perm-internal: 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

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

Value

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

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.