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

In perm: Exact or Asymptotic Permutation Tests

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

perm documentation built on Aug. 25, 2023, 1:07 a.m.