You can actually also get results from fisher.test when one of the entries is 0.
One of your confidence limits will just be either 0 or Inf.
But that should hardly be a surprise.
You could also try the twoby2 command from the Epi package which will summarize
your
table analysis nicely.
> m
[,1] [,2]
[1,] 360 0
[2,] 7 120
> fisher.test(m)
Fisher's Exact Test for Count Data
data: m
p-value < 2.2e-16
alternative hypothesis: true odds ratio is not equal to 1
95 percent confidence interval:
1204.706 Inf
sample estimates:
odds ratio
Inf
> fisher.test(m[,2:1])
Fisher's Exact Test for Count Data
data: m[, 2:1]
p-value < 2.2e-16
alternative hypothesis: true odds ratio is not equal to 1
95 percent confidence interval:
0.0000000000 0.0008300781
sample estimates:
> twoby2(m)
2 by 2 table analysis:
------------------------------------------------------
Outcome : Col 1
Comparing : Row 1 vs. Row 2
Col 1 Col 2 P(Col 1) 95% conf. interval
Row 1 360 0 1.0000 NaN 1.0000
Row 2 7 120 0.0551 0.0265 0.1111
95% conf. interval
Relative Risk: 18.1429 8.8303 37.2767
Sample Odds Ratio: Inf NaN Inf
Conditional MLE Odds Ratio: Inf 1204.7059 Inf
Probability difference: 0.9449 0.8896 0.9730
Exact P-value: 0
Asymptotic P-value: NaN
------------------------------------------------------
Best regards,
Bendix
_______________________________________________
Bendix Carstensen
Senior Statistician
Steno Diabetes Center
Niels Steensens Vej 2-4
DK-2820 Gentofte
Denmark
+45 44 43 87 38 (direct)
+45 30 75 87 38 (mobile)
b...@steno.dk http://www.biostat.ku.dk/~bxc
www.steno.dk
> -----Original Message-----
> From: r-sig-epi-boun...@stat.math.ethz.ch
> [mailto:r-sig-epi-boun...@stat.math.ethz.ch] On Behalf Of C.H.
> Sent: 5. marts 2010 12:49
> To: Pedro Emmanuel Alvarenga Americano do Brasil
> Cc: r-sig-epi@stat.math.ethz.ch
> Subject: Re: [R-sig-Epi] epitools::oddsratio error numbers
> close to zero in cells?
>
> It is possible to calculate the OR with non-zero cells using
> fisher.test
>
> > m<-matrix(c(360,7,4,120),byrow=F,nrow=2,ncol=2)
> > fisher.test(m)$estimate
> odds ratio
> 1419.605
> > fisher.test(m)$conf.int
> [1] 407.324 8192.000
> attr(,"conf.level")
> [1] 0.95
>
> For cases with zero cell, it is a problem. A typical work
> round (by usual software such as Revman, Prism or SPSS) is to
> add 0.5 to all cells to prevent the problem of division of
> zero. I don't know if any packages implemented this.
>
>
>
> On Fri, Mar 5, 2010 at 9:02 AM, Pedro Emmanuel Alvarenga
> Americano do Brasil <emmanuel.bra...@gmail.com> wrote:
> > Hello all,
> >
> > I was runing some analysis here and found an error with
> epitools::oddsratio.
> > First I tought it was in my data, later I tought I was running the
> > function incorrectly but I now realize that there is something with
> > numbers close to zero or cells with zero...
> >
> > below the same error with a simulated data... but it
> happens exactly
> > the same with mine wich has one cell with 1.
> >
> >> m<-matrix(c(360,7,0,120),byrow=F,nrow=2,ncol=2)
> >> m
> > [,1] [,2]
> > [1,] 360 0
> > [2,] 7 120
> >> oddsratio(m)
> > Erro em uniroot(function(or) { :
> > f() values at end points not of opposite sign
> >
> >> m<-matrix(c(360,7,4,120),byrow=F,nrow=2,ncol=2)
> >> m
> > [,1] [,2]
> > [1,] 360 4
> > [2,] 7 120
> >> oddsratio(m)
> > Erro em uniroot(function(or) { :
> > f() values at end points not of opposite sign
> >
> >> m<-matrix(c(360,7,7,120),byrow=F,nrow=2,ncol=2)
> >> m
> > [,1] [,2]
> > [1,] 360 7
> > [2,] 7 120
> >> oddsratio(m)
> > $data
> > Outcome
> > Predictor Disease1 Disease2 Total
> > Exposed1 360 7 367
> > Exposed2 7 120 127
> > Total 367 127 494
> >
> > $measure
> > odds ratio with 95% C.I.
> > Predictor estimate lower upper
> > Exposed1 1.0000 NA NA
> > Exposed2 806.1128 300.7302 2560
> >
> > $p.value
> > two-sided
> > Predictor midp.exact fisher.exact chi.square
> > Exposed1 NA NA NA
> > Exposed2 0 1.896808e-96 4.400778e-94
> >
> > Is it impoossible to estimate OR confidence intervals with
> tables with
> > very low numbers? Any work around sugestions?
> >
> > Abraço forte e que a força esteja com você,
> >
> > Dr. Pedro Emmanuel A. A. do Brasil
> > Instituto de Pesquisa Clínica Evandro Chagas Fundação
> Oswaldo Cruz Rio
> > de Janeiro - Brasil
> >
> > [[alternative HTML version deleted]]
> >
> >
> > _______________________________________________
> > R-sig-Epi@stat.math.ethz.ch mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-sig-epi
> >
> >
>
>
>
> --
> CH Chan
> Research Assistant - KWH
> http://www.macgrass.com
>
> _______________________________________________
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