quartetCutTestInd {MSCquartets}

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

Allman ES, Baños H, Mitchell JD, Rhodes JA (2024). “TINNIK: Inference of the Tree of Blobs of Species Networks Under the Coalescent.” draft.

See Also

quartetCutTest, quartetTestPlot, quartetStarTestInd, quartetTableResolved

Examples

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