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 -- Regards, Peng _______________________________________________ SciPy-User mailing list [hidden email] https://mail.python.org/mailman/listinfo/scipy-user |
On Sat, Apr 6, 2019 at 9:02 AM Peng Yu <[hidden email]> 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 > _______________________________________________ > SciPy-User mailing list > [hidden email] > https://mail.python.org/mailman/listinfo/scipy-user _______________________________________________ SciPy-User mailing list [hidden email] https://mail.python.org/mailman/listinfo/scipy-user |
Also see:
https://github.com/brentp/fishers_exact_test/issues/18 .... it's a **much** faster implementation of fisher's exact, and also differs from scipy.stats.fisher_exact. I think the brentp implementation is the same as R's -- actually would be good to test this and update the issue. - Stuart On Sat, Apr 6, 2019 at 6:22 AM <[hidden email]> wrote: > > On Sat, Apr 6, 2019 at 9:02 AM Peng Yu <[hidden email]> 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 > > _______________________________________________ > > SciPy-User mailing list > > [hidden email] > > https://mail.python.org/mailman/listinfo/scipy-user > _______________________________________________ > SciPy-User mailing list > [hidden email] > https://mail.python.org/mailman/listinfo/scipy-user SciPy-User mailing list [hidden email] https://mail.python.org/mailman/listinfo/scipy-user |
Also:
BUG: stats: fisher_exact returns incorrect p-value https://github.com/scipy/scipy/issues/4130 - Stu On Sat, Apr 6, 2019 at 12:37 PM Stuart Reynolds <[hidden email]> wrote: > > Also see: > https://github.com/brentp/fishers_exact_test/issues/18 > .... it's a **much** faster implementation of fisher's exact, and also > differs from scipy.stats.fisher_exact. > I think the brentp implementation is the same as R's -- actually would > be good to test this and update the issue. > > - Stuart > > > On Sat, Apr 6, 2019 at 6:22 AM <[hidden email]> wrote: > > > > On Sat, Apr 6, 2019 at 9:02 AM Peng Yu <[hidden email]> 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 > > > _______________________________________________ > > > SciPy-User mailing list > > > [hidden email] > > > https://mail.python.org/mailman/listinfo/scipy-user > > _______________________________________________ > > SciPy-User mailing list > > [hidden email] > > https://mail.python.org/mailman/listinfo/scipy-user SciPy-User mailing list [hidden email] https://mail.python.org/mailman/listinfo/scipy-user |
But I don't see the computation of the odds ratio.
On 4/6/19, Stuart Reynolds <[hidden email]> wrote: > Also: > > BUG: stats: fisher_exact returns incorrect p-value > https://github.com/scipy/scipy/issues/4130 > > - Stu -- Regards, Peng _______________________________________________ SciPy-User mailing list [hidden email] https://mail.python.org/mailman/listinfo/scipy-user |
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