hypergeom.test: Hypergeometric test
In hypergea: Hypergeometric Tests

Description Usage Arguments Details Value Source References See Also Examples

Performs exact hypergeometric tests for IxJ and 2x2x2 contingency tables

1 2	hypergeom.test(x, alternative = "two.sided", pval.method = "fisheR", nthreads = 2, ...)

`x`	an integer array (or matrix) without missing values
`alternative`	a character string specifying the alternative hypothesis, must be one of “two.sided” (default), “greater” or “less”
`pval.method`	a character vector specifying which approach should be used to determine the p-value in a two-sided test. Can be “fisheR”, “minimum.likelihood” or “double”. Ignored if ‘alternative’ is “less” or “greater”
`nthreads`	the number of threads that should be used
`...`	additional arguments. Currently not used

There is a lot of discussion about the correct way to calculate a p-value in a two sided test. Thus, several alternatives are possible (see Agresti (1992) for a short discussion and further references).

Three types of two-sided p-values are implemented. The first one (default) is the approach used by the Fisher's test implementation In R. It is currently used only for 2x2 tables. It is similar to the minimum-likelihood approach, which is also usable. The third one is the so-called doubling approach. In case of tables with I!=2 and J=!2 or 2x2x2 tables instead of the fisheR implementation the minimum-likelihood implementation is applied.

If pval.method is longer than one, all corresponding p-values are provided in the output, but only the first one is shown when calling output-object. If pval.method is NULL, all p-values are provided in the output, but only the first one (currently “fisheR”) is shown when calling output-object.

A list with class ‘"htest"’ containing the following components

`statistic`	the value observed if the cell of interest
`p.value`	the p-value for the selected test
`estimate`	the sample odds ratio calculated from ‘x’
`alternative`	a character string describing the alternative hypothesis
`method`	a character string indicating what type of hypergeometric test was performed
`conf.int`	the 95% confidence interval of the odds ratio

The code for 2x2x2 hypergeometric test is a C translation of the Fortran algorithm of Zelterman (1999).

Agresti, Alan (1992) A survey of exact inference for contingency tables. Statistical Science Vol. 7, No. 1 (Feb., 1992), pp. 131-153

Zelterman, Daniel (1999) Models for Discrete Data. Oxford University Press

fisher.test to calculate p-values for 2\times 2 tables

	##########
	## example from Zelterman (1999), p. 119, Table 4.1
	## mice were exposed to a fungicide (or not), some have a tumor
	##########
	dmn <- list(Tumor=c('y', 'n'), Exposition=c('y', 'n'))
	CT <- matrix(c(4,12,5,74), nrow=2, dimnames=dmn)
	## Not run: CT
	hypergeom.test(CT)

	## Not run: 
	##########
	## example from Agresti (1992), Table 2
	## Fisher's tea tasting experiment
	##########
	dmn <- list('poured first'=c('m', 't'), guess=c('m', 't'))
	CT <- matrix(c(3,1,1,3), nrow=2, dimnames=dmn)
	hypergeom.test(CT, alternative="two.sided")
	hypergeom.test(CT, alternative="two.sided", pval.method="double")
	out <- hypergeom.test(CT, alternative="two.sided", pval.method=NULL)
	hypergeom.test(CT, alternative="less")
	hypergeom.test(CT, alternative="greater")
	
## End(Not run)


	##########
	## example from Zelterman (1999), p. 44, Table 1.2
	## Response to three drugs
	##########
	dmn <- list(A=c('F', 'U'), B=c('F', 'U'), C=c('F', 'U'))
	CT <- array(c(6,16,2,4,2,4,6,6), dim=c(2,2,2), dimnames=dmn)
	## Not run: CT
	hypergeom.test(CT)