exact2x2-internal {exact2x2}R Documentation

Internal functions for exact2x2. Not to be called by user.

Description

The function exact2x2Pvals can calculate p-values for a vector of odds ratios. The function exact2x2CI is the code that calculates the confidence intervals for the two-sided Fisher's exact test and Blaker's exact test.

Usage

exact2x2Pvals(x, or, relErr=1+10^(-7),method = "minlike")
exact2x2CI(x, method="minlike", conf.level=0.95, tol=0.00001, orRange=c(10^-10,10^10))
mcnemar.exact.calc(bb,cc,or,alternative,tsmethod="central",conf.level=.95)

Arguments

x matrix representing 2 by 2 table
or odds ratio, may be a vector
relErr relative error. This is used to handle true ties on the computer. (see details).
method either "minlike","blaker", "central"
conf.level confidence level
tol tolerance
orRange range for search for odds ratio confidence interval
alternative indicates the alternative hypothesis and must be one of "two.sided", "greater" or "less".

Details

P-values for both the two-sided Fisher's exact and Blaker's exact test add probabilities from the opposite tail if either the cumulative probabilities (for Blaker's test) or the probabilities (Fisher's test) are less than or equal to those of the observed tail. Since sometimes the p-value at odds ratio=1 is important, we may have problems if the opposite tail is some very small different probability due to computer rounding, when mathematically the probabilities are exactly the same and should be included. To get around this problem fisher.test uses relErr so that it chooses all d<= d[i]*relErr and if mathematically d[i] is equal to another value in d but there is a slightly computer rounding error, that value will be included. We use the same tactic here.

The function mcnemar.exact.calc is just a simple call to binom.test with p=.5.

Value

Output from exact2x2Pvals is a LIST, with

or vector of odds ratios
pvals vector of two-sided p-values

Output from exact2x2CI is a confidence interval with attributes: conf.level and conf.int.prec (a list of the bounds on the precision of the limits).

See Also

exact2x2


[Package exact2x2 version 1.0-0 Index]