exact2x2 (version 1.4.0)

exact2x2-internal: 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),tsmethod = "minlike", alternative="two.sided")
exact2x2CI(x, tsmethod="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).

tsmethod

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".

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).

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="" a="" slightly="" computer="" rounding="" error,="" that="" will="" be="" included.="" we="" use="" the="" same="" tactic="" here.="" function="" mcnemar.exact.calc is just a simple call to binom.test with p=.5.

See Also

exact2x2