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

Description Usage Arguments Details Value References See Also Examples

View source: R/TreeQuartetHypTest.R

Description

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

Usage

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quartetTreeTestInd(
  rqt,
  model = "T3",
  lambda = 0,
  method = "MLest",
  smallcounts = "approximate",
  bootstraps = 10^4,
  speciestree = NULL
)

Arguments

rqt

table of resolved quartet counts, as produced by quartetTableResolved, or quartetStarTestInd

model

"T1" for a specific species tree topology, or "T3" for any species tree topology, with these models explained more fully by \insertCiteMAR19;textualMSCquartets

lambda

power divergence statistic parameter (e.g., 0 for likelihood ratio statistic, 1 for Chi-squared statistic)

method

"MLest", "conservative", or "bootstrap"; see quartetTreeTest 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

speciestree

species tree, in Newick as text, to determine quartet for T1 test; required for model="T1", ignored for model="T3"

Details

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

Value

if model="T3", a copy of rqt with a new column "p_T3" appended with p-values for each quartet; if model="T1", a copy of rqt with 2 columns appended: "p_T1" with p-values, and "qindex" giving index of quartet consistent with specified species tree, i.e., 1 if 12|34 on species tree, 2 if 13|24, 3 if 14|23

References

\insertRef

MAR19MSCquartets

See Also

quartetTreeTest, quartetTestPlot, quartetStarTestInd, quartetTableResolved

Examples

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gtrees=read.tree(file=system.file("extdata","dataGeneTreeSample",package="MSCquartets"))
tnames=c("t1","t2","t3","t4","t5","t6")
QT=quartetTable(gtrees,tnames)
RQT=quartetTableResolved(QT)
stree="(((t5,t6),t4),((t1,t2),t3));"
pTable3=quartetTreeTestInd(RQT,"T3")
quartetTablePrint(pTable3[1:6,])
stree="((((t5,t6),t4),t7),((t8,t9),((t1,t2),t3)));"
pTable1=quartetTreeTestInd(RQT,"T1",speciestree=stree)
quartetTablePrint(pTable1[1:6,])

MSCquartets documentation built on Jan. 8, 2021, 2:10 a.m.