getOddsRatio: Odds ratio

In hypergea: Hypergeometric Tests

Description

This function calculates odds ratios for 2x2 and 2x2x2 contingency tables.

Usage

getOddsRatio(x, za=TRUE)

Arguments

x	a contingency table (array or matrix)
za	zero adjustment, i.e. how to behave in case of zeros (logical). If FALSE than odds ratios as calculated. If TRUE, each cell is adjusted by addition of a small number (0.5).

Details

If x is a 2x2 table then the odds ratio is returned, defined as

OR=(x_00 x_11 )/( x_10 x_01 )

If x is a 2x2 table then Bartlett's ratio of odds ratios is calculated, defined as

OR=(x_000 x_111 x_011 x_101 )/( x_101 x_001 x_100 x_111 )

To be able to calculate odds ratios even for huge numbers, the log of each cell count is taken.

Calculation of an odds ratio becomes difficult in presence of zeros. Depending on the position(s) of zero(s) in the table, the ratio becomes zero, NaN or Inf. This corresponds to the behaviour of the fisher.test in such a case. However, another strategy is (Haldane) to add a small number (0.5) to each cell when the table contains at least one zero.

Note that this routine calculates the sample odds ratio (also: unconditional Maximum Likelihood estimate). This is different to other routines like fisher.test, which calculate the conditional Maximum Likelihood Estimate (MLE).

Value

the odds ratio (numeric) if x is a 2x2 or 2x2x2 table, NA otherwise

References

MARTIN A. HAMILTON (1979) CHOOSING THE PARAMETER FOR A 2 x 2 TABLE OR A 2 x 2 x 2 TABLE ANALYSIS. Am. J. Epidemiol. (1979) 109 (3): 362-375

See Also

fisher.test, vcd package for visualisation of contingency tables

Examples

CT <- matrix(c(1:4), nrow=2)
getOddsRatio(CT)

CT <- array(c(1:8), dim=c(2,2,2))
getOddsRatio(CT)

Example output

hypergea 1.3.6 loaded

[1] 0.6666667
[1] 0.7

hypergea documentation built on May 2, 2019, 2:40 a.m.