R: Auxiliary for controling permutation tests

permControl {perm} | R Documentation

## Auxiliary for controling permutation tests

### Description

A function to create a list of arguments for `permTS`, `permKS` or `permTREND`.

### Usage

    permControl(cm=NULL,nmc=10^3-1,seed=1234321,digits=12,
        p.conf.level=.99,setSEED=TRUE,tsmethod="central")

### Arguments

`cm` | a choose(n,m) by n matrix, used if method='exact.ce', ignored otherwise
`nmc` | number of Monte Carlo replications, used if method='exact.mc', ignored otherwise
`seed` | value used in `set.seed` if method='exact.mc', ignored otherwise
`setSEED` | logical, set to FALSE when performing simulations that use method='exact.mc'
`p.conf.level` | confidence level for p value estimate, used if method='exact.mc', ignored otherwise
`digits` | number of digits to use in `signif` for precision of test statistics
`tsmethod` | method for calculating two-sided p-values, character, either 'central' or 'abs' (see details)

### Details

When `cm`=NULL the resulting matrix is created by `chooseMatrix`, it may be optionally provided here only so that `chooseMatrix` does not need to be repeatedly called in simulations. Also when doing simulations with method='exact.mc', use setSEED=FALSE so that the seed is not reset to the same value each time you call the permutation test function.

See `calcPvalsMC` for description of how p.conf.level is used.

The two-sided method is given by `tsmethod`. The default 'central' two-sided method is just p=min(1, 2*min(pless,pgreater)), where pless and pgreater are the one-sided p-values. The name 'central' follows the convention of the `exact2x2` and `exactci` packages; so that for example, a two-sample permutation test on a binary response with tsmethod='central' will match the Central Fisher's Exact test (see Fay, 2010). The option tsmethod='abs' defines another method for defining the two-sided p-value. We define it for complete enumeration, but the algorithms may differ. Let Tj be the vector of length N of all possible values of the test statistic under each of N possible permutations. The p-value with tsmethod='abs' is defined as 1/N times the number of times `abs(Tj-mean(Tj)) >= abs(T0-mean(Tj))`, where T0 is the observed value of the test statistic. This option matches the default two-sided method for the `coin` package.

### Value

An list with the arguments as components.

### References

Fay, M.P. (2010). Confidence intervals that match Fisher's exact or Blaker's exact tests. Biostatistics 11(2):373-373.

[Package perm version 1.0-0.0 Index]