Description Usage Arguments Details Value References See Also Examples
View source: R/TreeQuartetHypTest.R
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.
1 2 3 4 5 6 7 8 9  quartetTreeTestInd(
rqt,
model = "T3",
lambda = 0,
method = "MLest",
smallcounts = "approximate",
bootstraps = 10^4,
speciestree = NULL
)

rqt 
table of resolved quartet counts, as produced by 
model 

lambda 
power divergence statistic parameter (e.g., 0 for likelihood ratio statistic, 1 for Chisquared statistic) 
method 

smallcounts 

bootstraps 
number of samples for bootstrapping 
speciestree 
species tree, in Newick as text, to determine quartet for T1 test; required for 
This function assumes all quartets are resolved. The test performed and the arguments
are described more fully in QuartetTreeTest
.
if model="T3"
, a copy of rqt
with a new column "p_T3"
appended with pvalues for each quartet;
if model="T1"
, a copy of rqt
with 2 columns appended: "p_T1"
with pvalues, and "qindex"
giving index of quartet consistent with specified species tree,
i.e., 1 if 1234 on species tree, 2 if 1324, 3 if 1423
MAR19MSCquartets
quartetTreeTest
, quartetTestPlot
, quartetStarTestInd
, quartetTableResolved
1 2 3 4 5 6 7 8 9 10  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,])

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