R: Internal Functions for perm package: Not to be called by User

perm-internal {perm} | R Documentation

## Internal Functions for perm package: Not to be called by User

### Description

These functions are where the algorithms are done. There is much room for improvement in the speed of the exact functions.

### Usage

    ksample.exact.mc(scores, group, nmc = 10^4 - 1, seed = 1234321, digits = 12, p.conf.level = 0.99, setSEED = TRUE)
    ksample.pclt(scores, group)
    trend.exact.mc(scores, group, alternative = "two.sided", nmc = 10^3 - 1, seed = 1234321, digits = 12, p.conf.level = 0.99, setSEED = TRUE)
    trend.pclt(scores, group)
    twosample.exact.ce(scores, group, cm = NULL, digits = 12)
    twosample.exact.mc(scores, group, alternative = "two.sided", nmc = 10^4 - 1, seed = 1234321, digits = 12, p.conf.level = 0.99, setSEED = TRUE)
    twosample.pclt(scores, group)

    twosample.exact.network(scores, group, digits = 12)
    getcnt(nodehk, cnt.edge, edgesize)

### Arguments

`scores` | vector of response scores
`group` | covariate vector
`alternative` | one of 'less', 'greater', 'two.sided' or 'two.sidedAbs'
`nmc` | number of Monte Carlo replications
`seed` | random number seed
`digits` | digits for rounding of test statistic, equal to that many digits are called tied
`p.conf.level` | confidence level for p-value, used with mc methods
`setSEED` | logical, set to FALSE when performing simulations on mc methods
`cm` | for speed you can input the matrix created from chooseMatrix (see `chooseMatrix`). If NULL it is created.
`nodehk` | nodes for which indeces of arcs are needed
`cnt.edge` | vector of first index for each node
`edgesize` | vector of number of arcs for each node

### Details

Network algorithm is very basic, only works for two group tests. The function `getcnt` (called by twosample.exact.network) gets a vector of indeces representing arcs for set of nodes.

### Value

The function `getcnt` returns a vector of indeces representing arcs for set of nodes

[Package perm version 1.0-0.0 Index]