quartetTreeTestInd: 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 a species tree under the MSC

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

quartetTreeTestInd(
  rqt,
  model = "T3",
  lambda = 0,
  method = "MLest",
  smallsample = "precomputed",
  smallcounts = "precomputed",
  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
smallsample	"precomputed" or "bootstrap", method of obtaining p-value when sample is small (<30)
smallcounts	"precomputed" or "bootstrap", 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

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 Oct. 31, 2024, 1:08 a.m.