in mcnemar.test).
Mike
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Michael P. Fay, PhD
Mathematical Statistician
National Institute of Allergy and Infectious Diseases
Tel: 301-451-5124 Fax:301-480-0912
(U.S. postal mail address)
6700B Rockledge Drive MSC 7609
Bethesda, MD 20892-7609
(Overnight mail address)
6700-A Rockledge Drive, Room 5133
Bethesda, MD 20817
http://www3.niaid.nih.gov/about/organization/dcr/BRB/staff/michael.htm
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