permp

0th

Percentile

Exact permutation p-values

Calculates exact p-values for permutation tests with permutations sampled with replacement.

Keywords
htest
Usage
permp(x, nperm, n1, n2, total.nperm=NULL, method="auto", twosided=TRUE)
Arguments
x
numeric vector or array giving the number of permutations that yield test statistics at least as extreme as that observed.
nperm
number of permutations performed.
n1
sample size of group 1. Not required if total.nperm is supplied.
n2
sample size of group 2. Not required if total.nperm is supplied.
total.nperm
total number of permutations allowable from the design of the experiment.
method
computation method, possible values are "exact", "approximate" or "auto".
twosided
logical, is the test two-sided so that the test statistic is symmetric between the two groups?
Details

This function can be used for calculating exact p-values for permutation tests where permutations are sampled with replacement, using theory and methods developed by Phipson and Smyth (2010). total.nperm is the total number of distinct values of the test statistic that are possible. This is generally equal to the number of possible permutations, unless a two-sided test is conducted with equal sample sizes, in which case total.nperm is half the number of permutations, because the test statistic must then be symmetric in the two groups. total.nperm can be supplied directly by the user, alternatively it will be computed from n1 and n2. When method="exact", the p-values are computed to full machine precision by evaluating a summation. When method="approximate", an approximation is used that is faster and uses less memory. If method="auto", the exact calculation is used when total.nperm is less than or equal to 10,000, otherwise the approximation is used.

Value

  • vector or array of p-values, of same dimensions as x

References

Phipson, B and Smyth, GK (2010). Exact permutation p-values when permutations are randomly drawn. Technical Report, Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia.

Aliases
  • permp
Examples
#  Consider a two-sided permutation test with 99 permutations, 
#  5 reaching the statistically significant threshold. 
#  Assume a two group experiment with 6 in each group.
#  Input total.nperm=462

permp(x=5, nperm=99, total.nperm=462)

# Input n1=6 and n2=6

permp(x=5, nperm=99, n1=6, n2=6)

# Suppose we have a vector of p-values taking on the values 0 to 10 for the same experiment described above.

x<-0:10
permp(x=x, nperm=99, total.nperm=462)
Documentation reproduced from package statmod, version 1.4.13, License: LGPL (>= 2)

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