NANUQdist  R Documentation 
Computes the quartet distance tables for the NANUQ algorithm of \insertCiteABR19;textualMSCquartets, using precomputed pvalues for quartets, for each of several levels specified. Distance tables are written to files, in nexus format.
NANUQdist(
pTable,
outfile = "NANUQdist",
alpha = 0.05,
beta = 0.95,
plot = TRUE
)
pTable 
a table of resolved quartets and pvalues, as previously computed by 
outfile 
a character string giving an output file name stub for
saving a 
alpha 
a value or vector of significance levels for judging pvalues testing a null hypothesis of no hybridization for each quartet; a smaller value applies a more liberal test for a tree (more trees), hence a stricter requirement for suspecting hybridization (fewer reticulations) 
beta 
a value or vector of significance levels for judging pvalues testing
a null hypothesis of a star tree for each quartet; a smaller value applies a more liberal
test for a star tree (more polytomies), hence a stricter requirment for suspecting a resolved tree;
if vectors, 
plot 

If plots are produced, each point represents an empirical quartet concordance factor, colorcoded to represent test results giving interpretation as network, resolved tree, or star tree.
If alpha
and beta
are vectors, they must be of the same length k. Then the ith entries are
paired to produce k plots and k distance tables/output files. This is equivalent to k
calls to NANUQdist
with paired scalar values from the vectors of alpha
and beta
.
See the documentation for quartetNetworkDist
for an explanation of a small, rarely noticeable,
stochastic element of the algorithm.
a NANUQ distance table, or a list of such tables if alpha
and beta
are vectors (returned invisibly)
ABR19MSCquartets
NANUQ
, quartetTreeTestInd
, quartetStarTestInd
data(pTableYeastRokas)
dist=NANUQdist(pTableYeastRokas, alpha=.05, beta=.95, outfile = NULL)
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