Re: Why stats.fisher_exact gives results different from R?

On Sat, Apr 6, 2019 at 9:02 AM Peng Yu <[email protected]> wrote:
>
> See below for the output of python and R.
>
> Why there is a difference in the odds ratio? Given that R is most
> widely used by statisticians, I'd prefer the python version print the
> same results. Also, confidence intervals are missing in the python's
> output.
>
> >>> stats.fisher_exact([[8, 2], [1, 5]])
> (20.0, 0.03496503496503495)
>
> R> fisher.test(rbind(c(8, 2), c(1,5)))
>
>     Fisher's Exact Test for Count Data
>
> data:  rbind(c(8, 2), c(1, 5))
> p-value = 0.03497
> alternative hypothesis: true odds ratio is not equal to 1
> 95 percent confidence interval:
>     1.008849 1049.791446
> sample estimates:
> odds ratio
>   15.46969

estimate
an estimate of the odds ratio. Note that the conditional Maximum
Likelihood Estimate (MLE) rather than the unconditional MLE (the
sample odds ratio) is used. Only present in the 2 by 2 case.
https://stat.ethz.ch/R-manual/R-devel/library/stats/html/fisher.test.html

scipy shows sample odds ratio

The R help page does not show which confidence interval method they
use, and I don't remember or never knew.

Josef

>
> --
> Regards,
> Peng
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