Thank you Marc :)
It Certainly helped me to get the exact value of P.
How to understand when to apply mcnemar.exact or just mcnemar.test?
I'm a beginner to biostatistics.

Manoj Aravind

On Tue, Dec 28, 2010 at 11:00 PM, Marc Schwartz <marc_schwartz@me.com>wrote:

>
> On Dec 28, 2010, at 11:05 AM, Manoj Aravind wrote:
>
> > Hi friends,
> > I get different values for McNemar's test in R and SPSS. Which one should
> i
> > rely on when the p values differ.
> > I came across this problem when i started learning R and seriously give
> up
> > on SPSS or any other proprietary software.
> > Thank u in advance
> >
> > Output in SPSS follows
> >
> > *Crosstab*
> >
> >
> >               hsc
> >
> > Total
> >
> >     ABN
> >
> > NE
> >
> > ABN
> >
> > tvs
> >
> > ABN
> >
> > Count
> >
> > 40
> >
> > 3
> >
> > 43
> >
> >     Row %
> >
> > 93.0%
> >
> > 7.0%
> >
> > 100.0%
> >
> >     COL%
> >
> > 78.4%
> >
> > 30.0%
> >
> > 70.5%
> >
> >  NE
> >
> > Count
> >
> > 11
> >
> > 7
> >
> > 18
> >
> >     Row %
> >
> > 61.1%
> >
> > 38.9%
> >
> > 100.0%
> >
> >     COL%
> >
> > 21.6%
> >
> > 70.0%
> >
> > 29.5%
> >
> > Total
> >
> > Count
> >
> > 51
> >
> > 10
> >
> > 61
> >
> >  Row %
> >
> > 83.6%
> >
> > 16.4%
> >
> > 100.0%
> >
> >  COL%
> >
> > 100.0%
> >
> > 100.0%
> >
> > 100.0%
> >
> >
> >
> > * Chi-Square Tests*
> >
> >
> >      Value
> >
> > Exact Sig. (2-sided)
> >
> > McNemar Test
> >
> >  .057(a)
> >
> > N of Valid Cases
> >
> > 61
> >
> >   a Binomial distribution used.
> >
> > Output from R is as follows....
> >
> >> tvshsc<-
> >
> > + matrix(c(40,11,3,7),
> >
> > + nrow=2,
> >
> > + dimnames=list("TVS"=c("ABN","NE"),
> >
> > + "HSC"=c("ABN","NE")))
> >
> >> tvshsc
> >
> >     HSC
> >
> > TVS   ABN NE
> >
> >  ABN  40  3
> >
> >  NE   11  7
> >
> >> mcnemar.test(tvshsc)
> >
> >
> > McNemar's Chi-squared test with continuity correction
> >
> >
> > data:  tvshsc
> >
> > McNemar's chi-squared = 3.5, df = 1, p-value = 0.06137
> >
> > Regards
> >
> > Dr. B Manoj Aravind
>
>
> The SPSS test appears to be an exact test, whereas the default R function
> does not perform an exact test, so you are not comparing Apples to Apples...
>
> Try this using the 'exact2x2' CRAN package:
>
> > require(exact2x2)
> Loading required package: exact2x2
> Loading required package: exactci
>
> > mcnemar.exact(matrix(c(40, 11, 3, 7), 2, 2))
>
>        Exact McNemar test (with central confidence intervals)
>
> data:  matrix(c(40, 11, 3, 7), 2, 2)
> b = 3, c = 11, p-value = 0.05737
> alternative hypothesis: true odds ratio is not equal to 1
> 95 percent confidence interval:
>  0.04885492 1.03241985
> sample estimates:
> odds ratio
>  0.2727273
>
>
> HTH,
>
> Marc Schwartz
>
>

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