Produce simplex plot with results of quartet hypothesis tests
Plot a 2-d probability simplex, with points for all quartet count vectors. Colors indicate rejection or failure to reject for tests at specified levels.
quartetTestPlot(pTable, test, alpha = 0.05, beta = 1, cex = 1)
pTable |
table of quartets and p-values, as produced by |
test |
model to use, for tree null hypothesis; options are |
alpha |
significance level for tree test with null hypothesis given by |
beta |
significance level for test with null hypothesis star tree;
test results plotted only if |
cex |
scaling factor for size of plotted symbols |
The first argument of this function is a table of quartets and p-values. The
plot may show results of either the T1 or T3
test, with or without a star tree test (depending on whether a "p_star" column is in the table and/or beta =1).
The p-values must be computed by previous calls to
quartetTreeTestInd (for "T1" or "T3" p-values)
and quartetStarTestInd (for "star" p-values). The NANUQ and NANUQdist
functions include calls to these tree test functions.
gtrees=read.tree(file=system.file("extdata","dataGeneTreeSample",package="MSCquartets"))
tnames=c("t1","t2","t3","t4","t5","t6")
QT=quartetTable(gtrees,tnames[1:6])
RQT=quartetTableResolved(QT)
stree="(((t5,t6),t4),((t1,t2),t3));"
pTable=quartetTreeTestInd(RQT,"T1",speciestree=stree)
pTable=quartetStarTestInd(pTable)
quartetTestPlot(pTable, "T1", alpha=.05, beta=.95)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.