quartetCutTestInd: Multiple independent hypothesis tests for quartet counts...

In MSCquartets: Analyzing Gene Tree Quartets under the Multi-Species Coalescent

Multiple independent hypothesis tests for quartet counts fitting the Cut model under the NMSC

Description

Perform a hypothesis test for all quartet counts in an input table, as if the counts for different choices of 4 taxa are independent.

Usage

quartetCutTestInd(
  rqt,
  lambda = 0,
  method = "MLest",
  smallcounts = "approximate",
  bootstraps = 10^4
)

Arguments

rqt	table of resolved quartet counts, as produced by quartetTableResolved, or quartetStarTestInd
lambda	power divergence statistic parameter (e.g., 0 for likelihood ratio statistic, 1 for Chi-squared statistic)
method	"MLest", "conservative", or "bootstrap"; see quartetCutTest for explanation
smallcounts	"bootstrap" or "approximate", method of obtaining p-value when some counts are small, so the chosen method is inappropriate
bootstraps	number of samples for bootstrapping

Details

This function assumes all quartets are resolved. The test performed and the arguments are described more fully in quartetCutTest.

Value

a copy of rqt with two columns appended: "p_cut" with p-values and "cutindex" giving index 1,2, or 3 of ML estimate of quartet tree of blobs (1 if 12|34, 2 if 13|24, 3 if 14|23) under Cut model.

References

\insertRef

ABMR24MSCquartets

See Also

quartetCutTest, quartetTestPlot, quartetStarTestInd, quartetTableResolved

Examples

data(pTableYeastRokas)
pT=pTableYeastRokas[1:10,1:11]
pTable=quartetCutTestInd(pT)

MSCquartets documentation built on Oct. 31, 2024, 1:08 a.m.