calcPvalsMC: Internal functions: Calculate p-values from Complete Enumeration or Monte Carlo

Description

These internal functions are not meant to be called directly. This help is to explain the functions. The function calcPvals calculates p-values from a set of either completely enumerated test statistics (in which case all wgts are equal to one) or a set of test statistics from a network algorithm (in which case the wgts come from the network algorithm). The function calcPvalsMC calculates p-values and the associated confidence intervals from a Monte Carlo simulation. The p-values are estimated by (S+1)/(N+1) where S is the number of more extreme test statistics, and N is the number of Monte Carlo simulations. This estimator is guaranteed to be valid, and the confidence interval is the appropriate one associated with this estimator (see e.g., Fay, Kim, and Hachey, 2007).

Usage

calcPvalsMC(Tj, T0, digits, alternative = NULL, twosidedTstat = FALSE, p.conf.level=0.99)
calcPvals(Tj, T0, digits, denom = NULL, wgts = NULL, twosidedTstat = FALSE)
pCI(S, N, p.conf.level = 0.99)

Arguments

numeric vector of values of test statistic

observed value of test statistic

digits

number of significant digits for rounding (see details)

alternative

character vector: one of "less", "greater", "two.sided"

twosidedTstat

logical, TRUE denotes test statistic is twosided

denom

total number of test statistics

wgts

vector of weights the same length as Tj, NULL gives all ones

number of Monte Carlo replications equal or more extreme than T0

number of Monte Carlo replications

p.conf.level

confidence level for confidence intervals about Monte Carlo p-values

References

Fay, MP, Kim, H-J, Hachey, M (2007). Journal of Computational and Graphical Statistics. 16:946-957. Available at http://www3.niaid.nih.gov/about/organization/dcr/BRB/staff/michael.htm

Description

Usage

Arguments

References

See Also