propAlt: Proportion of alternate hypotheses

In nickmckay/GeoChronR: Tools to Analyze and Visualize Time-Uncertain Data

Proportion of alternate hypotheses

Description

This is an internal function that calculates an estimate of a, the proportion of alternative hypotheses, using one of several methods.

Usage

propAlt(
  pvals,
  adjustment.method = "mean",
  adjustment.args = list(edf.lower = 0.8, num.steps = 20)
)

Arguments

pvals	a vector of pvals on which to conduct the multiple testing
adjustment.method	method for increasing the power of the procedure by estimating the proportion of alternative p-values, one of "mean", the modified Storey estimator that we suggest in Ventura et al. (2004), "storey", the method of Storey (2002), or "two-stage", the iterative approach of Benjamini et al. (2001)
adjustment.args	arguments to adjustment.method; see propAlt() for description, but note that for "two-stage", qlevel and fdr.method are taken from the qlevel and method arguments to fdr()

Value

estimate of a, the number of alternative hypotheses

Author(s)

Chris Paciorek

See Also

Other FDR: fdr(), fdr.master(), fdrBasic(), storey()

Examples

## Not run: 
a <- propAlt(pvals,adjustment.method="mean")

## End(Not run)

nickmckay/GeoChronR documentation built on Sept. 17, 2024, 10:13 a.m.